Single Cell Analysis (308)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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 SNeuron.2017 Aug 30;28858614
Using Longitudinal Data on Career Outcomes to Promote Improvements and Diversity in Graduate Education.Feig, Andrew L; Robinson, Leah; Yan, Song; Byrd, Mark; Mathur, AmbikaChange.2016;28804143
Acoustofluidic bacteria separation.Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E; Zeng, Xiangqun; Huang, Tony JunJournal of micromechanics and microengineering : structures, devices, and systems.2017 Jan 01;28798539
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, ChantaleClinical cancer research : an official journal of the American Association for Cancer Research.2017 Jul 28;28754817
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, KunScientific reports.2017 Jul 20;28729663
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 SNature biotechnology.2017 Aug;28714966
Unmassked: Single-Cell Profiling of Immune Cell Populations in Tumors.Varadarajan, NavinMolecular therapy : the journal of the American Society of Gene Therapy.2017 Aug 02;28684257
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, ArjunNature.;28607484
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, YuriCritical reviews in immunology.2016;28605344
Visualizing adenosine-to-inosine RNA editing in single mammalian cells.Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara HNature methods.2017 Jun 12;28604724
Single image super-resolution via an iterative reproducing kernel Hilbert space method.Deng, Liang-Jian; Guo, Weihong; Huang, Ting-ZhuIEEE transactions on circuits and systems for video technology : a publication of the Circuits and Systems Society.2016 Nov;28603404
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, HongkuiNature communications.2017 Jun 01;28569837
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, DenisNature communications.2017 May 26;28548090
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, JuliaPloS one.2017;28542304
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 ConsortiumHuman genetics.2017 Jul;28528403
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 LauraNature protocols.2017 Jun;28518171
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 JCell reports.2017 May 09;28494873
Assessment of Single Cell RNA-Seq Normalization Methods.Ding, Bo; Zheng, Lina; Wang, WeiG3 (Bethesda, Md.).2017 Jul 05;28468817
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 SNature methods.2017 Jun;28417997
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 AStem cell reports.2017 Apr 11;28410643
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 AStem cell reports.2017 Apr 11;28410642
Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.Greenwald, William W; Li, He; Smith, Erin N; Benaglio, Paola; Nariai, Naoki; Frazer, Kelly ABMC bioinformatics.2017 Apr 07;28388874
Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells.DeBoever, Christopher; Li, He; Jakubosky, David; Benaglio, Paola; Reyna, Joaquin; Olson, Katrina M; Huang, Hui; Biggs, William; Sandoval, Efren; D'Antonio, Matteo; Jepsen, Kristen; Matsui, Hiroko; Arias, Angelo; Ren, Bing; Nariai, Naoki; Smith, Erin N; D'Antonio-Chronowska, Agnieszka; Farley, Emma K; Frazer, Kelly ACell stem cell.2017 Apr 06;28388430
Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics.Panopoulos, Athanasia D; Smith, Erin N; Arias, Angelo D; Shepard, Peter J; Hishida, Yuriko; Modesto, Veronica; Diffenderfer, Kenneth E; Conner, Clay; Biggs, William; Sandoval, Efren; D'Antonio-Chronowska, Agnieszka; Berggren, W Travis; Izpisua Belmonte, Juan Carlos; Frazer, Kelly ACell stem cell.2017 Apr 06;28388429
Diagnosis of prostate cancer by desorption electrospray ionization mass spectrometric imaging of small metabolites and lipids.Banerjee, Shibdas; Zare, Richard N; Tibshirani, Robert J; Kunder, Christian A; Nolley, Rosalie; Fan, Richard; Brooks, James D; Sonn, Geoffrey AProceedings of the National Academy of Sciences of the United States of America.2017 Mar 28;28292895
3D Clumped Cell Segmentation Using Curvature Based Seeded Watershed.Atta-Fosu, Thomas; Guo, Weihong; Jeter, Dana; Mizutani, Claudia M; Stopczynski, Nathan; Sousa-Neves, RuiJournal of imaging.2016 Dec;28280723
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.Gierahn, Todd M; Wadsworth 2nd, Marc H; Hughes, Travis K; Bryson, Bryan D; Butler, Andrew; Satija, Rahul; Fortune, Sarah; Love, J Christopher; Shalek, Alex KNature methods.2017 Apr;28192419
Mechanisms of Cardiomyocyte Proliferation and Differentiation in Development and Regeneration.Yester, Jessie Wettig; Kühn, BernhardCurrent cardiology reports.2017 Feb;28185170
Tumor evolution: Linear, branching, neutral or punctuated?Davis, Alexander; Gao, Ruli; Navin, NicholasBiochimica et biophysica acta.2017 04;28110020
Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics.Spaethling, Jennifer M; Na, Young-Ji; Lee, Jaehee; Ulyanova, Alexandra V; Baltuch, Gordon H; Bell, Thomas J; Brem, Steven; Chen, H Isaac; Dueck, Hannah; Fisher, Stephen A; Garcia, Marcela P; Khaladkar, Mugdha; Kung, David K; Lucas Jr, Timothy H; O'Rourke, Donald M; Stefanik, Derek; Wang, Jinhui; Wolf, John A; Bartfai, Tamas; Grady, M Sean; Sul, Jai-Yoon; Kim, Junhyong; Eberwine, James HCell reports.2017 Jan 17;28099855
New-generation mass spectrometry expands the toolbox of cell and developmental biology.Lombard-Banek, Camille; Portero, Erika P; Onjiko, Rosemary M; Nemes, PeterGenesis (New York, N.Y. : 2000).2017 Jan;28095647
Hybrid Dielectric-loaded Nanoridge Plasmonic Waveguide for Low-Loss Light Transmission at the Subwavelength Scale.Zhang, Bin; Bian, Yusheng; Ren, Liqiang; Guo, Feng; Tang, Shi-Yang; Mao, Zhangming; Liu, Xiaomin; Sun, Jinju; Gong, Jianying; Guo, Xiasheng; Huang, Tony JunScientific reports.2017 Jan 16;28091583
Acoustic actuation of bioinspired microswimmers.Kaynak, Murat; Ozcelik, Adem; Nourhani, Amir; Lammert, Paul E; Crespi, Vincent H; Huang, Tony JunLab on a chip.2017 Jan 31;27991641
Gamma frequency entrainment attenuates amyloid load and modifies microglia.Iaccarino, Hannah F; Singer, Annabelle C; Martorell, Anthony J; Rudenko, Andrii; Gao, Fan; Gillingham, Tyler Z; Mathys, Hansruedi; Seo, Jinsoo; Kritskiy, Oleg; Abdurrob, Fatema; Adaikkan, Chinnakkaruppan; Canter, Rebecca G; Rueda, Richard; Brown, Emery N; Boyden, Edward S; Tsai, Li-HueiNature.2016 12 07;27929004
Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements.Hormoz, Sahand; Singer, Zakary S; Linton, James M; Antebi, Yaron E; Shraiman, Boris I; Elowitz, Michael BCell systems.;27883889
Assessing characteristics of RNA amplification methods for single cell RNA sequencing.Dueck, Hannah R; Ai, Rizi; Camarena, Adrian; Ding, Bo; Dominguez, Reymundo; Evgrafov, Oleg V; Fan, Jian-Bing; Fisher, Stephen A; Herstein, Jennifer S; Kim, Tae Kyung; Kim, Jae Mun Hugo; Lin, Ming-Yi; Liu, Rui; Mack, William J; McGroty, Sean; Nguyen, Joseph D; Salathia, Neeraj; Shallcross, Jamie; Souaiaia, Tade; Spaethling, Jennifer M; Walker, Christopher P; Wang, Jinhui; Wang, Kai; Wang, Wei; Wildberg, Andre; Zheng, Lina; Chow, Robert H; Eberwine, James; Knowles, James A; Zhang, Kun; Kim, JunhyongBMC genomics.2016 Nov 24;27881084
In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus.Shah, Sheel; Lubeck, Eric; Zhou, Wen; Cai, LongNeuron.2016 Oct 19;27764670
Enhancing Graduate and Postdoctoral Education To Create a Sustainable Biomedical Workforce.Fuhrmann, Cynthia NHuman gene therapy.2016 Nov;27762630
Acoustofluidic coating of particles and cells.Ayan, Bugra; Ozcelik, Adem; Bachman, Hunter; Tang, Shi-Yang; Xie, Yuliang; Wu, Mengxi; Li, Peng; Huang, Tony JunLab on a chip.2016 Nov 01;27754503
Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks.Simmons, Alan J; Scurrah, Cherié R; McKinley, Eliot T; Herring, Charles A; Irish, Jonathan M; Washington, M Kay; Coffey, Robert J; Lau, Ken SScience signaling.2016 Oct 11;27729552
Cleaning patch-clamp pipettes for immediate reuse.Kolb, I; Stoy, W A; Rousseau, E B; Moody, O A; Jenkins, A; Forest, C RScientific reports.2016 Oct 11;27725751
Optical method for automated measurement of glass micropipette tip geometry.Stockslager, Max A; Capocasale, Christopher M; Holst, Gregory L; Simon, Michael D; Li, Yuanda; McGruder, Dustin J; Rousseau, Erin B; Stoy, William A; Sulchek, Todd; Forest, Craig RPrecision engineering.2016 Oct;27672230
Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM).Kumar, Abhishek; Christensen, Ryan; Guo, Min; Chandris, Panos; Duncan, William; Wu, Yicong; Santella, Anthony; Moyle, Mark; Winter, Peter W; Colón-Ramos, Daniel; Bao, Zhirong; Shroff, HariThe Biological bulletin.2016 Aug;27638693
Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.Gao, Ruli; Davis, Alexander; McDonald, Thomas O; Sei, Emi; Shi, Xiuqing; Wang, Yong; Tsai, Pei-Ching; Casasent, Anna; Waters, Jill; Zhang, Hong; Meric-Bernstam, Funda; Michor, Franziska; Navin, Nicholas ENature genetics.2016 Oct;27526321
The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan.Kotzin, Jonathan J; Spencer, Sean P; McCright, Sam J; Kumar, Dinesh B Uthaya; Collet, Magalie A; Mowel, Walter K; Elliott, Ellen N; Uyar, Asli; Makiya, Michelle A; Dunagin, Margaret C; Harman, Christian C D; Virtue, Anthony T; Zhu, Stella; Bailis, Will; Stein, Judith; Hughes, Cynthia; Raj, Arjun; Wherry, E John; Goff, Loyal A; Klion, Amy D; Rinn, John L; Williams, Adam; Flavell, Richard A; Henao-Mejia, JorgeNature.2016 Sep 08;27525555
Acoustofluidic Rotational Manipulation of Cells and Organisms Using Oscillating Solid Structures.Ozcelik, Adem; Nama, Nitesh; Huang, Po-Hsun; Kaynak, Murat; McReynolds, Melanie R; Hanna-Rose, Wendy; Huang, Tony JunSmall (Weinheim an der Bergstrasse, Germany).2016 Oct;27515787
Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.Mann, Karen M; Newberg, Justin Y; Black, Michael A; Jones, Devin J; Amaya-Manzanares, Felipe; Guzman-Rojas, Liliana; Kodama, Takahiro; Ward, Jerrold M; Rust, Alistair G; van der Weyden, Louise; Yew, Christopher Chin Kuan; Waters, Jill L; Leung, Marco L; Rogers, Keith; Rogers, Susan M; McNoe, Leslie A; Selvanesan, Luxmanan; Navin, Nicholas; Jenkins, Nancy A; Copeland, Neal G; Mann, Michael BNature biotechnology.2016 Sep;27479497
Acoustofluidic actuation of in situ fabricated microrotors.Kaynak, Murat; Ozcelik, Adem; Nama, Nitesh; Nourhani, Amir; Lammert, Paul E; Crespi, Vincent H; Huang, Tony JunLab on a chip.2016 Sep 21;27466140
KIF1A/UNC-104 Transports ATG-9 to Regulate Neurodevelopment and Autophagy at Synapses.Stavoe, Andrea K H; Hill, Sarah E; Hall, David H; Colón-Ramos, Daniel ADevelopmental cell.2016 Jul 25;27396362
Integration of autopatching with automated pipette and cell detection in vitro.Wu, Qiuyu; Kolb, Ilya; Callahan, Brendan M; Su, Zhaolun; Stoy, William; Kodandaramaiah, Suhasa B; Neve, Rachael L; Zeng, Hongkui; Boyden, Ed S; Forest, Craig R; Chubykin, Alexander AJournal of neurophysiology.2016 Jul 6;27385800
Probe for the measurement of cell surface pH in vivo and ex vivo.Anderson, Michael; Moshnikova, Anna; Engelman, Donald M; Reshetnyak, Yana K; Andreev, Oleg AProceedings of the National Academy of Sciences of the United States of America.2016 Jul 19;27382181
Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies.Tillberg, Paul W; Chen, Fei; Piatkevich, Kiryl D; Zhao, Yongxin; Yu, Chih-Chieh Jay; English, Brian P; Gao, Linyi; Martorell, Anthony; Suk, Ho-Jun; Yoshida, Fumiaki; DeGennaro, Ellen M; Roossien, Douglas H; Gong, Guanyu; Seneviratne, Uthpala; Tannenbaum, Nature biotechnology.2016 Jul 4;27376584
Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.Shah, Sheel; Lubeck, Eric; Schwarzkopf, Maayan; He, Ting-Fang; Greenbaum, Alon; Sohn, Chang Ho; Lignell, Antti; Choi, Harry M T; Gradinaru, Viviana; Pierce, Niles A; Cai, LongDevelopment (Cambridge, England).2016 Aug 01;27342713
A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd AGenes & development.2016 Jun 15;27340175
Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain.Lake, Blue B; Ai, Rizi; Kaeser, Gwendolyn E; Salathia, Neeraj S; Yung, Yun C; Liu, Rui; Wildberg, Andre; Gao, Derek; Fung, Ho-Lim; Chen, Song; Vijayaraghavan, Raakhee; Wong, Julian; Chen, Allison; Sheng, Xiaoyan; Kaper, Fiona; Shen, Richard; Ronaghi, Mostafa; Fan, Jian-Bing; Wang, Wei; Chun, Jerold; Zhang, KunScience (New York, N.Y.).2016 Jun 24;27339989
Rapid formation of size-controllable multicellular spheroids via 3D acoustic tweezers.Chen, Kejie; Wu, Mengxi; Guo, Feng; Li, Peng; Chan, Chung Yu; Mao, Zhangming; Li, Sixing; Ren, Liqiang; Zhang, Rui; Huang, Tony JunLab on a chip.2016 Jul 5;27327102
In Situ and In Vivo Molecular Analysis by Coherent Raman Scattering Microscopy.Liao, Chien-Sheng; Cheng, Ji-XinAnnual review of analytical chemistry (Palo Alto, Calif.).2016 Jun 12;27306307
Constitutive Lck Activity Drives Sensitivity Differences between CD8+ Memory T Cell Subsets.Moogk, Duane; Zhong, Shi; Yu, Zhiya; Liadi, Ivan; Rittase, William; Fang, Victoria; Dougherty, Janna; Perez-Garcia, Arianne; Osman, Iman; Zhu, Cheng; Varadarajan, Navin; Restifo, Nicholas P; Frey, Alan B; Krogsgaard, MichelleJournal of immunology (Baltimore, Md. : 1950).2016 Jul 15;27271569
Dense transcript profiling in single cells by image correlation decoding.Coskun, Ahmet F; Cai, LongNature methods.2016 Aug;27271198
What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism.Symmons, Orsolya; Raj, ArjunMolecular cell.2016 Jun 2;27259209
A shared neural ensemble links distinct contextual memories encoded close in time.Cai, Denise J; Aharoni, Daniel; Shuman, Tristan; Shobe, Justin; Biane, Jeremy; Song, Weilin; Wei, Brandon; Veshkini, Michael; La-Vu, Mimi; Lou, Jerry; Flores, Sergio E; Kim, Isaac; Sano, Yoshitake; Zhou, Miou; Baumgaertel, Karsten; Lavi, Ayal; Kamata, Masakazu; Tuszynski, Mark; Mayford, Mark; Golshani, Peyman; Silva, Alcino JNature.2016 06 02;27251287
Monitoring Enzymatic Reactions in Real Time Using Venturi Easy Ambient Sonic-Spray Ionization Mass Spectrometry.Jansson, Erik T; Dulay, Maria T; Zare, Richard NAnalytical chemistry.2016 Jun 21;27249533
Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers.Cole, Russell H; Gartner, Zev J; Abate, Adam RJournal of visualized experiments : JoVE.2016 May 05;27214249
Evaluation of a BGO-Based PET System for Single-Cell Tracking Performance by Simulation and Phantom Studies.Ouyang, Yu; Kim, Tae Jin; Pratx, GuillemMolecular imaging.2016;27175009
Approaches to Inactivate Genes in Zebrafish.Parant, John M; Yeh, Jing-Ruey JoannaAdvances in experimental medicine and biology.2016;27165349
Investigation of micromixing by acoustically oscillated sharp-edges.Nama, Nitesh; Huang, Po-Hsun; Huang, Tony Jun; Costanzo, FrancescoBiomicrofluidics.2016 Mar;27158292
Imaging Specific Genomic DNA in Living Cells.Chen, Baohui; Guan, Juan; Huang, BoAnnual review of biophysics.2016 Jul 5;27145877
High-Resolution Live-Cell Imaging and Analysis by Laser Desorption/Ionization Droplet Delivery Mass Spectrometry.Lee, Jae Kyoo; Jansson, Erik T; Nam, Hong Gil; Zare, Richard NAnalytical chemistry.2016 May 17;27110027
Monovar: single-nucleotide variant detection in single cells.Zafar, Hamim; Wang, Yong; Nakhleh, Luay; Navin, Nicholas; Chen, KenNature methods.;27088313
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping.Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA.Molecular Cell2016 April 5V:62 P:1-1127067601
Generation of Catalytic Antibodies Is an Intrinsic Property of an Individual's Immune System: A Study on a Large Cohort of Renal Transplant Patients.Mahendra, Ankit; Peyron, Ivan; Thaunat, Olivier; Dollinger, Cécile; Gilardin, Laurent; Sharma, Meenu; Wootla, Bharath; Rao, Desirazu N; Padiolleau-Lefevre, Séverine; Boquet, Didier; More, Abhijit; Varadarajan, Navin; Kaveri, Srini V; Legendre, Christophe; Lacroix-Desmazes, SébastienJournal of immunology (Baltimore, Md. : 1950).2016 May 15;27067006
Regulation of ribosomal RNA expression across the lifespan is fine-tuned by maternal diet before implantation.Denisenko, Oleg; Lucas, Emma S; Sun, Congshan; Watkins, Adam J; Mar, Daniel; Bomsztyk, Karol; Fleming, Tom PBiochimica et biophysica acta.2016 Jul;27060415
Rotational manipulation of single cells and organisms using acoustic waves.Ahmed, Daniel; Ozcelik, Adem; Bojanala, Nagagireesh; Nama, Nitesh; Upadhyay, Awani; Chen, Yuchao; Hanna-Rose, Wendy; Huang, Tony JunNature communications.2016;27004764
Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo.Onjiko, Rosemary M; Morris, Sydney E; Moody, Sally A; Nemes, PeterThe Analyst.2016 Jun 21;27004603
Versatile protein tagging in cells with split fluorescent protein.Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A; Ishikawa, Hiroaki; Leonetti, Manuel D; Marshall, Wallace F; Weissman, Jonathan S; Huang, BoNature communications.2016;26988139
High resolution laser mass spectrometry bioimaging.Murray, Kermit K; Seneviratne, Chinthaka A; Ghorai, SumanMethods (San Diego, Calif.).2016 Jul 15;26972785
Denoising Stimulated Raman Spectroscopic Images by Total Variation Minimization.Liao, Chien-Sheng; Choi, Joon Hee; Zhang, Delong; Chan, Stanley H; Cheng, Ji-XinThe journal of physical chemistry. C, Nanomaterials and interfaces.2015 Aug 20;26955400
Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant.Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, ArjunGenes & development.2016 Mar 1;26944681
Assembly and operation of the autopatcher for automated intracellular neural recording in vivo.Kodandaramaiah, Suhasa B; Holst, Gregory L; Wickersham, Ian R; Singer, Annabelle C; Franzesi, Giovanni Talei; McKinnon, Michael L; Forest, Craig R; Boyden, Edward SNature protocols.2016 Apr;26938115
Spatial colocalization and functional link of purinosomes with mitochondria.French, Jarrod B; Jones, Sara A; Deng, Huayun; Pedley, Anthony M; Kim, Doory; Chan, Chung Yu; Hu, Haibei; Pugh, Raymond J; Zhao, Hong; Zhang, Youxin; Huang, Tony Jun; Fang, Ye; Zhuang, Xiaowei; Benkovic, Stephen JScience (New York, N.Y.).2016 Feb 12;733-726912862
Dynamics of epigenetic regulation at the single-cell level.Bintu, Lacramioara; Yong, John; Antebi, Yaron E; McCue, Kayla; Kazuki, Yasuhiro; Uno, Narumi; Oshimura, Mitsuo; Elowitz, Michael BScience (New York, N.Y.).2016 Feb 12;26912859
Establishment of human iPSC-based models for the study and targeting of glioma initiating cells.Sancho-Martinez, Ignacio; Nivet, Emmanuel; Xia, Yun; Hishida, Tomoaki; Aguirre, Aitor; Ocampo, Alejandro; Ma, Li; Morey, Robert; Krause, Marie N; Zembrzycki, Andreas; Ansorge, Olaf; Vazquez-Ferrer, Eric; Dubova, Ilir; Reddy, Pradeep; Lam, David; Hishida, Yuriko; Wu, Min-Zu; Esteban, Concepcion Rodriguez; O'Leary, Dennis; Wahl, Geoffrey M; Verma, Inder M; Laurent, Louise C; Izpisua Belmonte, Juan CarlosNature communications.2016;26899176
Single-Cell Detection of Secreted A? and sAPP? from Human IPSC-Derived Neurons and Astrocytes.Liao, Mei-Chen; Muratore, Christina R; Gierahn, Todd M; Sullivan, Sarah E; Srikanth, Priya; De Jager, Philip L; Love, J Christopher; Young-Pearse, Tracy LThe Journal of neuroscience : the official journal of the Society for Neuroscience.2016 Feb 3;1730-4626843653
HistoMosaic Detecting KRAS G12V Mutation Across Colorectal Cancer Tissue Slices through in Situ PCR.Raub, Christopher B; Lee, Chen-Chung; Shibata, Darryl; Taylor, Clive; Kartalov, EmilAnalytical chemistry.2016 Mar 01;26820161
Three-dimensional manipulation of single cells using surface acoustic waves.Guo, Feng; Mao, Zhangming; Chen, Yuchao; Xie, Zhiwei; Lata, James P; Li, Peng; Ren, Liqiang; Liu, Jiayang; Yang, Jian; Dao, Ming; Suresh, Subra; Huang, Tony JunProceedings of the National Academy of Sciences of the United States of America.2016 Feb 9;26811444
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.Fan, Jean; Salathia, Neeraj; Liu, Rui; Kaeser, Gwendolyn E; Yung, Yun C; Herman, Joseph L; Kaper, Fiona; Fan, Jian-Bing; Zhang, Kun; Chun, Jerold; Kharchenko, Peter VNature methods.2016 Mar;241-426780092
A robust nonlinear tissue-component discrimination method for computational pathology.Sarnecki, Jacob S; Burns, Kathleen H; Wood, Laura D; Waters, Kevin M; Hruban, Ralph H; Wirtz, Denis; Wu, Pei-HsunLaboratory investigation; a journal of technical methods and pathology.2016 Jan 18;26779829
System for Rapid, Precise Modulation of Intraocular Pressure, toward Minimally-Invasive In Vivo Measurement of Intracranial Pressure.Stockslager, Max A; Samuels, Brian C; Allingham, R Rand; Klesmith, Zoe A; Schwaner, Stephen A; Forest, Craig R; Ethier, C RossPloS one.2016;26771837
High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury.Jeong, Heejin; Na, Young-Ji; Lee, Kihwan; Kim, Yong Ho; Lee, Yunsin; Kang, Minho; Jiang, Bao-Chun; Yeom, Young Il; Wu, Long-Jun; Gao, Yong-Jing; Kim, Junhyong; Oh, Seog BaePain.2016 Apr;26761385
Highly multiplexed targeted DNA sequencing from single nuclei.Leung, Marco L; Wang, Yong; Kim, Charissa; Gao, Ruli; Jiang, Jerry; Sei, Emi; Navin, Nicholas ENature protocols.2016 Feb;26741407
Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.Chen, Baohui; Hu, Jeffrey; Almeida, Ricardo; Liu, Harrison; Balakrishnan, Sanjeev; Covill-Cooke, Christian; Lim, Wendell A; Huang, BoNucleic acids research.2016 Jan 5;26740581
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi; Kim, Tae Kyung; Jarsky, Tim; Yao, Zizhen; Levi, Boaz; Gray, Lucas T; Sorensen, Staci A; Dolbeare, Tim; Bertagnolli, Darren; Goldy, Jeff; Shapovalova, Nadiya; Parry, Sheana; Lee, Changkyu; Smith, Kimberly; Bernard, Amy; Madisen, Linda; Sunkin, Susan M; Hawrylycz, Michael; Koch, Christof; Zeng, HongkuiNature neuroscience.2016 Feb;26727548
Probing Cell Deformability via Acoustically Actuated Bubbles.Xie, Yuliang; Nama, Nitesh; Li, Peng; Mao, Zhangming; Huang, Po-Hsun; Zhao, Chenglong; Costanzo, Francesco; Huang, Tony JunSmall (Weinheim an der Bergstrasse, Germany).2016 Feb 17;26715211
Experimental and numerical studies on standing surface acoustic wave microfluidics.Mao, Zhangming; Xie, Yuliang; Guo, Feng; Ren, Liqiang; Huang, Po-Hsun; Chen, Yuchao; Rufo, Joseph; Costanzo, Francesco; Huang, Tony JunLab on a chip.2016 Feb 7;26698361
Generation and functional assessment of 3D multicellular spheroids in droplet based microfluidics platform.Sabhachandani, P; Motwani, V; Cohen, N; Sarkar, S; Torchilin, V; Konry, TLab on a chip.2016 Jan 26;497-50526686985
Exploring Memory Representations with Activity-Based Genetics.Mayford, Mark; Reijmers, LeonCold Spring Harbor perspectives in biology.2015 Dec 18;26684182
Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status.Vir, Pooja; Arrigucci, Riccardo; Lakehal, Karim; Davidow, Amy L; Pine, Richard; Tyagi, Sanjay; Bushkin, Yuri; Lardizabal, Alfred; Gennaro, Maria LauraPloS one.2015;26658491
The Mechanobiology of Aging.Phillip, Jude M; Aifuwa, Ivie; Walston, Jeremy; Wirtz, DenisAnnual review of biomedical engineering.2015;26643020
Untwisting the Caenorhabditis elegans embryo.Christensen, Ryan Patrick; Bokinsky, Alexandra; Santella, Anthony; Wu, Yicong; Marquina-Solis, Javier; Guo, Min; Kovacevic, Ismar; Kumar, Abhishek; Winter, Peter W; Tashakkori, Nicole; McCreedy, Evan; Liu, Huafeng; McAuliffe, Matthew; Mohler, William; Colón-Ramos, Daniel A; Bao, Zhirong; Shroff, HarieLife.2015 Dec 03;26633880
Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function.Dueck, Hannah; Eberwine, James; Kim, JunhyongBioEssays : news and reviews in molecular, cellular and developmental biology.2016 Feb;26625861
T Cell Dynamic Activation and Functional Analysis in Nanoliter Droplet Microarray.Sarkar, Saheli; Motwani, Vinny; Sabhachandani, Pooja; Cohen, Noa; Konry, TaniaJournal of clinical & cellular immunology.2015 Jun;26613065
Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially.Roy, Debasmita; Michaelson, David; Hochman, Tsivia; Santella, Anthony; Bao, Zhirong; Goldberg, Judith D; Hubbard, E Jane AlbertDevelopmental biology.2016 Jan 1;261-7126577869
Acceleration of reaction in charged microdroplets.Lee, Jae Kyoo; Banerjee, Shibdas; Nam, Hong Gil; Zare, Richard NQuarterly reviews of biophysics.2015 Nov;26537403
Collective cancer cell invasion induced by coordinated contractile stresses.Jimenez Valencia, Angela M; Wu, Pei-Hsun; Yogurtcu, Osman N; Rao, Pranay; DiGiacomo, Josh; Godet, Inês; He, Lijuan; Lee, Meng-Horng; Gilkes, Daniele; Sun, Sean X; Wirtz, DenisOncotarget.2015 Dec 22;26528856
Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-?-induced apoptosis in vivo.Simmons, Alan J; Banerjee, Amrita; McKinley, Eliot T; Scurrah, Cherie' R; Herring, Charles A; Gewin, Leslie S; Masuzaki, Ryota; Karp, Seth J; Franklin, Jeffrey L; Gerdes, Michael J; Irish, Jonathan M; Coffey, Robert J; Lau, Ken SMolecular systems biology.2015 Oct;83526519361
Modeling developmental neuropsychiatric disorders with iPSC technology: challenges and opportunities.Young-Pearse, Tracy L; Morrow, Eric MCurrent opinion in neurobiology.2016 Feb;66-7326517284
Local 3D matrix confinement determines division axis through cell shape.He, Lijuan; Chen, Weitong; Wu, Pei-Hsun; Jimenez, Angela; Wong, Bin Sheng; San, Angela; Konstantopoulos, Konstantinos; Wirtz, DenisOncotarget.2016 Feb 09;26515603
Reusable acoustic tweezers for disposable devices.Guo, Feng; Xie, Yuliang; Li, Sixing; Lata, James; Ren, Liqiang; Mao, Zhangming; Ren, Baiyang; Wu, Mengxi; Ozcelik, Adem; Huang, Tony JunLab on a chip.2015 Dec 21;4517-2326507411
Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model.Santella, Anthony; Kovacevic, Ismar; Herndon, Laura A; Hall, David H; Du, Zhuo; Bao, ZhirongNucleic acids research.2016 Jan 4;26503254
Senescent stromal cells induce cancer cell migration via inhibition of RhoA/ROCK/myosin-based cell contractility.Aifuwa, Ivie; Giri, Anjil; Longe, Nick; Lee, Sang Hyuk; An, Steven S; Wirtz, DenisOncotarget.2015 Oct 13;30516-3126483365
Induced pluripotent stem cells as a discovery tool for Alzheimer?s disease.Sullivan, Sarah E; Young-Pearse, Tracy LBrain research.2015 Oct 13;26459988
Phenotypic drug profiling in droplet microfluidics for better targeting of drug-resistant tumors.Sarkar, S; Cohen, N; Sabhachandani, P; Konry, TLab on a chip.2015 Dec 7;4441-5026456240
The origin and implementation of the Broadening Experiences in Scientific Training programs: an NIH common fund initiative.F.J. Meyers, A. Mathur, C.N. Fuhrmann, T.C. O’Brien, I. Wefes, P.A. Labosky, D.S. Duncan, A. August, A. Feig, K.L. Gould, M.J. Friedlander, C.B. Schaffer, A. Van Wart, and R. ChalkleyThe FASEB Journal2015 Oct 2;26432783
Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?Mellis, Ian A; Raj, ArjunGenome research.2015 Oct;1466-7226430156
Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions.Fraley, Stephanie I; Wu, Pei-Hsun; He, Lijuan; Feng, Yunfeng; Krisnamurthy, Ranjini; Longmore, Gregory D; Wirtz, DenisScientific reports.2015;1458026423227
Acousto-plasmofluidics: Acoustic modulation of surface plasmon resonance in microfluidic systems.Ahmed, Daniel; Peng, Xiaolei; Ozcelik, Adem; Zheng, Yuebing; Huang, Tony JunAIP advances.2015 Sep;26421224
Cellular Deconstruction: Finding Meaning in Individual Cell Variation.Eberwine, James; Kim, JunhyongTrends in cell biology.2015 Oct;569-7826410403
Functional enrichment by direct plasmid recovery after fluorescence activated cell sorting.Ramesh, Balakrishnan; Frei, Christopher S; Cirino, Patrick C; Varadarajan, NavinBioTechniques.2015 Sep;157-6126345509
Thermally multiplexed polymerase chain reaction.Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig RBiomicrofluidics.2015 Jul;26339317
A spatiotemporally controllable chemical gradient generator via acoustically oscillating sharp-edge structures.Huang, Po-Hsun; Chan, Chung Yu; Li, Peng; Nama, Nitesh; Xie, Yuliang; Wei, Cheng-Hsin; Chen, Yuchao; Ahmed, Daniel; Huang, Tony JunLab on a chip.2015 Nov 7;4166-7626338516
Normal mammary epithelial cells promote carcinoma basement membrane invasion by inducing microtubule-rich protrusions.Lee, Meng-Horng; Wu, Pei-Hsun; Gilkes, Daniele; Aifuwa, Ivie; Wirtz, DenisOncotarget.2015 Oct 20;32634-4526334095
Acoustofluidic Fluorescence Activated Cell Sorter.Nawaz, Ahmad Ahsan; Chen, Yuchao; Nama, Nitesh; Nissly, Ruth Helmus; Ren, Liqiang; Ozcelik, Adem; Wang, Lin; McCoy, J Philip; Levine, Stewart J; Huang, Tony JunAnalytical chemistry.2015 Dec 15;26331909
Tuning Sensitivity of CAR to EGFR Density Limits Recognition of Normal Tissue While Maintaining Potent Antitumor Activity.Caruso, Hillary G; Hurton, Lenka V; Najjar, Amer; Rushworth, David; Ang, Sonny; Olivares, Simon; Mi, Tiejuan; Switzer, Kirsten; Singh, Harjeet; Huls, Helen; Lee, Dean A; Heimberger, Amy B; Champlin, Richard E; Cooper, Laurence J NCancer research.2015 Sep 1;3505-1826330164
The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo.Du, Zhuo; Santella, Anthony; He, Fei; Shah, Pavak K; Kamikawa, Yuko; Bao, ZhirongDevelopmental cell.2015 Sep 14;592-60726321128
A high-throughput acoustic cell sorter.Ren, Liqiang; Chen, Yuchao; Li, Peng; Mao, Zhangming; Huang, Po-Hsun; Rufo, Joseph; Guo, Feng; Wang, Lin; McCoy, J Philip; Levine, Stewart J; Huang, Tony JunLab on a chip.2015 Oct 7;3870-926289231
Stress Enables Reinforcement-Elicited Serotonergic Consolidation of Fear Memory.Baratta, Michael V; Kodandaramaiah, Suhasa B; Monahan, Patrick E; Yao, Junmei; Weber, Michael D; Lin, Pei-Ann; Gisabella, Barbara; Petrossian, Natalie; Amat, Jose; Kim, Kyungman; Yang, Aimei; Forest, Craig R; Boyden, Edward S; Goosens, Ki ABiological psychiatry.2016 May 15;26248536
Imaging Tumor Acidity: pH-Low Insertion Peptide Probe for Optoacoustic Tomography.Reshetnyak, Yana KClinical cancer research : an official journal of the American Association for Cancer Research.2015 Jul 29;26224874
Exploring bubble oscillation and mass transfer enhancement in acoustic-assisted liquid-liquid extraction with a microfluidic device.Xie, Yuliang; Chindam, Chandraprakash; Nama, Nitesh; Yang, Shikuan; Lu, Mengqian; Zhao, Yanhui; Mai, John D; Costanzo, Francesco; Huang, Tony JunScientific reports.2015;1257226223474
Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis.McMillen, Patrick; Holley, Scott ACurrent opinion in cell biology.2015 Oct;48-5326189063
C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types.Vidal, Berta; Santella, Anthony; Serrano-Saiz, Esther; Bao, Zhirong; Chuang, Chiou-Fen; Hobert, OliverDevelopment (Cambridge, England).2015 Jul 15;26153233
Plasmofluidics: Merging Light and Fluids at the Micro-/Nanoscale.Wang, Mingsong; Zhao, Chenglong; Miao, Xiaoyu; Zhao, Yanhui; Rufo, Joseph; Liu, Yan Jun; Huang, Tony Jun; Zheng, YuebingSmall (Weinheim an der Bergstrasse, Germany).2015 Sep 16;4423-4426140612
Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis.Gonzalez, Jacob; Qi, Hongying; Liu, Na; Lin, HaifanCell reports.2015 Jul 7;150-6126119740
Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip.Shaffer, Sydney M; Joshi, Rohan P; Chambers, Benjamin S; Sterken, David; Biaesch, Andrew G; Gabrieli, David J; Li, Yang; Feemster, Kristen A; Hensley, Scott E; Issadore, David; Raj, ArjunLab on a chip.2015 Aug 7;3170-8226113495
Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules.Yu, Yu; Gaillard, Stephanie; Phillip, Jude M; Huang, Tai-Chung; Pinto, Sneha M; Tessarollo, Nayara G; Zhang, Zhen; Pandey, Akhilesh; Wirtz, Denis; Ayhan, Ayse; Davidson, Ben; Wang, Tian-Li; Shih, Ie-MingCancer cell.2015 Jul 13;82-9626096845
POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA.Elewa, Ahmed; Shirayama, Masaki; Kaymak, Ebru; Harrison, Paul F; Powell, David R; Du, Zhuo; Chute, Christopher D; Woolf, Hannah; Yi, Dongni; Ishidate, Takao; Srinivasan, Jagan; Bao, Zhirong; Beilharz, Traude H; Ryder, Sean P; Mello, Craig CDevelopmental cell.2015 Jul 6;26096734
Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING).Merouane, Amine; Rey-Villamizar, Nicolas; Lu, Yanbin; Liadi, Ivan; Romain, Gabrielle; Lu, Jennifer; Singh, Harjeet; Cooper, Laurence J N; Varadarajan, Navin; Roysam, BadrinathBioinformatics (Oxford, England).2015 Oct 1;3189-9726059718
Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.Dueck, Hannah; Khaladkar, Mugdha; Kim, Tae Kyung; Spaethling, Jennifer M; Francis, Chantal; Suresh, Sangita; Fisher, Stephen A; Seale, Patrick; Beck, Sheryl G; Bartfai, Tamas; Kuhn, Bernhard; Eberwine, James; Kim, JunhyongGenome biology.2015;12226056000
Mechanical Allostery: Evidence for a Force Requirement in the Proteolytic Activation of Notch.Gordon, Wendy R; Zimmerman, Brandon; He, Li; Miles, Laura J; Huang, Jiuhong; Tiyanont, Kittichoat; McArthur, Debbie G; Aster, Jon C; Perrimon, Norbert; Loparo, Joseph J; Blacklow, Stephen CDevelopmental cell.2015 Jun 22;729-3626051539
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.Santella, Anthony; Catena, Raúl; Kovacevic, Ismar; Shah, Pavak; Yu, Zidong; Marquina-Solis, Javier; Kumar, Abhishek; Wu, Yicong; Schaff, James; Colón-Ramos, Daniel; Shroff, Hari; Mohler, William A; Bao, ZhirongBMC bioinformatics.2015;18926051157
Scalable microfluidics for single-cell RNA printing and sequencing.Bose, Sayantan; Wan, Zhenmao; Carr, Ambrose; Rizvi, Abbas H; Vieira, Gregory; Pe'er, Dana; Sims, Peter AGenome biology.2015;12026047807
Variations in dysfunction of sister chromatid cohesion in esco2 mutant zebrafish reflect the phenotypic diversity of Roberts syndrome.Percival, Stefanie M; Thomas, Holly R; Amsterdam, Adam; Carroll, Andrew J; Lees, Jacqueline A; Yost, H Joseph; Parant, John MDisease models & mechanisms.2015 Aug 1;941-5526044958
Compact and modular multicolour fluorescence detector for droplet microfluidics.Cole, Russell H; de Lange, Niek; Gartner, Zev J; Abate, Adam RLab on a chip.2015 Jul 7;2754-826032595
A New Interleukin-13 Amino-Coated Gadolinium Metallofullerene Nanoparticle for Targeted MRI Detection of Glioblastoma Tumor Cells.Li, Tinghui; Murphy, Susan; Kiselev, Boris; Bakshi, Kanwarpal S; Zhang, Jianyuan; Eltahir, Amnah; Zhang, Yafen; Chen, Ying; Zhu, Jie; Davis, Richey M; Madsen, Louis A; Morris, John R; Karolyi, Daniel R; LaConte, Stephen M; Sheng, Zhi; Dorn, Harry CJournal of the American Chemical Society.2015 Jun 24;7881-826022213
Numerical study of acoustophoretic motion of particles in a PDMS microchannel driven by surface acoustic waves.Nama, Nitesh; Barnkob, Rune; Mao, Zhangming; Kähler, Christian J; Costanzo, Francesco; Huang, Tony JunLab on a chip.2015 Jun 21;2700-926001199
Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.Klein, Allon M; Mazutis, Linas; Akartuna, Ilke; Tallapragada, Naren; Veres, Adrian; Li, Victor; Peshkin, Leonid; Weitz, David A; Kirschner, Marc WCell.2015 May 21;1187-20126000487
Rapid and Localized Mechanical Stimulation and Adhesion Assay: TRPM7 Involvement in Calcium Signaling and Cell Adhesion.Nishitani, Wagner Shin; Alencar, Adriano Mesquita; Wang, YingxiaoPloS one.2015;e012644025946314
Tuning noise in gene expression.Tyagi, SanjayMolecular systems biology.2015 May;80525943344
Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo.Onjiko, Rosemary M; Moody, Sally A; Nemes, PeterProceedings of the National Academy of Sciences of the United States of America.2015 May 26;6545-5025941375
Transforming training to reflect the workforce.Mathur, Ambika; Meyers, Frederick J; Chalkley, Roger; O'Brien, Theresa C; Fuhrmann, Cynthia NScience translational medicine.2015 Apr 29;285ed425925677
Closed-loop, ultraprecise, automated craniotomies.Pak, Nikita; Siegle, Joshua H; Kinney, Justin P; Denman, Daniel J; Blanche, Timothy J; Boyden, Edward SJournal of neurophysiology.2015 Jun 1;3943-5325855700
SNES: single nucleus exome sequencing.Leung, Marco L; Wang, Yong; Waters, Jill; Navin, Nicholas EGenome biology.2015;5525853327
Acoustic separation of circulating tumor cells.Li, Peng; Mao, Zhangming; Peng, Zhangli; Zhou, Lanlan; Chen, Yuchao; Huang, Po-Hsun; Truica, Cristina I; Drabick, Joseph J; El-Deiry, Wafik S; Dao, Ming; Suresh, Subra; Huang, Tony JunProceedings of the National Academy of Sciences of the United States of America.2015 Apr 21;4970-525848039
Neuregulin stimulation of cardiomyocyte regeneration in mice and human myocardium reveals a therapeutic window.Polizzotti, Brian D; Ganapathy, Balakrishnan; Walsh, Stuart; Choudhury, Sangita; Ammanamanchi, Niyatie; Bennett, David G; dos Remedios, Cristobal G; Haubner, Bernhard J; Penninger, Josef M; Kühn, BernhardScience translational medicine.2015 Apr 1;281ra4525834111
Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure.Hashem, Sherin I; Perry, Cynthia N; Bauer, Matthieu; Han, Sangyoon; Clegg, Stacey D; Ouyang, Kunfu; Deacon, Dekker C; Spinharney, Mary; Panopoulos, Athanasia D; Izpisua Belmonte, Juan Carlos; Frazer, Kelly A; Chen, Ju; Gong, Qiuming; Zhou, Zhengfeng; Chi,Stem cells (Dayton, Ohio).2015 Jul;2343-5025826782
The tissue mechanics of vertebrate body elongation and segmentation.McMillen, Patrick; Holley, Scott ACurrent opinion in genetics & development.2015 Jun;106-1125796079
Microdroplet fusion mass spectrometry for fast reaction kinetics.Lee, Jae Kyoo; Kim, Samuel; Nam, Hong Gil; Zare, Richard NProceedings of the National Academy of Sciences of the United States of America.2015 Mar 31;25775573
Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development.Kurian, Leo; Aguirre, Aitor; Sancho-Martinez, Ignacio; Benner, Christopher; Hishida, Tomoaki; Nguyen, Thai B; Reddy, Pradeep; Nivet, Emmanuel; Krause, Marie N; Nelles, David A; Rodriguez Esteban, Concepcion; Campistol, Josep M; Yeo, Gene W; Izpisua BelmonCirculation.2015 Apr 7;1278-9025739401
Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.Malhotra, Ankit; Wang, Yong; Waters, Jill; Chen, Ken; Meric-Bernstam, Funda; Hall, Ira M; Navin, Nicholas EGenome medicine.2015;625729435
Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model.Wu, Pei-Hsun; Giri, Anjil; Wirtz, DenisNature protocols.2015 Mar;517-2725719270
Normalization and noise reduction for single cell RNA-seq experiments.Ding, Bo; Zheng, Lina; Zhu, Yun; Li, Nan; Jia, Haiyang; Ai, Rizi; Wildberg, Andre; Wang, WeiBioinformatics (Oxford, England).2015 Jul 1;2225-725717193
Individual Motile CD4(+) T Cells Can Participate in Efficient Multikilling through Conjugation to Multiple Tumor Cells.Liadi, Ivan; Singh, Harjeet; Romain, Gabrielle; Rey-Villamizar, Nicolas; Merouane, Amine; Adolacion, Jay R T; Kebriaei, Partow; Huls, Helen; Qiu, Peng; Roysam, Badrinath; Cooper, Laurence J N; Varadarajan, NavinCancer immunology research.2015 May;473-8225711538
COX-2 dependent regulation of mechanotransduction in human breast cancer cells.Yoon, A-Rum; Stasinopoulos, Ioannis; Kim, Jae Hun; Yong, Hwan Mee; Kilic, Onur; Wirtz, Denis; Bhujwalla, Zaver M; An, Steven SCancer biology & therapy.2015;430-725701047
Cytoskeletal tension induces the polarized architecture of the nucleus.Kim, Dong-Hwee; Wirtz, DenisBiomaterials.2015 Apr;161-7225701041
Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.Lee, Je Hyuk; Daugharthy, Evan R; Scheiman, Jonathan; Kalhor, Reza; Ferrante, Thomas C; Terry, Richard; Turczyk, Brian M; Yang, Joyce L; Lee, Ho Suk; Aach, John; Zhang, Kun; Church, George MNature protocols.2015 Mar;442-5825675209
Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-? response to viral infection.Patil, Sonali; Fribourg, Miguel; Ge, Yongchao; Batish, Mona; Tyagi, Sanjay; Hayot, Fernand; Sealfon, Stuart CScience signaling.2015 Feb 10;ra1625670204
Distinct mechanisms regulating mechanical force-induced Ca²? signals at the plasma membrane and the ER in human MSCs.Kim, Tae-Jin; Joo, Chirlmin; Seong, Jihye; Vafabakhsh, Reza; Botvinick, Elliot L; Berns, Michael W; Palmer, Amy E; Wang, Ning; Ha, Taekjip; Jakobsson, Eric; Sun, Jie; Wang, YingxiaoeLife.2015;e0487625667984
Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony JunSmall (Weinheim an der Bergstrasse, Germany).2015 Jun;2733-725641793
Controlling lipid micelle stability using oligonucleotide headgroups.Wilner, Samantha E; Sparks, Samuel E; Cowburn, David; Girvin, Mark E; Levy, MatthewJournal of the American Chemical Society.2015 Feb 18;2171-425634639
Advanced targeted nanomedicine.Arachchige, Mohan C M; Reshetnyak, Yana K; Andreev, Oleg AJournal of biotechnology.2015 May 20;88-9725615945
Optical clearing in dense connective tissues to visualize cellular connectivity in situ.Calve, Sarah; Ready, Andrew; Huppenbauer, Christopher; Main, Russell; Neu, Corey PPloS one.2015;e011666225581165
Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.Kim, Daniel H; Marinov, Georgi K; Pepke, Shirley; Singer, Zakary S; He, Peng; Williams, Brian; Schroth, Gary P; Elowitz, Michael B; Wold, Barbara JCell stem cell.2015 Jan 8;88-10125575081
Single-neuron isolation for RNA analysis using pipette capture and laser capture microdissection.Lovatt, Ditte; Bell, Thomas; Eberwine, JamesCold Spring Harbor protocols.2015 Jan;pdb.prot07243925561613
Efficient delivery and functional expression of transfected modified mRNA in human embryonic stem cell-derived retinal pigmented epithelial cells.Hansson, Magnus L; Albert, Silvia; González Somermeyer, Louisa; Peco, Rubén; Mejía-Ramírez, Eva; Montserrat, Núria; Izpisua Belmonte, Juan CarlosThe Journal of biological chemistry.2015 Feb 27;5661-7225555917
A FRET-Based Biosensor for Imaging SYK Activities in Living Cells.Xiang, Xue; Sun, Jie; Wu, Jianhua; He, Hai-Tao; Wang, Yingxiao; Zhu, ChengCellular and molecular bioengineering.2011 Dec;670-67725541586
Controlling cell-cell interactions using surface acoustic waves.Guo, Feng; Li, Peng; French, Jarrod B; Mao, Zhangming; Zhao, Hong; Li, Sixing; Nama, Nitesh; Fick, James R; Benkovic, Stephen J; Huang, Tony JunProceedings of the National Academy of Sciences of the United States of America.2015 Jan 6;43-825535339
E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis.Du, Zhuo; He, Fei; Yu, Zidong; Bowerman, Bruce; Bao, ZhirongDevelopmental biology.2015 Feb 15;267-7925523393
In vivo activation of a conserved microRNA program induces mammalian heart regeneration.Aguirre, Aitor; Montserrat, Nuria; Zacchigna, Serena; Nivet, Emmanuel; Hishida, Tomoaki; Krause, Marie N; Kurian, Leo; Ocampo, Alejandro; Vazquez-Ferrer, Eric; Rodriguez-Esteban, Concepcion; Kumar, Sachin; Moresco, James J; Yates 3rd, John R; Campistol, JCell stem cell.2014 Nov 6;589-60425517466
Transcriptional expression of myelin basic protein in oligodendrocytes depends on functional syntaxin 4: a potential correlation with autocrine signaling.Bijlard, Marjolein; Klunder, Bert; de Jonge, Jenny C; Nomden, Anita; Tyagi, Sanjay; de Vries, Hans; Hoekstra, Dick; Baron, WiaMolecular and cellular biology.2015 Feb;675-8725512606
Profiling T cell activation using single-molecule fluorescence in situ hybridization and flow cytometry.Bushkin, Yuri; Radford, Felix; Pine, Richard; Lardizabal, Alfred; Mangura, Bonita T; Gennaro, Maria Laura; Tyagi, SanjayJournal of immunology (Baltimore, Md. : 1950).2015 Jan 15;836-4125505292
High-throughput genome editing and phenotyping facilitated by high resolution melting curve analysis.Thomas, Holly R; Percival, Stefanie M; Yoder, Bradley K; Parant, John MPloS one.2014;e11463225503746
Single-cell variation leads to population invariance in NF-*B signaling dynamics.Hughey, Jacob J; Gutschow, Miriam V; Bajar, Bryce T; Covert, Markus WMolecular biology of the cell.2015 Feb 1;583-9025473117
RE: stem cells loaded with multimechanistic oncolytic herpes simplex virus variants for brain tumor therapy.Krause, Marie N; Sancho-Martinez, Ignacio; Izpisua Belmonte, Juan CarlosJournal of the National Cancer Institute.2015 Jan;36825473104
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Optical clearing in collagen- and proteoglycan-rich osteochondral tissues.Neu, C P; Novak, T; Gilliland, K F; Marshall, P; Calve, SOsteoarthritis and cartilage / OARS, Osteoarthritis Research Society.2015 Mar;405-1325454370
Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording.Harrison, Reid R; Kolb, Ilya; Kodandaramaiah, Suhasa B; Chubykin, Alexander A; Yang, Aimei; Bear, Mark F; Boyden, Edward S; Forest, Craig RJournal of neurophysiology.2015 Feb 15;1275-8225429119
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Acoustofluidic chemical waveform generator and switch.Ahmed, Daniel; Muddana, Hari S; Lu, Mengqian; French, Jarrod B; Ozcelik, Adem; Fang, Ye; Butler, Peter J; Benkovic, Stephen J; Manz, Andreas; Huang, Tony JunAnalytical chemistry.2014 Dec 2;11803-1025405550
Standing surface acoustic wave (SSAW)-based cell washing.Li, Sixing; Ding, Xiaoyun; Mao, Zhangming; Chen, Yuchao; Nama, Nitesh; Guo, Feng; Li, Peng; Wang, Lin; Cameron, Craig E; Huang, Tony JunLab on a chip.2015 Jan 7;331-825372273
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Dual-view plane illumination microscopy for rapid and spatially isotropic imaging.Kumar, Abhishek; Wu, Yicong; Christensen, Ryan; Chandris, Panagiotis; Gandler, William; McCreedy, Evan; Bokinsky, Alexandra; Colon-Ramos, Daniel A; Bao, Zhirong; McAuliffe, Matthew; Rondeau, Gary; Shroff, HariNature protocols.2014 Nov;2555-7325299154
The KRUPPEL-like transcription factor DATILOGRAFO is required in specific cholinergic neurons for sexual receptivity in Drosophila females.Schinaman, Joseph Moeller; Giesey, Rachel Lynn; Mizutani, Claudia Mieko; Lukacsovich, Tamas; Sousa-Neves, RuiPLoS biology.2014 Oct;e100196425291190
Tip-enhanced laser ablation sample transfer for biomolecule mass spectrometry.Ghorai, Suman; Seneviratne, Chinthaka A; Murray, Kermit KJournal of the American Society for Mass Spectrometry.2015 Jan;63-7025287125
Functional imaging in OA: role of imaging in the evaluation of tissue biomechanics.Neu, C POsteoarthritis and cartilage / OARS, Osteoarthritis Research Society.2014 Oct;1349-5925278049
Muscling up the heart: a preadolescent cardiomyocyte proliferation contributes to heart growth.Zhang, Cheng-Hai; Kuhn, BernhardCirculation research.2014 Sep 26;690-225258401
Antibody Fc engineering improves frequency and promotes kinetic boosting of serial killing mediated by NK cells.Romain, Gabrielle; Senyukov, Vladimir; Rey-Villamizar, Nicolas; Merouane, Amine; Kelton, William; Liadi, Ivan; Mahendra, Ankit; Charab, Wissam; Georgiou, George; Roysam, Badrinath; Lee, Dean A; Varadarajan, NavinBlood.2014 Nov 20;3241-925232058
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Loss of IP3R-dependent Ca2+ signalling in thymocytes leads to aberrant development and acute lymphoblastic leukemia.Ouyang, Kunfu; Leandro Gomez-Amaro, Rafael; Stachura, David L; Tang, Huayuan; Peng, Xiaohong; Fang, Xi; Traver, David; Evans, Sylvia M; Chen, JuNature communications.2014 Sep 12;25215520
Sorting out where fibroblasts come from.Moore-Morris, Thomas; Tallquist, Michelle D; Evans, Sylvia MCirculation research.2014 Sep 12;602-425214570
Conversion of human fibroblasts into monocyte-like progenitor cells.Pulecio, Julian; Nivet, Emmanuel; Sancho-Martinez, Ignacio; Vitaloni, Marianna; Guenechea, Guillermo; Xia, Yun; Kurian, Leo; Dubova, Ilir; Bueren, Juan; Laricchia-Robbio, Leopoldo; Izpisua Belmonte, Juan CarlosStem cells (Dayton, Ohio).2014 Nov;2923-3825175072
Modeling of the dorsal gradient across species reveals interaction between embryo morphology and Toll signaling pathway during evolution.Ambrosi, Priscilla; Chahda, Juan Sebastian; Koslen, Hannah R; Chiel, Hillel J; Mizutani, Claudia MiekoPLoS computational biology.2014 Aug;e100380725165818
Spatial and temporal organization of signaling pathways.Housden, Benjamin E; Perrimon, NorbertTrends in biochemical sciences.2014 Oct;457-6425155749
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, VivianaCell2014 Aug 14945-5825088144
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
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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 KMolecular pharmaceutics.2014 Aug 4;2896-90525004202
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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.2014;433024999918
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, BrNature neuroscience2014 Aug1123-924997763
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; EsCell stem cell.2014 Jul 3;31-624996168
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
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 PJournal of biomechanics.2014 Aug 22;2801-624968943
A semi-local neighborhood-based framework for probabilistic cell lineage tracing.Santella, Anthony; Du, Zhuo; Bao, ZhirongBMC bioinformatics.2014;21724964866
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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 investigation2014 Jul 12921-3424937432
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Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2.Xu, Shuwa; Tyagi, Sanjay; Schedl, PaulPLoS genetics2014 Maye100438024830287
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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
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
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Local mechanical response of cells to the controlled rotation of magnetic nanorods.Castillo, Matias; Ebensperger, Roberto; Wirtz, Denis; Walczak, Magdalena; Hurtado, Daniel E; Celedon, AlfredoJournal of biomedical materials research. Part B, Applied biomaterials.2014 Nov;1779-8524700696
Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools.Doupé, David P; Perrimon, NorbertScience signaling.2014 Apr 1;re124692594
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
Single-cell in situ RNA profiling by sequential hybridization.Lubeck, Eric; Coskun, Ahmet F; Zhiyentayev, Timur; Ahmad, Mubhij; Cai, LongNature methods2014 Apr360-124681720
Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ.Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, MonaPloS one2014e9348824675777
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
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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, JuPLoS genetics.2014 Feb;e100411424586179
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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
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Tumor evolution in response to chemotherapy: phenotype versus genotype.Navin, Nicholas ECell reports2014 Feb 13417-924529750
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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 BelmontProtein & cell.2014 Jan;59-6824474197
Single-cell technologies for monitoring immune systems.Chattopadhyay, Pratip K; Gierahn, Todd M; Roederer, Mario; Love, J ChristopherNature immunology2014 Feb128-3524448570
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
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
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
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
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 CarlosThe Journal of biological chemistry.2014 Feb 21;4594-924362028
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
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 LProceedings of the National Academy of Sciences of the United States of America.2014 Jan 21;E384-9324324133
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
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
PIWI proteins are essential for early Drosophila embryogenesis.Mani, Sneha Ramesh; Megosh, Heather; Lin, HaifanDevelopmental biology2013 Oct 31NULL24184635
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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 TJournal of the American College of Cardiology.2014 Feb 4;358-6824140660
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, FaHuman molecular genetics.2014 Mar 1;1134-5024108106
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
Genetically encoded fluorescent biosensors for live-cell imaging of MT1-MMP protease activity.Ouyang, Mingxing; Lu, Shaoying; Wang, YingxiaoMethods in molecular biology (Clifton, N.J.).2014;24052388
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Tracking immune cells in vivo using magnetic resonance imaging.Ahrens, Eric T; Bulte, Jeff W MNature reviews. Immunology.2013 Oct;24013185
Epigenetic alterations in acute kidney injury.Bomsztyk, Karol; Denisenko, OlegSeminars in nephrology2013 Jul327-4024011575
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 HJournal of cellular physiology.2014 Mar;362-7323996089
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, LiGenome biology.2013;R8723972288
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
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 FCell stem cell.2013 Aug 1;246-5423910086
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
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
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 ENature2013 Aug 29589-9223873040
Developmental biology. Enhancing pluripotency and lineage specification.Xie, Wei; Ren, BingScience (New York, N.Y.)2013 Jul 19245-723869010
Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis.Moore, Julia L; Du, Zhuo; Bao, ZhirongDevelopment (Cambridge, England).2013 Aug;23861063
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
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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
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 MCirculation research2013 Aug 2399-40723743334
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
Single-cell transcriptomics for drug target discovery.Spaethling, Jennifer M; Eberwine, James HCurrent opinion in pharmacology.2013 Oct;786-9023725882
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; NCell2013 May 231134-4823664764
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
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
Interstitial friction greatly impacts membrane mechanics.Wirtz, DenisBiophysical journal2013 Mar 191217-823528079
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
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
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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
Thymosin *4 is not required for embryonic viability or vascular development.Banerjee, Indroneal; Moore Morris, Thomas; Evans, Sylvia M; Chen, JuCirculation research.2013 Feb 1;e25-823371905
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 CarlosNature communications.2013;138223340422
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, RongAnalytical chemistry2013 Feb 192548-5623339603
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
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
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
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
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
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
Beating in a dish: new hopes for cardiomyocyte regeneration.Gu, Ying; Yi, Fei; Liu, Guang-Hui; Izpisua Belmonte, Juan CarlosCell research.2013 Mar;314-623184058
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-HoDevelopmental biology.2013 Feb 01;23165293
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
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 CarlosThe Journal of biological chemistry.2012 Nov 23;40767-7823019325
Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins.Ramesh, Balakrishnan; Sendra, Victor G; Cirino, Patrick C; Varadarajan, NavinThe Journal of biological chemistry.2012 Nov 9;23019324
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 CarlosProceedings of the National Academy of Sciences of the United States of America.2012 Oct 02;22991473
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
The dawn of angiogenesis modeling: regenerating vasculature from human pluripotent stem cells.Yi, Fei; Qu, Jing; Liu, Guang-Hui; Izpisua Belmonte, Juan CarlosCell research.2013 Jan;5-Mar22964710
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
Cut and paste: restoring cellular function by gene correction.Liu, Guang-Hui; Sancho-Martinez, Ignacio; Izpisua Belmonte, Juan CarlosCell research.2012 Feb;22143565
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 BelmCell research.2012 Jan;168-7722064701
Purging and isolating pluripotent cells, ''sweet'' dreams become true?Sancho-Martinez, Ignacio; Nivet, Emmanuel; Izpisua Belmonte, Juan CarlosCell research.2011 Nov;22025252