Single Cell Analysis Program (SCAP)
Single Cell Analysis Program (SCAP)
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Authors | Journal | PubMedID | Publication Date |
|---|---|---|---|---|
| Molecular mechanisms of experience-dependent plasticity in visual cortex. | Tropea, Daniela; Van Wart, Audra; Sur, Mriganka | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 18977729 | 2009 Feb 12 |
| 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 |
| 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 |
| 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 |
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| A multimodal cell census and atlas of the mammalian primary motor cortex. | BRAIN Initiative Cell Census Network (BICCN) | Nature | 34616075 | 2021 10 |
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| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum, Nongluk; Diep, Dinh; Chen, Song; Lake, Blue B; Zhang, Kun | Nature protocols | 34650278 | 2021 11 |
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| Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion. | Ghosh, Soham; Scott, Adrienne K; Seelbinder, Benjamin; Barthold, Jeanne E; Martin, Brittany M St; Kaonis, Samantha; Schneider, Stephanie E; Henderson, Jonathan T; Neu, Corey P | Biophysical journal | 34800469 | 2022 Jan 04 |
| DynaMorph: self-supervised learning of morphodynamic states of live cells. | Wu, Zhenqin; Chhun, Bryant B; Popova, Galina; Guo, Syuan-Ming; Kim, Chang N; Yeh, Li-Hao; Nowakowski, Tomasz; Zou, James; Mehta, Shalin B | Molecular biology of the cell | 35138913 | 2022 05 15 |
| Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. | Jiang, Shengdian; Wang, Yimin; Liu, Lijuan; Ding, Liya; Ruan, Zongcai; Dong, Hong-Wei; Ascoli, Giorgio A; Hawrylycz, Michael; Zeng, Hongkui; Peng, Hanchuan | Neuroinformatics | 35182359 | 2022 Feb 19 |
| In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. | D'Antonio, Matteo; Nguyen, Jennifer P; Arthur, Timothy D; Matsui, Hiroko; Donovan, Margaret K R; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | PLoS computational biology | 35226669 | 2022 Feb |
| Correction to: Unveiling Complexity and Multipotentiality of Early Heart Fields. | Circulation research | 35239406 | 2022 Mar 04 | |
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| Altered adult neurogenesis and gliogenesis in patients with mesial temporal lobe epilepsy. | Ammothumkandy, Aswathy; Ravina, Kristine; Wolseley, Victoria; Tartt, Alexandria N; Yu, Pen-Ning; Corona, Luis; Zhang, Naibo; Nune, George; Kalayjian, Laura; Mann, J John; Rosoklija, Gorazd B; Arango, Victoria; Dwork, Andrew J; Lee, Brian; Smith, J A D; Song, Dong; Berger, Theodore W; Heck, Christianne; Chow, Robert H; Boldrini, Maura; Liu, Charles Y; Russin, Jonathan J; Bonaguidi, Michael A | Nature neuroscience | 35383330 | 2022 Apr |
| The nested embryonic dorsal domains of BMP-target genes are not scaled to size during the evolution of Drosophila species. | Chahda, Juan Sebastian; Ambrosi, Priscilla; Mizutani, Claudia M | Journal of experimental zoology. Part B, Molecular and developmental evolution | 35451554 | 2022 Apr 22 |
| Deep learning identification of stiffness markers in breast cancer. | Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis | Biomaterials | 35537336 | 2022 06 |
| Astrocyte ethanol exposure reveals persistent and defined calcium response subtypes and associated gene signatures. | Kim, Hyun-Bum; Lu, Youtao; Oh, Seonkyung C; Morris, Jacqueline; Miyashiro, Kevin; Kim, Junhyong; Eberwine, James; Sul, Jai-Yoon | The Journal of biological chemistry | 35716779 | 2022 Jun 16 |
| Shifting machine learning for healthcare from development to deployment and from models to data. | Zhang, Angela; Xing, Lei; Zou, James; Wu, Joseph C | Nature biomedical engineering | 35788685 | 2022 Jul 04 |
| Development of an Interferon-Gamma Release Assay (IGRA) to Aid Diagnosis of Histoplasmosis. | Datta, Kausik; LaRue, Richard; Permpalung, Nitipong; Das, Sukanya; Zhang, Sean; Mehta Steinke, Seema; Bushkin, Yuri; Nosanchuk, Joshua D; Marr, Kieren A | Journal of clinical microbiology | 36190260 | 2022 Oct 19 |
| CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. | Jalloh, Sallieu; Olejnik, Judith; Berrigan, Jacob; Nisa, Annuurun; Suder, Ellen L; Akiyama, Hisashi; Lei, Maohua; Ramaswamy, Sita; Tyagi, Sanjay; Bushkin, Yuri; Mühlberger, Elke; Gummuluru, Suryaram | PLoS pathogens | 36279285 | 2022 Oct |
| Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in <i>C. elegans</i>. | Kim, Jun; Jimenez, David S; Ragipani, Bhavana; Zhang, Bo; Street, Lena A; Kramer, Maxwell; Albritton, Sarah E; Winterkorn, Lara H; Morao, Ana K; Ercan, Sevinc | eLife | 36331876 | 2022 11 04 |
| Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. | D'Antonio, Matteo; Nguyen, Jennifer P; Arthur, Timothy D; iPSCORE Consortium; Matsui, Hiroko; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | Nature communications | 36854752 | 2023 Feb 28 |
| Career self-efficacy disparities in underrepresented biomedical scientist trainees. | Chatterjee, Deepshikha; Jacob, Gabrielle A; Varvayanis, Susi Sturzenegger; Wefes, Inge; Chalkley, Roger; Nogueira, Ana T; Fuhrmann, Cynthia N; Varadarajan, Janani; Hubbard, Nisaan M; Gaines, Christiann H; Layton, Rebekah L; Chaudhary, Sunita | PloS one | 36857379 | 2023 |
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| 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 |
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| 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 |
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| Modulations of Homeostatic ACE2, CD147, GRP78 Pathways Correlate with Vascular and Endothelial Performance Markers during Pulmonary SARS-CoV-2 Infection. | Nisa, Annuurun; Kumar, Ranjeet; Ramasamy, Santhamani; Kolloli, Afsal; Olejnik, Judith; Jalloh, Sallieu; Gummuluru, Suryaram; Subbian, Selvakumar; Bushkin, Yuri | Cells | 38474396 | 2024 Feb 29 |
| Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues. | Shin, Tay Won; Wang, Hao; Zhang, Chi; An, Bobae; Lu, Yangning; Zhang, Elizabeth; Lu, Xiaotang; Karagiannis, Emmanouil D; Kang, Jeong Seuk; Emenari, Amauche; Symvoulidis, Panagiotis; Asano, Shoh; Lin, Leanne; Costa, Emma K; IMAXT Grand Challenge Consortium; Marblestone, Adam H; Kasthuri, Narayanan; Tsai, Li-Huei; Boyden, Edward S | bioRxiv : the preprint server for biology | 38496681 | 2024 Mar 08 |
| Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor, Kian; Chen, Chien-Ju; Lee, Ho Suk; Cai, Matthew; Nafisi, Mahsa; Que, Richard; Palmer, Carter R; Yuan, Yixu; Zhang, Yida; Li, Xuwen; Song, Jinghui; Knoten, Amanda; Lake, Blue B; Gaut, Joseph P; Keene, C Dirk; Lein, Ed; Kharchenko, Peter V; Chun, Jerold; Jain, Sanjay; Fan, Jian-Bing; Zhang, Kun | Nature communications | 38509069 | 2024 Mar 20 |
| Small Extracellular Vesicles Promote Stiffness-mediated Metastasis. | Sneider, Alexandra; Liu, Ying; Starich, Bartholomew; Du, Wenxuan; Nair, Praful R; Marar, Carolyn; Faqih, Najwa; Ciotti, Gabrielle E; Kim, Joo Ho; Krishnan, Sejal; Ibrahim, Salma; Igboko, Muna; Locke, Alexus; Lewis, Daniel M; Hong, Hanna; Karl, Michelle N; Vij, Raghav; Russo, Gabriella C; Gómez-de-Mariscal, Estibaliz; Habibi, Mehran; Muñoz-Barrutia, Arrate; Gu, Luo; Eisinger-Mathason, T S Karin; Wirtz, Denis | Cancer research communications | 38630893 | 2024 May 09 |
| Tumor proliferation and invasion are intrinsically coupled and unraveled through tunable spheroid and physics-based models. | Crawford, Ashleigh J; Gomez-Cruz, Clara; Russo, Gabriella C; Huang, Wilson; Bhorkar, Isha; Roy, Triya; Muñoz-Barrutia, Arrate; Wirtz, Denis; Garcia-Gonzalez, Daniel | Acta biomaterialia | 38160858 | 2024 Feb |
| Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections. | Yip, Mighten C; Gonzalez, Mercedes M; Lewallen, Colby F; Landry, Corey R; Kolb, Ilya; Yang, Bo; Stoy, William M; Fong, Ming-Fai; Rowan, Matthew J M; Boyden, Edward S; Forest, Craig R | bioRxiv : the preprint server for biology | 39185225 | 2024 Aug 15 |
| Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. | Arthur, Timothy D; Nguyen, Jennifer P; D'Antonio-Chronowska, Agnieszka; Matsui, Hiroko; Silva, Nayara S; Joshua, Isaac N; iPSCORE Consortium; Luchessi, André D; Greenwald, William W Young; D'Antonio, Matteo; Pera, Martin F; Frazer, Kelly A | Nature communications | 38395976 | 2024 Feb 23 |
