Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Title | Authors | Journal | PubMedID | Publication Date |
---|---|---|---|---|
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-Cheng | Nature biotechnology. | 30371680 | 2018 Oct 29; |
Protein identification strategies in MALDI imaging mass spectrometry: a brief review. | Ryan, Daniel J; Spraggins, Jeffrey M; Caprioli, Richard M | Current opinion in chemical biology. | 30476689 | 2019 02; |
Forecasting innovations in science, technology, and education. | Börner, Katy; Rouse, William B; Trunfio, Paul; Stanley, H Eugene | Proceedings of the National Academy of Sciences of the United States of America. | 30530683 | 2018 12 11; |
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. | Stoeckius, Marlon; Zheng, Shiwei; Houck-Loomis, Brian; Hao, Stephanie; Yeung, Bertrand Z; Mauck 3rd, William M; Smibert, Peter; Satija, Rahul | Genome biology. | 30567574 | 2018 12 19; |
Data visualization literacy: Definitions, conceptual frameworks, exercises, and assessments. | Börner, Katy; Bueckle, Andreas; Ginda, Michael | Proceedings of the National Academy of Sciences of the United States of America. | 30718386 | 2019 Feb 05; |
Dhaka: Variational Autoencoder for Unmasking Tumor Heterogeneity from Single Cell Genomic Data. | Rashid, Sabrina; Shah, Sohrab; Bar-Joseph, Ziv; Pandya, Ravi | Bioinformatics (Oxford, England). | 30768159 | 2019 Feb 15; |
The single-cell transcriptional landscape of mammalian organogenesis. | Cao, Junyue; Spielmann, Malte; Qiu, Xiaojie; Huang, Xingfan; Ibrahim, Daniel M; Hill, Andrew J; Zhang, Fan; Mundlos, Stefan; Christiansen, Lena; Steemers, Frank J; Trapnell, Cole; Shendure, Jay | Nature. | 30787437 | 2019 02; |
Cell lineage inference from SNP and scRNA-Seq data. | Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv | Nucleic acids research. | 30820578 | 2019 Jun 04; |
Multiple TOF/TOF Events in a Single Laser Shot for Multiplexed Lipid Identifications in MALDI Imaging Mass Spectrometry. | Prentice, Boone M; McMillen, Josiah C; Caprioli, Richard M | International journal of mass spectrometry. | 30906202 | 2019 Mar; |
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng, Chee-Huat Linus; Lawson, Michael; Zhu, Qian; Dries, Ruben; Koulena, Noushin; Takei, Yodai; Yun, Jina; Cronin, Christopher; Karp, Christoph; Yuan, Guo-Cheng; Cai, Long | Nature. | 30911168 | 2019 Apr; |
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. | Rodriques, Samuel G; Stickels, Robert R; Goeva, Aleksandrina; Martin, Carly A; Murray, Evan; Vanderburg, Charles R; Welch, Joshua; Chen, Linlin M; Chen, Fei; Macosko, Evan Z | Science (New York, N.Y.). | 30923225 | 2019 03 29; |
Imaging mass spectrometry enables molecular profiling of mouse and human pancreatic tissue. | Prentice, Boone M; Hart, Nathaniel J; Phillips, Neil; Haliyur, Rachana; Judd, Audra; Armandala, Radhika; Spraggins, Jeffrey M; Lowe, Cindy L; Boyd, Kelli L; Stein, Roland W; Wright, Christopher V; Norris, Jeremy L; Powers, Alvin C; Brissova, Marcela; Caprioli, Richard M | Diabetologia. | 30955045 | 2019 06; |
The 2019 mathematical oncology roadmap. | Rockne, Russell C; Hawkins-Daarud, Andrea; Swanson, Kristin R; Sluka, James P; Glazier, James A; Macklin, Paul; Hormuth, David A; Jarrett, Angela M; Lima, Ernesto A B F; Tinsley Oden, J; Biros, George; Yankeelov, Thomas E; Curtius, Kit; Al Bakir, Ibrahim; Wodarz, Dominik; Komarova, Natalia; Aparicio, Luis; Bordyuh, Mykola; Rabadan, Raul; Finley, Stacey D; Enderling, Heiko; Caudell, Jimmy; Moros, Eduardo G; Anderson, Alexander R A; Gatenby, Robert A; Kaznatcheev, Artem; Jeavons, Peter; Krishnan, Nikhil; Pelesko, Julia; Wadhwa, Raoul R; Yoon, Nara; Nichol, Daniel; Marusyk, Andriy; Hinczewski, Michael; Scott, Jacob G | Physical biology. | 30991381 | 2019 Jun 19; |
Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. | Lin, Chieh; Bar-Joseph, Ziv | Bioinformatics (Oxford, England). | 31038684 | 2019 Apr 30; |
Visualizing learner engagement, performance, and trajectories to evaluate and optimize online course design. | Ginda, Michael; Richey, Michael C; Cousino, Mark; Börner, Katy | PloS one. | 31059546 | 2019; |
SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi, Jocelyn Y; Lapan, Sylvain W; Beliveau, Brian J; West, Emma R; Zhu, Allen; Sasaki, Hiroshi M; Saka, Sinem K; Wang, Yu; Cepko, Constance L; Yin, Peng | Nature methods. | 31110282 | 2019 Jun; |
MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. | Ryan, Daniel J; Patterson, Nathan Heath; Putnam, Nicole E; Wilde, Aimee D; Weiss, Andy; Perry, William J; Cassat, James E; Skaar, Eric P; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry. | 31149808 | 2019 06 18; |
Comprehensive Integration of Single-Cell Data. | Stuart, Tim; Butler, Andrew; Hoffman, Paul; Hafemeister, Christoph; Papalexi, Efthymia; Mauck 3rd, William M; Hao, Yuhan; Stoeckius, Marlon; Smibert, Peter; Satija, Rahul | Cell. | 31178118 | 2019 Jun 13; |
Two Specific Sulfatide Species Are Dysregulated during Renal Development in a Mouse Model of Alport Syndrome. | Gessel, Megan M; Spraggins, Jeffrey M; Voziyan, Paul A; Abrahamson, Dale R; Caprioli, Richard M; Hudson, Billy G | Lipids. | 31197846 | 2019 06; |
A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. | Judd, Audra M; Gutierrez, Danielle B; Moore, Jessica L; Patterson, Nathan Heath; Yang, Junhai; Romer, Carrie E; Norris, Jeremy L; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 31254303 | 2019 Aug; |
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. | Saka, Sinem K; Wang, Yu; Kishi, Jocelyn Y; Zhu, Allen; Zeng, Yitian; Xie, Wenxin; Kirli, Koray; Yapp, Clarence; Cicconet, Marcelo; Beliveau, Brian J; Lapan, Sylvain W; Yin, Siyuan; Lin, Millicent; Boyden, Edward S; Kaeser, Pascal S; Pihan, German; Church, George M; Yin, Peng | Nature biotechnology. | 31427819 | 2019 Sep; |
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa, José L; Hill, Andrew J; Qiu, Xiaojie; Jackson, Dana; Shendure, Jay; Trapnell, Cole | Nature genetics. | 31477929 | 2019 Sep; |
Supervised classification enables rapid annotation of cell atlases. | Pliner, Hannah A; Shendure, Jay; Trapnell, Cole | Nature methods. | 31501545 | 2019 Oct; |
High-Parameter Immune Profiling with CyTOF. | Sahaf, Bita; Rahman, Adeeb; Maecker, Holden T; Bendall, Sean C | Methods in molecular biology (Clifton, N.J.). | 31502160 | 2020; |
High-Performance Molecular Imaging with MALDI Trapped Ion-Mobility Time-of-Flight (timsTOF) Mass Spectrometry. | Spraggins, Jeffrey M; Djambazova, Katerina V; Rivera, Emilio S; Migas, Lukasz G; Neumann, Elizabeth K; Fuetterer, Arne; Suetering, Juergen; Goedecke, Niels; Ly, Alice; Van de Plas, Raf; Caprioli, Richard M | Analytical chemistry. | 31593446 | 2019 11 19; |
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. | HuBMAP Consortium | Nature. | 31597973 | 2019 10; |
Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. | Verbeeck, Nico; Caprioli, Richard M; Van de Plas, Raf | Mass spectrometry reviews. | 31602691 | 2020 May; |
Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host. | Perry, William J; Spraggins, Jeffrey M; Sheldon, Jessica R; Grunenwald, Caroline M; Heinrichs, David E; Cassat, James E; Skaar, Eric P; Caprioli, Richard M | Proceedings of the National Academy of Sciences of the United States of America. | 31611408 | 2019 10 29; |
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen, Song; Lake, Blue B; Zhang, Kun | Nature biotechnology. | 31611697 | 2019 12; |
High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry. | Yin, Ruichuan; Burnum-Johnson, Kristin E; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Nature protocols. | 31723300 | 2019 12; |
Deep learning for inferring gene relationships from single-cell expression data. | Yuan, Ye; Bar-Joseph, Ziv | Proceedings of the National Academy of Sciences of the United States of America | 31822622 | 2019 Dec 10 |
Toward a Common Coordinate Framework for the Human Body. | Rood, Jennifer E; Stuart, Tim; Ghazanfar, Shila; Biancalani, Tommaso; Fisher, Eyal; Butler, Andrew; Hupalowska, Anna; Gaffney, Leslie; Mauck, William; Eraslan, Gökçen; Marioni, John C; Regev, Aviv; Satija, Rahul | Cell. | 31835027 | 2019 Dec 12; |
Uncovering Matrix Effects on Lipid Analyses in MALDI Imaging Mass Spectrometry Experiments. | Perry, William J; Patterson, Nathan Heath; Prentice, Boone M; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 31860760 | 2019 Dec 20; |
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister, Christoph; Satija, Rahul | Genome biology. | 31870423 | 2019 12 23; |
Immune monitoring using mass cytometry and related high-dimensional imaging approaches. | Hartmann, Felix J; Bendall, Sean C | Nature reviews. Rheumatology. | 31892734 | 2020 02; |
Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-?m spatial resolution. | Piehowski, Paul D; Zhu, Ying; Bramer, Lisa M; Stratton, Kelly G; Zhao, Rui; Orton, Daniel J; Moore, Ronald J; Yuan, Jia; Mitchell, Hugh D; Gao, Yuqian; Webb-Robertson, Bobbie-Jo M; Dey, Sudhansu K; Kelly, Ryan T; Burnum-Johnson, Kristin E | Nature communications. | 31911630 | 2020 Jan 07; |
Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. | Hurley, Killian; Ding, Jun; Villacorta-Martin, Carlos; Herriges, Michael J; Jacob, Anjali; Vedaie, Marall; Alysandratos, Konstantinos D; Sun, Yuliang L; Lin, Chieh; Werder, Rhiannon B; Huang, Jessie; Wilson, Andrew A; Mithal, Aditya; Mostoslavsky, Gustavo; Oglesby, Irene; Caballero, Ignacio S; Guttentag, Susan H; Ahangari, Farida; Kaminski, Naftali; Rodriguez-Fraticelli, Alejo; Camargo, Fernando; Bar-Joseph, Ziv; Kotton, Darrell N | Cell stem cell | 32004478 | 2020 04 02 |
Inferring TF activation order in time series scRNA-Seq studies. | Lin, Chieh; Ding, Jun; Bar-Joseph, Ziv | PLoS computational biology | 32069291 | 2020 02 |
Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review. | Perry, William J; Weiss, Andy; Van de Plas, Raf; Spraggins, Jeffrey M; Caprioli, Richard M; Skaar, Eric P | Current opinion in chemical biology. | 32087551 | 2020 Apr; |
RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. | Wei, Christopher Jen-Yue; Zhang, Kun | Genome research. | 32127417 | 2020 Apr; |
Multiplexed single-cell morphometry for hematopathology diagnostics. | Tsai, Albert G; Glass, David R; Juntilla, Marisa; Hartmann, Felix J; Oak, Jean S; Fernandez-Pol, Sebastian; Ohgami, Robert S; Bendall, Sean C | Nature medicine. | 32161403 | 2020 03; |
Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology. | 32221477 | 2020 07; |
Discovering New Lipidomic Features Using Cell Type Specific Fluorophore Expression to Provide Spatial and Biological Specificity in a Multimodal Workflow with MALDI Imaging Mass Spectrometry. | Jones, Marissa A; Cho, Sung Hoon; Patterson, Nathan Heath; Van de Plas, Raf; Spraggins, Jeffrey M; Boothby, Mark R; Caprioli, Richard M | Analytical chemistry. | 32298091 | 2020 05 19; |
Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features. | Islam, Mirazul; Chen, Bob; Spraggins, Jeffrey M; Kelly, Ryan T; Lau, Ken S | Gastroenterology. | 32417404 | 2020 Aug; |
The Importance of Clinical Tissue Imaging. | Spraggins, Jeffrey M; Schwamborn, Kristina; Heeren, Ron M A; Eberlin, Livia S | Clinical mass spectrometry (Del Mar, Calif.). | 32483555 | 2019 Apr; |
Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. | Zafar, Hamim; Lin, Chieh; Bar-Joseph, Ziv | Nature communications | 32546686 | 2020 Jun 16 |
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. | Ji, Andrew L; Rubin, Adam J; Thrane, Kim; Jiang, Sizun; Reynolds, David L; Meyers, Robin M; Guo, Margaret G; George, Benson M; Mollbrink, Annelie; Bergenstråhle, Joseph; Larsson, Ludvig; Bai, Yunhao; Zhu, Bokai; Bhaduri, Aparna; Meyers, Jordan M; Rovira-Clavé, Xavier; Hollmig, S Tyler; Aasi, Sumaira Z; Nolan, Garry P; Lundeberg, Joakim; Khavari, Paul A | Cell. | 32579974 | 2020 Jul 23; |
A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. | Keyes, Timothy J; Domizi, Pablo; Lo, Yu-Chen; Nolan, Garry P; Davis, Kara L | Cytometry. Part A : the journal of the International Society for Analytical Cytology. | 32602650 | 2020 08; |
Lipid Landscape of the Human Retina and Supporting Tissues Revealed by High-Resolution Imaging Mass Spectrometry. | Anderson, David M G; Messinger, Jeffrey D; Patterson, Nathan H; Rivera, Emilio S; Kotnala, Ankita; Spraggins, Jeffrey M; Caprioli, Richard M; Curcio, Christine A; Schey, Kevin L | Journal of the American Society for Mass Spectrometry | 32628476 | 2020 Dec 02 |
An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. | Glass, David R; Tsai, Albert G; Oliveria, John Paul; Hartmann, Felix J; Kimmey, Samuel C; Calderon, Ariel A; Borges, Luciene; Glass, Marla C; Wagar, Lisa E; Davis, Mark M; Bendall, Sean C | Immunity. | 32668225 | 2020 Jul 14; |
Localization of the lens intermediate filament switch by imaging mass spectrometry. | Wang, Zhen; Ryan, Daniel J; Schey, Kevin L | Experimental eye research | 32682822 | 2020 09 |
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. | Shafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M; Liu, Kelvin J; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M; Vollger, Mitchell R; Monlong, Jean; Garrison, Erik; Eichler, Evan E; Salama, Sofie; Haussler, David; Green, Richard E; Akeson, Mark; Phillippy, Adam; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Paten, Benedict | Nature biotechnology. | 32686750 | 2020 09; |
Progenitor identification and SARS-CoV-2 infection in long-term human distal lung organoid cultures. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; van Unen, Vincent; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | bioRxiv : the preprint server for biology | 32743583 | 2020 Jul 27 |
An Integrated Microfluidic Probe for Mass Spectrometry Imaging of Biological Samples*. | Li, Xiangtang; Yin, Ruichuan; Hu, Hang; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Angewandte Chemie (International ed. in English) | 32743957 | 2020 12 07 |
Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. | Schürch, Christian M; Bhate, Salil S; Barlow, Graham L; Phillips, Darci J; Noti, Luca; Zlobec, Inti; Chu, Pauline; Black, Sarah; Demeter, Janos; McIlwain, David R; Kinoshita, Shigemi; Samusik, Nikolay; Goltsev, Yury; Nolan, Garry P | Cell. | 32763154 | 2020 Sep 03; |
Tetraspanin-7 regulation of L-type voltage-dependent calcium channels controls pancreatic β-cell insulin secretion. | Dickerson, Matthew T; Dadi, Prasanna K; Butterworth, Regan B; Nakhe, Arya Y; Graff, Sarah M; Zaborska, Karolina E; Schaub, Charles M; Jacobson, David A | The Journal of physiology | 32790176 | 2020 Nov |
Single-cell metabolic profiling of human cytotoxic T cells. | Hartmann, Felix J; Mrdjen, Dunja; McCaffrey, Erin; Glass, David R; Greenwald, Noah F; Bharadwaj, Anusha; Khair, Zumana; Verberk, Sanne G S; Baranski, Alex; Baskar, Reema; Graf, William; Van Valen, David; Van den Bossche, Jan; Angelo, Michael; Bendall, Sean C | Nature biotechnology. | 32868913 | 2020 Aug 31; |
Identifying signaling genes in spatial single-cell expression data. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 32886099 | 2021 05 17 |
Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine. | Neumann, Elizabeth K; Djambazova, Katerina V; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of the American Society for Mass Spectrometry | 32886506 | 2020 Dec 02 |
The impact of air transport availability on research collaboration: A case study of four universities. | Ploszaj, Adam; Yan, Xiaoran; Börner, Katy | PloS one | 32886681 | 2020 |
Targeting Phosphotyrosine in Native Proteins with Conditional, Bispecific Antibody Traps. | Zhou, Xin X; Bracken, Colton J; Zhang, Kaihua; Zhou, Jie; Mou, Yun; Wang, Lei; Cheng, Yifan; Leung, Kevin K; Wells, James A | Journal of the American Chemical Society | 32924468 | 2020 10 14 |
Changes to Zonular Tension Alters the Subcellular Distribution of AQP5 in Regions of Influx and Efflux of Water in the Rat Lens. | Petrova, Rosica S; Bavana, Nandini; Zhao, Rusin; Schey, Kevin L; Donaldson, Paul J | Investigative ophthalmology & visual science | 32945844 | 2020 09 01 |
Integrating ion mobility and imaging mass spectrometry for comprehensive analysis of biological tissues: A brief review and perspective. | Rivera, Emilio S; Djambazova, Katerina V; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M | Journal of mass spectrometry : JMS. | 32955134 | 2020 Jul 04; |
A Generic Framework and Library for Exploration of Small Multiples through Interactive Piling. | Lekschas, Fritz; Zhou, Xinyi; Chen, Wei; Gehlenborg, Nils; Bach, Benjamin; Pfister, Hanspeter | IEEE transactions on visualization and computer graphics | 33026994 | 2021 02 |
Landscape of coordinated immune responses to H1N1 challenge in humans. | Rahil, Zainab; Leylek, Rebecca; Schürch, Christian M; Chen, Han; Bjornson-Hooper, Zach; Christensen, Shannon R; Gherardini, Pier Federico; Bhate, Salil S; Spitzer, Matthew H; Fragiadakis, Gabriela K; Mukherjee, Nilanjan; Kim, Nelson; Jiang, Sizun; Yo, Jennifer; Gaudilliere, Brice; Affrime, Melton; Bock, Bonnie; Hensley, Scott E; Idoyaga, Juliana; Aghaeepour, Nima; Kim, Kenneth; Nolan, Garry P; McIlwain, David R | The Journal of clinical investigation. | 33044226 | 2020 Nov 02; |
CDKL5: a promising new therapeutic target for acute kidney injury? | de Caestecker, Mark P | American journal of physiology. Renal physiology. | 33073588 | 2020 Oct 19; |
Iterative point set registration for aligning scRNA-seq data. | Alavi, Amir; Bar-Joseph, Ziv | PLoS computational biology | 33108369 | 2020 10 |
Guidelines for reporting single-cell RNA-seq experiments. | Füllgrabe, Anja; George, Nancy; Green, Matthew; Nejad, Parisa; Aronow, Bruce; Fexova, Silvie Korena; Fischer, Clay; Freeberg, Mallory Ann; Huerta, Laura; Morrison, Norman; Scheuermann, Richard H; Taylor, Deanne; Vasilevsky, Nicole; Clarke, Laura; Gehlenborg, Nils; Kent, Jim; Marioni, John; Teichmann, Sarah; Brazma, Alvis; Papatheodorou, Irene | Nature biotechnology | 33188371 | 2020 12 |
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. | Liu, Yang; Yang, Mingyu; Deng, Yanxiang; Su, Graham; Enninful, Archibald; Guo, Cindy C; Tebaldi, Toma; Zhang, Di; Kim, Dongjoo; Bai, Zhiliang; Norris, Eileen; Pan, Alisia; Li, Jiatong; Xiao, Yang; Halene, Stephanie; Fan, Rong | Cell. | 33188776 | 2020 Dec 10; |
A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project. | El-Achkar, Tarek M; Eadon, Michael T; Menon, Rajasree; Lake, Blue B; Sigdel, Tara K; Alexandrov, Theodore; Parikh, Samir; Zhang, Guanshi; Dobi, Dejan; Dunn, Kenneth W; Otto, Edgar A; Anderton, Christopher R; Carson, Jonas M; Luo, Jinghui; Park, Chris; Hamidi, Habib; Zhou, Jian; Hoover, Paul; Schroeder, Andrew; Joanes, Marianinha; Azeloglu, Evren U; Sealfon, Rachel; Winfree, Seth; Steck, Becky; He, Yongqun; D'Agati, Vivette; Iyengar, Ravi; Troyanskaya, Olga G; Barisoni, Laura; Gaut, Joseph; Zhang, Kun; Laszik, Zoltan; Rovin, Brad H; Dagher, Pierre C; Sharma, Kumar; Sarwal, Minnie M; Hodgin, Jeffrey B; Alpers, Charles E; Kretzler, Matthias; Jain, Sanjay | Physiological genomics | 33197228 | 2021 Jan 01 |
Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data. | Uzun, Yasin; Wu, Hao; Tan, Kai | Genome research | 33219054 | 2021 Jan |
Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. | Martin, Kendall; Zhang, Tong; Zhang, Pengfei; Chrisler, William B; Thomas, Fillmore L; Liu, Fen; Liu, Tao; Qian, Wei-Jun; Smith, Richard D; Shi, Tujin | Journal of visualized experiments : JoVE. | 33226031 | 2020 11 06; |
Progenitor identification and SARS-CoV-2 infection in human distal lung organoids. | Salahudeen, Ameen A; Choi, Shannon S; Rustagi, Arjun; Zhu, Junjie; van Unen, Vincent; de la O, Sean M; Flynn, Ryan A; Margalef-Català, Mar; Santos, António J M; Ju, Jihang; Batish, Arpit; Usui, Tatsuya; Zheng, Grace X Y; Edwards, Caitlin E; Wagar, Lisa E; Luca, Vincent; Anchang, Benedict; Nagendran, Monica; Nguyen, Khanh; Hart, Daniel J; Terry, Jessica M; Belgrader, Phillip; Ziraldo, Solongo B; Mikkelsen, Tarjei S; Harbury, Pehr B; Glenn, Jeffrey S; Garcia, K Christopher; Davis, Mark M; Baric, Ralph S; Sabatti, Chiara; Amieva, Manuel R; Blish, Catherine A; Desai, Tushar J; Kuo, Calvin J | Nature | 33238290 | 2020 12 |
Effect of MALDI matrices on lipid analyses of biological tissues using MALDI-2 postionization mass spectrometry. | McMillen, Josiah C; Fincher, Jarod A; Klein, Dustin R; Spraggins, Jeffrey M; Caprioli, Richard M | Journal of mass spectrometry : JMS. | 33241625 | 2020 Dec; |
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data. | Yuan, Ye; Bar-Joseph, Ziv | Genome biology | 33303016 | 2020 Dec 10 |
RIPK3-mediated inflammation is a conserved β cell response to ER stress. | Yang, Bingyuan; Maddison, Lisette A; Zaborska, Karolina E; Dai, Chunhua; Yin, Linlin; Tang, Zihan; Zang, Liqing; Jacobson, David A; Powers, Alvin C; Chen, Wenbiao | Science advances | 33355143 | 2020 Dec |
Phase identification for dynamic CT enhancements with generative adversarial network. | Tang, Yucheng; Gao, Riqiang; Lee, Ho Hin; Chen, Yunqiang; Gao, Dashan; Bermudez, Camilo; Bao, Shunxing; Huo, Yuankai; Savoie, Brent V; Landman, Bennett A | Medical physics | 33410167 | 2021 Mar |
Quantitative Mass Spectrometry Imaging of Biological Systems. | Unsihuay, Daisy; Mesa Sanchez, Daniela; Laskin, Julia | Annual review of physical chemistry | 33441032 | 2021 Apr 20 |
Supervised Adversarial Alignment of Single-Cell RNA-seq Data. | Ge, Songwei; Wang, Haohan; Alavi, Amir; Xing, Eric; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 33470876 | 2021 05 |
Integrated spatial genomics reveals global architecture of single nuclei. | Takei, Yodai; Yun, Jina; Zheng, Shiwei; Ollikainen, Noah; Pierson, Nico; White, Jonathan; Shah, Sheel; Thomassie, Julian; Suo, Shengbao; Eng, Chee-Huat Linus; Guttman, Mitchell; Yuan, Guo-Cheng; Cai, Long | Nature | 33505024 | 2021 02 |
Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. | Kennedy-Darling, Julia; Bhate, Salil S; Hickey, John W; Black, Sarah; Barlow, Graham L; Vazquez, Gustavo; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | European journal of immunology | 33548142 | 2021 May |
Body Part Regression With Self-Supervision. | Tang, Yucheng; Gao, Riqiang; Han, Shizhong; Chen, Yunqiang; Gao, Dashan; Nath, Vishwesh; Bermudez, Camilo; Savona, Michael R; Bao, Shunxing; Lyu, Ilwoo; Huo, Yuankai; Landman, Bennett A | IEEE transactions on medical imaging | 33560981 | 2021 May |
Spatial Segmentation of Mass Spectrometry Imaging Data by Combining Multivariate Clustering and Univariate Thresholding. | Hu, Hang; Yin, Ruichuan; Brown, Hilary M; Laskin, Julia | Analytical chemistry | 33570915 | 2021 02 23 |
Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. | Tsai, Chia-Feng; Zhang, Pengfei; Scholten, David; Martin, Kendall; Wang, Yi-Ting; Zhao, Rui; Chrisler, William B; Patel, Dhwani B; Dou, Maowei; Jia, Yuzhi; Reduzzi, Carolina; Liu, Xia; Moore, Ronald J; Burnum-Johnson, Kristin E; Lin, Miao-Hsia; Hsu, Chuan-Chih; Jacobs, Jon M; Kagan, Jacob; Srivastava, Sudhir; Rodland, Karin D; Steven Wiley, H; Qian, Wei-Jun; Smith, Richard D; Zhu, Ying; Cristofanilli, Massimo; Liu, Tao; Liu, Huiping; Shi, Tujin | Communications biology | 33649493 | 2021 Mar 01 |
Advances in Proximity Ligation in situ Hybridization (PLISH). | Nagendran, Monica; Andruska, Adam M; Harbury, Pehr B; Desai, Tushar J | Bio-protocol | 33659462 | 2020 Nov 05 |
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Characteristics of p.Gln368Ter Myocilin Variant and Influence of Polygenic Risk on Glaucoma Penetrance in the UK Biobank. | Zebardast, Nazlee; Sekimitsu, Sayuri; Wang, Jiali; Elze, Tobias; Gharahkhani, Puya; Cole, Brian S; Lin, Michael M; Segrè, Ayellet V; Wiggs, Janey L; International Glaucoma Genetics Consortium | Ophthalmology | 33713785 | 2021 Sep |
Islet sympathetic innervation and islet neuropathology in patients with type 1 diabetes. | Campbell-Thompson, Martha; Butterworth, Elizabeth A; Boatwright, J Lucas; Nair, Malavika A; Nasif, Lith H; Nasif, Kamal; Revell, Andy Y; Riva, Alberto; Mathews, Clayton E; Gerling, Ivan C; Schatz, Desmond A; Atkinson, Mark A | Scientific reports | 33753784 | 2021 Mar 22 |
Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. | Gerbasi, Vincent R; Melani, Rafael D; Abbatiello, Susan E; Belford, Michael W; Huguet, Romain; McGee, John P; Dayhoff, Dawson; Thomas, Paul M; Kelleher, Neil L | Analytical chemistry | 33844503 | 2021 04 27 |
CytoTalk: De novo construction of signal transduction networks using single-cell transcriptomic data. | Hu, Yuxuan; Peng, Tao; Gao, Lin; Tan, Kai | Science advances | 33853780 | 2021 Apr |
Deep learning of gene relationships from single cell time-course expression data. | Yuan, Ye; Bar-Joseph, Ziv | Briefings in bioinformatics | 33876191 | 2021 09 02 |
SpatialDWLS: accurate deconvolution of spatial transcriptomic data. | Dong, Rui; Yuan, Guo-Cheng | Genome biology | 33971932 | 2021 05 10 |
Pancreas Optical Clearing and 3-D Microscopy in Health and Diabetes. | Campbell-Thompson, Martha; Tang, Shiue-Cheng | Frontiers in endocrinology | 33981285 | 2021 |
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Multiomics Imaging Using High-Energy Water Gas Cluster Ion Beam Secondary Ion Mass Spectrometry [(H2O)n-GCIB-SIMS] of Frozen-Hydrated Cells and Tissue. | Tian, Hua; Sheraz Née Rabbani, Sadia; Vickerman, John C; Winograd, Nicholas | Analytical chemistry | 34038090 | 2021 06 08 |
New Interface for Faster Proteoform Analysis: Immunoprecipitation Coupled with SampleStream-Mass Spectrometry. | Santos Seckler, Henrique Dos; Park, Hae-Min; Lloyd-Jones, Cameron M; Melani, Rafael D; Camarillo, Jeannie M; Wilkins, John T; Compton, Philip D; Kelleher, Neil L | Journal of the American Society for Mass Spectrometry | 34043341 | 2021 Jul 07 |
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Successive High-Resolution (H2O)n-GCIB and C60-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue. | Tian, Hua; Sparvero, Louis J; Anthonymuthu, Tamil Selvan; Sun, Wan-Yang; Amoscato, Andrew A; He, Rong-Rong; Bayır, Hülya; Kagan, Valerian E; Winograd, Nicholas | Analytical chemistry | 34075742 | 2021 Jun 15 |
Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging. | Phillips, Darci; Schürch, Christian M; Khodadoust, Michael S; Kim, Youn H; Nolan, Garry P; Jiang, Sizun | Frontiers in immunology | 34093591 | 2021 |
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CODEX multiplexed tissue imaging with DNA-conjugated antibodies. | Black, Sarah; Phillips, Darci; Hickey, John W; Kennedy-Darling, Julia; Venkataraaman, Vishal G; Samusik, Nikolay; Goltsev, Yury; Schürch, Christian M; Nolan, Garry P | Nature protocols | 34215862 | 2021 08 |
Acceleration of age-induced proteolysis in the guinea pig lens nucleus by in vivo exposure to hyperbaric oxygen: A mass spectrometry analysis. | Giblin, Frank J; Anderson, David M G; Han, Jun; Rose, Kristie L; Wang, Zhen; Schey, Kevin L | Experimental eye research | 34233175 | 2021 09 |
Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices. | Alseekh, Saleh; Aharoni, Asaph; Brotman, Yariv; Contrepois, Kévin; D'Auria, John; Ewald, Jan; C Ewald, Jennifer; Fraser, Paul D; Giavalisco, Patrick; Hall, Robert D; Heinemann, Matthias; Link, Hannes; Luo, Jie; Neumann, Steffen; Nielsen, Jens; Perez de Souza, Leonardo; Saito, Kazuki; Sauer, Uwe; Schroeder, Frank C; Schuster, Stefan; Siuzdak, Gary; Skirycz, Aleksandra; Sumner, Lloyd W; Snyder, Michael P; Tang, Huiru; Tohge, Takayuki; Wang, Yulan; Wen, Weiwei; Wu, Si; Xu, Guowang; Zamboni, Nicola; Fernie, Alisdair R | Nature methods | 34239102 | 2021 07 |
Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. | Martin, Kendall; Zhang, Tong; Lin, Tai-Tu; Habowski, Amber N; Zhao, Rui; Tsai, Chia-Feng; Chrisler, William B; Sontag, Ryan L; Orton, Daniel J; Lu, Yong-Jie; Rodland, Karin D; Yang, Bin; Liu, Tao; Smith, Richard D; Qian, Wei-Jun; Waterman, Marian L; Wiley, H Steven; Shi, Tujin | Journal of proteome research | 34351778 | 2021 09 03 |
Community-wide hackathons to identify central themes in single-cell multi-omics. | Lê Cao, Kim-Anh; Abadi, Al J; Davis-Marcisak, Emily F; Hsu, Lauren; Arora, Arshi; Coullomb, Alexis; Deshpande, Atul; Feng, Yuzhou; Jeganathan, Pratheepa; Loth, Melanie; Meng, Chen; Mu, Wancen; Pancaldi, Vera; Sankaran, Kris; Righelli, Dario; Singh, Amrit; Sodicoff, Joshua S; Stein-O'Brien, Genevieve L; Subramanian, Ayshwarya; Welch, Joshua D; You, Yue; Argelaguet, Ricard; Carey, Vincent J; Dries, Ruben; Greene, Casey S; Holmes, Susan; Love, Michael I; Ritchie, Matthew E; Yuan, Guo-Cheng; Culhane, Aedin C; Fertig, Elana | Genome biology | 34353350 | 2021 08 05 |
Construction of a Multi-Phase Contrast Computed Tomography Kidney Atlas. | Lee, Ho Hin; Tang, Yucheng; Xu, Kaiwen; Bao, Shunxing; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Heinrich, Mattias; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 34354322 | 2021 |
Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study. | IMPACC Manuscript Writing Team; IMPACC Network Steering Committee | Science immunology | 34376480 | 2021 08 10 |
Protocol for multimodal analysis of human kidney tissue by imaging mass spectrometry and CODEX multiplexed immunofluorescence. | Neumann, Elizabeth K; Patterson, Nathan Heath; Allen, Jamie L; Migas, Lukasz G; Yang, Haichun; Brewer, Maya; Anderson, David M; Harvey, Jennifer; Gutierrez, Danielle B; Harris, Raymond C; deCaestecker, Mark P; Fogo, Agnes B; Van de Plas, Raf; Caprioli, Richard M; Spraggins, Jeffrey M | STAR protocols | 34430920 | 2021 Sep 17 |
α-Cyano-4-hydroxycinnamic Acid and Tri-Potassium Citrate Salt Pre-Coated Silicon Nanopost Array Provides Enhanced Lipid Detection for High Spatial Resolution MALDI Imaging Mass Spectrometry. | Dufresne, Martin; Fincher, Jarod A; Patterson, Nathan Heath; Schey, Kevin L; Norris, Jeremy L; Caprioli, Richard M; Spraggins, Jeffrey M | Analytical chemistry | 34449196 | 2021 09 14 |
Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations. | Tideman, Leonoor E M; Migas, Lukasz G; Djambazova, Katerina V; Patterson, Nathan Heath; Caprioli, Richard M; Spraggins, Jeffrey M; Van de Plas, Raf | Analytica chimica acta | 34482894 | 2021 Sep 08 |
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Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. | Lohoff, T; Ghazanfar, S; Missarova, A; Koulena, N; Pierson, N; Griffiths, J A; Bardot, E S; Eng, C-H L; Tyser, R C V; Argelaguet, R; Guibentif, C; Srinivas, S; Briscoe, J; Simons, B D; Hadjantonakis, A-K; Göttgens, B; Reik, W; Nichols, J; Cai, L; Marioni, J C | Nature biotechnology | 34489600 | 2022 Jan |
Renal Cortex, Medulla and Pelvicaliceal System Segmentation on Arterial Phase CT Images with Random Patch-based Networks. | Tang, Yucheng; Gao, Riqiang; Lee, Ho Hin; Xu, Zhoubing; Savoie, Brent V; Bao, Shunxing; Huo, Yuankai; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Spraggins, Jeffrey; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 34531632 | 2021 |
Spatially Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier. | Wang, Zhen; Cantrell, Lee S; Schey, Kevin L | Investigative ophthalmology & visual science | 34554179 | 2021 09 02 |
Advances in spatial transcriptomic data analysis. | Dries, Ruben; Chen, Jiaji; Del Rossi, Natalie; Khan, Mohammed Muzamil; Sistig, Adriana; Yuan, Guo-Cheng | Genome research | 34599004 | 2021 Oct |
Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. | Neumann, Elizabeth K; Patterson, Nathan Heath; Rivera, Emilio S; Allen, Jamie L; Brewer, Maya; deCaestecker, Mark P; Caprioli, Richard M; Fogo, Agnes B; Spraggins, Jeffrey M | Kidney international | 34619231 | 2021 Oct 05 |
In-depth triacylglycerol profiling using MS3 Q-Trap mass spectrometry. | Cabruja, Matias; Priotti, Josefina; Domizi, Pablo; Papsdorf, Katharina; Kroetz, Deanna L; Brunet, Anne; Contrepois, Kévin; Snyder, Michael P | Analytica chimica acta | 34625255 | 2021 Nov 01 |
rPAC: Route based pathway analysis for cohorts of gene expression data sets. | Joshi, Pujan; Basso, Brent; Wang, Honglin; Hong, Seung-Hyun; Giardina, Charles; Shin, Dong-Guk | Methods (San Diego, Calif.) | 34628030 | 2021 Oct 07 |
A Pilot Study of Urine Proteomics in Covid-19-associated Acute Kidney Injury. | Ye, Yinyin; Swensen, Adam C; Wang, Yang; Kaushal, Madhurima; Salamon, Diane; Knoten, Amanda; Nicora, Carrie D; Marks, Laura; Gaut, Joseph P; Vijayan, Anitha; Orton, Daniel J; Mudd, Philip A; Parikh, Chirag R; Qian, Wei-Jun; O'Halloran, Jane A; Piehowski, Paul D; Jain, Sanjay | Kidney international reports | 34642644 | 2021 Oct 07 |
Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum, Nongluk; Diep, Dinh; Chen, Song; Lake, Blue B; Zhang, Kun | Nature protocols | 34650278 | 2021 11 |
RAP-NET: COARSE-TO-FINE MULTI-ORGAN SEGMENTATION WITH SINGLE RANDOM ANATOMICAL PRIOR. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Abramson, Richard G; Huo, Yuankai; Landman, Bennett A | Proceedings. IEEE International Symposium on Biomedical Imaging | 34667487 | 2021 Apr |
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Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. | Biancalani, Tommaso; Scalia, Gabriele; Buffoni, Lorenzo; Avasthi, Raghav; Lu, Ziqing; Sanger, Aman; Tokcan, Neriman; Vanderburg, Charles R; Segerstolpe, Åsa; Zhang, Meng; Avraham-Davidi, Inbal; Vickovic, Sanja; Nitzan, Mor; Ma, Sai; Subramanian, Ayshwarya; Lipinski, Michal; Buenrostro, Jason; Brown, Nik Bear; Fanelli, Duccio; Zhuang, Xiaowei; Macosko, Evan Z; Regev, Aviv | Nature methods | 34711971 | 2021 Nov |
Mass spectrometry-based targeted proteomics for analysis of protein mutations. | Lin, Tai-Tu; Zhang, Tong; Kitata, Reta B; Liu, Tao; Smith, Richard D; Qian, Wei-Jun; Shi, Tujin | Mass spectrometry reviews | 34719806 | 2021 Oct 31 |
Editorial: Footprints of Immune Cells in the Type 1 Diabetic Pancreas. | Brusko, Todd M; Mallone, Roberto; Rodriguez-Calvo, Teresa | Frontiers in endocrinology | 34721308 | 2021 |
Deep Learning Approach for Dynamic Sparse Sampling for High-Throughput Mass Spectrometry Imaging. | Helminiak, David; Hu, Hang; Laskin, Julia; Ye, Dong Hye | IS&T International Symposium on Electronic Imaging | 34722959 | 2021 |
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Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. | Shafin, Kishwar; Pesout, Trevor; Chang, Pi-Chuan; Nattestad, Maria; Kolesnikov, Alexey; Goel, Sidharth; Baid, Gunjan; Kolmogorov, Mikhail; Eizenga, Jordan M; Miga, Karen H; Carnevali, Paolo; Jain, Miten; Carroll, Andrew; Paten, Benedict | Nature methods | 34725481 | 2021 Nov |
Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations. | Stachtea, Xanthi; Loughrey, Maurice B; Salvucci, Manuela; Lindner, Andreas U; Cho, Sanghee; McDonough, Elizabeth; Sood, Anup; Graf, John; Santamaria-Pang, Alberto; Corwin, Alex; Laurent-Puig, Pierre; Dasgupta, Sonali; Shia, Jinru; Owens, Jonathan R; Abate, Samantha; Van Schaeybroeck, Sandra; Lawler, Mark; Prehn, Jochen H M; Ginty, Fiona; Longley, Daniel B | Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc | 34732839 | 2021 Nov 03 |
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Anatomical structures, cell types and biomarkers of the Human Reference Atlas. | Börner, Katy; Teichmann, Sarah A; Quardokus, Ellen M; Gee, James C; Browne, Kristen; Osumi-Sutherland, David; Herr 2nd, Bruce W; Bueckle, Andreas; Paul, Hrishikesh; Haniffa, Muzlifah; Jardine, Laura; Bernard, Amy; Ding, Song-Lin; Miller, Jeremy A; Lin, Shin; Halushka, Marc K; Boppana, Avinash; Longacre, Teri A; Hickey, John; Lin, Yiing; Valerius, M Todd; He, Yongqun; Pryhuber, Gloria; Sun, Xin; Jorgensen, Marda; Radtke, Andrea J; Wasserfall, Clive; Ginty, Fiona; Ho, Jonhan; Sunshine, Joel; Beuschel, Rebecca T; Brusko, Maigan; Lee, Sujin; Malhotra, Rajeev; Jain, Sanjay; Weber, Griffin | Nature cell biology | 34750582 | 2021 11 |
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures. | Ding, Hongxu; Anastopoulos, Ioannis; Bailey 4th, Andrew D; Stuart, Joshua; Paten, Benedict | Nature communications | 34764310 | 2021 11 11 |
Magnetic resonance linear accelerator technology and adaptive radiation therapy: An overview for clinicians. | Hall, William A; Paulson, Eric; Li, X Allen; Erickson, Beth; Schultz, Christopher; Tree, Alison; Awan, Musaddiq; Low, Daniel A; McDonald, Brigid A; Salzillo, Travis; Glide-Hurst, Carri K; Kishan, Amar U; Fuller, Clifton D | CA: a cancer journal for clinicians | 34792808 | 2022 01 |
Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma. | Phillips, Darci; Matusiak, Magdalena; Gutierrez, Belén Rivero; Bhate, Salil S; Barlow, Graham L; Jiang, Sizun; Demeter, Janos; Smythe, Kimberly S; Pierce, Robert H; Fling, Steven P; Ramchurren, Nirasha; Cheever, Martin A; Goltsev, Yury; West, Robert B; Khodadoust, Michael S; Kim, Youn H; Schürch, Christian M; Nolan, Garry P | Nature communications | 34795254 | 2021 Nov 18 |
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. | Greenwald, Noah F; Miller, Geneva; Moen, Erick; Kong, Alex; Kagel, Adam; Dougherty, Thomas; Fullaway, Christine Camacho; McIntosh, Brianna J; Leow, Ke Xuan; Schwartz, Morgan Sarah; Pavelchek, Cole; Cui, Sunny; Camplisson, Isabella; Bar-Tal, Omer; Singh, Jaiveer; Fong, Mara; Chaudhry, Gautam; Abraham, Zion; Moseley, Jackson; Warshawsky, Shiri; Soon, Erin; Greenbaum, Shirley; Risom, Tyler; Hollmann, Travis; Bendall, Sean C; Keren, Leeat; Graf, William; Angelo, Michael; Van Valen, David | Nature biotechnology | 34795433 | 2021 Nov 18 |
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. | Hickey, John W; Neumann, Elizabeth K; Radtke, Andrea J; Camarillo, Jeannie M; Beuschel, Rebecca T; Albanese, Alexandre; McDonough, Elizabeth; Hatler, Julia; Wiblin, Anne E; Fisher, Jeremy; Croteau, Josh; Small, Eliza C; Sood, Anup; Caprioli, Richard M; Angelo, R Michael; Nolan, Garry P; Chung, Kwanghun; Hewitt, Stephen M; Germain, Ronald N; Spraggins, Jeffrey M; Lundberg, Emma; Snyder, Michael P; Kelleher, Neil L; Saka, Sinem K | Nature methods | 34811556 | 2022 03 |
Cross-Laboratory Standardization of Preclinical Lipidomics Using Differential Mobility Spectrometry and Multiple Reaction Monitoring. | Ghorasaini, Mohan; Mohammed, Yassene; Adamski, Jerzy; Bettcher, Lisa; Bowden, John A; Cabruja, Matias; Contrepois, Kévin; Ellenberger, Mathew; Gajera, Bharat; Haid, Mark; Hornburg, Daniel; Hunter, Christie; Jones, Christina M; Klein, Theo; Mayboroda, Oleg; Mirzaian, Mina; Moaddel, Ruin; Ferrucci, Luigi; Lovett, Jacqueline; Nazir, Kenneth; Pearson, Mackenzie; Ubhi, Baljit K; Raftery, Daniel; Riols, Fabien; Sayers, Rebekah; Sijbrands, Eric J G; Snyder, Michael P; Su, Baolong; Velagapudi, Vidya; Williams, Kevin J; de Rijke, Yolanda B; Giera, Martin | Analytical chemistry | 34859676 | 2021 12 14 |
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq. | Missarova, Alsu; Jain, Jaison; Butler, Andrew; Ghazanfar, Shila; Stuart, Tim; Brusko, Maigan; Wasserfall, Clive; Nick, Harry; Brusko, Todd; Atkinson, Mark; Satija, Rahul; Marioni, John C | Genome biology | 34872616 | 2021 12 06 |
Multicellular modules as clinical diagnostic and therapeutic targets. | Baertsch, Marc-A; Nolan, Garry P; Hickey, John W | Trends in cancer | 34872889 | 2022 Mar |
Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. | Kotnala, Ankita; Anderson, David M G; Patterson, Nathan Heath; Cantrell, Lee S; Messinger, Jeffrey D; Curcio, Christine A; Schey, Kevin L | Journal of mass spectrometry : JMS | 34881479 | 2021 Dec |
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. | Zhao, Tongtong; Chiang, Zachary D; Morriss, Julia W; LaFave, Lindsay M; Murray, Evan M; Del Priore, Isabella; Meli, Kevin; Lareau, Caleb A; Nadaf, Naeem M; Li, Jilong; Earl, Andrew S; Macosko, Evan Z; Jacks, Tyler; Buenrostro, Jason D; Chen, Fei | Nature | 34912115 | 2022 01 |
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. | Sirén, Jouni; Monlong, Jean; Chang, Xian; Novak, Adam M; Eizenga, Jordan M; Markello, Charles; Sibbesen, Jonas A; Hickey, Glenn; Chang, Pi-Chuan; Carroll, Andrew; Gupta, Namrata; Gabriel, Stacey; Blackwell, Thomas W; Ratan, Aakrosh; Taylor, Kent D; Rich, Stephen S; Rotter, Jerome I; Haussler, David; Garrison, Erik; Paten, Benedict | Science (New York, N.Y.) | 34914532 | 2021 12 17 |
A census of the lung: CellCards from LungMAP. | Sun, Xin; Perl, Anne-Karina; Li, Rongbo; Bell, Sheila M; Sajti, Eniko; Kalinichenko, Vladimir V; Kalin, Tanya V; Misra, Ravi S; Deshmukh, Hitesh; Clair, Geremy; Kyle, Jennifer; Crotty Alexander, Laura E; Masso-Silva, Jorge A; Kitzmiller, Joseph A; Wikenhe | Developmental cell | 34936882 | 2022 Jan 10 |
Author Correction: Single-cell chromatin state analysis with Signac. | Nature methods | 34997233 | 2022 Feb | |
Comparison and evaluation of statistical error models for scRNA-seq. | Choudhary, Saket; Satija, Rahul | Genome biology | 35042561 | 2022 01 18 |
Self-supervised clustering of mass spectrometry imaging data using contrastive learning. | Hu, Hang; Bindu, Jyothsna Padmakumar; Laskin, Julia | Chemical science | 35059155 | 2021 Dec 22 |
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. | Risom, Tyler; Glass, David R; Averbukh, Inna; Liu, Candace C; Baranski, Alex; Kagel, Adam; McCaffrey, Erin F; Greenwald, Noah F; Rivero-Gutiérrez, Belén; Strand, Siri H; Varma, Sushama; Kong, Alex; Keren, Leeat; Srivastava, Sucheta; Zhu, Chunfang; Khair, Zumana; Veis, Deborah J; Deschryver, Katherine; Vennam, Sujay; Maley, Carlo; Hwang, E Shelley; Marks, Jeffrey R; Bendall, Sean C; Colditz, Graham A; West, Robert B; Angelo, Michael | Cell | 35063072 | 2022 01 20 |
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Temporal modelling using single-cell transcriptomics. | Ding, Jun; Sharon, Nadav; Bar-Joseph, Ziv | Nature reviews. Genetics | 35102309 | 2022 06 |
Histo-Fetch - On-the-Fly Processing of Gigapixel Whole Slide Images Simplifies and Speeds Neural Network Training. | Lutnick, Brendon; Murali, Leema Krishna; Ginley, Brandon; Rosenberg, Avi Z; Sarder, Pinaki | Journal of pathology informatics | 35136674 | 2022 |
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. | Deng, Yanxiang; Bartosovic, Marek; Kukanja, Petra; Zhang, Di; Liu, Yang; Su, Graham; Enninful, Archibald; Bai, Zhiliang; Castelo-Branco, Gonçalo; Fan, Rong | Science (New York, N.Y.) | 35143307 | 2022 02 11 |
Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. | Baskar, Reema; Kimmey, Sam C; Bendall, Sean C | Trends in cell biology | 35181197 | 2022 Feb 16 |
Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? | Plubell, Deanna L; Käll, Lukas; Webb-Robertson, Bobbie-Jo; Bramer, Lisa M; Ives, Ashley; Kelleher, Neil L; Smith, Lloyd M; Montine, Thomas J; Wu, Christine C; MacCoss, Michael J | Journal of proteome research | 35220718 | 2022 Apr 01 |
Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. | Kruse, Angela R S; Spraggins, Jeffrey M | Frontiers in physiology | 35222094 | 2022 |
Machine Learning Classifies Ferroptosis and Apoptosis Cell Death Modalities with TfR1 Immunostaining. | Jin, Jenny; Schorpp, Kenji; Samaga, Daniel; Unger, Kristian; Hadian, Kamyar; Stockwell, Brent R | ACS chemical biology | 35230809 | 2022 Mar 18 |
Ductal Carcinoma In Situ of Breast: From Molecular Etiology to Therapeutic Management. | Hophan, Shelby Lynn; Odnokoz, Olena; Liu, Huiping; Luo, Yuan; Khan, Seema; Gradishar, William; Zhou, Zhuan; Badve, Sunil; Torres, Mylin A; Wan, Yong | Endocrinology | 35245349 | 2022 Apr 01 |
Limited extent and consequences of pancreatic SARS-CoV-2 infection. | van der Heide, Verena; Jangra, Sonia; Cohen, Phillip; Rathnasinghe, Raveen; Aslam, Sadaf; Aydillo, Teresa; Geanon, Daniel; Handler, Diana; Kelley, Geoffrey; Lee, Brian; Rahman, Adeeb; Dawson, Travis; Qi, Jingjing; D'Souza, Darwin; Kim-Schulze, Seunghee; Panzer, Julia K; Caicedo, Alejandro; Kusmartseva, Irina; Posgai, Amanda L; Atkinson, Mark A; Albrecht, Randy A; García-Sastre, Adolfo; Rosenberg, Brad R; Schotsaert, Michael; Homann, Dirk | Cell reports | 35247306 | 2022 Feb 21 |
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. | Li, Dongshunyi; Velazquez, Jeremy J; Ding, Jun; Hislop, Joshua; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Genome biology | 35255944 | 2022 Mar 07 |
MITI minimum information guidelines for highly multiplexed tissue images. | Schapiro, Denis; Yapp, Clarence; Sokolov, Artem; Reynolds, Sheila M; Chen, Yu-An; Sudar, Damir; Xie, Yubin; Muhlich, Jeremy; Arias-Camison, Raquel; Arena, Sarah; Taylor, Adam J; Nikolov, Milen; Tyler, Madison; Lin, Jia-Ren; Burlingame, Erik A; Human Tumor Atlas Network; Chang, Young H; Farhi, Samouil L; Thorsson, Vésteinn; Venkatamohan, Nithya; Drewes, Julia L; Pe'er, Dana; Gutman, David A; Herrmann, Markus D; Gehlenborg, Nils; Bankhead, Peter; Roland, Joseph T; Herndon, John M; Snyder, Michael P; Angelo, Michael; Nolan, Garry; Swedlow, Jason R; Schultz, Nikolaus; Merrick, Daniel T; Mazzili, Sarah A; Cerami, Ethan; Rodig, Scott J; Santagata, Sandro; Sorger, Peter K | Nature methods | 35277708 | 2022 03 |
Clinical Implementation and Initial Experience With a 1.5 Tesla MR-Linac for MR-Guided Radiation Therapy for Gynecologic Cancer: An R-IDEAL Stage 1 and 2a First in Humans Feasibility Study of New Technology Implementation. | Lakomy, David S; Yang, Jinzhong; Vedam, Sastry; Wang, Jihong; Lee, Belinda; Sobremonte, Angela; Castillo, Pamela; Hughes, Neil; Mohammedsaid, Mustefa; Jhingran, Anuja; Klopp, Ann H; Choi, Seungtaek; Fuller, C David; Lin, Lilie L | Practical radiation oncology | 35278717 | 2022 Jul-Aug |
Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. | LeDuc, Richard D; Deutsch, Eric W; Binz, Pierre-Alain; Fellers, Ryan T; Cesnik, Anthony J; Klein, Joshua A; Van Den Bossche, Tim; Gabriels, Ralf; Yalavarthi, Arshika; Perez-Riverol, Yasset; Carver, Jeremy; Bittremieux, Wout; Kawano, Shin; Pullman, Benjamin; Bandeira, Nuno; Kelleher, Neil L; Thomas, Paul M; Vizcaíno, Juan Antonio | Journal of proteome research | 35290070 | 2022 Apr 01 |
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. | Zhang, Bingjie; Srivastava, Avi; Mimitou, Eleni; Stuart, Tim; Raimondi, Ivan; Hao, Yuhan; Smibert, Peter; Satija, Rahul | Nature biotechnology | 35332340 | 2022 Aug |
Integrated single-cell sequencing and histopathological analyses reveal diverse injury and repair responses in a participant with acute kidney injury: a clinical-molecular-pathologic correlation. | Menon, Rajasree; Bomback, Andrew S; Lake, Blue B; Stutzke, Christy; Grewenow, Stephanie M; Menez, Steven; D'Agati, Vivette D; Jain, Sanjay; Kidney Precision Medicine Project | Kidney international | 35339536 | 2022 Jun |
Referenced Kendrick Mass Defect Annotation and Class-Based Filtering of Imaging MS Lipidomics Experiments. | Richardson, Luke T; Neumann, Elizabeth K; Caprioli, Richard M; Spraggins, Jeffrey M; Solouki, Touradj | Analytical chemistry | 35344335 | 2022 04 12 |
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. | Goenka, Sneha D; Gorzynski, John E; Shafin, Kishwar; Fisk, Dianna G; Pesout, Trevor; Jensen, Tanner D; Monlong, Jean; Chang, Pi-Chuan; Baid, Gunjan; Bernstein, Jonathan A; Christle, Jeffrey W; Dalton, Karen P; Garalde, Daniel R; Grove, Megan E; Guillory, Joseph; Kolesnikov, Alexey; Nattestad, Maria; Ruzhnikov, Maura R Z; Samadi, Mehrzad; Sethia, Ankit; Spiteri, Elizabeth; Wright, Christopher J; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J; Carroll, Andrew; Paten, Benedict; Ashley, Euan A | Nature biotechnology | 35347328 | 2022 Jul |
Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF). | Liu, Candace C; Bosse, Marc; Kong, Alex; Kagel, Adam; Kinders, Robert; Hewitt, Stephen M; Varma, Sushama; van de Rijn, Matt; Nowak, Stanisław H; Bendall, Sean C; Angelo, Michael | Laboratory investigation; a journal of technical methods and pathology | 35351966 | 2022 07 |
Complete genomic and epigenetic maps of human centromeres. | Altemose, Nicolas; Logsdon, Glennis A; Bzikadze, Andrey V; Sidhwani, Pragya; Langley, Sasha A; Caldas, Gina V; Hoyt, Savannah J; Uralsky, Lev; Ryabov, Fedor D; Shew, Colin J; Sauria, Michael E G; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A; Dvorkina, Tatiana; Kunyavskaya, Olga; Vollger, Mitchell R; Rhie, Arang; McCartney, Ann M; Asri, Mobin; Lorig-Roach, Ryan; Shafin, Kishwar; Lucas, Julian K; Aganezov, Sergey; Olson, Daniel; de Lima, Leonardo Gomes; Potapova, Tamara; Hartley, Gabrielle A; Haukness, Marina; Kerpedjiev, Peter; Gusev, Fedor; Tigyi, Kristof; Brooks, Shelise; Young, Alice; Nurk, Sergey; Koren, Sergey; Salama, Sofie R; Paten, Benedict; Rogaev, Evgeny I; Streets, Aaron; Karpen, Gary H; Dernburg, Abby F; Sullivan, Beth A; Straight, Aaron F; Wheeler, Travis J; Gerton, Jennifer L; Eichler, Evan E; Phillippy, Adam M; Timp, Winston; Dennis, Megan Y; O'Neill, Rachel J; Zook, Justin M; Schatz, Michael C; Pevzner, Pavel A; Diekhans, Mark; Langley, Charles H; Alexandrov, Ivan A; Miga, Karen H | Science (New York, N.Y.) | 35357911 | 2022 04 |
A complete reference genome improves analysis of human genetic variation. | Aganezov, Sergey; Yan, Stephanie M; Soto, Daniela C; Kirsche, Melanie; Zarate, Samantha; Avdeyev, Pavel; Taylor, Dylan J; Shafin, Kishwar; Shumate, Alaina; Xiao, Chunlin; Wagner, Justin; McDaniel, Jennifer; Olson, Nathan D; Sauria, Michael E G; Vollger, Mitchell R; Rhie, Arang; Meredith, Melissa; Martin, Skylar; Lee, Joyce; Koren, Sergey; Rosenfeld, Jeffrey A; Paten, Benedict; Layer, Ryan; Chin, Chen-Shan; Sedlazeck, Fritz J; Hansen, Nancy F; Miller, Danny E; Phillippy, Adam M; Miga, Karen H; McCoy, Rajiv C; Dennis, Megan Y; Zook, Justin M; Schatz, Michael C | Science (New York, N.Y.) | 35357935 | 2022 04 |
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. | Mc Cartney, Ann M; Shafin, Kishwar; Alonge, Michael; Bzikadze, Andrey V; Formenti, Giulio; Fungtammasan, Arkarachai; Howe, Kerstin; Jain, Chirag; Koren, Sergey; Logsdon, Glennis A; Miga, Karen H; Mikheenko, Alla; Paten, Benedict; Shumate, Alaina; Soto, Daniela C; Sović, Ivan; Wood, Jonathan M D; Zook, Justin M; Phillippy, Adam M; Rhie, Arang | Nature methods | 35361931 | 2022 06 |
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation. | Formenti, Giulio; Rhie, Arang; Walenz, Brian P; Thibaud-Nissen, Françoise; Shafin, Kishwar; Koren, Sergey; Myers, Eugene W; Jarvis, Erich D; Phillippy, Adam M | Nature methods | 35361932 | 2022 06 |
Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. | Fan, Rong; Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph; Hafler, David | Research square | 35378748 | 2022 Mar 30 |
Analyzing Spatial Transcriptomics Data Using Giotto. | Del Rossi, Natalie; Chen, Jiaji G; Yuan, Guo-Cheng; Dries, Ruben | Current protocols | 35384407 | 2022 Apr |
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. | Bailey, Andrew D; Talkish, Jason; Ding, Hongxu; Igel, Haller; Duran, Alejandra; Mantripragada, Shreya; Paten, Benedict; Ares, Manuel | eLife | 35384842 | 2022 Apr 06 |
Cell Trafficking at the Intersection of the Tumor-Immune Compartments. | Du, Wenxuan; Nair, Praful; Johnston, Adrian; Wu, Pei-Hsun; Wirtz, Denis | Annual review of biomedical engineering | 35385679 | 2022 Jun 06 |
Mapping the Proteoform Landscape of Five Human Tissues. | Drown, Bryon S; Jooß, Kevin; Melani, Rafael D; Lloyd-Jones, Cameron; Camarillo, Jeannie M; Kelleher, Neil L | Journal of proteome research | 35413190 | 2022 05 06 |
Interactive single-cell data analysis using Cellar. | Hasanaj, Euxhen; Wang, Jingtao; Sarathi, Arjun; Ding, Jun; Bar-Joseph, Ziv | Nature communications | 35422041 | 2022 04 14 |
Membrane marker selection for segmenting single cell spatial proteomics data. | Dayao, Monica T; Brusko, Maigan; Wasserfall, Clive; Bar-Joseph, Ziv | Nature communications | 35422106 | 2022 04 14 |
A single-cell regulatory map of postnatal lung alveologenesis in humans and mice. | Duong, Thu Elizabeth; Wu, Yan; Sos, Brandon Chin; Dong, Weixiu; Limaye, Siddharth; Rivier, Lauraine H; Myers, Greg; Hagood, James S; Zhang, Kun | Cell genomics | 35434692 | 2022 Mar 09 |
Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. | Glass, Marla C; Glass, David R; Oliveria, John-Paul; Mbiribindi, Berenice; Esquivel, Carlos O; Krams, Sheri M; Bendall, Sean C; Martinez, Olivia M | Cell reports | 35443184 | 2022 04 19 |
Proteoform-Selective Imaging of Tissues Using Mass Spectrometry. | Yang, Manxi; Hu, Hang; Su, Pei; Thomas, Paul M; Camarillo, Jeannie M; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Kelleher, Neil L; Laskin, Julia | Angewandte Chemie (International ed. in English) | 35446460 | 2022 07 18 |
Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. | Baskar, Reema; Chen, Amy F; Favaro, Patricia; Reynolds, Warren; Mueller, Fabian; Borges, Luciene; Jiang, Sizun; Park, Hyun Shin; Kool, Eric T; Greenleaf, William J; Bendall, Sean C | Cell reports methods | 35463156 | 2022 Mar 28 |
Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. | Andreasson, Johan O L; Gotrik, Michael R; Wu, Michelle J; Wayment-Steele, Hannah K; Kladwang, Wipapat; Portela, Fernando; Wellington-Oguri, Roger; Eterna Participants; Das, Rhiju; Greenleaf, William J | Proceedings of the National Academy of Sciences of the United States of America | 35471911 | 2022 05 03 |
Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. | Ding, Jun; Alavi, Amir; Ebrahimkhani, Mo R; Bar-Joseph, Ziv | Cell reports methods | 35474899 | 2021 Oct 25 |
A complete pedigree-based graph workflow for rare candidate variant analysis. | Markello, Charles; Huang, Charles; Rodriguez, Alex; Carroll, Andrew; Chang, Pi-Chuan; Eizenga, Jordan; Markello, Thomas; Haussler, David; Paten, Benedict | Genome research | 35483961 | 2022 May |
NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. | Chen, Amy F; Parks, Benjamin; Kathiria, Arwa S; Ober-Reynolds, Benjamin; Goronzy, Jorg J; Greenleaf, William J | Nature methods | 35501385 | 2022 05 |
Unilateral Radiation Therapy for Tonsillar Cancer: Treatment Outcomes in the Era of Human Papillomavirus, Positron-Emission Tomography, and Intensity Modulated Radiation Therapy. | Taku, Nicolette; Chronowski, Gregory; Brandon Gunn, G; Morrison, William H; Gross, Neil D; Moreno, Amy C; Ferrarotto, Renata; Frank, Steven J; Fuller, C David; Goepfert, Ryan P; Phan, Jack; Lai, Stephen Y; Reddy, Jay P; Rosenthal, David I; Garden, Adam S | International journal of radiation oncology, biology, physics | 35504500 | 2022 Aug 01 |
PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. | Chen, Xu; Calandrelli, Riccardo; Girardini, John; Yan, Zhangming; Tan, Zhiqun; Xu, Xiangmin; Hiniker, Annie; Zhong, Sheng | Cell metabolism | 35508105 | 2022 05 03 |
Multi-contrast computed tomography healthy kidney atlas. | Lee, Ho Hin; Tang, Yucheng; Xu, Kaiwen; Bao, Shunxing; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Heinrich, Mattias; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Computers in biology and medicine | 35533459 | 2022 07 |
Deep learning identification of stiffness markers in breast cancer. | Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis | Biomaterials | 35537336 | 2022 06 |
Epigenetic Regulation of Heart-ECHS. | Gan, Lu; Pei, Liming | JACC. Basic to translational science | 35540104 | 2022 Apr |
Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web. | Manz, Trevor; Gold, Ilan; Patterson, Nathan Heath; McCallum, Chuck; Keller, Mark S; Herr 2nd, Bruce W; Börner, Katy; Spraggins, Jeffrey M; Gehlenborg, Nils | Nature methods | 35545714 | 2022 May |
Nuclear oligo hashing improves differential analysis of single-cell RNA-seq. | Kim, Hyeon-Jin; Booth, Greg; Saunders, Lauren; Srivatsan, Sanjay; McFaline-Figueroa, José L; Trapnell, Cole | Nature communications | 35562344 | 2022 May 13 |
New Views of Old Proteins: Clarifying the Enigmatic Proteome. | Burnum-Johnson, Kristin E; Conrads, Thomas P; Drake, Richard R; Herr, Amy E; Iyengar, Ravi; Kelly, Ryan T; Lundberg, Emma; MacCoss, Michael J; Naba, Alexandra; Nolan, Garry P; Pevzner, Pavel A; Rodland, Karin D; Sechi, Salvatore; Slavov, Nikolai; Spraggins, Jeffrey M; Van Eyk, Jennifer E; Vidal, Marc; Vogel, Christine; Walt, David R; Kelleher, Neil L | Molecular & cellular proteomics : MCP | 35654359 | 2022 Jul |
A reference tissue atlas for the human kidney. | Hansen, Jens; Sealfon, Rachel; Menon, Rajasree; Eadon, Michael T; Lake, Blue B; Steck, Becky; Anjani, Kavya; Parikh, Samir; Sigdel, Tara K; Zhang, Guanshi; Velickovic, Dusan; Barwinska, Daria; Alexandrov, Theodore; Dobi, Dejan; Rashmi, Priyanka; Otto, Edgar A; Rivera, Miguel; Rose, Michael P; Anderton, Christopher R; Shapiro, John P; Pamreddy, Annapurna; Winfree, Seth; Xiong, Yuguang; He, Yongqun; de Boer, Ian H; Hodgin, Jeffrey B; Barisoni, Laura; Naik, Abhijit S; Sharma, Kumar; Sarwal, Minnie M; Zhang, Kun; Himmelfarb, Jonathan; Rovin, Brad; El-Achkar, Tarek M; Laszik, Zoltan; He, John Cijiang; Dagher, Pierre C; Valerius, M Todd; Jain, Sanjay; Satlin, Lisa M; Troyanskaya, Olga G; Kretzler, Matthias; Iyengar, Ravi; Azeloglu, Evren U; Kidney Precision Medicine Project | Science advances | 35675394 | 2022 Jun 10 |
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. | Becker, Winston R; Nevins, Stephanie A; Chen, Derek C; Chiu, Roxanne; Horning, Aaron M; Guha, Tuhin K; Laquindanum, Rozelle; Mills, Meredith; Chaib, Hassan; Ladabaum, Uri; Longacre, Teri; Shen, Jeanne; Esplin, Edward D; Kundaje, Anshul; Ford, James M; Curtis, Christina; Snyder, Michael P; Greenleaf, William J | Nature genetics | 35726067 | 2022 Jul |
Unsupervised cell functional annotation for single-cell RNA-seq. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Genome research | 35764397 | 2022 Jun 28 |
High-Throughput Nano-DESI Mass Spectrometry Imaging of Biological Tissues Using an Integrated Microfluidic Probe. | Li, Xiangtang; Hu, Hang; Yin, Ruichuan; Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K; Laskin, Julia | Analytical chemistry | 35770488 | 2022 07 12 |
scSTEM: clustering pseudotime ordered single-cell data. | Song, Qi; Wang, Jingtao; Bar-Joseph, Ziv | Genome biology | 35799304 | 2022 07 07 |
Ferroptosis turns 10: Emerging mechanisms, physiological functions, and therapeutic applications. | Stockwell, Brent R | Cell | 35803244 | 2022 07 07 |
Hanging drop sample preparation improves sensitivity of spatial proteomics. | Kwon, Yumi; Piehowski, Paul D; Zhao, Rui; Sontag, Ryan L; Moore, Ronald J; Burnum-Johnson, Kristin E; Smith, Richard D; Qian, Wei-Jun; Kelly, Ryan T; Zhu, Ying | Lab on a chip | 35838077 | 2022 Jul 26 |
Rapid Multivariate Analysis Approach to Explore Differential Spatial Protein Profiles in Tissue. | Sharman, Kavya; Patterson, Nathan Heath; Weiss, Andy; Neumann, Elizabeth K; Guiberson, Emma R; Ryan, Daniel J; Gutierrez, Danielle B; Spraggins, Jeffrey M; Van de Plas, Raf; Skaar, Eric P; Caprioli, Richard M | Journal of proteome research | 35849531 | 2023 May 05 |
Overcoming Selection Bias In Synthetic Lethality Prediction. | Seale, Colm; Tepeli, Yasin; Gonçalves, Joana P | Bioinformatics (Oxford, England) | 35876858 | 2022 Jul 25 |
Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. | Su, Pei; McGee, John P; Durbin, Kenneth R; Hollas, Michael A R; Yang, Manxi; Neumann, Elizabeth K; Allen, Jamie L; Drown, Bryon S; Butun, Fatma Ayaloglu; Greer, Joseph B; Early, Bryan P; Fellers, Ryan T; Spraggins, Jeffrey M; Laskin, Julia; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Science advances | 35947651 | 2022 Aug 12 |
Revving an Engine of Human Metabolism: Activity Enhancement of Triosephosphate Isomerase via Hemi-Phosphorylation. | Schachner, Luis F; Soye, Benjamin Des; Ro, Soo; Kenney, Grace E; Ives, Ashley N; Su, Taojunfeng; Goo, Young Ah; Jewett, Michael C; Rosenzweig, Amy C; Kelleher, Neil L | ACS chemical biology | 35951581 | 2022 Aug 11 |
Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. | Ozonoff, Al; Schaenman, Joanna; Jayavelu, Naresh Doni; Milliren, Carly E; Calfee, Carolyn S; Cairns, Charles B; Kraft, Monica; Baden, Lindsey R; Shaw, Albert C; Krammer, Florian; van Bakel, Harm; Esserman, Denise A; Liu, Shanshan; Sesma, Ana Fernandez; Simon, Viviana; Hafler, David A; Montgomery, Ruth R; Kleinstein, Steven H; Levy, Ofer; Bime, Christian; Haddad, Elias K; Erle, David J; Pulendran, Bali; Nadeau, Kari C; Davis, Mark M; Hough, Catherine L; Messer, William B; Higuita, Nelson I Agudelo; Metcalf, Jordan P; Atkinson, Mark A; Brakenridge, Scott C; Corry, David; Kheradmand, Farrah; Ehrlich, Lauren I R; Melamed, Esther; McComsey, Grace A; Sekaly, Rafick; Diray-Arce, Joann; Peters, Bjoern; Augustine, Alison D; Reed, Elaine F; Altman, Matthew C; Becker, Patrice M; Rouphael, Nadine; IMPACC study group members | EBioMedicine | 35952496 | 2022 Sep |
Spatial profiling of chromatin accessibility in mouse and human tissues. | Deng, Yanxiang; Bartosovic, Marek; Ma, Sai; Zhang, Di; Kukanja, Petra; Xiao, Yang; Su, Graham; Liu, Yang; Qin, Xiaoyu; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Xu, Mina L; Halene, Stephanie; Craft, Joseph E; Leong, Kam W; Boldrini, Maura; Castelo-Branco, Gonçalo; Fan, Rong | Nature | 35978191 | 2022 09 |
UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. | Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv | Journal of computational biology : a journal of computational molecular cell biology | 36036832 | 2022 Nov |
Pharmacological inhibition and reversal of pancreatic acinar ductal metaplasia. | da Silva, Lais; Jiang, Jinmai; Perkins, Corey; Atanasova, Kalina Rosenova; Bray, Julie K; Bulut, Gamze; Azevedo-Pouly, Ana; Campbell-Thompson, Martha; Yang, Xiaozhi; Hakimjavadi, Hesamedin; Chamala, Srikar; Ratnayake, Ranjala; Gharaibeh, Raad Z; Li, Chenglong; Luesch, Hendrik; Schmittgen, Thomas D | Cell death discovery | 36055991 | 2022 Sep 02 |
Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. | Zemaitis, Kevin J; Veličković, Dušan; Kew, William; Fort, Kyle L; Reinhardt-Szyba, Maria; Pamreddy, Annapurna; Ding, Yanli; Kaushik, Dharam; Sharma, Kumar; Makarov, Alexander A; Zhou, Mowei; Paša-Tolić, Ljiljana | Analytical chemistry | 36067026 | 2022 09 20 |
Incidence Trends of New-Onset Diabetes in Children and Adolescents Before and During the COVID-19 Pandemic: Findings From Florida. | Guo, Yi; Bian, Jiang; Chen, Aokun; Wang, Fei; Posgai, Amanda L; Schatz, Desmond A; Shenkman, Elizabeth A; Atkinson, Mark A | Diabetes | 36094294 | 2022 Dec 01 |
CINS: Cell Interaction Network inference from Single cell expression data. | Yuan, Ye; Cosme Jr, Carlos; Adams, Taylor Sterling; Schupp, Jonas; Sakamoto, Koji; Xylourgidis, Nikos; Ruffalo, Matthew; Li, Jiachen; Kaminski, Naftali; Bar-Joseph, Ziv | PLoS computational biology | 36095011 | 2022 09 |
Polyphony: An Interactive Transfer Learning Framework for Single-Cell Data Analysis. | Cheng, Furui; Keller, Mark S; Qu, Huamin; Gehlenborg, Nils; Wang, Qianwen | IEEE transactions on visualization and computer graphics | 36155452 | 2022 Sep 26 |
GBZ file format for pangenome graphs. | Sirén, Jouni; Paten, Benedict | Bioinformatics (Oxford, England) | 36179091 | 2022 Nov 15 |
Anatomic nomenclature and 3-dimensional regional model of the human ovary: call for a new paradigm. | O'Neill, Kathleen E; Maher, Jacqueline Y; Laronda, Monica M; Duncan, Francesca E; LeDuc, Richard D; Lujan, Marla E; Oktay, Kutluk H; Pouch, Alison M; Segars, James H; Tsui, Elizabeth L; Zelinski, Mary B; Halvorson, Lisa M; Gomez-Lobo, Veronica | American journal of obstetrics and gynecology | 36191605 | 2023 Mar |
The expanding vistas of spatial transcriptomics. | Tian, Luyi; Chen, Fei; Macosko, Evan Z | Nature biotechnology | 36192637 | 2022 Oct 03 |
Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. | Ramos, Erika K; Tsai, Chia-Feng; Jia, Yuzhi; Cao, Yue; Manu, Megan; Taftaf, Rokana; Hoffmann, Andrew D; El-Shennawy, Lamiaa; Gritsenko, Marina A; Adorno-Cruz, Valery; Schuster, Emma J; Scholten, David; Patel, Dhwani; Liu, Xia; Patel, Priyam; Wray, Brian; Zhang, Youbin; Zhang, Shanshan; Moore, Ronald J; Mathews, Jeremy V; Schipma, Matthew J; Liu, Tao; Tokars, Valerie L; Cristofanilli, Massimo; Shi, Tujin; Shen, Yang; Dashzeveg, Nurmaa K; Liu, Huiping | eLife | 36193887 | 2022 Oct 04 |
A Parallelization Strategy for the Time Efficient Analysis of Thousands of LC/MS Runs in High-Performance Computing Environment. | van Zalm, Patrick; Viodé, Arthur; Smolen, Kinga; Fatou, Benoit; Hayati, Arash Nemati; Schlaffner, Christoph N; Levy, Ofer; Steen, Judith; Steen, Hanno | Journal of proteome research | 36201825 | 2022 Nov 04 |
Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program. | Shapira, Suzanne N; Naji, Ali; Atkinson, Mark A; Powers, Alvin C; Kaestner, Klaus H | Cell metabolism | 36206763 | 2022 Sep 30 |
Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing. | Kishi, Jocelyn Y; Liu, Ninning; West, Emma R; Sheng, Kuanwei; Jordanides, Jack J; Serrata, Matthew; Cepko, Constance L; Saka, Sinem K; Yin, Peng | Nature methods | 36216958 | 2022 Nov |
Spatial epitope barcoding reveals clonal tumor patch behaviors. | Rovira-Clavé, Xavier; Drainas, Alexandros P; Jiang, Sizun; Bai, Yunhao; Baron, Maya; Zhu, Bokai; Dallas, Alec E; Lee, Myung Chang; Chu, Theresa P; Holzem, Alessandra; Ayyagari, Ramya; Bhattacharya, Debadrita; McCaffrey, Erin F; Greenwald, Noah F; Markovic | Cancer cell | 36240778 | 2022 Nov 14 |
Annotation of spatially resolved single-cell data with STELLAR. | Brbić, Maria; Cao, Kaidi; Hickey, John W; Tan, Yuqi; Snyder, Michael P; Nolan, Garry P; Leskovec, Jure | Nature methods | 36280720 | 2022 Nov |
Supervised Deep Generation of High-Resolution Arterial Phase Computed Tomography Kidney Substructure Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Fogo, Agnes B; Harris, Raymond; de Caestecker, Mark P; Spraggins, Jeffrey M; Heinrich, Mattias; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 36303577 | 2022 Feb-Mar |
Creating a common language for the subanatomy of the ovary. | Tsui, Elizabeth L; O'Neill, Kathleen E; LeDuc, Richard D; Shikanov, Ariella; Gomez-Lobo, Veronica; Laronda, Monica M | Biology of reproduction | 36308436 | 2023 Jan 14 |
Single-cell spatial proteomic imaging for human neuropathology. | Vijayaragavan, Kausalia; Cannon, Bryan J; Tebaykin, Dmitry; Bossé, Marc; Baranski, Alex; Oliveria, J P; Bukhari, Syed A; Mrdjen, Dunja; Corces, M Ryan; McCaffrey, Erin F; Greenwald, Noah F; Sigal, Yari; Marquez, Diana; Khair, Zumana; Bruce, Trevor; Goldston, Mako; Bharadwaj, Anusha; Montine, Kathleen S; Angelo, R Michael; Montine, Thomas J; Bendall, Sean C | Acta neuropathologica communications | 36333818 | 2022 Nov 04 |
Gestationally dependent immune organization at the maternal-fetal interface. | Moore, Amber R; Vivanco Gonzalez, Nora; Plummer, Katherine A; Mitchel, Olivia R; Kaur, Harleen; Rivera, Moises; Collica, Brian; Goldston, Mako; Filiz, Ferda; Angelo, Michael; Palmer, Theo D; Bendall, Sean C | Cell reports | 36384130 | 2022 Nov 15 |
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. | Shao, Xinhao; Gomez, Clarissa D; Kapoor, Nandini; Considine, James M; Grams, Christopher; Gao, Yu Tom; Naba, Alexandra | Nucleic acids research | 36399478 | 2022 Nov 18 |
Multiset multicover methods for discriminative marker selection. | Hasanaj, Euxhen; Alavi, Amir; Gupta, Anupam; Póczos, Barnabás; Bar-Joseph, Ziv | Cell reports methods | 36452867 | 2022 Nov 21 |
An optimized approach and inflation media for obtaining complimentary mass spectrometry-based omics data from human lung tissue. | Lukowski, Jessica K; Olson, Heather; Velickovic, Marija; Wang, Juan; Kyle, Jennifer E; Kim, Young-Mo; Williams, Sarah M; Zhu, Ying; Huyck, Heidi L; McGraw, Matthew D; Poole, Cory; Rogers, Lisa; Misra, Ravi; Alexandrov, Theodore; Ansong, Charles; Pryhuber, Gloria S; Clair, Geremy; Adkins, Joshua N; Carson, James P; Anderton, Christopher R | Frontiers in molecular biosciences | 36465564 | 2022 |
Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. | Tang, Xiaofang; Luo, Yingjun; Yuan, Dongqiang; Calandrelli, Riccardo; Malhi, Naseeb Kaur; Sriram, Kiran; Miao, Yifei; Lou, Chih-Hong; Tsark, Walter; Tapia, Alonso; Chen, Aleysha T; Zhang, Guangyu; Roeth, Daniel; Kalkum, Markus; Wang, Zhao V; Chien, Shu; N | The Journal of clinical investigation | 36512424 | 2023 Feb 01 |
Tissue registration and exploration user interfaces in support of a human reference atlas. | Börner, Katy; Bueckle, Andreas; Herr 2nd, Bruce W; Cross, Leonard E; Quardokus, Ellen M; Record, Elizabeth G; Ju, Yingnan; Silverstein, Jonathan C; Browne, Kristen M; Jain, Sanjay; Wasserfall, Clive H; Jorgensen, Marda L; Spraggins, Jeffrey M; Patterson, N Heath; Weber, Griffin M | Communications biology | 36513738 | 2022 Dec 13 |
Evaluation of cell segmentation methods without reference segmentations. | Chen, Haoran; Murphy, Robert F | Molecular biology of the cell | 36515991 | 2023 May 15 |
Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. | Stuart, Tim; Hao, Stephanie; Zhang, Bingjie; Mekerishvili, Levan; Landau, Dan A; Maniatis, Silas; Satija, Rahul; Raimondi, Ivan | Nature biotechnology | 36536150 | 2023 Jun |
Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. | Swahn, Hannah; Li, Kun; Duffy, Tomas; Olmer, Merissa; D'Lima, Darryl D; Mondala, Tony S; Natarajan, Padmaja; Head, Steven R; Lotz, Martin K | Annals of the rheumatic diseases | 36564153 | 2023 Mar |
Machine-learning based investigation of prognostic indicators for oncological outcome of pancreatic ductal adenocarcinoma. | Chang, Jeremy; Liu, Yanan; Saey, Stephanie A; Chang, Kevin C; Shrader, Hannah R; Steckly, Kelsey L; Rajput, Maheen; Sonka, Milan; Chan, Carlos H F | Frontiers in oncology | 36568148 | 2022 |
Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. | Liao, Yen-Chen; Fulcher, James M; Degnan, David J; Williams, Sarah M; Bramer, Lisa M; Veličković, Dušan; Zemaitis, Kevin J; Veličković, Marija; Sontag, Ryan L; Moore, Ronald J; Paša-Tolić, Ljiljana; Zhu, Ying; Zhou, Mowei | Molecular & cellular proteomics : MCP | 36603806 | 2023 Feb |
193 nm Ultraviolet Photodissociation for the Characterization of Singly Charged Proteoforms Generated by MALDI. | Zemaitis, Kevin J; Zhou, Mowei; Kew, William; Paša-Tolić, Ljiljana | Journal of the American Society for Mass Spectrometry | 36622763 | 2023 Feb 01 |
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. | Sibbesen, Jonas A; Eizenga, Jordan M; Novak, Adam M; Sirén, Jouni; Chang, Xian; Garrison, Erik; Paten, Benedict | Nature methods | 36646895 | 2023 Feb |
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. | Tsai, Chia-Feng; Wang, Yi-Ting; Hsu, Chuan-Chih; Kitata, Reta Birhanu; Chu, Rosalie K; Velickovic, Marija; Zhao, Rui; Williams, Sarah M; Chrisler, William B; Jorgensen, Marda L; Moore, Ronald J; Zhu, Ying; Rodland, Karin D; Smith, Richard D; Wasserfall, Clive H; Shi, Tujin; Liu, Tao | Communications biology | 36653408 | 2023 Jan 18 |
Human pancreatic capillaries and nerve fibers persist in type 1 diabetes despite beta cell loss. | Richardson, Tiffany M; Saunders, Diane C; Haliyur, Rachana; Shrestha, Shristi; Cartailler, Jean-Philippe; Reinert, Rachel B; Petronglo, Jenna; Bottino, Rita; Aramandla, Radhika; Bradley, Amber M; Jenkins, Regina; Phillips, Sharon; Kang, Hakmook; Human Pancreas Analysis Program; Caicedo, Alejandro; Powers, Alvin C; Brissova, Marcela | American journal of physiology. Endocrinology and metabolism | 36696598 | 2023 Mar 01 |
A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases. | Conlin, Christopher C; Feng, Christine H; Digma, Leonardino A; Rodríguez-Soto, Ana E; Kuperman, Joshua M; Rakow-Penner, Rebecca; Karow, David S; White, Nathan S; Seibert, Tyler M; Hahn, Michael E; Dale, Anders M | Radiology. Imaging cancer | 36705559 | 2023 Jan |
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov, Mikhail; Billingsley, Kimberley J; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Jerez, Pilar Alvarez; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; North American Brain Expression Consortium (NABEC); Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W; Traynor, Bryan J; Miga, Karen H; Jain, Miten; Timp, Winston; Phillippy, Adam M; Chaisson, Mark; Sedlazeck, Fritz J; Blauwendraat, Cornelis; Paten, Benedict | bioRxiv : the preprint server for biology | 36711673 | 2023 Apr 05 |
Integration of spatial and single-cell data across modalities with weak linkage. | Chen, Shuxiao; Zhu, Bokai; Huang, Sijia; Hickey, John W; Lin, Kevin Z; Snyder, Michael; Greenleaf, William J; Nolan, Garry P; Zhang, Nancy R; Ma, Zongming | bioRxiv : the preprint server for biology | 36711792 | 2023 Jan 16 |
Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | bioRxiv : the preprint server for biology | 36711953 | 2023 Jan 06 |
Multimodal characterization of antigen-specific CD8 + T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | bioRxiv : the preprint server for biology | 36747786 | 2023 Jan 24 |
Optimal gap-affine alignment in O(s) space. | Marco-Sola, Santiago; Eizenga, Jordan M; Guarracino, Andrea; Paten, Benedict; Garrison, Erik; Moreto, Miquel | Bioinformatics (Oxford, England) | 36749013 | 2023 Feb 03 |
Using single cell atlas data to reconstruct regulatory networks. | Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv | Nucleic acids research | 36762475 | 2023 Apr 24 |
Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN. | Rosen, Yanay; Brbić, Maria; Roohani, Yusuf; Swanson, Kyle; Li, Ziang; Leskovec, Jure | bioRxiv : the preprint server for biology | 36778387 | 2023 Sep 24 |
Super-resolution SRS microscopy with A-PoD. | Jang, Hongje; Li, Yajuan; Fung, Anthony A; Bagheri, Pegah; Hoang, Khang; Skowronska-Krawczyk, Dorota; Chen, Xiaoping; Wu, Jane Y; Bintu, Bogdan; Shi, Lingyan | Nature methods | 36797410 | 2023 Mar |
Conundrums of choice of 'normal' kidney tissue for single cell studies. | Jain, Sanjay | Current opinion in nephrology and hypertension | 36811638 | 2023 May 01 |
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. | Liu, Yang; DiStasio, Marcello; Su, Graham; Asashima, Hiromitsu; Enninful, Archibald; Qin, Xiaoyu; Deng, Yanxiang; Nam, Jungmin; Gao, Fu; Bordignon, Pino; Cassano, Marco; Tomayko, Mary; Xu, Mina; Halene, Stephanie; Craft, Joseph E; Hafler, David; Fan, Rong | Nature biotechnology | 36823353 | 2023 Oct |
Spatially Aware Transformer Networks for Contextual Prediction of Diabetic Nephropathy Progression from Whole Slide Images. | Shickel, Benjamin; Lucarelli, Nicholas; Rao, Adish S; Yun, Donghwan; Moon, Kyung Chul; Han, Seung Seok; Sarder, Pinaki | medRxiv : the preprint server for health sciences | 36865174 | 2023 Feb 23 |
Phased nanopore assembly with Shasta and modular graph phasing with GFAse. | Lorig-Roach, Ryan; Meredith, Melissa; Monlong, Jean; Jain, Miten; Olsen, Hugh; McNulty, Brandy; Porubsky, David; Montague, Tessa; Lucas, Julian; Condon, Chris; Eizenga, Jordan; Juul, Sissel; McKenzie, Sean; Simmonds, Sara E; Park, Jimin; Asri, Mobin; Koren, Sergey; Eichler, Evan; Axel, Richard; Martin, Bruce; Carnevali, Paolo; Miga, Karen; Paten, Benedict | bioRxiv : the preprint server for biology | 36865218 | 2023 Feb 22 |
OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hart | bioRxiv : the preprint server for biology | 36865282 | 2023 May 07 |
Computational Pathology Fusing Spatial Technologies. | Border, Samuel; Lucarelli, Nicholas; Eadon, Michael T; El-Achkar, Tarek M; Jain, Sanjay; Sarder, Pinaki | Clinical journal of the American Society of Nephrology : CJASN | 36913267 | 2023 Mar 13 |
Nano-DESI Mass Spectrometry Imaging of Proteoforms in Biological Tissues with High Spatial Resolution. | Yang, Manxi; Unsihuay, Daisy; Hu, Hang; Nguele Meke, Frederick; Qu, Zihan; Zhang, Zhong-Yin; Laskin, Julia | Analytical chemistry | 36917636 | 2023 Mar 28 |
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives. | Naba, Alexandra | Molecular & cellular proteomics : MCP | 36918099 | 2023 Mar 12 |
Spatial epigenome-transcriptome co-profiling of mammalian tissues. | Zhang, Di; Deng, Yanxiang; Kukanja, Petra; Agirre, Eneritz; Bartosovic, Marek; Dong, Mingze; Ma, Cong; Ma, Sai; Su, Graham; Bao, Shuozhen; Liu, Yang; Xiao, Yang; Rosoklija, Gorazd B; Dwork, Andrew J; Mann, J John; Leong, Kam W; Boldrini, Maura; Wang, Liya; Haeussler, Maximilian; Raphael, Benjamin J; Kluger, Yuval; Castelo-Branco, Gonçalo; Fan, Rong | Nature | 36922587 | 2023 Apr |
Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. | Mastracci, Teresa L; Apte, Minoti; Amundadottir, Laufey T; Alvarsson, Alexandra; Artandi, Steven; Bellin, Melena D; Bernal-Mizrachi, Ernesto; Caicedo, Alejandro; Campbell-Thompson, Martha; Cruz-Monserrate, Zobeida; El Ouaamari, Abdelfattah; Gaulton, Kyle J; Geisz, Andrea; Goodarzi, Mark O; Hara, Manami; Hull-Meichle, Rebecca L; Kleger, Alexander; Klein, Alison P; Kopp, Janel L; Kulkarni, Rohit N; Muzumdar, Mandar D; Naren, Anjaparavanda P; Oakes, Scott A; Olesen, Søren S; Phelps, Edward A; Powers, Alvin C; Stabler, Cherie L; Tirkes, Temel; Whitcomb, David C; Yadav, Dhiraj; Yong, Jing; Zaghloul, Norann A; Pandol, Stephen J; Sander, Maike | Diabetes | 36940317 | 2023 Apr 01 |
Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. | Robinson, Makeda L; Glass, David R; Duran, Veronica; Agudelo Rojas, Olga Lucia; Sanz, Ana Maria; Consuegra, Monika; Sahoo, Malaya Kumar; Hartmann, Felix J; Bosse, Marc; Gelvez, Rosa Margarita; Bueno, Nathalia; Pinsky, Benjamin A; Montoya, Jose G; Maecker, Holden; Estupiñan Cardenas, Maria Isabel; Villar Centeno, Luis Angel; Garrido, Elsa Marina Rojas; Rosso, Fernando; Bendall, Sean C; Einav, Shirit | Science advances | 36961888 | 2023 Mar 24 |
Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas. | Herr 2nd, Bruce W; Hardi, Josef; Quardokus, Ellen M; Bueckle, Andreas; Chen, Lu; Wang, Fusheng; Caron, Anita R; Osumi-Sutherland, David; Musen, Mark A; Börner, Katy | Scientific data | 36973309 | 2023 Mar 27 |
A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics. | Viode, Arthur; van Zalm, Patrick; Smolen, Kinga K; Fatou, Benoit; Stevenson, David; Jha, Meenakshi; Levy, Ofer; Steen, Judith; Steen, Hanno; IMPACC Network | Science advances | 36989362 | 2023 Mar 29 |
Prospective validation of diffusion-weighted MRI as a biomarker of tumor response and oncologic outcomes in head and neck cancer: Results from an observational biomarker pre-qualification study. | Joint Head and Neck Radiotherapy-MRI Development Cooperative; Mohamed, Abdallah S R; Abusaif, Abdelrahman; He, Renjie; Wahid, Kareem A; Salama, Vivian; Youssef, Sara; McDonald, Brigid A; Naser, Mohamed; Ding, Yao; Salzillo, Travis C; AboBakr, Moamen A; Wang, Jihong; Lai, Stephen Y; Fuller, Clifton D | Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology | 36990394 | 2023 Jun |
Gene panel selection for targeted spatial transcriptomics. | Zhang, Yida; Petukhov, Viktor; Biederstedt, Evan; Que, Richard; Zhang, Kun; Kharchenko, Peter V | bioRxiv : the preprint server for biology | 36993340 | 2023 Mar 24 |
Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. | Gupta, Rajat M; Schnitzler, Gavin R; Fang, Shi; Lee-Kim, Vivian S; Barry, Aurelie | Arteriosclerosis, thrombosis, and vascular biology | 36994731 | 2023 May |
Systems biology approaches to unravel lymphocyte subsets and function. | Kim, YeEun; Greenleaf, William J; Bendall, Sean C | Current opinion in immunology | 37028221 | 2023 Jun |
Foundation models for generalist medical artificial intelligence. | Moor, Michael; Banerjee, Oishi; Abad, Zahra Shakeri Hossein; Krumholz, Harlan M; Leskovec, Jure; Topol, Eric J; Rajpurkar, Pranav | Nature | 37045921 | 2023 Apr |
MALDI IMS-Derived Molecular Contour Maps: Augmenting Histology Whole-Slide Images. | Sharman, Kavya; Patterson, Nathan Heath; Migas, Lukasz G; Neumann, Elizabeth K; Allen, Jamie; Gibson-Corley, Katherine N; Spraggins, Jeffrey M; Van de Plas, Raf; Skaar, Eric P; Caprioli, Richard M | Journal of the American Society for Mass Spectrometry | 37061946 | 2023 May 03 |
Uncovering the spatial landscape of molecular interactions within the tumor microenvironment through latent spaces. | Deshpande, Atul; Loth, Melanie; Sidiropoulos, Dimitrios N; Zhang, Shuming; Yuan, Long; Bell, Alexander T F; Zhu, Qingfeng; Ho, Won Jin; Santa-Maria, Cesar; Gilkes, Daniele M; Williams, Stephen R; Uytingco, Cedric R; Chew, Jennifer; Hartnett, Andrej; Bent, Zachary W; Favorov, Alexander V; Popel, Aleksander S; Yarchoan, Mark; Kiemen, Ashley; Wu, Pei-Hsun; Fujikura, Kohei; Wirtz, Denis; Wood, Laura D; Zheng, Lei; Jaffee, Elizabeth M; Anders, Robert A; Danilova, Ludmila; Stein-O'Brien, Genevieve; Kagohara, Luciane T; Fertig, Elana J | Cell systems | 37080163 | 2023 Apr 19 |
Erratum. Integrated Physiology of the Exocrine and Endocrine Compartments in Pancreatic Diseases: Workshop Proceedings. Diabetes 2023;72:433-448. | Mastracci, Teresa L; Apte, Minoti; Amundadottir, Laufey T; Alvarsson, Alexandra; Artandi, Steven; Bellin, Melena D; Bernal-Mizrachi, Ernesto; Caicedo, Alejandro; Campbell-Thompson, Martha; Cruz-Monserrate, Zobeida; Ouaamari, Abdelfattah El; Gaulton, Kyle J; Geisz, Andrea; Goodarzi, Mark O; Hara, Manami; Hull-Meichle, Rebecca L; Kleger, Alexander; Klein, Alison P; Kopp, Janel L; Kulkarni, Rohit N; Muzumdar, Mandar D; Naren, Anjaparavanda P; Oakes, Scott A; Olesen, Søren S; Phelps, Edward A; Powers, Alvin C; Stabler, Cherie L; Tirkes, Temel; Whitcomb, David C; Yadav, Dhiraj; Yong, Jing; Zaghloul, Norann A; Pandol, Stephen J; Sander, Maike | Diabetes | 37116182 | 2023 Aug 01 |
Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra | bioRxiv : the preprint server for biology | 37131773 | 2023 Apr 20 |
Pangenome graph construction from genome alignments with Minigraph-Cactus. | Hickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M; Eizenga, Jordan M; Gao, Yan; Human Pangenome Reference Consortium; Marschall, Tobias; Li, Heng; Paten, Benedict | Nature biotechnology | 37165083 | 2023 May 10 |
A draft human pangenome reference. | Liao, Wen-Wei; Asri, Mobin; Ebler, Jana; Doerr, Daniel; Haukness, Marina; Hickey, Glenn; Lu, Shuangjia; Lucas, Julian K; Monlong, Jean; Abel, Haley J; Buonaiuto, Silvia; Chang, Xian H; Cheng, Haoyu; Chu, Justin; Colonna, Vincenza; Eizenga, Jordan M; Feng, Xiaowen; Fischer, Christian; Fulton, Robert S; Garg, Shilpa; Groza, Cristian; Guarracino, Andrea; Harvey, William T; Heumos, Simon; Howe, Kerstin; Jain, Miten; Lu, Tsung-Yu; Markello, Charles; Martin, Fergal J; Mitchell, Matthew W; Munson, Katherine M; Mwaniki, Moses Njagi; Novak, Adam M; Olsen, Hugh E; Pesout, Trevor; Porubsky, David; Prins, Pjotr; Sibbesen, Jonas A; Sirén, Jouni; Tomlinson, Chad; Villani, Flavia; Vollger, Mitchell R; Antonacci-Fulton, Lucinda L; Baid, Gunjan; Baker, Carl A; Belyaeva, Anastasiya; Billis, Konstantinos; Carroll, Andrew; Chang, Pi-Chuan; Cody, Sarah; Cook, Daniel E; Cook-Deegan, Robert M; Cornejo, Omar E; Diekhans, Mark; Ebert, Peter; Fairley, Susan; Fedrigo, Olivier; Felsenfeld, Adam L; Formenti, Giulio; Frankish, Adam; Gao, Yan; Garrison, Nanibaa' A; Giron, Carlos Garcia; Green, Richard E; Haggerty, Leanne; Hoekzema, Kendra; Hourlier, Thibaut; Ji, Hanlee P; Kenny, Eimear E; Koenig, Barbara A; Kolesnikov, Alexey; Korbel, Jan O; Kordosky, Jennifer; Koren, Sergey; Lee, HoJoon; Lewis, Alexandra P; Magalhães, Hugo; Marco-Sola, Santiago; Marijon, Pierre; McCartney, Ann; McDaniel, Jennifer; Mountcastle, Jacquelyn; Nattestad, Maria; Nurk, Sergey; Olson, Nathan D; Popejoy, Alice B; Puiu, Daniela; Rautiainen, Mikko; Regier, Allison A; Rhie, Arang; Sacco, Samuel; Sanders, Ashley D; Schneider, Valerie A; Schultz, Baergen I; Shafin, Kishwar; Smith, Michael W; Sofia, Heidi J; Abou Tayoun, Ahmad N; Thibaud-Nissen, Françoise; Tricomi, Francesca Floriana; Wagner, Justin; Walenz, Brian; Wood, Jonathan M D; Zimin, Aleksey V; Bourque, Guillaume; Chaisson, Mark J P; Flicek, Paul; Phillippy, Adam M; Zook, Justin M; Eichler, Evan E; Haussler, David; Wang, Ting; Jarvis, Erich D; Miga, Karen H; Garrison, Erik; Marschall, Tobias; Hall, Ira M; Li, Heng; Paten, Benedict | Nature | 37165242 | 2023 May |
High-Throughput Mass Spectrometry Imaging of Biological Systems: Current Approaches and Future Directions. | Jiang, Li-Xue; Yang, Manxi; Wali, Syeda Nazifa; Laskin, Julia | Trends in analytical chemistry : TRAC | 37206615 | 2023 Jun |
Prospective on Imaging Mass Spectrometry in Clinical Diagnostics. | Moore, Jessica L; Patterson, Nathan Heath; Norris, Jeremy L; Caprioli, Richard M | Molecular & cellular proteomics : MCP | 37209813 | 2023 Sep |
Stabilized mosaic single-cell data integration using unshared features. | Ghazanfar, Shila; Guibentif, Carolina; Marioni, John C | Nature biotechnology | 37231260 | 2023 May 25 |
Dictionary learning for integrative, multimodal and scalable single-cell analysis. | Hao, Yuhan; Stuart, Tim; Kowalski, Madeline H; Choudhary, Saket; Hoffman, Paul; Hartman, Austin; Srivastava, Avi; Molla, Gesmira; Madad, Shaista; Fernandez-Granda, Carlos; Satija, Rahul | Nature biotechnology | 37231261 | 2023 May 25 |
Bioorthogonal Chemical Imaging of Cell Metabolism Regulated by Aromatic Amino Acids. | Bagheri, Pegah; Hoang, Khang; Kuo, Chan-Yu; Trivedi, Hetvi; Jang, Hongje; Shi, Lingyan | Journal of visualized experiments : JoVE | 37246865 | 2023 May 12 |
Polygenic prediction of preeclampsia and gestational hypertension. | Honigberg, Michael C; Truong, Buu; Khan, Raiyan R; Xiao, Brenda; Bhatta, Laxmi; Vy, Ha My T; Guerrero, Rafael F; Schuermans, Art; Selvaraj, Margaret Sunitha; Patel, Aniruddh P; Koyama, Satoshi; Cho, So Mi Jemma; Vellarikkal, Shamsudheen Karuthedath; Trinder, Mark; Urbut, Sarah M; Gray, Kathryn J; Brumpton, Ben M; Patil, Snehal; Zöllner, Sebastian; Antopia, Mariah C; Saxena, Richa; Nadkarni, Girish N; Do, Ron; Yan, Qi; Pe'er, Itsik; Verma, Shefali Setia; Gupta, Rajat M; Haas, David M; Martin, Hilary C; van Heel, David A; Laisk, Triin; Natarajan, Pradeep | Nature medicine | 37248299 | 2023 Jun |
Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer. | Dashzeveg, Nurmaa K; Jia, Yuzhi; Zhang, Youbin; Gerratana, Lorenzo; Patel, Priyam; Shajahan, Asif; Dandar, Tsogbadrakh; Ramos, Erika K; Almubarak, Hannah F; Adorno-Cruz, Valery; Taftaf, Rokana; Schuster, Emma J; Scholten, David; Sokolowski, Michael T; Reduzzi, Carolina; El-Shennawy, Lamiaa; Hoffmann, Andrew D; Manai, Maroua; Zhang, Qiang; D'Amico, Paolo; Azadi, Parastoo; Colley, Karen J; Platanias, Leonidas C; Shah, Ami N; Gradishar, William J; Cristofanilli, Massimo; Muller, William A; Cobb, Brian A; Liu, Huiping | Cancer discovery | 37272843 | 2023 Jun 05 |
The technological landscape and applications of single-cell multi-omics. | Baysoy, Alev; Bai, Zhiliang; Satija, Rahul; Fan, Rong | Nature reviews. Molecular cell biology | 37280296 | 2023 Oct |
An integrated cell atlas of the lung in health and disease. | Sikkema, Lisa; Ramírez-Suástegui, Ciro; Strobl, Daniel C; Gillett, Tessa E; Zappia, Luke; Madissoon, Elo; Markov, Nikolay S; Zaragosi, Laure-Emmanuelle; Ji, Yuge; Ansari, Meshal; Arguel, Marie-Jeanne; Apperloo, Leonie; Banchero, Martin; Bécavin, Christophe; Berg, Marijn; Chichelnitskiy, Evgeny; Chung, Mei-I; Collin, Antoine; Gay, Aurore C A; Gote-Schniering, Janine; Hooshiar Kashani, Baharak; Inecik, Kemal; Jain, Manu; Kapellos, Theodore S; Kole, Tessa M; Leroy, Sylvie; Mayr, Christoph H; Oliver, Amanda J; von Papen, Michael; Peter, Lance; Taylor, Chase J; Walzthoeni, Thomas; Xu, Chuan; Bui, Linh T; De Donno, Carlo; Dony, Leander; Faiz, Alen; Guo, Minzhe; Gutierrez, Austin J; Heumos, Lukas; Huang, Ni; Ibarra, Ignacio L; Jackson, Nathan D; Kadur Lakshminarasimha Murthy, Preetish; Lotfollahi, Mohammad; Tabib, Tracy; Talavera-López, Carlos; Travaglini, Kyle J; Wilbrey-Clark, Anna; Worlock, Kaylee B; Yoshida, Masahiro; Lung Biological Network Consortium; van den Berge, Maarten; Bossé, Yohan; Desai, Tushar J; Eickelberg, Oliver; Kaminski, Naftali; Krasnow, Mark A; Lafyatis, Robert; Nikolic, Marko Z; Powell, Joseph E; Rajagopal, Jayaraj; Rojas, Mauricio; Rozenblatt-Rosen, Orit; Seibold, Max A; Sheppard, Dean; Shepherd, Douglas P; Sin, Don D; Timens, Wim; Tsankov, Alexander M; Whitsett, Jeffrey; Xu, Yan; Banovich, Nicholas E; Barbry, Pascal; Duong, Thu Elizabeth; Falk, Christine S; Meyer, Kerstin B; Kropski, Jonathan A; Pe'er, Dana; Schiller, Herbert B; Tata, Purushothama Rao; Schultze, Joachim L; Teichmann, Sara A; Misharin, Alexander V; Nawijn, Martijn C; Luecken, Malte D; Theis, Fabian J | Nature medicine | 37291214 | 2023 Jun |
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Ginley, Brandon; Lucarelli, Nicholas; Zee, Jarcy; Jain, Sanjay; Han, Seung Sook; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Jen, Kuang-Yu; Sarder, Pinaki | bioRxiv : the preprint server for biology | 37292965 | 2023 May 18 |
Tissue Mass Spectrometry: How Solid Is Our Future? | Unsihuay, Daisy; Phipps, William S; Paulovich, Amanda G; Chapman, Jessica R; Ducret, Axel; Eberlin, Livia S; Spraggins, Jeffrey M; Goodwin, Richard J A | Clinical chemistry | 37293883 | 2023 Jul 05 |
Ex Vivo OCT-Based Multimodal Imaging of Human Donor Eyes for Research into Age-Related Macular Degeneration. | Messinger, Jeffrey D; Brinkmann, Max; Kimble, James A; Berlin, Andreas; Freund, K Bailey; Grossman, Gregory H; Ach, Thomas; Curcio, Christine A | Journal of visualized experiments : JoVE | 37306417 | 2023 May 26 |
Semantic-Aware Contrastive Learning for Multi-Object Medical Image Segmentation. | Lee, Ho Hin; Tang, Yucheng; Yang, Qi; Yu, Xin; Cai, Leon Y; Remedios, Lucas W; Bao, Shunxing; Landman, Bennett A; Huo, Yuankai | IEEE journal of biomedical and health informatics | 37310834 | 2023 Sep |
Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. | Diray-Arce, Joann; Fourati, Slim; Doni Jayavelu, Naresh; Patel, Ravi; Maguire, Cole; Chang, Ana C; Dandekar, Ravi; Qi, Jingjing; Lee, Brian H; van Zalm, Patrick; Schroeder, Andrew; Chen, Ernie; Konstorum, Anna; Brito, Anderson; Gygi, Jeremy P; Kho, Alvin; Chen, Jing; Pawar, Shrikant; Gonzalez-Reiche, Ana Silvia; Hoch, Annmarie; Milliren, Carly E; Overton, James A; Westendorf, Kerstin; IMPACC Network; Cairns, Charles B; Rouphael, Nadine; Bosinger, Steven E; Kim-Schulze, Seunghee; Krammer, Florian; Rosen, Lindsey; Grubaugh, Nathan D; van Bakel, Harm; Wilson, Michael; Rajan, Jayant; Steen, Hanno; Eckalbar, Walter; Cotsapas, Chris; Langelier, Charles R; Levy, Ofer; Altman, Matthew C; Maecker, Holden; Montgomery, Ruth R; Haddad, Elias K; Sekaly, Rafick P; Esserman, Denise; Ozonoff, Al; Becker, Patrice M; Augustine, Alison D; Guan, Leying; Peters, Bjoern; Kleinstein, Steven H | Cell reports. Medicine | 37327781 | 2023 Jun 20 |
Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. | Gosline, Sara J C; Veličković, Marija; Pino, James C; Day, Le Z; Attah, Isaac K; Swensen, Adam C; Danna, Vincent; Posso, Camilo; Rodland, Karin D; Chen, Jing; Matthews, Clayton E; Campbell-Thompson, Martha; Laskin, Julia; Burnum-Johnson, Kristin; Zhu, Ying; Piehowski, Paul D | Molecular & cellular proteomics : MCP | 37328065 | 2023 Aug |
Surgical management of lymphedema: Does a microsurgeon's bias exist? | Friedman, Rosie; Ismail Aly, Mohamed Eldardiri; Singhal, Dhruv | Microsurgery | 37339916 | 2023 Sep |
Proteome Landscapes of Human Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma. | Yi, Xiao; Zhu, Jiang; Liu, Wei; Peng, Li; Lu, Cong; Sun, Ping; Huang, Lingling; Nie, Xiu; Huang, Shi'ang; Guo, Tiannan; Zhu, Yi | Molecular & cellular proteomics : MCP | 37353004 | 2023 Aug |
Potential and risks of artificial intelligence models: Common in medicine practice and special in pediatric urology. | Wen, Yi; Di, Huajie | Journal of pediatric urology | 37355343 | 2023 Oct |
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. | Dayao, Monica T; Trevino, Alexandro; Kim, Honesty; Ruffalo, Matthew; D'Angio, H Blaize; Preska, Ryan; Duvvuri, Umamaheswar; Mayer, Aaron T; Bar-Joseph, Ziv | Bioinformatics (Oxford, England) | 37387167 | 2023 Jun 30 |
IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley, Benjamin; Woloszcuk, Kyra; Hou, Jintong; Connors, Jennifer; Cusimano, Gina; Bell, Mathew; Taramangalam, Bhavani; Fourati, Slim; Mege, Nathan; Bernui, Mariana; Altman, Matthew; Krammer, Florian; van Bakel, Harm; Maecker, Holden; Wigdahl, Brian; Cairns, Charles; Haddad, Elias; Comunale, Mary | Research square | 37398192 | 2023 Jun 02 |
SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | bioRxiv : the preprint server for biology | 37398213 | 2023 Jun 16 |
Ubiquitin-specific peptidase 22 controls integrin-dependent cancer cell stemness and metastasis. | Liu, Kun; Gao, Qiong; Jia, Yuzhi; Wei, Juncheng; Chaudhuri, Shuvam; Wang, Shengnan; Tang, Amy; Mani, Nikita; Iyer, Radhika; Cheng, Yang; Gao, Beixue; Lu, Weiyuan; Sun, Zhaolin; Liu, Huiping; Fang, Deyu | Research square | 37398311 | 2023 Jun 16 |
Spatial proteomics reveals human microglial states shaped by anatomy and neuropathology. | Mrdjen, Dunja; Amouzgar, Meelad; Cannon, Bryan; Liu, Candace; Spence, Angie; McCaffrey, Erin; Bharadwaj, Anusha; Tebaykin, Dmitry; Bukhari, Syed; Hartmann, Felix J; Kagel, Adam; Vijayaragavan, Kausalia; Oliveria, John Paul; Yakabi, Koya; Serrano, Geidy E; Corrada, Maria M; Kawas, Claudia H; Camacho, Christine; Bosse, Marc; Tibshirani, Robert; Beach, Thomas G; Angelo, Michael; Montine, Thomas; Bendall, Sean C | Research square | 37398389 | 2023 Jun 02 |
Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. | Hislop, Joshua; Alavi, Amir; Song, Qi; Schoenberger, Rayna; Kamyar, Keshavarz F; LeGraw, Ryan; Velazquez, Jeremy; Mokhtari, Tahere; Taheri, Mohammad Nasser; Rytel, Matthew; de Sousa Lopes, Susana M Chuva; Watkins, Simon; Stolz, Donna; Kiani, Samira; Sozen, Berna; Bar-Joseph, Ziv; Ebrahimkhani, Mo R | bioRxiv : the preprint server for biology | 37398391 | 2023 Jul 24 |
Joint profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations in single cells of the human brain. | Luo, Zhifei; Wen, Xingzhao; Zhao, Wenxin; Nguyen, Tri C; Wan, Xueyi; Richard, John Lalith Charles; Zhong, Sheng | bioRxiv : the preprint server for biology | 37425846 | 2023 Jun 28 |
OME-Zarr: a cloud-optimized bioimaging file format with international community support. | Moore, Josh; Basurto-Lozada, Daniela; Besson, Sébastien; Bogovic, John; Bragantini, Jordão; Brown, Eva M; Burel, Jean-Marie; Casas Moreno, Xavier; de Medeiros, Gustavo; Diel, Erin E; Gault, David; Ghosh, Satrajit S; Gold, Ilan; Halchenko, Yaroslav O; Hartley, Matthew; Horsfall, Dave; Keller, Mark S; Kittisopikul, Mark; Kovacs, Gabor; Küpcü Yoldaş, Aybüke; Kyoda, Koji; le Tournoulx de la Villegeorges, Albane; Li, Tong; Liberali, Prisca; Lindner, Dominik; Linkert, Melissa; Lüthi, Joel; Maitin-Shepard, Jeremy; Manz, Trevor; Marconato, Luca; McCormick, Matthew; Lange, Merlin; Mohamed, Khaled; Moore, William; Norlin, Nils; Ouyang, Wei; Özdemir, Bugra; Palla, Giovanni; Pape, Constantin; Pelkmans, Lucas; Pietzsch, Tobias; Preibisch, Stephan; Prete, Martin; Rzepka, Norman; Samee, Sameeul; Schaub, Nicholas; Sidky, Hythem; Solak, Ahmet Can; Stirling, David R; Striebel, Jonathan; Tischer, Christian; Toloudis, Daniel; Virshup, Isaac; Walczysko, Petr; Watson, Alan M; Weisbart, Erin; Wong, Frances; Yamauchi, Kevin A; Bayraktar, Omer; Cimini, Beth A; Gehlenborg, Nils; Haniffa, Muzlifah; Hotaling, Nathan; Onami, Shuichi; Royer, Loic A; Saalfeld, Stephan; Stegle, Oliver; Theis, Fabian J; Swedlow, Jason R | Histochemistry and cell biology | 37428210 | 2023 Sep |
SCS: cell segmentation for high-resolution spatial transcriptomics. | Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv | Nature methods | 37429992 | 2023 Aug |
Nanospray Desorption Electrospray Ionization (Nano-DESI) Mass Spectrometry Imaging with High Ion Mobility Resolution. | Jiang, Li-Xue; Hernly, Emerson; Hu, Hang; Hilger, Ryan T; Neuweger, Heiko; Yang, Manxi; Laskin, Julia | Journal of the American Society for Mass Spectrometry | 37463098 | 2023 Aug 02 |
Unsupervised Registration Refinement for Generating Unbiased Eye Atlas. | Lee, Ho Hin; Tang, Yucheng; Bao, Shunxing; Yang, Qi; Xu, Xin; Schey, Kevin L; Spraggins, Jeffrey M; Huo, Yuankai; Landman, Bennett A | Proceedings of SPIE--the International Society for Optical Engineering | 37465097 | 2023 Feb |
A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease. | Canela, Victor Hugo; Bowen, William S; Ferreira, Ricardo Melo; Syed, Farooq; Lingeman, James E; Sabo, Angela R; Barwinska, Daria; Winfree, Seth; Lake, Blue B; Cheng, Ying-Hua; Gaut, Joseph P; Ferkowicz, Michael; LaFavers, Kaice A; Zhang, Kun; Coe, Fredric L; Worcester, Elaine; Kidney Precision Medicine Project; Jain, Sanjay; Eadon, Michael T; Williams Jr, James C; El-Achkar, Tarek M | Nature communications | 37468493 | 2023 Jul 19 |
Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature. | Boppana, Avinash; Lee, Sujin; Malhotra, Rajeev; Halushka, Marc; Gustilo, Katherine S; Quardokus, Ellen M; Herr 2nd, Bruce W; Börner, Katy; Weber, Griffin M | Scientific data | 37468503 | 2023 Jul 19 |
Segmentation of human functional tissue units in support of a Human Reference Atlas. | Jain, Yashvardhan; Godwin, Leah L; Ju, Yingnan; Sood, Naveksha; Quardokus, Ellen M; Bueckle, Andreas; Longacre, Teri; Horning, Aaron; Lin, Yiing; Esplin, Edward D; Hickey, John W; Snyder, Michael P; Patterson, Nathan Heath; Spraggins, Jeffrey M; Börner, Katy | Communications biology | 37468557 | 2023 Jul 19 |
An atlas of healthy and injured cell states and niches in the human kidney. | Lake, Blue B; Menon, Rajasree; Winfree, Seth; Hu, Qiwen; Melo Ferreira, Ricardo; Kalhor, Kian; Barwinska, Daria; Otto, Edgar A; Ferkowicz, Michael; Diep, Dinh; Plongthongkum, Nongluk; Knoten, Amanda; Urata, Sarah; Mariani, Laura H; Naik, Abhijit S; Eddy, Sean; Zhang, Bo; Wu, Yan; Salamon, Diane; Williams, James C; Wang, Xin; Balderrama, Karol S; Hoover, Paul J; Murray, Evan; Marshall, Jamie L; Noel, Teia; Vijayan, Anitha; Hartman, Austin; Chen, Fei; Waikar, Sushrut S; Rosas, Sylvia E; Wilson, Francis P; Palevsky, Paul M; Kiryluk, Krzysztof; Sedor, John R; Toto, Robert D; Parikh, Chirag R; Kim, Eric H; Satija, Rahul; Greka, Anna; Macosko, Evan Z; Kharchenko, Peter V; Gaut, Joseph P; Hodgin, Jeffrey B; KPMP Consortium; Eadon, Michael T; Dagher, Pierre C; El-Achkar, Tarek M; Zhang, Kun; Kretzler, Matthias; Jain, Sanjay | Nature | 37468583 | 2023 Jul |
Organization of the human intestine at single-cell resolution. | Hickey, John W; Becker, Winston R; Nevins, Stephanie A; Horning, Aaron; Perez, Almudena Espin; Zhu, Chenchen; Zhu, Bokai; Wei, Bei; Chiu, Roxanne; Chen, Derek C; Cotter, Daniel L; Esplin, Edward D; Weimer, Annika K; Caraccio, Chiara; Venkataraaman, Vishal; Schürch, Christian M; Black, Sarah; Brbić, Maria; Cao, Kaidi; Chen, Shuxiao; Zhang, Weiruo; Monte, Emma; Zhang, Nancy R; Ma, Zongming; Leskovec, Jure; Zhang, Zhengyan; Lin, Shin; Longacre, Teri; Plevritis, Sylvia K; Lin, Yiing; Nolan, Garry P; Greenleaf, William J; Snyder, Michael | Nature | 37468586 | 2023 Jul |
Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. | Quardokus, Ellen M; Saunders, Diane C; McDonough, Elizabeth; Hickey, John W; Werlein, Christopher; Surrette, Christine; Rajbhandari, Presha; Casals, Anna Martinez; Tian, Hua; Lowery, Lisa; Neumann, Elizabeth K; Björklund, Frida; Neelakantan, Taruna V; Croteau, Josh; Wiblin, Anne E; Fisher, Jeremy; Livengood, April J; Dowell, Karen G; Silverstein, Jonathan C; Spraggins, Jeffrey M; Pryhuber, Gloria S; Deutsch, Gail; Ginty, Fiona; Nolan, Garry P; Melov, Simon; Jonigk, Danny; Caldwell, Michael A; Vlachos, Ioannis S; Muller, Werner; Gehlenborg, Nils; Stockwell, Brent R; Lundberg, Emma; Snyder, Michael P; Germain, Ronald N; Camarillo, Jeannie M; Kelleher, Neil L; Börner, Katy; Radtke, Andrea J | Nature methods | 37468619 | 2023 Aug |
KRAS(G12D) drives lepidic adenocarcinoma through stem-cell reprogramming. | Juul, Nicholas H; Yoon, Jung-Ki; Martinez, Marina C; Rishi, Neha; Kazadaeva, Yana I; Morri, Maurizio; Neff, Norma F; Trope, Winston L; Shrager, Joseph B; Sinha, Rahul; Desai, Tushar J | Nature | 37468622 | 2023 Jul |
Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). | Jain, Sanjay; Pei, Liming; Spraggins, Jeffrey M; Angelo, Michael; Carson, James P; Gehlenborg, Nils; Ginty, Fiona; Gonçalves, Joana P; Hagood, James S; Hickey, John W; Kelleher, Neil L; Laurent, Louise C; Lin, Shin; Lin, Yiing; Liu, Huiping; Naba, Alexandra; Nakayasu, Ernesto S; Qian, Wei-Jun; Radtke, Andrea; Robson, Paul; Stockwell, Brent R; Van de Plas, Raf; Vlachos, Ioannis S; Zhou, Mowei; HuBMAP Consortium; Börner, Katy; Snyder, Michael P | Nature cell biology | 37468756 | 2023 Aug |
3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. | Ghose, Soumya; Ju, Yingnan; McDonough, Elizabeth; Ho, Jonhan; Karunamurthy, Arivarasan; Chadwick, Chrystal; Cho, Sanghee; Rose, Rachel; Corwin, Alex; Surrette, Christine; Martinez, Jessica; Williams, Eric; Sood, Anup; Al-Kofahi, Yousef; Falo Jr, Louis D; Börner, Katy; Ginty, Fiona | Communications biology | 37468758 | 2023 Jul 19 |
Non-Linear Lymphatic Anatomy in Breast Cancer Patients Prior to Axillary Lymph Node Dissection: A Risk Factor For Lymphedema Development. | Kinney, JacqueLyn R; Friedman, Rosie; Kim, Erin; Tillotson, Elizabeth; Shillue, Kathy; Lee, Bernard T; Singhal, Dhruv | Journal of mammary gland biology and neoplasia | 37480365 | 2023 Jul 22 |
Editorial: Global excellence in inflammatory diseases: North America 2021. | Kusner, Linda L; Misra, Ravi S; Lucas, Rudolf | Frontiers in immunology | 37483602 | 2023 |
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases. | Ober-Reynolds, Benjamin; Wang, Chen; Ko, Justin M; Rios, Eon J; Aasi, Sumaira Z; Davis, Mark M; Oro, Anthony E; Greenleaf, William J | Nature genetics | 37500727 | 2023 Aug |
Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms. | Jain, Yashvardhan; Godwin, Leah L; Joshi, Sripad; Mandarapu, Shriya; Le, Trang; Lindskog, Cecilia; Lundberg, Emma; Börner, Katy | Nature communications | 37537179 | 2023 Aug 03 |
Matrisome AnalyzeR - a suite of tools to annotate and quantify ECM molecules in big datasets across organisms. | Petrov, Petar B; Considine, James M; Izzi, Valerio; Naba, Alexandra | Journal of cell science | 37555624 | 2023 Sep 01 |
Systematic Sampling of the Female Reproductive System for Molecular Characterization. | Fisher, Stephen A; Grijalva, Marielena; Guo, Rong; Johnston, Sarah A; Laurent, Louise C; Nguyen, Hieu; Renz, John; Rosario, Jean G; Rudich, Steven; Gregory, Brian D; Kim, Junhyong; O'Neill, Kathleen | Current protocols | 37584588 | 2023 Aug |
Segmentation quality assessment by automated detection of erroneous surface regions in medical images. | Zaman, Fahim Ahmed; Zhang, Lichun; Zhang, Honghai; Sonka, Milan; Wu, Xiaodong | Computers in biology and medicine | 37591161 | 2023 Sep |
Edematous Dermal Thickening on Magnetic Resonance Imaging as a Biomarker for Lymphatic Surgical Outcomes. | Kinney, JacqueLyn R; Babapour, Sara; Kim, Erin; Friedman, Rosie; Singhal, Dhruv; Lee, Bernard T; Tsai, Leo L | Medicina (Kaunas, Lithuania) | 37629659 | 2023 Jul 26 |
Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter; Yuan, Yixu; Zhang, Yida; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | bioRxiv : the preprint server for biology | 37645998 | 2023 Aug 19 |
Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. | Favaro, Patricia; Glass, David R; Borges, Luciene; Baskar, Reema; Reynolds, Warren; Ho, Daniel; Bruce, Trevor; Tebaykin, Dmitry; Scanlon, Vanessa M; Shestopalov, Ilya; Bendall, Sean C | bioRxiv : the preprint server for biology | 37693547 | 2023 Aug 30 |
Transcriptomic profiling of tissue environments critical for post-embryonic patterning and morphogenesis of zebrafish skin. | Aman, Andrew J; Saunders, Lauren M; Carr, August A; Srivatasan, Sanjay; Eberhard, Colten; Carrington, Blake; Watkins-Chow, Dawn; Pavan, William J; Trapnell, Cole; Parichy, David M | eLife | 37695017 | 2023 Sep 11 |
Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. | Kolmogorov, Mikhail; Billingsley, Kimberley J; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Alvarez Jerez, Pilar; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W; Traynor, Bryan J; Miga, Karen H; Jain, Miten; Timp, Winston; Phillippy, Adam M; Chaisson, Mark; Sedlazeck, Fritz J; Blauwendraat, Cornelis; Paten, Benedict | Nature methods | 37710018 | 2023 Oct |
Early cancer detection by SERS spectroscopy and machine learning. | Shi, Lingyan; Li, Yajuan; Li, Zhi | Light, science & applications | 37714845 | 2023 Sep 15 |
Multimodal single-cell datasets characterize antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection. | Zhang, Bingjie; Upadhyay, Rabi; Hao, Yuhan; Samanovic, Marie I; Herati, Ramin S; Blair, John D; Axelrad, Jordan; Mulligan, Mark J; Littman, Dan R; Satija, Rahul | Nature immunology | 37735591 | 2023 Oct |
Local read haplotagging enables accurate long-read small variant calling. | Kolesnikov, Alexey; Cook, Daniel; Nattestad, Maria; McNulty, Brandy; Gorzynski, John; Goenka, Sneha; Ashley, Euan A; Jain, Miten; Miga, Karen H; Paten, Benedict; Chang, Pi-Chuan; Carroll, Andrew; Shafin, Kishwar | bioRxiv : the preprint server for biology | 37745389 | 2023 Sep 12 |
Navigating the kidney organoid: insights into assessment and enhancement of nephron function. | Tabibzadeh, Nahid; Satlin, Lisa M; Jain, Sanjay; Morizane, Ryuji | American journal of physiology. Renal physiology | 37767571 | 2023 Dec 01 |
Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. | Piyadasa, Hadeesha; Oberlton, Benjamin; Kong, Alex; Camacho Fullaway, Christine; Reddy Varra, Sricharan; Sowers, Cameron; Tsai, Albert G | Journal of visualized experiments : JoVE | 37782085 | 2023 Sep 15 |
A monolithic microfluidic probe for ambient mass spectrometry imaging of biological tissues. | Jiang, Li-Xue; Polack, Matthias; Li, Xiangtang; Yang, Manxi; Belder, Detlev; Laskin, Julia | Lab on a chip | 37782224 | 2023 Oct 24 |
Mechano-induced homotypic patterned domain formation by monocytes. | Wirtz, Denis; Du, Wenxuan; Zhu, Jingyi; Wu, Yufei; Kiemen, Ashley; Wan, Zeqi; Hanna, Eban; Sun, Sean | Research square | 37790337 | 2023 Sep 22 |
The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. | Pepin, Mark E; Gupta, Rajat | The American journal of pathology | 37827214 | 2023 Oct 10 |
High-resolution integrated microfluidic probe for mass spectrometry imaging of biological tissues. | Li, Xiangtang; Hu, Hang; Laskin, Julia | Analytica chimica acta | 37827646 | 2023 Oct 23 |
Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee, John P; Su, Pei; Durbin, Kenneth R; Hollas, Michael A R; Bateman, Nicholas W; Maxwell, G Larry; Conrads, Thomas P; Fellers, Ryan T; Melani, Rafael D; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Nature communications | 37838706 | 2023 Oct 14 |
Functional Tissue Units in the Human Reference Atlas. | Bidanta, Supriya; Börner, Katy; Herr 2nd, Bruce W; Nagy, Marcell; Gustilo, Katherine S; Bajema, Rachel; Maier, Libby; Molontay, Roland; Weber, Griffin | bioRxiv : the preprint server for biology | 37905079 | 2023 Oct 26 |
Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia. | Tan, Kai; Xu, Jason; Chen, Changya; Vincent, Tiffaney; Pölönen, Petri; Hu, Jianzhong; Yoshimura, Satoshi; Yu, Wenbao; Sussman, Jonathan; Chen, Chia-Hui; Li, Elizabeth; Diorio, Caroline; Shraim, Rawan; Newman, Haley; Uppuluri, Lahari; Li, Alexander; Chen, Gregory; Bandyopadhyay, Shovik; Wu, David; Ding, Yang-Yang; Xu, Jessica; Lim, Tristan; Hsu, Miles; Thadi, Anusha; Ahn, Kyung Jin; Wu, Chi-Yun; Peng, Jacqueline; Sun, Yusha; Wang, Alice; Mehta, Rushabh; Frank, David; Meyer, Lauren; Loh, Mignon; Raetz, Elizabeth; Chen, Zhiguo; Wood, Brent; Devidas, Meenakshi; Dunsmore, Kimberly; Winter, Stuart; Chang, Ti-Cheng; Wu, Gang; Pounds, Stanley; Zhang, Nancy; Carroll, William; Hunger, Stephen; Bernt, Kathrin; Yang, Jun; Mullighan, Charles; Teachey, David | Research square | 37961674 | 2023 Oct 30 |
Dimension-agnostic and granularity-based spatially variable gene identification using BSP. | Wang, Juexin; Li, Jinpu; Kramer, Skyler T; Su, Li; Chang, Yuzhou; Xu, Chunhui; Eadon, Michael T; Kiryluk, Krzysztof; Ma, Qin; Xu, Dong | Nature communications | 37963892 | 2023 Nov 14 |
Correlating Deep Learning-Based Automated Reference Kidney Histomorphometry with Patient Demographics and Creatinine. | Lucarelli, Nicholas; Ginley, Brandon; Zee, Jarcy; Mimar, Sayat; Paul, Anindya S; Jain, Sanjay; Han, Seung Seok; Rodrigues, Luis; Ozrazgat-Baslanti, Tezcan; Wong, Michelle L; Nadkarni, Girish; Clapp, William L; Jen, Kuang-Yu; Sarder, Pinaki | Kidney360 | 37966063 | 2023 Dec 01 |
Multimodal imaging of metabolic activities for distinguishing subtypes of breast cancer. | Li, Zhi; Nguyen, Chloe; Jang, Hongje; Hoang, David; Min, SoeSu; Ackerstaff, Ellen; Koutcher, Jason A; Shi, Lingyan | Biomedical optics express | 38021123 | 2023 Nov 01 |
Human mobility networks reveal increased segregation in large cities. | Nilforoshan, Hamed; Looi, Wenli; Pierson, Emma; Villanueva, Blanca; Fishman, Nic; Chen, Yiling; Sholar, John; Redbird, Beth; Grusky, David; Leskovec, Jure | Nature | 38030732 | 2023 Dec |
Author Correction: Automated imaging and identification of proteoforms directly from ovarian cancer tissue. | McGee, John P; Su, Pei; Durbin, Kenneth R; Hollas, Michael A R; Bateman, Nicholas W; Maxwell, G Larry; Conrads, Thomas P; Fellers, Ryan T; Melani, Rafael D; Camarillo, Jeannie M; Kafader, Jared O; Kelleher, Neil L | Nature communications | 38040721 | 2023 Dec 01 |
Advances in Imaging Mass Spectrometry for Biomedical and Clinical Research. | Djambazova, Katerina V; van Ardenne, Jacqueline M; Spraggins, Jeffrey M | Trends in analytical chemistry : TRAC | 38045023 | 2023 Dec |
A Foundation Model for Cell Segmentation. | Israel, Uriah; Marks, Markus; Dilip, Rohit; Li, Qilin; Schwartz, Morgan; Pradhan, Elora; Pao, Edward; Li, Shenyi; Pearson-Goulart, Alexander; Perona, Pietro; Gkioxari, Georgia; Barnowski, Ross; Yue, Yisong; Van Valen, David | bioRxiv : the preprint server for biology | 38045277 | 2023 Nov 20 |
DRAVA: Aligning Human Concepts with Machine Learning Latent Dimensions for the Visual Exploration of Small Multiples. | Wang, Qianwen; L'Yi, Sehi; Gehlenborg, Nils | Proceedings of the SIGCHI conference on human factors in computing systems. CHI Conference | 38074525 | 2023 Apr |
T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. | Hickey, John W; Haist, Maximillian; Horowitz, Nina; Caraccio, Chiara; Tan, Yuqi; Rech, Andrew J; Baertsch, Marc-Andrea; Rovira-Clavé, Xavier; Zhu, Bokai; Vazquez, Gustavo; Barlow, Graham; Agmon, Eran; Goltsev, Yury; Sunwoo, John B; Covert, Markus; Nolan, | Cell reports | 38085642 | 2023 Dec 26 |
Modelling post-implantation human development to yolk sac blood emergence. | Hislop, Joshua; Song, Qi; Keshavarz F, Kamyar; Alavi, Amir; Schoenberger, Rayna; LeGraw, Ryan; Velazquez, Jeremy J; Mokhtari, Tahere; Taheri, Mohammad Naser; Rytel, Matthew; Chuva de Sousa Lopes, Susana M; Watkins, Simon; Stolz, Donna; Kiani, Samira; Soze | Nature | 38092041 | 2024 Feb |
Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell, Andrew J C; Weir, Jackson A; Nadaf, Naeem M; Shabet, Matthew; Kumar, Vipin; Kambhampati, Sandeep; Raichur, Ruth; Marrero, Giovanni J; Liu, Sophia; Balderrama, Karol S; Vanderburg, Charles R; Shanmugam, Vignesh; Tian, Luyi; Iorgulescu, J Bryan; Yoon, Charles H; Wu, Catherine J; Macosko, Evan Z; Chen, Fei | Nature | 38093010 | 2024 Jan |
Parsing 20 Years of Public Data by AI Maps Trends in Proteomics and Forecasts Technology. | Green, Josiah J; Grimm, Chase; Fristo, Andre; Byrum, Joseph; Kelleher, Neil L | Journal of proteome research | 38096378 | 2024 Feb 02 |
Spatial pharmacology using mass spectrometry imaging. | Rajbhandari, Presha; Neelakantan, Taruna V; Hosny, Noreen; Stockwell, Brent R | Trends in pharmacological sciences | 38103980 | 2024 Jan |
Integrating Multiplexed Imaging and Multiscale Modeling Identifies Tumor Phenotype Transformation as a Critical Component of Therapeutic T Cell Efficacy. | Hickey, John W; Agmon, Eran; Horowitz, Nina; Lamore, Matthew; Sunwoo, John; Covert, Markus; Nolan, Garry P | bioRxiv : the preprint server for biology | 38106218 | 2023 Dec 08 |
Discussion: Commercial Insurance Rates and Coding for Lymphedema Procedures: The Current State of Confusion and Need for Consensus. | Friedman, Rosie; Lee, Bernard T; Chatterjee, Abhishek; Singhal, Dhruv | Plastic and reconstructive surgery | 38127452 | 2024 Jan 01 |
Thermal-plex: fluidic-free, rapid sequential multiplexed imaging with DNA-encoded thermal channels. | Hong, Fan; Kishi, Jocelyn Y; Delgado, Ryan N; Jeong, Jiyoun; Saka, Sinem K; Su, Hanquan; Cepko, Constance L; Yin, Peng | Nature methods | 38151595 | 2024 Feb |
Engineering self-propelled tumor-infiltrating CAR T cells using synthetic velocity receptors. | Johnston, Adrian C; Alicea, Gretchen M; Lee, Cameron C; Patel, Payal V; Hanna, Eban A; Vaz, Eduarda; Forjaz, André; Wan, Zeqi; Nair, Praful R; Lim, Yeongseo; Chen, Tina; Du, Wenxuan; Kim, Dongjoo; Nichakawade, Tushar D; Rebecca, Vito W; Bonifant, Challice L; Fan, Rong; Kiemen, Ashley L; Wu, Pei-Hsun; Wirtz, Denis | bioRxiv : the preprint server for biology | 38168186 | 2024 Mar 26 |
Personalized Pangenome References. | Sirén, Jouni; Eskandar, Parsa; Ungaro, Matteo Tommaso; Hickey, Glenn; Eizenga, Jordan M; Novak, Adam M; Chang, Xian; Chang, Pi-Chuan; Kolmogorov, Mikhail; Carroll, Andrew; Monlong, Jean; Paten, Benedict | bioRxiv : the preprint server for biology | 38168361 | 2023 Dec 15 |
Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. | Ozonoff, Al; Jayavelu, Naresh Doni; Liu, Shanshan; Melamed, Esther; Milliren, Carly E; Qi, Jingjing; Geng, Linda N; McComsey, Grace A; Cairns, Charles B; Baden, Lindsey R; Schaenman, Joanna; Shaw, Albert C; Samaha, Hady; Seyfert-Margolis, Vicki; Krammer, Florian; Rosen, Lindsey B; Steen, Hanno; Syphurs, Caitlin; Dandekar, Ravi; Shannon, Casey P; Sekaly, Rafick P; Ehrlich, Lauren I R; Corry, David B; Kheradmand, Farrah; Atkinson, Mark A; Brakenridge, Scott C; Higuita, Nelson I Agudelo; Metcalf, Jordan P; Hough, Catherine L; Messer, William B; Pulendran, Bali; Nadeau, Kari C; Davis, Mark M; Sesma, Ana Fernandez; Simon, Viviana; van Bakel, Harm; Kim-Schulze, Seunghee; Hafler, David A; Levy, Ofer; Kraft, Monica; Bime, Chris; Haddad, Elias K; Calfee, Carolyn S; Erle, David J; Langelier, Charles R; Eckalbar, Walter; Bosinger, Steven E; IMPACC Network; Peters, Bjoern; Kleinstein, Steven H; Reed, Elaine F; Augustine, Alison D; Diray-Arce, Joann; Maecker, Holden T; Altman, Matthew C; Montgomery, Ruth R; Becker, Patrice M; Rouphael, Nadine | Nature communications | 38172101 | 2024 Jan 03 |
Lysolipids are prominent in subretinal drusenoid deposits, a high-risk phenotype in age-related macular degeneration. | Anderson, David M G; Kotnala, Ankita; Migas, Lukasz G; Patterson, Nathan Heath; Tideman, Léonore; Cao, Dongfeng; Adhikari, Bibek; Messinger, Jeffrey D; Ach, Thomas; Tortorella, Sara; Van de Plas, Raf; Curcio, Christine A; Schey, Kevin L | Frontiers in ophthalmology | 38186747 | 2023 |
scResolve: Recovering single cell expression profiles from multi-cellular spatial transcriptomics. | Chen, Hao; Lee, Young Je; Ovando, Jose A; Rosas, Lorena; Rojas, Mauricio; Mora, Ana L; Bar-Joseph, Ziv; Lugo-Martinez, Jose | bioRxiv : the preprint server for biology | 38187629 | 2023 Dec 19 |
Unsupervised and supervised discovery of tissue cellular neighborhoods from cell phenotypes. | Hu, Yuxuan; Rong, Jiazhen; Xu, Yafei; Xie, Runzhi; Peng, Jacqueline; Gao, Lin; Tan, Kai | Nature methods | 38191930 | 2024 Jan 08 |
IgM N-glycosylation correlates with COVID-19 severity and rate of complement deposition. | Haslund-Gourley, Benjamin S; Woloszczuk, Kyra; Hou, Jintong; Connors, Jennifer; Cusimano, Gina; Bell, Mathew; Taramangalam, Bhavani; Fourati, Slim; Mege, Nathan; Bernui, Mariana; Altman, Matthew C; Krammer, Florian; van Bakel, Harm; IMPACC Network; Maecker, Holden T; Rouphael, Nadine; Diray-Arce, Joann; Wigdahl, Brian; Kutzler, Michele A; Cairns, Charles B; Haddad, Elias K; Comunale, Mary Ann | Nature communications | 38195739 | 2024 Jan 09 |
Host-Microbe Multi-omic Profiling Identifies a Unique Program of COVID-19 Inflammatory Dysregulation in Solid Organ Transplant Recipients. | Langelier, Charles; Pickering, Harry; Schaenman, Joanna; Phan, Hoang; Maguire, Cole; Tsitsiklis, Alexandra; Rouphael, Nadine; Higuita, Nelson; Atkinson, Mark; Breckenridge, Scott; Fung, Monica; Messer, William; IMPACC Network; Salehi-Rad, Ramin; Altman, M | Research square | 38196658 | 2023 Dec 20 |
The chromatin landscape of healthy and injured cell types in the human kidney. | Gisch, Debora L; Brennan, Michelle; Lake, Blue B; Basta, Jeannine; Keller, Mark S; Melo Ferreira, Ricardo; Akilesh, Shreeram; Ghag, Reetika; Lu, Charles; Cheng, Ying-Hua; Collins, Kimberly S; Parikh, Samir V; Rovin, Brad H; Robbins, Lynn; Stout, Lisa; Conklin, Kimberly Y; Diep, Dinh; Zhang, Bo; Knoten, Amanda; Barwinska, Daria; Asghari, Mahla; Sabo, Angela R; Ferkowicz, Michael J; Sutton, Timothy A; Kelly, Katherine J; De Boer, Ian H; Rosas, Sylvia E; Kiryluk, Krzysztof; Hodgin, Jeffrey B; Alakwaa, Fadhl; Winfree, Seth; Jefferson, Nichole; Türkmen, Aydın; Gaut, Joseph P; Gehlenborg, Nils; Phillips, Carrie L; El-Achkar, Tarek M; Dagher, Pierre C; Hato, Takashi; Zhang, Kun; Himmelfarb, Jonathan; Kretzler, Matthias; Mollah, Shamim; Kidney Precision Medicine Project (KPMP); Jain, Sanjay; Rauchman, Michael; Eadon, Michael T | Nature communications | 38199997 | 2024 Jan 10 |
Toward a common standard for data and specimen provenance in life sciences. | Wittner, Rudolf; Holub, Petr; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Plass, Markus; Allocca, Clare; Betsou, Fay; Burdett, Tony; Cancio, Ibon; Chapman, Adriane; Chapman, Martin; Courtot, Mélanie; Curcin, Vasa; Eder, Johann; Elliot, Mark; Exter, Katrina; Goble, Carole; Golebiewski, Martin; Kisler, Bron; Kremer, Andreas; Leo, Simone; Lin-Gibson, Sheng; Marsano, Anna; Mattavelli, Marco; Moore, Josh; Nakae, Hiroki; Perseil, Isabelle; Salman, Ayat; Sluka, James; Soiland-Reyes, Stian; Strambio-De-Castillia, Caterina; Sussman, Michael; Swedlow, Jason R; Zatloukal, Kurt; Geiger, Jörg | Learning health systems | 38249839 | 2024 Jan |
Lymphatic Microsurgical Preventative Healing Approach for the Primary Prevention of Lymphedema: A 4-Year Follow-Up. | Friedman, Rosie; Johnson, Anna Rose; Brunelle, Cheryl L; Chang, David W; Coriddi, Michelle; Dayan, Joseph H; Mehrara, Babak J; Skoracki, Roman; Taghian, Alphonse G; Singhal, Dhruv | Plastic and reconstructive surgery | 38266142 | 2024 Feb 01 |
Super-Resolution Stimulated Raman Scattering Microscopy with Graphical User Interface-Supported A-PoD. | Jang, Hongje; Li, Yajuan; Wu, Shuang; Shi, Lingyan | Current protocols | 38270527 | 2024 Jan |
Gene panel selection for targeted spatial transcriptomics. | Zhang, Yida; Petukhov, Viktor; Biederstedt, Evan; Que, Richard; Zhang, Kun; Kharchenko, Peter V | Genome biology | 38273415 | 2024 Jan 25 |
Expanding the coverage of spatial proteomics: a machine learning approach. | Sun, Huangqingbo; Li, Jiayi; Murphy, Robert F | Bioinformatics (Oxford, England) | 38310340 | 2024 Feb 01 |
Convergence of coronary artery disease genes onto endothelial cell programs. | Schnitzler, Gavin R; Kang, Helen; Fang, Shi; Angom, Ramcharan S; Lee-Kim, Vivian S; Ma, X Rosa; Zhou, Ronghao; Zeng, Tony; Guo, Katherine; Taylor, Martin S; Vellarikkal, Shamsudheen K; Barry, Aurelie E; Sias-Garcia, Oscar; Bloemendal, Alex; Munson, Glen; Guckelberger, Philine; Nguyen, Tung H; Bergman, Drew T; Hinshaw, Stephen; Cheng, Nathan; Cleary, Brian; Aragam, Krishna; Lander, Eric S; Finucane, Hilary K; Mukhopadhyay, Debabrata; Gupta, Rajat M; Engreitz, Jesse M | Nature | 38326615 | 2024 Feb |
Far-red chemigenetic biosensors for multi-dimensional and super-resolved kinase activity imaging. | Frei, Michelle S; Sanchez, Samantha A; Liu, Longwei; Schneider, Falk; Wang, Zichen; Hakozaki, Hiroyuki; Li, Yajuan; Lyons, Anne C; Rohm, Theresa V; Olefsky, Jerrold M; Shi, Lingyan; Schöneberg, Johannes; Fraser, Scott E; Mehta, Sohum; Wang, Yingxiao; Zhang, Jin | bioRxiv : the preprint server for biology | 38370804 | 2024 Feb 11 |
Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. | Bai, Zhiliang; Zhang, Dingyao; Gao, Yan; Tao, Bo; Bao, Shuozhen; Enninful, Archibald; Zhang, Daiwei; Su, Graham; Tian, Xiaolong; Zhang, Ningning; Xiao, Yang; Liu, Yang; Gerstein, Mark; Li, Mingyao; Xing, Yi; Lu, Jun; Xu, Mina L; Fan, Rong | bioRxiv : the preprint server for biology | 38370833 | 2024 Feb 08 |
vSPACE: Exploring Virtual Spatial Representation of Articular Chondrocytes at the Single-Cell Level. | Zhang, Chenyu; Wang, Honglin; Hong, Seung-Hyun; Olmer, Merissa; Swahn, Hannah; Lotz, Martin K; Maye, Peter; Rowe, David; Shin, Dong-Guk | bioRxiv : the preprint server for biology | 38370845 | 2024 Feb 10 |
Multi-molecular hyperspectral PRM-SRS microscopy. | Zhang, Wenxu; Li, Yajuan; Fung, Anthony A; Li, Zhi; Jang, Hongje; Zha, Honghao; Chen, Xiaoping; Gao, Fangyuan; Wu, Jane Y; Sheng, Huaxin; Yao, Junjie; Skowronska-Krawczyk, Dorota; Jain, Sanjay; Shi, Lingyan | Nature communications | 38383552 | 2024 Feb 21 |
Host-Microbe Multiomic Profiling Reveals Age-Dependent COVID-19 Immunopathology. | Van Phan, Hoang; Tsitsiklis, Alexandra; Maguire, Cole P; Haddad, Elias K; Becker, Patrice M; Kim-Schulze, Seunghee; Lee, Brian; Chen, Jing; Hoch, Annmarie; Pickering, Harry; Van Zalm, Patrick; Altman, Matthew C; Augustine, Alison D; Calfee, Carolyn S; Bosinger, Steve; Cairns, Charles; Eckalbar, Walter; Guan, Leying; Jayavelu, Naresh Doni; Kleinstein, Steven H; Krammer, Florian; Maecker, Holden T; Ozonoff, Al; Peters, Bjoern; Rouphael, Nadine; IMPACC Network; Montgomery, Ruth R; Reed, Elaine; Schaenman, Joanna; Steen, Hanno; Levy, Ofer; Diray-Arce, Joann; Langelier, Charles R | medRxiv : the preprint server for health sciences | 38405760 | 2024 Feb 13 |
Spatial top-down proteomics for the functional characterization of human kidney. | Zemaitis, Kevin J; Fulcher, James M; Kumar, Rashmi; Degnan, David J; Lewis, Logan A; Liao, Yen-Chen; Veličković, Marija; Williams, Sarah M; Moore, Ronald J; Bramer, Lisa M; Veličković, Dušan; Zhu, Ying; Zhou, Mowei; Paša-Tolić, Ljiljana | bioRxiv : the preprint server for biology | 38405958 | 2024 Feb 13 |
A Panoramic View of Cell Population Dynamics in Mammalian Aging. | Zhang, Zehao; Schaefer, Chloe; Jiang, Weirong; Lu, Ziyu; Lee, Jasper; Sziraki, Andras; Abdulraouf, Abdulraouf; Wick, Brittney; Haeussler, Maximilian; Li, Zhuoyan; Molla, Gesmira; Satija, Rahul; Zhou, Wei; Cao, Junyue | bioRxiv : the preprint server for biology | 38496474 | 2024 Mar 05 |
Predicting drug outcome of population via clinical knowledge graph. | Brbić, Maria; Yasunaga, Michihiro; Agarwal, Prabhat; Leskovec, Jure | medRxiv : the preprint server for health sciences | 38496488 | 2024 Mar 08 |
Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. | Kwon, Yumi; Woo, Jongmin; Yu, Fengchao; Williams, Sarah M; Markillie, Lye Meng; Moore, Ronald J; Nakayasu, Ernesto S; Chen, Jing; Campbell-Thompson, Martha; Mathews, Clayton E; Nesvizhskii, Alexey I; Qia, Wei-Jun; Zhu, Ying | bioRxiv : the preprint server for biology | 38496682 | 2024 Mar 04 |
Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter R; Yuan, Yixu; Zhang, Yida; Li, Xuwen; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, C Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | Nature communications | 38509069 | 2024 Mar 20 |
3DCellComposer - A Versatile Pipeline Utilizing 2D Cell Segmentation Methods for 3D Cell Segmentation. | Chen, Haoran; Murphy, Robert F | bioRxiv : the preprint server for biology | 38559093 | 2024 Mar 12 |
Mapping the Cellular Biogeography of Human Bone Marrow Niches Using Single-Cell Transcriptomics and Proteomic Imaging. | Bandyopadhyay, Shovik; Duffy, Michael; Ahn, Kyung Jin; Pang, Minxing; Smith, David; Duncan, Gwendolyn; Sussman, Jonathan; Zhang, Iris; Huang, Jeffrey; Lin, Yulieh; Xiong, Barbara; Imtiaz, Tamjid; Chen, Chia-Hui; Thadi, Anusha; Chen, Changya; Xu, Jason; Reichart, Melissa; Pillai, Vinodh; Snaith, Oraine; Oldridge, Derek; Bhattacharyya, Siddharth; Maillard, Ivan; Carroll, Martin; Nelson, Charles; Qin, Ling; Tan, Kai | bioRxiv : the preprint server for biology | 38559168 | 2024 Mar 16 |
Blind Polarization Demultiplexing of Shaped QAM Signals Assisted by Temporal Correlations. | Bajaj, Vinod; Van de Plas, Raf; Wahls, Sander | Journal of lightwave technology : a joint IEEE/OSA publication | 38586243 | 2024 Jan 15 |