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Single Cell Analysis (86)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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 ENature2014 Aug 14155-6025079324
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, YingxiaoBiomaterials2014 Jun 24NULL24973298
High-sensitivity measurements of multiple kinase activities in live single cells.Regot, Sergi; Hughey, Jacob J; Bajar, Bryce T; Carrasco, Silvia; Covert, Markus WCell2014 Jun 191724-3424949979
Tight coupling between nucleus and cell migration through the perinuclear actin cap.Kim, Dong-Hwee; Cho, Sangkyun; Wirtz, DenisJournal of cell science2014 Jun 12528-4124639463
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, AlipashaNature methods2014 May 18NULL24836920
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 NJournal of immunotherapy (Hagerstown, Md. : 1997)2014 May204-1324714354
Genetic characteristics and pathogenic mechanisms of periodontal pathogens.Amano, A; Chen, C; Honma, K; Li, C; Settem, R P; Sharma, AAdvances in dental research2014 May15-2224736700
Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2.Xu, Shuwa; Tyagi, Sanjay; Schedl, PaulPLoS genetics2014 Maye100438024830287
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, KonstantinosCell2014 Apr 24611-2324726433
Single-cell in situ RNA profiling by sequential hybridization.Lubeck, Eric; Coskun, Ahmet F; Zhiyentayev, Timur; Ahmad, Mubhij; Cai, LongNature methods2014 Apr360-124681720
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 JThe Journal of clinical investigation2014 Apr 1NULL24691442
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.)2014 Mar 211360-324578530
Three-dimensional cell migration does not follow a random walk.Wu, Pei-Hsun; Giri, Anjil; Sun, Sean X; Wirtz, DenisProceedings of the National Academy of Sciences of the United States of America2014 Mar 183949-5424594603
The role of mechanical tension on lipid raft dependent PDGF-induced TRPC6 activation.Lei, Lei; Lu, Shaoying; Wang, Yi; Kim, Taejin; Mehta, Dolly; Wang, YingxiaoBiomaterials2014 Mar2868-7724397990
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 AlvesCytokine2014 Mar46-5324548424
Tumor evolution in response to chemotherapy: phenotype versus genotype.Navin, Nicholas ECell reports2014 Feb 13417-924529750
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, JNature methods2014 Feb190-624412976
Single-cell technologies for monitoring immune systems.Chattopadhyay, Pratip K; Gierahn, Todd M; Roederer, Mario; Love, J ChristopherNature immunology2014 Feb128-3524448570
A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans.Cheng, Ya-An; Jee, Jason; Hsu, Genie; Huang, Yanyan; Chen, Casey; Lin, Chun-PinJournal of the Formosan Medical Association = Taiwan yi zhi2014 Feb114-2324530245
Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images.Gierahn, Todd M; Loginov, Denis; Love, J ChristopherJournal of proteome research2014 Jan 24NULL24417579
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, ZhirongCell2014 Jan 16359-7224439388
PIWI proteins are essential for early Drosophila embryogenesis.Mani, Sneha Ramesh; Megosh, Heather; Lin, HaifanDevelopmental biology2014 Jan 15340-924184635
Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ.Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, MonaPloS one2014e9348824675777
In vivo robotics: the automation of neuroscience and other intact-system biological fields.Kodandaramaiah, Suhasa B; Boyden, Edward S; Forest, Craig RAnnals of the New York Academy of Sciences2013 Dec63-7123841584
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, KunNature biotechnology2013 Dec1126-3224213699
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, YingxiaoProceedings of the National Academy of Sciences of the United States of America2013 Nov 2619372-724222685
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, HariNature biotechnology2013 Nov1032-824108093
PIWI proteins are essential for early Drosophila embryogenesis.Mani, Sneha Ramesh; Megosh, Heather; Lin, HaifanDevelopmental biology2013 Oct 31NULL24184635
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 WDevelopment (Cambridge, England)2013 Sep3882-9123946444
Genetic analysis of mate discrimination in Drosophila simulans.Chu, Y; Yang, E; Schinaman, J M; Chahda, J S; Sousa-Neves, REvolution; international journal of organic evolution2013 Aug2335-4723888855
Single cell spectroscopy: Noninvasive measures of small-scale structure and function.Mousoulis, Charilaos; Xu, Xin; Reiter, David A; Neu, Corey PMethods (San Diego, Calif.)2013 Jul 22NULL23886910
In vivo robotics: the automation of neuroscience and other intact-system biological fields.Kodandaramaiah, Suhasa B; Boyden, Edward S; Forest, Craig RAnnals of the New York Academy of Sciences2013 Jul 10NULL23841584
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, DenisFASEB journal : official publication of the Federation of American Societies for Experimental Biology2013 Jul2667-7623538711
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 PPLoS computational biology2013 Jule100314523874187
Epigenetic alterations in acute kidney injury.Bomsztyk, Karol; Denisenko, OlegSeminars in nephrology2013 Jul327-4024011575
Detection and isolation of auto-reactive human antibodies from primary B cells.Sendra, Victor G; Lie, Anthony; Romain, Gabrielle; Agarwal, Sandeep K; Varadarajan, NavinMethods (San Diego, Calif.)2013 Jun 26NULL23811296
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, YingxiaoNature communications2013 Jun 24203723792876
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, YingxiaoBiomaterials2013 May3807-1523465490
Mechanotransduction at focal adhesions: from physiology to cancer development.Seong, Jihye; Wang, Ning; Wang, YingxiaoJournal of cellular and molecular medicine2013 May597-60423601032
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 MiekoCurrent biology : CB2013 Apr 22710-623583556
Focal adhesion size uniquely predicts cell migration.Kim, Dong-Hwee; Wirtz, DenisFASEB journal : official publication of the Federation of American Societies for Experimental Biology2013 Apr1351-6123254340
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, HongkACS nano2013 Mar 261850-6623514423
Interstitial friction greatly impacts membrane mechanics.Wirtz, DenisBiophysical journal2013 Mar 191217-823528079
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, DenisIntegrative biology : quantitative biosciences from nano to macro2013 Mar523-3423319145
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, CMolecular oral microbiology2013 Feb17-Jan23194436
FRET imaging of calcium signaling in live cells in the microenvironment.Qian, Tongcheng; Lu, Shaoying; Ma, Hongwei; Fang, Jing; Zhong, Wenxuan; Wang, YingxiaoIntegrative biology : quantitative biosciences from nano to macro2013 Jan 28431-823250282
Dimensional control of cancer cell migration.Konstantopoulos, Konstantinos; Wu, Pei-Hsun; Wirtz, DenisBiophysical journal2013 Jan 22279-8023442847
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 EJournal of bacteriology2013 Jan156-6623104812
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 WPloS one2013e5322223301045
Quantitative high-throughput single-cell cytotoxicity assay for T cells.Liadi, Ivan; Roszik, Jason; Romain, Gabrielle; Cooper, Laurence J N; Varadarajan, NavinJournal of visualized experiments : JoVE2013e5005823407457
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 NPloS one2013e6413823741305
Barriers to transmission of transcriptional noise in a c-fos c-jun pathway.Shah, Khyati; Tyagi, SanjayMolecular systems biology201368724022005
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 AScientific reports2013356024356337
Probing Endoplasmic Reticulum Dynamics using Fluorescence Imaging and Photobleaching Techniques.Costantini, Lindsey; Snapp, ErikCurrent protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.]201321.7.1-21.7.2924510787
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 ChristopherAnalytical chemistry2012 Dec 1810531-623205933
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, YJournal of microscopy2012 Oct77-8922971220
Elimination of dendritic spines with long-term memory is specific to active circuits.Sanders, Jeff; Cowansage, Kiriana; Baumgartel, Karsten; Mayford, MarkThe Journal of neuroscience : the official journal of the Society for Neuroscience2012 Sep 512570-822956846
Single-cell systems biology by super-resolution imaging and combinatorial labeling.Lubeck, Eric; Cai, LongNature methods2012 Jul743-822660740
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, RogerJournal of bacteriology2012 Apr183722408240
Genome sequence of a novel species, Propionibacterium humerusii.Butler-Wu, Susan M; Sengupta, Dhruba J; Kittichotirat, Weerayuth; Matsen 3rd, Frederick A; Bumgarner, Roger EJournal of bacteriology2011 Jul367821571999
Development of an animal model for Aggregatibacter actinomycetemcomitans biofilm-mediated oral osteolytic infection: a preliminary study.Freire, Marcelo O; Sedghizadeh, Parish P; Schaudinn, Christoph; Gorur, Amita; Downey, Jennifer S; Choi, Jeong-Ho; Chen, Weizhen; Kook, Joong-Ki; Chen, Casey; Goodman, Steven D; Zadeh, Homayoun HJournal of periodontology2011 May778-8921222546
Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.Kittichotirat, Weerayuth; Bumgarner, Roger E; Asikainen, Sirkka; Chen, CaseyPloS one2011e2242021811606
Occurrence of Aggregatibacter actinomycetemcomitans serotypes in subgingival plaque from United States subjects.Chen, C; Wang, T; Chen, WMolecular oral microbiology2010 Jun207-1420536748
Genome sequence of naturally competent Aggregatibacter actinomycetemcomitans serotype a strain D7S-1.Chen, Casey; Kittichotirat, Weerayuth; Chen, Weizhen; Downey, Jennifer S; Si, Yan; Bumgarner, RogerJournal of bacteriology2010 May2643-420348265
Markedly different genome arrangements between serotype a strains and serotypes b or c strains of Aggregatibacter actinomycetemcomitans.Kittichotirat, Weerayuth; Bumgarner, Roger; Chen, CaseyBMC genomics201048920825670
Genome sequence of Aggregatibacter actinomycetemcomitans serotype c strain D11S-1.Chen, Casey; Kittichotirat, Weerayuth; Si, Yan; Bumgarner, RogerJournal of bacteriology2009 Dec7378-919820097
The derivation of diagnostic markers of chronic myeloid leukemia progression from microarray data.Oehler, Vivian G; Yeung, Ka Yee; Choi, Yongjae E; Bumgarner, Roger E; Raftery, Adrian E; Radich, Jerald PBlood2009 Oct 83292-819654405
Protinfo PPC: a web server for atomic level prediction of protein complexes.Kittichotirat, Weerayuth; Guerquin, Michal; Bumgarner, Roger E; Samudrala, RamNucleic acids research2009 JulW519-2519420059
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.Annest, Amalia; Bumgarner, Roger E; Raftery, Adrian E; Yeung, Ka YeeBMC bioinformatics20097219245714
Adherence of Aggregatibacter actinomycetemcomitans via serotype-specific polysaccharide antigens in lipopolysaccharides.Fujise, O; Wang, Y; Chen, W; Chen, COral microbiology and immunology2008 Jun226-3318402609
Identification of strain-specific DNA of Actinobacillus actinomycetemcomitans by representational difference analysis.Mena, J; Chen, COral microbiology and immunology2007 Dec429-3217949347
Genomic distribution and functions of uptake signal sequences in Actinobacillus actinomycetemcomitans.Wang, Ying; Orvis, Joshua; Dyer, David; Chen, CaseyMicrobiology (Reading, England)2006 Nov3319-2517074902
Identification of a genomic island of Actinobacillus actinomycetemcomitans.Chen, Weizhen; Wang, Ying; Chen, CaseyJournal of periodontology.2005 Nov2052-6016277576
Genetic basis for conversion of rough-to-smooth colony morphology in Actinobacillus actinomycetemcomitans.Wang, Ying; Liu, Amy; Chen, CaseyInfection and immunity. 2005 Jun3749-5315908406
Cytokine responses of human gingival fibroblasts to Actinobacillus actinomycetemcomitans cytolethal distending toxin.Belibasakis, G N; Johansson, A; Wang, Y; Chen, C; Lagergard, T; Kalfas, S; Lerner, U HCytokine. 2005 Apr 2156-6315804596
The cytolethal distending toxin induces receptor activator of NF-kappaB ligand expression in human gingival fibroblasts and periodontal ligament cells.Belibasakis, G N; Johansson, A; Wang, Y; Chen, C; Kalfas, S; Lerner, U HInfection and immunity. 2005 Jan342-5115618171
Clonal distribution of natural competence in Actinobacillus actinomycetemcomitans.Fujise, O; Lakio, L; Wang, Y; Asikainen, S; Chen, COral microbiology and immunology. 2004 Oct340-215327649
Cell cycle arrest of human gingival fibroblasts and periodontal ligament cells by Actinobacillus actinomycetemcomitans: involvement of the cytolethal distending toxin.Belibasakis, G N; Mattsson, A; Wang, Y; Chen, C; Johansson, AAPMIS : acta pathologica, microbiologica, et immunologica Scandinavica. 2004 Oct674-8515601319
Clonal diversity and stability of subgingival Eikenella corrodens.Fujise, O; Chen, W; Rich, S; Chen, CJournal of clinical microbiology. 2004 May2036-4215131167
Induction of T-cell apoptosis by Actinobacillus actinomycetemcomitans mutants with deletion of ltxA and cdtABC genes: possible activity of GroEL-like molecule.Nalbant, A; Chen, C; Wang, Y; Zadeh, H HOral microbiology and immunology. 2003 Dec339-4914622339
Type IV pilus gene homologs pilABCD are required for natural transformation in Actinobacillus actinomycetemcomitans.Wang, Ying; Shi, Wenyuan; Chen, Weizhen; Chen, CaseyGene. 2003 Jul 17249-5512909361
Natural transformation and DNA uptake signal sequences in Actinobacillus actinomycetemcomitans.Wang, Ying; Goodman, Steve D; Redfield, Rosemary J; Chen, CaseyJournal of bacteriology.2002 Jul3442-912057937
Susceptibilities of Eikenella corrodens, Prevotella intermedia, and Prevotella nigrescens clinical isolates to amoxicillin and tetracycline.Luong, N; Tsai, J; Chen, CAntimicrobial agents and chemotherapy.2001 Nov3253-511600394
Frequency of 530-bp deletion in Actinobacillus actinomycetemcomitans leukotoxin promoter region.Contreras, A; Rusitanonta, T; Chen, C; Wagner, W G; Michalowicz, B S; Slots, JOral microbiology and immunology. 2000 Oct338-4011154428
Molecular identification of Dialister pneumosintes in subgingival plaque of humans.Doan, N; Contreras, A; Flynn, J; Slots, J; Chen, CJournal of clinical microbiology.2000 Aug3043-710921975
Importance of Dialister pneumosintes in human periodontitis.Contreras, A; Doan, N; Chen, C; Rusitanonta, T; Flynn, M J; Slots, JOral microbiology and immunology.2000 Aug269-7211154414


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