Science of Behavior Change (186)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
PIVOT: platform for interactive analysis and visualization of transcriptomics data.Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, JunhyongBMC bioinformatics.2018 Jan 05;29304726
Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology.Kim, Jeong-Ki; Louhghalam, Arghavan; Lee, Geonhui; Schafer, Benjamin W; Wirtz, Denis; Kim, Dong-HweeNature communications.2017 Dec 14;29242553
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain.Lake, Blue B; Chen, Song; Sos, Brandon C; Fan, Jean; Kaeser, Gwendolyn E; Yung, Yun C; Duong, Thu E; Gao, Derek; Chun, Jerold; Kharchenko, Peter V; Zhang, KunNature biotechnology.2018 Jan;29227469
Identification of a neural crest stem cell niche by Spatial Genomic Analysis.Lignell, Antti; Kerosuo, Laura; Streichan, Sebastian J; Cai, Long; Bronner, Marianne ENature communications.2017 Nov 28;29184067
An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues.Shah, Pavak Kirit; Santella, Anthony; Jacobo, Adrian; Siletti, Kimberly; Hudspeth, A J; Bao, ZhirongDevelopmental cell.2017 Nov 20;29161596
Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut.Herring, Charles A; Banerjee, Amrita; McKinley, Eliot T; Simmons, Alan J; Ping, Jie; Roland, Joseph T; Franklin, Jeffrey L; Liu, Qi; Gerdes, Michael J; Coffey, Robert J; Lau, Ken SCell systems.2017 Nov 07;29153838
Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics.Guo, Feng; Li, Sixing; Caglar, Mehmet Umut; Mao, Zhangming; Liu, Wu; Woodman, Andrew; Arnold, Jamie J; Wilke, Claus O; Huang, Tony Jun; Cameron, Craig ECell reports.2017 Nov 07;29117571
Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues.Lin, Ming-Yi; Wang, Yi-Ling; Wu, Wan-Lin; Wolseley, Victoria; Tsai, Ming-Ting; Radic, Vladimir; Thornton, Matthew E; Grubbs, Brendan H; Chow, Robert H; Huang, I-ChuehScientific reports.2017 Nov 01;29093521
Acoustic streaming: an arbitrary Lagrangian-Eulerian perspective.Nama, Nitesh; Huang, Tony Jun; Costanzo, FrancescoJournal of fluid mechanics.2017 Aug 25;29051631
Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging.Piatkevich, Kiryl D; Suk, Ho-Jun; Kodandaramaiah, Suhasa B; Yoshida, Fumiaki; DeGennaro, Ellen M; Drobizhev, Mikhail; Hughes, Thomas E; Desimone, Robert; Boyden, Edward S; Verkhusha, Vladislav VBiophysical journal.2017 Nov 21;29017728
21st century neurobehavioral theories of decision making in addiction: Review and evaluation.Bickel, Warren K; Mellis, Alexandra M; Snider, Sarah E; Athamneh, Liqa N; Stein, Jeffrey S; Pope, Derek APharmacology, biochemistry, and behavior.2017 Sep 21;28942119
Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA.Mowel, Walter K; McCright, Sam J; Kotzin, Jonathan J; Collet, Magalie A; Uyar, Asli; Chen, Xin; DeLaney, Alexandra; Spencer, Sean P; Virtue, Anthony T; Yang, EnJun; Villarino, Alejandro; Kurachi, Makoto; Dunagin, Margaret C; Pritchard, Gretchen Harms; Stein, Judith; Hughes, Cynthia; Fonseca-Pereira, Diogo; Veiga-Fernandes, Henrique; Raj, Arjun; Kambayashi, Taku; Brodsky, Igor E; O'Shea, John J; Wherry, E John; Goff, Loyal A; Rinn, John L; Williams, Adam; Flavell, Richard A; Henao-Mejia, JorgeImmunity.2017 Sep 19;28930659
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
A magnetic micropore chip for rapid (Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, DavidLab on a chip.2017 Sep 12;28809985
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
Single cell transcriptomics of noncoding RNAs and their cell-specificity.Gawronski, Katerina A B; Kim, JunhyongWiley interdisciplinary reviews. RNA.2017 Nov;28762653
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
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
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
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
Mechanisms of Cardiomyocyte Proliferation and Differentiation in Development and Regeneration.Yester, Jessie Wettig; Kühn, BernhardCurrent cardiology reports.2017 Feb;28185170
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
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
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
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
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
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
Investigation of micromixing by acoustically oscillated sharp-edges.Nama, Nitesh; Huang, Po-Hsun; Huang, Tony Jun; Costanzo, FrancescoBiomicrofluidics.2016 Mar;27158292
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Tuning noise in gene expression.Tyagi, SanjayMolecular systems biology.2015 May;80525943344
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
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
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
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
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
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
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
Switching from protease-independent to protease-dependent cancer cell invasion.He, Lijuan; Wirtz, DenisBiophysical journal.2014 Dec 2;2484-525468324
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
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
Antisense RNA amplification for target assessment of total mRNA from a single cell.Morris, Jacqueline; Bell, Thomas J; Buckley, Peter T; Eberwine, James HCold Spring Harbor protocols.2014 Nov 03;25368303
Direct reactivation of a coherent neocortical memory of context.Cowansage, Kiriana K; Shuman, Tristan; Dillingham, Blythe C; Chang, Allene; Golshani, Peyman; Mayford, MarkNeuron.2014 Oct 22;25308330
Cardiac regeneration based on mechanisms of cardiomyocyte proliferation and differentiation.Senyo, Samuel E; Lee, Richard T; Kuhn, BernhardStem cell research.2014 Nov;532-4125306390
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
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
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
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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
A semi-local neighborhood-based framework for probabilistic cell lineage tracing.Santella, Anthony; Du, Zhuo; Bao, ZhirongBMC bioinformatics.2014;21724964866
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
Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2.Xu, Shuwa; Tyagi, Sanjay; Schedl, PaulPLoS genetics2014 Maye100438024830287
Hypoxia and the extracellular matrix: drivers of tumour metastasis.Gilkes, Daniele M; Semenza, Gregg L; Wirtz, DenisNature reviews. Cancer.2014 Jun;430-924827502
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
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
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
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
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
Nuclear envelope in nuclear positioning and cell migration.Razafsky, David; Wirtz, Denis; Hodzic, DidierAdvances in experimental medicine and biology.2014;471-9024563361
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
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
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
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
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
Barriers to transmission of transcriptional noise in a c-fos c-jun pathway.Shah, Khyati; Tyagi, SanjayMolecular systems biology201368724022005
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
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
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
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
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
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
Dimensional control of cancer cell migration.Konstantopoulos, Konstantinos; Wu, Pei-Hsun; Wirtz, DenisBiophysical journal2013 Jan 22279-8023442847
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
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
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
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
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