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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
Distinction between two populations of islet-1-positive cells in hearts of different murine strains. Khattar, Patricia; Friedrich, Felix W; Bonne, Gisèle; Carrier, Lucie; Eschenhagen, Thomas; Evans, Sylvia M; Schwartz, Ketty; Fiszman, Marc Y; Vilquin, Jean-Thomas Stem cells and development. 20942609 2011 06;
TACE/ADAM-17 phosphorylation by PKC-epsilon mediates premalignant changes in tobacco smoke-exposed lung cells. Lemjabbar-Alaoui, Hassan; Sidhu, Sukhvinder S; Mengistab, Aklilu; Gallup, Marianne; Basbaum, Carol PloS one. 21423656 2011 Mar 15;
The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. Panopoulos, Athanasia D; Yanes, Oscar; Ruiz, Sergio; Kida, Yasuyuki S; Diep, Dinh; Tautenhahn, Ralf; Herrerias, Aida; Batchelder, Erika M; Plongthongkum, Nongluk; Lutz, Margaret; Berggren, W Travis; Zhang, Kun; Evans, Ronald M; Siuzdak, Gary; Izpisua Belm Cell research. 22064701 2012 Jan;
Cut and paste: restoring cellular function by gene correction. Liu, Guang-Hui; Sancho-Martinez, Ignacio; Izpisua Belmonte, Juan Carlos Cell research. 22143565 2012 Feb;
Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual. Chen, Casey; Kittichotirat, Weerayuth; Chen, Weizhen; Downey, Jennifer S; Bumgarner, Roger Journal of bacteriology 22408240 2012 Apr
Single-cell systems biology by super-resolution imaging and combinatorial labeling. Lubeck, Eric; Cai, Long Nature methods 22660740 2012 Jul
Elimination of dendritic spines with long-term memory is specific to active circuits. Sanders, Jeff; Cowansage, Kiriana; Baumgartel, Karsten; Mayford, Mark The Journal of neuroscience : the official journal of the Society for Neuroscience 22956846 2012 Sep 5
The dawn of angiogenesis modeling: regenerating vasculature from human pluripotent stem cells. Yi, Fei; Qu, Jing; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos Cell research. 22964710 2013 Jan;
Red-shifted fluorescent proteins monitor enzymatic activity in live HT-1080 cells with fluorescence lifetime imaging microscopy (FLIM). Eichorst, J P; Clegg, R M; Wang, Y Journal of microscopy 22971220 2012 Oct
Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Ruiz, Sergio; Diep, Dinh; Gore, Athurva; Panopoulos, Athanasia D; Montserrat, Nuria; Plongthongkum, Nongluk; Kumar, Sachin; Fung, Ho-Lim; Giorgetti, Alessandra; Bilic, Josipa; Batchelder, Erika M; Zaehres, Holm; Kan, Natalia G; Schöler, Hans Robert; Mercola, Mark; Zhang, Kun; Izpisua Belmonte, Juan Carlos Proceedings of the National Academy of Sciences of the United States of America. 22991473 2012 Oct 02;
Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins. Ramesh, Balakrishnan; Sendra, Victor G; Cirino, Patrick C; Varadarajan, Navin The Journal of biological chemistry. 23019324 2012 Nov 9;
Generation of a drug-inducible reporter system to study cell reprogramming in human cells. Ruiz, Sergio; Panopoulos, Athanasia D; Montserrat, Nuria; Multon, Marie-Christine; Daury, Aurelie; Rocher, Corinne; Spanakis, Emmanuel; Batchelder, Erika M; Orsini, Cecile; Deleuze, Jean-Francois; Izpisua Belmonte, Juan Carlos The Journal of biological chemistry. 23019325 2012 Nov 23;
Characterization of the effects of an rpoC mutation that confers resistance to the Fst peptide toxin-antitoxin system toxin. Brinkman, Cassandra L; Bumgarner, Roger; Kittichotirat, Weerayuth; Dunman, Paul M; Kuechenmeister, Lisa J; Weaver, Keith E Journal of bacteriology 23104812 2013 Jan
Evolutionary conservation of Nkx2.5 autoregulation in the second heart field. Clark, Christopher D; Zhang, Boding; Lee, Benjamin; Evans, Samuel I; Lassar, Andrew B; Lee, Kyu-Ho Developmental biology. 23165293 2013 Feb 01;
Beating in a dish: new hopes for cardiomyocyte regeneration. Gu, Ying; Yi, Fei; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos Cell research. 23184058 2013 Mar;
Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans. Huang, Y; Kittichotirat, W; Mayer, M P A; Hall, R; Bumgarner, R; Chen, C Molecular oral microbiology 23194436 2013 Feb
Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. Yamanaka, Yvonne J; Szeto, Gregory L; Gierahn, Todd M; Forcier, Talitha L; Benedict, Kelly F; Brefo, Mavis S N; Lauffenburger, Douglas A; Irvine, Darrell J; Love, J Christopher Analytical chemistry 23205933 2012 Dec 18
FRET imaging of calcium signaling in live cells in the microenvironment. Qian, Tongcheng; Lu, Shaoying; Ma, Hongwei; Fang, Jing; Zhong, Wenxuan; Wang, Yingxiao Integrative biology : quantitative biosciences from nano to macro 23250282 2013 Jan 28
Focal adhesion size uniquely predicts cell migration. Kim, Dong-Hwee; Wirtz, Denis FASEB journal : official publication of the Federation of American Societies for Experimental Biology 23254340 2013 Apr
Single-cell and population NF-ýýB dynamic responses depend on lipopolysaccharide preparation. Gutschow, Miriam V; Hughey, Jacob J; Ruggero, Nicholas A; Bajar, Bryce T; Valle, Sean D; Covert, Markus W PloS one 23301045 2013
Functional interplay between the cell cycle and cell phenotypes. Chen, Wei-Chiang; Wu, Pei-Hsun; Phillip, Jude M; Khatau, Shyam B; Choi, Jae Min; Dallas, Matthew R; Konstantopoulos, Konstantinos; Sun, Sean X; Lee, Jerry S H; Hodzic, Didier; Wirtz, Denis Integrative biology : quantitative biosciences from nano to macro 23319145 2013 Mar
High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. Lu, Yao; Chen, Jonathan J; Mu, Luye; Xue, Qiong; Wu, Yu; Wu, Pei-Hsun; Li, Jie; Vortmeyer, Alexander O; Miller-Jensen, Kathryn; Wirtz, Denis; Fan, Rong Analytical chemistry 23339603 2013 Feb 19
Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming. Ruiz, Sergio; Gore, Athurva; Li, Zhe; Panopoulos, Athanasia D; Montserrat, Nuria; Fung, Ho-Lim; Giorgetti, Alessandra; Bilic, Josipa; Batchelder, Erika M; Zaehres, Holm; Scholer, Hans R; Zhang, Kun; Izpisua Belmonte, Juan Carlos Nature communications. 23340422 2013;
Thymosin *4 is not required for embryonic viability or vascular development. Banerjee, Indroneal; Moore Morris, Thomas; Evans, Sylvia M; Chen, Ju Circulation research. 23371905 2013 Feb 1;
Quantitative high-throughput single-cell cytotoxicity assay for T cells. Liadi, Ivan; Roszik, Jason; Romain, Gabrielle; Cooper, Laurence J N; Varadarajan, Navin Journal of visualized experiments : JoVE 23407457 2013
Dimensional control of cancer cell migration. Konstantopoulos, Konstantinos; Wu, Pei-Hsun; Wirtz, Denis Biophysical journal 23442847 2013 Jan 22
The antagonistic roles of PDGF and integrin ýývýý3 in regulating ROS production at focal adhesions. Lin, Li-Jung; Grimme, Jill M; Sun, Jie; Lu, Shaoying; Gai, Lisa; Cropek, Donald M; Wang, Yingxiao Biomaterials 23465490 2013 May
Nanotools for neuroscience and brain activity mapping. Alivisatos, A Paul; Andrews, Anne M; Boyden, Edward S; Chun, Miyoung; Church, George M; Deisseroth, Karl; Donoghue, John P; Fraser, Scott E; Lippincott-Schwartz, Jennifer; Looger, Loren L; Masmanidis, Sotiris; McEuen, Paul L; Nurmikko, Arto V; Park, Hongk ACS nano 23514423 2013 Mar 26
Interstitial friction greatly impacts membrane mechanics. Wirtz, Denis Biophysical journal 23528079 2013 Mar 19
Simultaneously defining cell phenotypes, cell cycle, and chromatin modifications at single-cell resolution. Chambliss, Allison B; Wu, Pei-Hsun; Chen, Wei-Chiang; Sun, Sean X; Wirtz, Denis FASEB journal : official publication of the Federation of American Societies for Experimental Biology 23538711 2013 Jul
Variation in the dorsal gradient distribution is a source for modified scaling of germ layers in Drosophila. Chahda, Juan Sebastian; Sousa-Neves, Rui; Mizutani, Claudia Mieko Current biology : CB 23583556 2013 Apr 22
Mechanotransduction at focal adhesions: from physiology to cancer development. Seong, Jihye; Wang, Ning; Wang, Yingxiao Journal of cellular and molecular medicine 23601032 2013 May
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Xie, Wei; Schultz, Matthew D; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W; Tian, Shulan; Hawkins, R David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; N Cell 23664764 2013 May 23
Single-cell transcriptomics for drug target discovery. Spaethling, Jennifer M; Eberwine, James H Current opinion in pharmacology. 23725882 2013 Oct;
Manufacture of clinical-grade CD19-specific T cells stably expressing chimeric antigen receptor using Sleeping Beauty system and artificial antigen presenting cells. Singh, Harjeet; Figliola, Matthew J; Dawson, Margaret J; Olivares, Simon; Zhang, Ling; Yang, Ge; Maiti, Sourindra; Manuri, Pallavi; Senyukov, Vladimir; Jena, Bipulendu; Kebriaei, Partow; Champlin, Richard E; Huls, Helen; Cooper, Laurence J N PloS one 23741305 2013
HCN4 dynamically marks the first heart field and conduction system precursors. Liang, Xingqun; Wang, Gang; Lin, Lizhu; Lowe, Jennifer; Zhang, Qingquan; Bu, Lei; Chen, Yihan; Chen, Ju; Sun, Yunfu; Evans, Sylvia M Circulation research 23743334 2013 Aug 2
Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2. Sun, Jie; Lu, Shaoying; Ouyang, Mingxing; Lin, Li-Jung; Zhuo, Yue; Liu, Bo; Chien, Shu; Neel, Benjamin G; Wang, Yingxiao Nature communications 23792876 2013 Jun 24
Detection and isolation of auto-reactive human antibodies from primary B cells. Sendra, Victor G; Lie, Anthony; Romain, Gabrielle; Agarwal, Sandeep K; Varadarajan, Navin Methods (San Diego, Calif.) 23811296 2013 Jun 26
In vivo robotics: the automation of neuroscience and other intact-system biological fields. Kodandaramaiah, Suhasa B; Boyden, Edward S; Forest, Craig R Annals of the New York Academy of Sciences 23841584 2013 Jul 10
In vivo robotics: the automation of neuroscience and other intact-system biological fields. Kodandaramaiah, Suhasa B; Boyden, Edward S; Forest, Craig R Annals of the New York Academy of Sciences 23841584 2013 Dec
Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis. Moore, Julia L; Du, Zhuo; Bao, Zhirong Development (Cambridge, England) 23861063 2013 Aug
Developmental biology. Enhancing pluripotency and lineage specification. Xie, Wei; Ren, Bing Science (New York, N.Y.) 23869010 2013 Jul 19
Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor. Peng, Tien; Tian, Ying; Boogerd, Cornelis J; Lu, Min Min; Kadzik, Rachel S; Stewart, Kathleen M; Evans, Sylvia M; Morrisey, Edward E Nature 23873040 2013 Aug 29
Statistical analysis of molecular signal recording. Glaser, Joshua I; Zamft, Bradley M; Marblestone, Adam H; Moffitt, Jeffrey R; Tyo, Keith; Boyden, Edward S; Church, George; Kording, Konrad P PLoS computational biology 23874187 2013 Jul
Single cell spectroscopy: Noninvasive measures of small-scale structure and function. Mousoulis, Charilaos; Xu, Xin; Reiter, David A; Neu, Corey P Methods (San Diego, Calif.) 23886910 2013 Jul 22
Genetic analysis of mate discrimination in Drosophila simulans. Chu, Y; Yang, E; Schinaman, J M; Chahda, J S; Sousa-Neves, R Evolution; international journal of organic evolution 23888855 2013 Aug
Efficient generation of human iPSCs by a synthetic self-replicative RNA. Yoshioka, Naohisa; Gros, Edwige; Li, Hai-Ri; Kumar, Shantanu; Deacon, Dekker C; Maron, Cornelia; Muotri, Alysson R; Chi, Neil C; Fu, Xiang-Dong; Yu, Benjamin D; Dowdy, Steven F Cell stem cell. 23910086 2013 Aug 1;
Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-? gene in acute kidney injury. Bomsztyk, Karol; Flanagin, Steve; Mar, Daniel; Mikula, Michal; Johnson, Ali; Zager, Richard; Denisenko, Oleg PloS one. 23936185 2013;
FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans. Minor, Paul J; He, Ting-Fang; Sohn, Chang Ho; Asthagiri, Anand R; Sternberg, Paul W Development (Cambridge, England) 23946444 2013 Sep
BreakTrans: uncovering the genomic architecture of gene fusions. Chen, Ken; Navin, Nicholas E; Wang, Yong; Schmidt, Heather K; Wallis, John W; Niu, Beifang; Fan, Xian; Zhao, Hao; McLellan, Michael D; Hoadley, Katherine A; Mardis, Elaine R; Ley, Timothy J; Perou, Charles M; Wilson, Richard K; Ding, Li Genome biology. 23972288 2013;
Morphological effects on expression of growth differentiation factor 15 (GDF15), a marker of metastasis. Aw Yong, Koh Meng; Zeng, Yu; Vindivich, Donald; Phillip, Jude M; Wu, Pei-Hsun; Wirtz, Denis; Getzenberg, Robert H Journal of cellular physiology. 23996089 2014 Mar;
Epigenetic alterations in acute kidney injury. Bomsztyk, Karol; Denisenko, Oleg Seminars in nephrology 24011575 2013 Jul
Tracking immune cells in vivo using magnetic resonance imaging. Ahrens, Eric T; Bulte, Jeff W M Nature reviews. Immunology 24013185 2013 10
Barriers to transmission of transcriptional noise in a c-fos c-jun pathway. Shah, Khyati; Tyagi, Sanjay Molecular systems biology 24022005 2013
Genetically encoded fluorescent biosensors for live-cell imaging of MT1-MMP protease activity. Ouyang, Mingxing; Lu, Shaoying; Wang, Yingxiao Methods in molecular biology (Clifton, N.J.). 24052388 2014;
Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. Wu, Yicong; Wawrzusin, Peter; Senseney, Justin; Fischer, Robert S; Christensen, Ryan; Santella, Anthony; York, Andrew G; Winter, Peter W; Waterman, Clare M; Bao, Zhirong; Colon-Ramos, Daniel A; McAuliffe, Matthew; Shroff, Hari Nature biotechnology 24108093 2013 Nov
Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model. Lyon, Robert C; Mezzano, Valeria; Wright, Adam T; Pfeiffer, Emily; Chuang, Joyce; Banares, Katherine; Castaneda, Allan; Ouyang, Kunfu; Cui, Li; Contu, Riccardo; Gu, Yusu; Evans, Sylvia M; Omens, Jeffrey H; Peterson, Kirk L; McCulloch, Andrew D; Sheikh, Fa Human molecular genetics. 24108106 2014 Mar 1;
Human heart rate: heritability of resting and stress values in twin pairs, and influence of genetic variation in the adrenergic pathway at a microribonucleic acid (microrna) motif in the 3'-UTR of cytochrome b561 [corrected]. Zhang, Kuixing; Deacon, Dekker C; Rao, Fangwen; Schork, Andrew J; Fung, Maple M; Waalen, Jill; Schork, Nicholas J; Nievergelt, Caroline M; Chi, Neil C; O'Connor, Daniel T Journal of the American College of Cardiology. 24140660 2014 Feb 4;
PIWI proteins are essential for early Drosophila embryogenesis. Mani, Sneha Ramesh; Megosh, Heather; Lin, Haifan Developmental biology 24184635 2013 Oct 31
PIWI proteins are essential for early Drosophila embryogenesis. Mani, Sneha Ramesh; Megosh, Heather; Lin, Haifan Developmental biology 24184635 2014 Jan 15
Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun Nature biotechnology 24213699 2013 Dec
Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins. Seong, Jihye; Tajik, Arash; Sun, Jie; Guan, Jun-Lin; Humphries, Martin J; Craig, Susan E; Shekaran, Asha; Garcia, Andres J; Lu, Shaoying; Lin, Michael Z; Wang, Ning; Wang, Yingxiao Proceedings of the National Academy of Sciences of the United States of America 24222685 2013 Nov 26
Hypoxia-inducible factors mediate coordinated RhoA-ROCK1 expression and signaling in breast cancer cells. Gilkes, Daniele M; Xiang, Lisha; Lee, Sun Joo; Chaturvedi, Pallavi; Hubbi, Maimon E; Wirtz, Denis; Semenza, Gregg L Proceedings of the National Academy of Sciences of the United States of America. 24324133 2014 Jan 21;
pH dependent transfer of nano-pores into membrane of cancer cells to induce apoptosis. Wijesinghe, Dayanjali; Arachchige, Mohan C M; Lu, Andrew; Reshetnyak, Yana K; Andreev, Oleg A Scientific reports 24356337 2013
A cut above the rest: targeted genome editing technologies in human pluripotent stem cells. Li, Mo; Suzuki, Keiichiro; Kim, Na Young; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos The Journal of biological chemistry. 24362028 2014 Feb 21;
The role of mechanical tension on lipid raft dependent PDGF-induced TRPC6 activation. Lei, Lei; Lu, Shaoying; Wang, Yi; Kim, Taejin; Mehta, Dolly; Wang, Yingxiao Biomaterials 24397990 2014 Mar
Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Lovatt, Ditte; Ruble, Brittani K; Lee, Jaehee; Dueck, Hannah; Kim, Tae Kyung; Fisher, Stephen; Francis, Chantal; Spaethling, Jennifer M; Wolf, John A; Grady, M Sean; Ulyanova, Alexandra V; Yeldell, Sean B; Griepenburg, Julianne C; Buckley, Peter T; Kim, J Nature methods 24412976 2014 Feb
Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images. Gierahn, Todd M; Loginov, Denis; Love, J Christopher Journal of proteome research 24417579 2014 Jan 24
De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. Du, Zhuo; Santella, Anthony; He, Fei; Tiongson, Michael; Bao, Zhirong Cell 24439388 2014 Jan 16
Single-cell technologies for monitoring immune systems. Chattopadhyay, Pratip K; Gierahn, Todd M; Roederer, Mario; Love, J Christopher Nature immunology 24448570 2014 Feb
Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Gu, Ying; Liu, Guang-Hui; Plongthongkum, Nongluk; Benner, Christopher; Yi, Fei; Qu, Jing; Suzuki, Keiichiro; Yang, Jiping; Zhang, Weiqi; Li, Mo; Montserrat, Nuria; Crespo, Isaac; Del Sol, Antonio; Esteban, Concepcion Rodriguez; Zhang, Kun; Izpisua Belmont Protein & cell. 24474197 2014 Jan;
Probing Endoplasmic Reticulum Dynamics using Fluorescence Imaging and Photobleaching Techniques. Costantini, Lindsey; Snapp, Erik Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.] 24510787 2013
Tumor evolution in response to chemotherapy: phenotype versus genotype. Navin, Nicholas E Cell reports 24529750 2014 Feb 13
A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans. Cheng, Ya-An; Jee, Jason; Hsu, Genie; Huang, Yanyan; Chen, Casey; Lin, Chun-Pin Journal of the Formosan Medical Association = Taiwan yi zhi 24530245 2014 Feb
The cytolethal distending toxin of Aggregatibacter actinomycetemcomitans inhibits macrophage phagocytosis and subverts cytokine production. Ando-Suguimoto, Ellen Sayuri; da Silva, Maike Paulino; Kawamoto, Dione; Chen, Casey; DiRienzo, Joseph M; Mayer, Marcia Pinto Alves Cytokine 24548424 2014 Mar
Nuclear envelope in nuclear positioning and cell migration. Razafsky, David; Wirtz, Denis; Hodzic, Didier Advances in experimental medicine and biology. 24563361 2014;
Highly multiplexed subcellular RNA sequencing in situ. Lee, Je Hyuk; Daugharthy, Evan R; Scheiman, Jonathan; Kalhor, Reza; Yang, Joyce L; Ferrante, Thomas C; Terry, Richard; Jeanty, Sauveur S F; Li, Chao; Amamoto, Ryoji; Peters, Derek T; Turczyk, Brian M; Marblestone, Adam H; Inverso, Samuel A; Bernard, Amy; Science (New York, N.Y.) 24578530 2014 Mar 21
Targeted ablation of nesprin 1 and nesprin 2 from murine myocardium results in cardiomyopathy, altered nuclear morphology and inhibition of the biomechanical gene response. Banerjee, Indroneal; Zhang, Jianlin; Moore-Morris, Thomas; Pfeiffer, Emily; Buchholz, Kyle S; Liu, Ao; Ouyang, Kunfu; Stroud, Matthew J; Gerace, Larry; Evans, Sylvia M; McCulloch, Andrew; Chen, Ju PLoS genetics. 24586179 2014 Feb;
Three-dimensional cell migration does not follow a random walk. Wu, Pei-Hsun; Giri, Anjil; Sun, Sean X; Wirtz, Denis Proceedings of the National Academy of Sciences of the United States of America 24594603 2014 Mar 18
Tight coupling between nucleus and cell migration through the perinuclear actin cap. Kim, Dong-Hwee; Cho, Sangkyun; Wirtz, Denis Journal of cell science 24639463 2014 Jun 1
Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ. Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, Mona PloS one 24675777 2014
Single-cell in situ RNA profiling by sequential hybridization. Lubeck, Eric; Coskun, Ahmet F; Zhiyentayev, Timur; Ahmad, Mubhij; Cai, Long Nature methods 24681720 2014 Apr
Excess PLAC8 promotes an unconventional ERK2-dependent EMT in colon cancer. Li, Cunxi; Ma, Haiting; Wang, Yang; Cao, Zheng; Graves-Deal, Ramona; Powell, Anne E; Starchenko, Alina; Ayers, Gregory D; Washington, Mary Kay; Kamath, Vidya; Desai, Keyur; Gerdes, Michael J; Solnica-Krezel, Lila; Coffey, Robert J The Journal of clinical investigation 24691442 2014 Apr 1
Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. Doupé, David P; Perrimon, Norbert Science signaling. 24692594 2014 Apr 1;
Local mechanical response of cells to the controlled rotation of magnetic nanorods. Castillo, Matias; Ebensperger, Roberto; Wirtz, Denis; Walczak, Magdalena; Hurtado, Daniel E; Celedon, Alfredo Journal of biomedical materials research. Part B, Applied biomaterials. 24700696 2014 Nov;
Mathematical approaches to modeling development and reprogramming. Morris, Rob; Sancho-Martinez, Ignacio; Sharpee, Tatyana O; Izpisua Belmonte, Juan Carlos Proceedings of the National Academy of Sciences of the United States of America. 24706886 2014 Apr 8;
Universal artificial antigen presenting cells to selectively propagate T cells expressing chimeric antigen receptor independent of specificity. Rushworth, David; Jena, Bipulendu; Olivares, Simon; Maiti, Sourindra; Briggs, Neima; Somanchi, Srinivas; Dai, Jianliang; Lee, Dean; Cooper, Laurence J N Journal of immunotherapy (Hagerstown, Md. : 1997) 24714354 2014 May
Atomic force microscopy-coupled microcoils for cellular-scale nuclear magnetic resonance spectroscopy. Mousoulis, Charilaos; Maleki, Teimour; Ziaie, Babak; Neu, Corey P Applied physics letters. 24719493 2013 Apr 08;
Water permeation drives tumor cell migration in confined microenvironments. Stroka, Kimberly M; Jiang, Hongyuan; Chen, Shih-Hsun; Tong, Ziqiu; Wirtz, Denis; Sun, Sean X; Konstantopoulos, Konstantinos Cell 24726433 2014 Apr 24
Genetic characteristics and pathogenic mechanisms of periodontal pathogens. Amano, A; Chen, C; Honma, K; Li, C; Settem, R P; Sharma, A Advances in dental research 24736700 2014 May
Hypoxia and the extracellular matrix: drivers of tumour metastasis. Gilkes, Daniele M; Semenza, Gregg L; Wirtz, Denis Nature reviews. Cancer. 24827502 2014 Jun;
Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2. Xu, Shuwa; Tyagi, Sanjay; Schedl, Paul PLoS genetics 24830287 2014 May
Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Prevedel, Robert; Yoon, Young-Gyu; Hoffmann, Maximilian; Pak, Nikita; Wetzstein, Gordon; Kato, Saul; Schrodel, Tina; Raskar, Ramesh; Zimmer, Manuel; Boyden, Edward S; Vaziri, Alipasha Nature methods 24836920 2014 May 18
The 3D Genome in Transcriptional Regulation and Pluripotency. Gorkin, David U; Leung, Danny; Ren, Bing Cell stem cell 24905166 2014 Jun 5
Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. Moore-Morris, Thomas; Guimaraes-Camboa, Nuno; Banerjee, Indroneal; Zambon, Alexander C; Kisseleva, Tatiana; Velayoudon, Aurelie; Stallcup, William B; Gu, Yusu; Dalton, Nancy D; Cedenilla, Marta; Gomez-Amaro, Rafael; Zhou, Bin; Brenner, David A; Peterson, The Journal of clinical investigation 24937432 2014 Jul 1
High-sensitivity measurements of multiple kinase activities in live single cells. Regot, Sergi; Hughey, Jacob J; Bajar, Bryce T; Carrasco, Silvia; Covert, Markus W Cell 24949979 2014 Jun 19
A semi-local neighborhood-based framework for probabilistic cell lineage tracing. Santella, Anthony; Du, Zhuo; Bao, Zhirong BMC bioinformatics. 24964866 2014;
Comparison of intervertebral disc displacements measured under applied loading with MRI at 3.0 T and 9.4 T. Chan, Deva D; Gossett, Paull C; Butz, Kent D; Nauman, Eric A; Neu, Corey P Journal of biomechanics. 24968943 2014 Aug 22;
The regulation of *-adrenergic receptor-mediated PKA activation by substrate stiffness via microtubule dynamics in human MSCs. Kim, Tae-Jin; Sun, Jie; Lu, Shaoying; Zhang, Jin; Wang, Yingxiao Biomaterials 24973298 2014 Jun 24
Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Suzuki, Keiichiro; Yu, Chang; Qu, Jing; Li, Mo; Yao, Xiaotian; Yuan, Tingting; Goebl, April; Tang, Senwei; Ren, Ruotong; Aizawa, Emi; Zhang, Fan; Xu, Xiuling; Soligalla, Rupa Devi; Chen, Feng; Kim, Jessica; Kim, Na Young; Liao, Hsin-Kai; Benner, Chris; Es Cell stem cell. 24996168 2014 Jul 3;
Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Chuong, Amy S; Miri, Mitra L; Busskamp, Volker; Matthews, Gillian A C; Acker, Leah C; Sorensen, Andreas T; Young, Andrew; Klapoetke, Nathan C; Henninger, Mike A; Kodandaramaiah, Suhasa B; Ogawa, Masaaki; Ramanlal, Shreshtha B; Bandler, Rachel C; Allen, Br Nature neuroscience 24997763 2014 Aug
Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. Liu, Guang-Hui; Suzuki, Keiichiro; Li, Mo; Qu, Jing; Montserrat, Nuria; Tarantino, Carolina; Gu, Ying; Yi, Fei; Xu, Xiuling; Zhang, Weiqi; Ruiz, Sergio; Plongthongkum, Nongluk; Zhang, Kun; Masuda, Shigeo; Nivet, Emmanuel; Tsunekawa, Yuji; Soligalla, Rupa Nature communications. 24999918 2014;
Regeneration: making muscle from hPSCs. Zhu, Xiping; Fu, Lina; Yi, Fei; Liu, Guang-Hui; Ocampo, Alejandro; Qu, Jing; Izpisua Belmonte, Juan Carlos Cell research. 25001388 2014 Oct;
Targeting breast tumors with pH (low) insertion peptides. Adochite, Ramona-Cosmina; Moshnikova, Anna; Carlin, Sean D; Guerrieri, Renato A; Andreev, Oleg A; Lewis, Jason S; Reshetnyak, Yana K Molecular pharmaceutics. 25004202 2014 Aug 4;
Dynamic heterogeneity and DNA methylation in embryonic stem cells. Singer, Zakary S; Yong, John; Tischler, Julia; Hackett, Jamie A; Altinok, Alphan; Surani, M Azim; Cai, Long; Elowitz, Michael B Molecular cell. 25038413 2014 Jul 17;
Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Wang, Yong; Waters, Jill; Leung, Marco L; Unruh, Anna; Roh, Whijae; Shi, Xiuqing; Chen, Ken; Scheet, Paul; Vattathil, Selina; Liang, Han; Multani, Asha; Zhang, Hong; Zhao, Rui; Michor, Franziska; Meric-Bernstam, Funda; Navin, Nicholas E Nature 25079324 2014 Aug 14
Single-cell imaging of mechanotransduction in endothelial cells. Lu, Shaoying; Wang, Yingxiao Progress in molecular biology and translational science. 25081613 2014;
Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing. Yang, Bin; Treweek, Jennifer B; Kulkarni, Rajan P; Deverman, Benjamin E; Chen, Chun-Kan; Lubeck, Eric; Shah, Sheel; Cai, Long; Gradinaru, Viviana Cell 25088144 2014 Aug 14
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iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Panopoulos, Athanasia D; D'Antonio, Matteo; Benaglio, Paola; Williams, Roy; Hashem, Sherin I; Schuldt, Bernhard M; DeBoever, Christopher; Arias, Angelo D; Garcia, Melvin; Nelson, Bradley C; Harismendy, Olivier; Jakubosky, David A; Donovan, Margaret K R; Greenwald, William W; Farnam, KathyJean; Cook, Megan; Borja, Victor; Miller, Carl A; Grinstein, Jonathan D; Drees, Frauke; Okubo, Jonathan; Diffenderfer, Kenneth E; Hishida, Yuriko; Modesto, Veronica; Dargitz, Carl T; Feiring, Rachel; Zhao, Chang; Aguirre, Aitor; McGarry, Thomas J; Matsui, Hiroko; Li, He; Reyna, Joaquin; Rao, Fangwen; O'Connor, Daniel T; Yeo, Gene W; Evans, Sylvia M; Chi, Neil C; Jepsen, Kristen; Nariai, Naoki; Müller, Franz-Josef; Goldstein, Lawrence S B; Izpisua Belmonte, Juan Carlos; Adler, Eric; Loring, Jeanne F; Berggren, W Travis; D'Antonio-Chronowska, Agnieszka; Smith, Erin N; Frazer, Kelly A Stem cell reports. 28392216 2017 Apr 03;
High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. D'Antonio, Matteo; Woodruff, Grace; Nathanson, Jason L; D'Antonio-Chronowska, Agnieszka; Arias, Angelo; Matsui, Hiroko; Williams, Roy; Herrera, Cheryl; Reyna, Sol M; Yeo, Gene W; Goldstein, Lawrence S B; Panopoulos, Athanasia D; Frazer, Kelly A Stem cell reports. 28392217 2017 Apr 04;
iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Panopoulos, Athanasia D; D'Antonio, Matteo; Benaglio, Paola; Williams, Roy; Hashem, Sherin I; Schuldt, Bernhard M; DeBoever, Christopher; Arias, Angelo D; Garcia, Melvin; Nelson, Bradley C; Harismendy, Olivier; Jakubosky, David A; Donovan, Margaret K R; Greenwald, William W; Farnam, KathyJean; Cook, Megan; Borja, Victor; Miller, Carl A; Grinstein, Jonathan D; Drees, Frauke; Okubo, Jonathan; Diffenderfer, Kenneth E; Hishida, Yuriko; Modesto, Veronica; Dargitz, Carl T; Feiring, Rachel; Zhao, Chang; Aguirre, Aitor; McGarry, Thomas J; Matsui, Hiroko; Li, He; Reyna, Joaquin; Rao, Fangwen; O'Connor, Daniel T; Yeo, Gene W; Evans, Sylvia M; Chi, Neil C; Jepsen, Kristen; Nariai, Naoki; Müller, Franz-Josef; Goldstein, Lawrence S B; Izpisua Belmonte, Juan Carlos; Adler, Eric; Loring, Jeanne F; Berggren, W Travis; D'Antonio-Chronowska, Agnieszka; Smith, Erin N; Frazer, Kelly A Stem cell reports. 28410642 2017 Apr 11;
High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. D'Antonio, Matteo; Woodruff, Grace; Nathanson, Jason L; D'Antonio-Chronowska, Agnieszka; Arias, Angelo; Matsui, Hiroko; Williams, Roy; Herrera, Cheryl; Reyna, Sol M; Yeo, Gene W; Goldstein, Lawrence S B; Panopoulos, Athanasia D; Frazer, Kelly A Stem cell reports. 28410643 2017 Apr 11;
Iterative expansion microscopy. Chang, Jae-Byum; Chen, Fei; Yoon, Young-Gyu; Jung, Erica E; Babcock, Hazen; Kang, Jeong Seuk; Asano, Shoh; Suk, Ho-Jun; Pak, Nikita; Tillberg, Paul W; Wassie, Asmamaw T; Cai, Dawen; Boyden, Edward S Nature methods. 28417997 2017 Jun;
In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry: Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo. Onjiko, Rosemary M; Portero, Erika P; Moody, Sally A; Nemes, Peter Analytical chemistry. 28434226 2017 Jul 05;
Assessment of Single Cell RNA-Seq Normalization Methods. Ding, Bo; Zheng, Lina; Wang, Wei G3 (Bethesda, Md.). 28468817 2017 Jul 05;
Development of an optimized synthetic Notch receptor as an in vivo cell-cell contact sensor. He, Li; Huang, Jiuhong; Perrimon, Norbert Proceedings of the National Academy of Sciences of the United States of America. 28490499 2017 05 23;
A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo. Yang, Yu-Ping; Ma, Haiting; Starchenko, Alina; Huh, Won Jae; Li, Wei; Hickman, F Edward; Zhang, Qin; Franklin, Jeffrey L; Mortlock, Douglas P; Fuhrmann, Sabine; Carter, Bruce D; Ihrie, Rebecca A; Coffey, Robert J Cell reports. 28494873 2017 May 09;
Visualizing Calcium Flux in Freely Moving Nematode Embryos. Ardiel, Evan L; Kumar, Abhishek; Marbach, Joseph; Christensen, Ryan; Gupta, Rishi; Duncan, William; Daniels, Jonathan S; Stuurman, Nico; Colón-Ramos, Daniel; Shroff, Hari Biophysical journal. 28494967 2017 May 09;
FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry. Arrigucci, Riccardo; Bushkin, Yuri; Radford, Felix; Lakehal, Karim; Vir, Pooja; Pine, Richard; Martin, December; Sugarman, Jeffrey; Zhao, Yanlin; Yap, George S; Lardizabal, Alfred A; Tyagi, Sanjay; Gennaro, Maria Laura Nature protocols. 28518171 2017 Jun;
Assessing the causal relationship between obesity and venous thromboembolism through a Mendelian Randomization study. Lindström, Sara; Germain, Marine; Crous-Bou, Marta; Smith, Erin N; Morange, Pierre-Emmanuel; van Hylckama Vlieg, Astrid; de Haan, Hugoline G; Chasman, Daniel; Ridker, Paul; Brody, Jennifer; de Andrade, Mariza; Heit, John A; Tang, Weihong; DeVivo, Immaculata; Grodstein, Francine; Smith, Nicholas L; Tregouet, David; Kabrhel, Christopher; INVENT Consortium Human genetics. 28528403 2017 Jul;
The ''new normal'': Adapting doctoral trainee career preparation for broad career paths in science. St Clair, Rebekah; Hutto, Tamara; MacBeth, Cora; Newstetter, Wendy; McCarty, Nael A; Melkers, Julia PloS one. 28542304 2017;
Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration. Jayatilaka, Hasini; Tyle, Pranay; Chen, Jonathan J; Kwak, Minsuk; Ju, Julia; Kim, Hyun Ji; Lee, Jerry S H; Wu, Pei-Hsun; Gilkes, Daniele M; Fan, Rong; Wirtz, Denis Nature communications. 28548090 2017 May 26;
Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain. Singer, Annabelle C; Talei Franzesi, Giovanni; Kodandaramaiah, Suhasa B; Flores, Francisco J; Cohen, Jeremy D; Lee, Albert K; Börgers, Christoph; Forest, Craig R; Kopell, Nancy J; Boyden, Edward S Journal of neurophysiology. 28566460 2017 May 31;
A robot for high yield electrophysiology and morphology of single neurons in vivo. Li, Lu; Ouellette, Benjamin; Stoy, William A; Garren, Emma J; Daigle, Tanya L; Forest, Craig R; Koch, Christof; Zeng, Hongkui Nature communications. 28569837 2017 Jun 01;
Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity. McKinley, Eliot T; Sui, Yunxia; Al-Kofahi, Yousef; Millis, Bryan A; Tyska, Matthew J; Roland, Joseph T; Santamaria-Pang, Alberto; Ohland, Christina L; Jobin, Christian; Franklin, Jeffrey L; Lau, Ken S; Gerdes, Michael J; Coffey, Robert J JCI insight. 28570279 2017 Jun 02;
Single image super-resolution via an iterative reproducing kernel Hilbert space method. Deng, Liang-Jian; Guo, Weihong; Huang, Ting-Zhu IEEE transactions on circuits and systems for video technology : a publication of the Circuits and Systems Society. 28603404 2016 Nov;
IgG Fc domains that bind C1q but not effector Fc? receptors delineate the importance of complement-mediated effector functions. Lee, Chang-Han; Romain, Gabrielle; Yan, Wupeng; Watanabe, Makiko; Charab, Wissam; Todorova, Biliana; Lee, Jiwon; Triplett, Kendra; Donkor, Moses; Lungu, Oana I; Lux, Anja; Marshall, Nicholas; Lindorfer, Margaret A; Goff, Odile Richard-Le; Balbino, Bianca; Kang, Tae Hyun; Tanno, Hidetaka; Delidakis, George; Alford, Corrine; Taylor, Ronald P; Nimmerjahn, Falk; Varadarajan, Navin; Bruhns, Pierre; Zhang, Yan Jessie; Georgiou, George Nature immunology. 28604720 2017 Aug;
Visualizing adenosine-to-inosine RNA editing in single mammalian cells. Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H Nature methods. 28604724 2017 Jun 12;
Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. Radford, Felix; Tyagi, Sanjay; Gennaro, Maria Laura; Pine, Richard; Bushkin, Yuri Critical reviews in immunology. 28605344 2016;
Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Shaffer, Sydney M; Dunagin, Margaret C; Torborg, Stefan R; Torre, Eduardo A; Emert, Benjamin; Krepler, Clemens; Beqiri, Marilda; Sproesser, Katrin; Brafford, Patricia A; Xiao, Min; Eggan, Elliott; Anastopoulos, Ioannis N; Vargas-Garcia, Cesar A; Singh, Abhyudai; Nathanson, Katherine L; Herlyn, Meenhard; Raj, Arjun Nature. 28607484 ;
A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve. Caravaca, A S; Tsaava, T; Goldman, L; Silverman, H; Riggott, G; Chavan, S S; Bouton, C; Tracey, K J; Desimone, R; Boyden, E S; Sohal, H S; Olofsson, P S Journal of neural engineering. 28628030 2017 12;
Tissue specific requirements for WNT11 in developing outflow tract and dorsal mesenchymal protrusion. van Vliet, Patrick P; Lin, Lizhu; Boogerd, Cornelis J; Martin, James F; Andelfinger, Gregor; Grossfeld, Paul D; Evans, Sylvia M Developmental biology. 28669819 2017 09 01;
Unmassked: Single-Cell Profiling of Immune Cell Populations in Tumors. Varadarajan, Navin Molecular therapy : the journal of the American Society of Gene Therapy. 28684257 2017 Aug 02;
Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. Zhao, Yongxin; Bucur, Octavian; Irshad, Humayun; Chen, Fei; Weins, Astrid; Stancu, Andreea L; Oh, Eun-Young; DiStasio, Marcello; Torous, Vanda; Glass, Benjamin; Stillman, Isaac E; Schnitt, Stuart J; Beck, Andrew H; Boyden, Edward S Nature biotechnology. 28714966 2017 Aug;
A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Lake, Blue B; Codeluppi, Simone; Yung, Yun C; Gao, Derek; Chun, Jerold; Kharchenko, Peter V; Linnarsson, Sten; Zhang, Kun Scientific reports. 28729663 2017 Jul 20;
Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry. Das, Dipjyoti; Chatti, Veena; Emonet, Thierry; Holley, Scott A Developmental cell. 28743003 2017 07 24;
Multifaceted role of BTLA in the control of CD8+ T cell fate after antigen encounter. Ritthipichai, Krit; Haymaker, Cara; Martinez-Paniagua, Melisa; Aschenbrenner, Andrew; Yi, Xiaohui; Zhang, Minying; Kale, Charuta; Hailemichael, Yared; Overwijk, Willem W; Vence, Luis; Roszik, Jason; Varadarajan, Navin; Nurieva, Roza; Radvanyi, Laszlo G; Hwu, Patrick; Bernatchez, Chantale Clinical cancer research : an official journal of the American Association for Cancer Research. 28754817 2017 Jul 28;
Single cell transcriptomics of noncoding RNAs and their cell-specificity. Gawronski, Katerina A B; Kim, Junhyong Wiley interdisciplinary reviews. RNA. 28762653 2017 Nov;
Neuronal cell-type classification: challenges, opportunities and the path forward. Zeng, Hongkui; Sanes, Joshua R Nature reviews. Neuroscience 28775344 2017 Sep
High-NA open-top selective-plane illumination microscopy for biological imaging. Mcgorty, Ryan; Xie, Dan; Huang, Bo Optics express. 28789271 2017 Jul 24;
Acoustofluidic bacteria separation. Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E; Zeng, Xiangqun; Huang, Tony Jun Journal of micromechanics and microengineering : structures, devices, and systems. 28798539 2017 Jan 01;
Using Longitudinal Data on Career Outcomes to Promote Improvements and Diversity in Graduate Education. Feig, Andrew L; Robinson, Leah; Yan, Song; Byrd, Mark; Mathur, Ambika Change. 28804143 2016;
A magnetic micropore chip for rapid ( Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, David Lab on a chip. 28809985 2017 Sep 12;
Dissociated and Reconstituted Cartilage Microparticles in Densified Collagen Induce Local hMSC Differentiation. Novak, Tyler; Seelbinder, Benjamin; Twitchell, Celina M; Voytik-Harbin Prof, Sherry L; Neu Prof, Corey P Advanced functional materials. 28824356 2016 Aug 09;
Single-cell profiling of dynamic cytokine secretion and the phenotype of immune cells. An, Xingyue; Sendra, Victor G; Liadi, Ivan; Ramesh, Balakrishnan; Romain, Gabrielle; Haymaker, Cara; Martinez-Paniagua, Melisa; Lu, Yanbin; Radvanyi, Laszlo G; Roysam, Badrinath; Varadarajan, Navin PloS one. 28837583 2017;
Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. Suk, Ho-Jun; van Welie, Ingrid; Kodandaramaiah, Suhasa B; Allen, Brian; Forest, Craig R; Boyden, Edward S Neuron. 28858614 2017 Aug 30;
Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Mowel, Walter K; McCright, Sam J; Kotzin, Jonathan J; Collet, Magalie A; Uyar, Asli; Chen, Xin; DeLaney, Alexandra; Spencer, Sean P; Virtue, Anthony T; Yang, EnJun; Villarino, Alejandro; Kurachi, Makoto; Dunagin, Margaret C; Pritchard, Gretchen Harms; Stein, Judith; Hughes, Cynthia; Fonseca-Pereira, Diogo; Veiga-Fernandes, Henrique; Raj, Arjun; Kambayashi, Taku; Brodsky, Igor E; O'Shea, John J; Wherry, E John; Goff, Loyal A; Rinn, John L; Williams, Adam; Flavell, Richard A; Henao-Mejia, Jorge Immunity. 28930659 2017 Sep 19;
21st century neurobehavioral theories of decision making in addiction: Review and evaluation. Bickel, Warren K; Mellis, Alexandra M; Snider, Sarah E; Athamneh, Liqa N; Stein, Jeffrey S; Pope, Derek A Pharmacology, biochemistry, and behavior. 28942119 2017 Sep 21;
Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. Suk, Ho-Jun; van Welie, Ingrid; Kodandaramaiah, Suhasa B; Allen, Brian; Forest, Craig R; Boyden, Edward S Neuron. 28957673 2017 Sep 27;
Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging. Piatkevich, Kiryl D; Suk, Ho-Jun; Kodandaramaiah, Suhasa B; Yoshida, Fumiaki; DeGennaro, Ellen M; Drobizhev, Mikhail; Hughes, Thomas E; Desimone, Robert; Boyden, Edward S; Verkhusha, Vladislav V Biophysical journal. 29017728 2017 Nov 21;
Acoustic streaming: an arbitrary Lagrangian-Eulerian perspective. Nama, Nitesh; Huang, Tony Jun; Costanzo, Francesco Journal of fluid mechanics. 29051631 2017 Aug 25;
Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. Onjiko, Rosemary M; Plotnick, David O; Moody, Sally A; Nemes, Peter Analytical methods : advancing methods and applications. 29062391 2017 Sep 14;
Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. Nariai, Naoki; Greenwald, William W; DeBoever, Christopher; Li, He; Frazer, Kelly A Genetics. 29074555 2017 12;
Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues. Lin, Ming-Yi; Wang, Yi-Ling; Wu, Wan-Lin; Wolseley, Victoria; Tsai, Ming-Ting; Radic, Vladimir; Thornton, Matthew E; Grubbs, Brendan H; Chow, Robert H; Huang, I-Chueh Scientific reports. 29093521 2017 Nov 01;
EB1 and cytoplasmic dynein mediate protrusion dynamics for efficient 3-dimensional cell migration. Jayatilaka, Hasini; Giri, Anjil; Karl, Michelle; Aifuwa, Ivie; Trenton, Nicholaus J; Phillip, Jude M; Khatau, Shyam; Wirtz, Denis FASEB journal : official publication of the Federation of American Societies for Experimental Biology. 29097501 2018 03;
Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. Guo, Feng; Li, Sixing; Caglar, Mehmet Umut; Mao, Zhangming; Liu, Wu; Woodman, Andrew; Arnold, Jamie J; Wilke, Claus O; Huang, Tony Jun; Cameron, Craig E Cell reports. 29117571 2017 Nov 07;
Profiling the transcriptome with RNA SPOTs. Eng, Chee-Huat Linus; Shah, Sheel; Thomassie, Julian; Cai, Long Nature methods. 29131163 2017 Dec;
Single-Cell Imaging Using Radioluminescence Microscopy Reveals Unexpected Binding Target for [18F]HFB. Kiru, Louise; Kim, Tae Jin; Shen, Bin; Chin, Frederick T; Pratx, Guillem Molecular imaging and biology. 29143174 2018 06;
Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Herring, Charles A; Banerjee, Amrita; McKinley, Eliot T; Simmons, Alan J; Ping, Jie; Roland, Joseph T; Franklin, Jeffrey L; Liu, Qi; Gerdes, Michael J; Coffey, Robert J; Lau, Ken S Cell systems. 29153838 2017 Nov 07;
Cell-type Dependent Alzheimer's Disease Phenotypes: Probing the Biology of Selective Neuronal Vulnerability. Muratore, Christina R; Zhou, Constance; Liao, Meichen; Fernandez, Marty A; Taylor, Walter M; Lagomarsino, Valentina N; Pearse 2nd, Richard V; Rice, Heather C; Negri, Joseph M; He, Amy; Srikanth, Priya; Callahan, Dana G; Shin, Taehwan; Zhou, Monica; Bennett, David A; Noggle, Scott; Love, J Christopher; Selkoe, Dennis J; Young-Pearse, Tracy L Stem cell reports. 29153990 2017 12 12;
An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues. Shah, Pavak Kirit; Santella, Anthony; Jacobo, Adrian; Siletti, Kimberly; Hudspeth, A J; Bao, Zhirong Developmental cell. 29161596 2017 Nov 20;
Functional MRI can detect changes in intratissue strains in a full thickness and critical sized ovine cartilage defect model. Chan, Deva D; Cai, Luyao; Butz, Kent D; Nauman, Eric A; Dickerson, Darryl A; Jonkers, Ilse; Neu, Corey P Journal of biomechanics. 29169631 2018 01 03;
Identification of a neural crest stem cell niche by Spatial Genomic Analysis. Lignell, Antti; Kerosuo, Laura; Streichan, Sebastian J; Cai, Long; Bronner, Marianne E Nature communications. 29184067 2017 Nov 28;
Eph-ephrin signaling modulated by polymerization and condensation of receptors. Ojosnegros, Samuel; Cutrale, Francesco; Rodríguez, Daniel; Otterstrom, Jason J; Chiu, Chi Li; Hortigüela, Verónica; Tarantino, Carolina; Seriola, Anna; Mieruszynski, Stephen; Martínez, Elena; Lakadamyali, Melike; Raya, Angel; Fraser, Scott E Proceedings of the National Academy of Sciences of the United States of America. 29192024 2017 Dec 12;
Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing. Morris, Jacqueline; Na, Young-Ji; Zhu, Hua; Lee, Jae-Hee; Giang, Hoa; Ulyanova, Alexandra V; Baltuch, Gordon H; Brem, Steven; Chen, H Isaac; Kung, David K; Lucas, Timothy H; O'Rourke, Donald M; Wolf, John A; Grady, M Sean; Sul, Jai-Yoon; Kim, Junhyong; Eb Cell reports. 29212019 2017 Dec 05;
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Lake, Blue B; Chen, Song; Sos, Brandon C; Fan, Jean; Kaeser, Gwendolyn E; Yung, Yun C; Duong, Thu E; Gao, Derek; Chun, Jerold; Kharchenko, Peter V; Zhang, Kun Nature biotechnology. 29227469 2018 Jan;
Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation. Lee, Jae Kyoo; Nam, Hong Gil; Zare, Richard N Quarterly reviews of biophysics. 29233214 2017 01;
Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology. Kim, Jeong-Ki; Louhghalam, Arghavan; Lee, Geonhui; Schafer, Benjamin W; Wirtz, Denis; Kim, Dong-Hwee Nature communications. 29242553 2017 Dec 14;
In Vivo Multiscale and Spatially-Dependent Biomechanics Reveals Differential Strain Transfer Hierarchy in Skeletal Muscle. Ghosh, Soham; Cimino, James G; Scott, Adrienne K; Damen, Frederick W; Phillips, Evan H; Veress, Alexander I; Neu, Corey P; Goergen, Craig J ACS biomaterials science & engineering. 29276759 2017 Nov 13;
Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice. Kolb, Ilya; Talei Franzesi, Giovanni; Wang, Michael; Kodandaramaiah, Suhasa B; Forest, Craig R; Boyden, Edward S; Singer, Annabelle C The Journal of neuroscience : the official journal of the Society for Neuroscience. 29279309 2018 Feb 14;
Mammalian Cell Division in 3D Matrices via Quantitative Confocal Reflection Microscopy. He, Lijuan; Sneider, Alexandra; Chen, Weitong; Karl, Michelle; Prasath, Vishnu; Wu, Pei-Hsun; Mattson, Gunnar; Wirtz, Denis Journal of visualized experiments : JoVE. 29286363 2017 11 29;
Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos. Onjiko, Rosemary M; Portero, Erika P; Moody, Sally A; Nemes, Peter Journal of visualized experiments : JoVE. 29286491 2017 Dec 22;
Multi-neuron intracellular recording in vivo via interacting autopatching robots. Kodandaramaiah, Suhasa B; Flores, Francisco J; Holst, Gregory L; Singer, Annabelle C; Han, Xue; Brown, Emery N; Boyden, Edward S; Forest, Craig R eLife. 29297466 2018 01 03;
Acoustofluidic devices controlled by cell phones. Bachman, Hunter; Huang, Po-Hsun; Zhao, Shuaiguo; Yang, Shujie; Zhang, Peiran; Fu, Hai; Huang, Tony Jun Lab on a chip. 29302660 2018 Jan 30;
PIVOT: platform for interactive analysis and visualization of transcriptomics data. Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong BMC bioinformatics. 29304726 2018 Jan 05;
Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A Development (Cambridge, England). 29311262 2018 01 08;
Survey of checkpoints along the pathway to diverse biomedical research faculty. Meyers, Lindsay C; Brown, Abigail M; Moneta-Koehler, Liane; Chalkley, Roger PloS one. 29338019 2018;
Cell Membrane Tracking in Living Brain Tissue Using Differential Interference Contrast Microscopy. Lee, John; Kolb, Ilya; Forest, Craig R; Rozell, Christopher J IEEE transactions on image processing : a publication of the IEEE Signal Processing Society. 29346099 2018 Apr;
Acoustofluidic waveguides for localized control of acoustic wavefront in microfluidics. Bian, Yusheng; Guo, Feng; Yang, Shujie; Mao, Zhangming; Bachman, Hunter; Tang, Shi-Yang; Ren, Liqiang; Zhang, Bin; Gong, Jianying; Guo, Xiasheng; Huang, Tony Jun Microfluidics and nanofluidics. 29358901 2017 Aug;
Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy. Chen, Andy Jing; Yuan, Xiaojing; Li, Junjie; Dong, Puting; Hamza, Iqbal; Cheng, Ji-Xin Analytical chemistry. 29401392 2018 03 06;
Mechanical regulation of stem-cell differentiation by the stretch-activated Piezo channel. He, Li; Si, Guangwei; Huang, Jiuhong; Samuel, Aravinthan D T; Perrimon, Norbert Nature. 29414942 2018 03 01;
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing Nature neuroscience. 29434377 2018 Mar;
Molecular Time Sharing through Dynamic Pulsing in Single Cells. Park, Jin; Dies, Marta; Lin, Yihan; Hormoz, Sahand; Smith-Unna, Stephanie E; Quinodoz, Sofia; Hernández-Jiménez, María Jesús; Garcia-Ojalvo, Jordi; Locke, James C W; Elowitz, Michael B Cell systems. 29454936 2018 Feb 28;
Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun Cell systems. 29454938 2018 Feb 28;
A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. Piatkevich, Kiryl D; Jung, Erica E; Straub, Christoph; Linghu, Changyang; Park, Demian; Suk, Ho-Jun; Hochbaum, Daniel R; Goodwin, Daniel; Pnevmatikakis, Eftychios; Pak, Nikita; Kawashima, Takashi; Yang, Chao-Tsung; Rhoades, Jeffrey L; Shemesh, Or; Asano, Shoh; Yoon, Young-Gyu; Freifeld, Limor; Saulnier, Jessica L; Riegler, Clemens; Engert, Florian; Hughes, Thom; Drobizhev, Mikhail; Szabo, Balint; Ahrens, Misha B; Flavell, Steven W; Sabatini, Bernardo L; Boyden, Edward S Nature chemical biology. 29483642 2018 Apr;
Direct measurement of bipolar cell responses to electrical stimulation in wholemount mouse retina. Walston, Steven T; Chow, Robert H; Weiland, James D Journal of neural engineering. 29513646 2018 08;
Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation. Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M; Norris, Jeremy L Journal of the American Society for Mass Spectrometry. 29536413 2018 Mar 13;
The successes and future prospects of the linear antisense RNA amplification methodology. Li, Jifen; Eberwine, James Nature protocols. 29599441 2018 05;
AceTree: a major update and case study in the long term maintenance of open-source scientific software. Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong BMC bioinformatics. 29618316 2018 Apr 04;
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Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density. Ma, Yitong; Budde, Mark W; Zhu, Junqin; Elowitz, Michael B bioRxiv : the preprint server for biology 37398290 2023 Jun 01
GPT detectors are biased against non-native English writers. Liang, Weixin; Yuksekgonul, Mert; Mao, Yining; Wu, Eric; Zou, James Patterns (New York, N.Y.) 37521038 2023 Jul 14
Tuning Methylation-Dependent Silencing Dynamics by Synthetic Modulation of CpG Density. Ma, Yitong; Budde, Mark W; Zhu, Junqin; Elowitz, Michael B ACS synthetic biology 37572041 2023 Sep 15
EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI). Ma, Yitong; Antebi, Yaron bioRxiv : the preprint server for biology 37609189 2023 Aug 09
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
Rational design and experimental evaluation of peptide ligands for the purification of adeno-associated viruses via affinity chromatography. Shastry, Shriarjun; Chu, Wenning; Barbieri, Eduardo; Greback-Clarke, Paul; Smith, William K; Cummings, Christopher; Minzoni, Arianna; Pancorbo, Jennifer; Gilleskie, Gary; Ritola, Kimberly; Daniele, Michael A; Johnson, Thomas F; Menegatti, Stefano Biotechnology journal 37728197 2023 Sep 20
Intervertebral Disc Elastography to Relate Shear Modulus and Relaxometry in Compression and Bending. Davis, Zachary R; Gossett, Paull C; Wilson, Robert L; Kim, Woong; Mei, Yue; Butz, Kent D; Emery, Nancy C; Nauman, Eric A; Avril, Stéphane; Neu, Corey P; Chan, Deva D bioRxiv : the preprint server for biology 37732250 2023 Sep 05
Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Jindal, Granton A; Bantle, Alexis T; Solvason, Joe J; Grudzien, Jessica L; D'Antonio-Chronowska, Agnieszka; Lim, Fabian; Le, Sophia H; Song, Benjamin P; Ragsac, Michelle F; Klie, Adam; Larsen, Reid O; Frazer, Kelly A; Farley, Emma K Developmental cell 37848026 2023 Nov 06
GenePT: A Simple But Hard-to-Beat Foundation Model for Genes and Cells Built From ChatGPT. Chen, Yiqun T; Zou, James bioRxiv : the preprint server for biology 37905130 2023 Oct 19
From goal to outcome: Analyzing the progression of biomedical sciences PhD careers in a longitudinal study using an expanded taxonomy. Brown, Abigail M; Meyers, Lindsay C; Varadarajan, Janani; Ward, Nicholas J; Cartailler, Jean-Philippe; Chalkley, Roger G; Gould, Kathleen L; Petrie, Kimberly A FASEB bioAdvances 37936923 2023 Nov
CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. Lu, Youtao; Lee, Jaehee; Li, Jifen; Allu, Srinivasa Rao; Wang, Jinhui; Kim, HyunBum; Bullaughey, Kevin L; Fisher, Stephen A; Nordgren, C Erik; Rosario, Jean G; Anderson, Stewart A; Ulyanova, Alexandra V; Brem, Steven; Chen, H Isaac; Wolf, John A; Grady, M Sean; Vinogradov, Sergei A; Kim, Junhyong; Eberwine, James Nature communications 37963886 2023 Nov 14

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