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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
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
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
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
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
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
Spatial pharmacology using mass spectrometry imaging. Rajbhandari, Presha; Neelakantan, Taruna V; Hosny, Noreen; Stockwell, Brent R Trends in pharmacological sciences 38103980 2024 Jan
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Early cancer detection by SERS spectroscopy and machine learning. Shi, Lingyan; Li, Yajuan; Li, Zhi Light, science & applications 37714845 2023 Sep 15
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
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
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
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
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
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
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
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
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
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
Editorial: Global excellence in inflammatory diseases: North America 2021. Kusner, Linda L; Misra, Ravi S; Lucas, Rudolf Frontiers in immunology 37483602 2023
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
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
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
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
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
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
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
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
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
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
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
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
SCS: cell segmentation for high-resolution spatial transcriptomics. Chen, Hao; Li, Dongshunyi; Bar-Joseph, Ziv Nature methods 37429992 2023 Aug
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
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
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
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
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
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
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
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
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
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
Surgical management of lymphedema: Does a microsurgeon's bias exist? Friedman, Rosie; Ismail Aly, Mohamed Eldardiri; Singhal, Dhruv Microsurgery 37339916 2023 Sep
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
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
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
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
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
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
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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
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
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
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives. Naba, Alexandra Molecular & cellular proteomics : MCP 36918099 2023 Mar 12
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
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
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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
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
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
Conundrums of choice of 'normal' kidney tissue for single cell studies. Jain, Sanjay Current opinion in nephrology and hypertension 36811638 2023 May 01
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
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
Using single cell atlas data to reconstruct regulatory networks. Song, Qi; Ruffalo, Matthew; Bar-Joseph, Ziv Nucleic acids research 36762475 2023 Apr 24
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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
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
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
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
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
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
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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
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
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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
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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
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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
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
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
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Identifying signaling genes in spatial single-cell expression data. Li, Dongshunyi; Ding, Jun; Bar-Joseph, Ziv Bioinformatics (Oxford, England) 32886099 2021 05 17
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;
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
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;
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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
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;
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
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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
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;
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;
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;
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;
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;
Tools for the analysis of high-dimensional single-cell RNA sequencing data. Wu, Yan; Zhang, Kun Nature reviews. Nephrology. 32221477 2020 07;
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;
RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells. Wei, Christopher Jen-Yue; Zhang, Kun Genome research. 32127417 2020 Apr;
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;
Inferring TF activation order in time series scRNA-Seq studies. Lin, Chieh; Ding, Jun; Bar-Joseph, Ziv PLoS computational biology 32069291 2020 02
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
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;
Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Hartmann, Felix J; Bendall, Sean C Nature reviews. Rheumatology. 31892734 2020 02;
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;
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;
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;
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
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;
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;
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;
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;
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. HuBMAP Consortium Nature. 31597973 2019 10;
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;
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;
Supervised classification enables rapid annotation of cell atlases. Pliner, Hannah A; Shendure, Jay; Trapnell, Cole Nature methods. 31501545 2019 Oct;
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;
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 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;
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;
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;
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;
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;
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;
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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;
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;
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;
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;
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;
Cell lineage inference from SNP and scRNA-Seq data. Ding, Jun; Lin, Chieh; Bar-Joseph, Ziv Nucleic acids research. 30820578 2019 Jun 04;
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;
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;
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;
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;
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;
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