Publications Search by Program
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The search results on this publication page are automated on a monthly schedule based on acknowledgment of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Single Cell Analysis (520)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| The epithelial polarity genes frazzled and GUK-holder adjust morphogen gradients to coordinate changes in cell position with cell fate specification. | Xue, Yongqiang; Krishnan, Aravindan; Chahda, Juan Sebastian; Schweickart, Robert Allen; Sousa-Neves, Rui; Mizutani, Claudia Mieko | PLoS biology | 2023 Mar | e3002021 | 36913435 |
| Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. | D'Antonio, Matteo; Nguyen, Jennifer P; Arthur, Timothy D; iPSCORE Consortium; Matsui, Hiroko; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | Nature communications | 2023 Feb 28 | 1132 | 36854752 |
| Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans. | Kim, Jun; Jimenez, David S; Ragipani, Bhavana; Zhang, Bo; Street, Lena A; Kramer, Maxwell; Albritton, Sarah E; Winterkorn, Lara H; Morao, Ana K; Ercan, Sevinc | eLife | 2022 11 04 | 36331876 | |
| CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. | Jalloh, Sallieu; Olejnik, Judith; Berrigan, Jacob; Nisa, Annuurun; Suder, Ellen L; Akiyama, Hisashi; Lei, Maohua; Ramaswamy, Sita; Tyagi, Sanjay; Bushkin, Yuri; Mühlberger, Elke; Gummuluru, Suryaram | PLoS pathogens | 2022 Oct | 36279285 | |
| Development of an Interferon-Gamma Release Assay (IGRA) to Aid Diagnosis of Histoplasmosis. | Datta, Kausik; LaRue, Richard; Permpalung, Nitipong; Das, Sukanya; Zhang, Sean; Mehta Steinke, Seema; Bushkin, Yuri; Nosanchuk, Joshua D; Marr, Kieren A | Journal of clinical microbiology | 2022 Oct 19 | 36190260 | |
| Shifting machine learning for healthcare from development to deployment and from models to data. | Zhang, Angela; Xing, Lei; Zou, James; Wu, Joseph C | Nature biomedical engineering | 2022 Jul 04 | 35788685 | |
| Astrocyte ethanol exposure reveals persistent and defined calcium response subtypes and associated gene signatures. | Kim, Hyun-Bum; Lu, Youtao; Oh, Seonkyung C; Morris, Jacqueline; Miyashiro, Kevin; Kim, Junhyong; Eberwine, James; Sul, Jai-Yoon | The Journal of biological chemistry | 2022 Jun 16 | 35716779 | |
| Deep learning identification of stiffness markers in breast cancer. | Sneider, Alexandra; Kiemen, Ashley; Kim, Joo Ho; Wu, Pei-Hsun; Habibi, Mehran; White, Marissa; Phillip, Jude M; Gu, Luo; Wirtz, Denis | Biomaterials | 2022 06 | 35537336 | |
| The nested embryonic dorsal domains of BMP-target genes are not scaled to size during the evolution of Drosophila species. | Chahda, Juan Sebastian; Ambrosi, Priscilla; Mizutani, Claudia M | Journal of experimental zoology. Part B, Molecular and developmental evolution | 2022 Apr 22 | 35451554 | |
| Altered adult neurogenesis and gliogenesis in patients with mesial temporal lobe epilepsy. | Ammothumkandy, Aswathy; Ravina, Kristine; Wolseley, Victoria; Tartt, Alexandria N; Yu, Pen-Ning; Corona, Luis; Zhang, Naibo; Nune, George; Kalayjian, Laura; Mann, J John; Rosoklija, Gorazd B; Arango, Victoria; Dwork, Andrew J; Lee, Brian; Smith, J A D; Song, Dong; Berger, Theodore W; Heck, Christianne; Chow, Robert H; Boldrini, Maura; Liu, Charles Y; Russin, Jonathan J; Bonaguidi, Michael A | Nature neuroscience | 2022 Apr | 35383330 | |
| CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. | Jalloh, Sallieu; Olejnik, Judith; Berrigan, Jacob; Nisa, Annuurun; Suder, Ellen L; Akiyama, Hisashi; Lei, Maohua; Tyagi, Sanjay; Bushkin, Yuri; Mühlberger, Elke; Gummuluru, Suryaram | bioRxiv : the preprint server for biology | 2022 Mar 30 | 35378756 | |
| In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. | D'Antonio, Matteo; Nguyen, Jennifer P; Arthur, Timothy D; Matsui, Hiroko; Donovan, Margaret K R; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | PLoS computational biology | 2022 Feb | 35226669 | |
| Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. | Jiang, Shengdian; Wang, Yimin; Liu, Lijuan; Ding, Liya; Ruan, Zongcai; Dong, Hong-Wei; Ascoli, Giorgio A; Hawrylycz, Michael; Zeng, Hongkui; Peng, Hanchuan | Neuroinformatics | 2022 Feb 19 | 35182359 | |
| DynaMorph: self-supervised learning of morphodynamic states of live cells. | Wu, Zhenqin; Chhun, Bryant B; Popova, Galina; Guo, Syuan-Ming; Kim, Chang N; Yeh, Li-Hao; Nowakowski, Tomasz; Zou, James; Mehta, Shalin B | Molecular biology of the cell | 2022 05 15 | 35138913 | |
| Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion. | Ghosh, Soham; Scott, Adrienne K; Seelbinder, Benjamin; Barthold, Jeanne E; Martin, Brittany M St; Kaonis, Samantha; Schneider, Stephanie E; Henderson, Jonathan T; Neu, Corey P | Biophysical journal | 2022 Jan 04 | 34800469 | |
| SuperSelective primer pairs for sensitive detection of rare somatic mutations. | Kramer, Fred Russell; Vargas, Diana Yaneth | Scientific reports | 2021 11 17 | 34789731 | |
| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum, Nongluk; Diep, Dinh; Chen, Song; Lake, Blue B; Zhang, Kun | Nature protocols | 2021 11 | 34650278 | |
| Reduction in gene expression noise by targeted increase in accessibility at gene loci. | Fraser, LaTasha C R; Dikdan, Ryan J; Dey, Supravat; Singh, Abhyudai; Tyagi, Sanjay | Proceedings of the National Academy of Sciences of the United States of America | 2021 Oct 19 | 34625470 | |
| A multimodal cell census and atlas of the mammalian primary motor cortex. | BRAIN Initiative Cell Census Network (BICCN) | Nature | 2021 10 | 34616075 | |
| Morphological diversity of single neurons in molecularly defined cell types. | Peng, Hanchuan; Xie, Peng; Liu, Lijuan; Kuang, Xiuli; Wang, Yimin; Qu, Lei; Gong, Hui; Jiang, Shengdian; Li, Anan; Ruan, Zongcai; Ding, Liya; Yao, Zizhen; Chen, Chao; Chen, Mengya; Daigle, Tanya L; Dalley, Rachel; Ding, Zhangcan; Duan, Yanjun; Feiner, Aaron; He, Ping; Hill, Chris; Hirokawa, Karla E; Hong, Guodong; Huang, Lei; Kebede, Sara; Kuo, Hsien-Chi; Larsen, Rachael; Lesnar, Phil; Li, Longfei; Li, Qi; Li, Xiangning; Li, Yaoyao; Li, Yuanyuan; Liu, An; Lu, Donghuan; Mok, Stephanie; Ng, Lydia; Nguyen, Thuc Nghi; Ouyang, Qiang; Pan, Jintao; Shen, Elise; Song, Yuanyuan; Sunkin, Susan M; Tasic, Bosiljka; Veldman, Matthew B; Wakeman, Wayne; Wan, Wan; Wang, Peng; Wang, Quanxin; Wang, Tao; Wang, Yaping; Xiong, Feng; Xiong, Wei; Xu, Wenjie; Ye, Min; Yin, Lulu; Yu, Yang; Yuan, Jia; Yuan, Jing; Yun, Zhixi; Zeng, Shaoqun; Zhang, Shichen; Zhao, Sujun; Zhao, Zijun; Zhou, Zhi; Huang, Z Josh; Esposito, Luke; Hawrylycz, Michael J; Sorensen, Staci A; Yang, X William; Zheng, Yefeng; Gu, Zhongze; Xie, Wei; Koch, Christof; Luo, Qingming; Harris, Julie A; Wang, Yun; Zeng, Hongkui | Nature | 2021 10 | 34616072 | |
| Cellular anatomy of the mouse primary motor cortex. | Muñoz-Castañeda, Rodrigo; Zingg, Brian; Matho, Katherine S; Chen, Xiaoyin; Wang, Quanxin; Foster, Nicholas N; Li, Anan; Narasimhan, Arun; Hirokawa, Karla E; Huo, Bingxing; Bannerjee, Samik; Korobkova, Laura; Park, Chris Sin; Park, Young-Gyun; Bienkowski, Michael S; Chon, Uree; Wheeler, Diek W; Li, Xiangning; Wang, Yun; Naeemi, Maitham; Xie, Peng; Liu, Lijuan; Kelly, Kathleen; An, Xu; Attili, Sarojini M; Bowman, Ian; Bludova, Anastasiia; Cetin, Ali; Ding, Liya; Drewes, Rhonda; D'Orazi, Florence; Elowsky, Corey; Fischer, Stephan; Galbavy, William; Gao, Lei; Gillis, Jesse; Groblewski, Peter A; Gou, Lin; Hahn, Joel D; Hatfield, Joshua T; Hintiryan, Houri; Huang, Junxiang Jason; Kondo, Hideki; Kuang, Xiuli; Lesnar, Philip; Li, Xu; Li, Yaoyao; Lin, Mengkuan; Lo, Darrick; Mizrachi, Judith; Mok, Stephanie; Nicovich, Philip R; Palaniswamy, Ramesh; Palmer, Jason; Qi, Xiaoli; Shen, Elise; Sun, Yu-Chi; Tao, Huizhong W; Wakemen, Wayne; Wang, Yimin; Yao, Shenqin; Yuan, Jing; Zhan, Huiqing; Zhu, Muye; Ng, Lydia; Zhang, Li I; Lim, Byung Kook; Hawrylycz, Michael; Gong, Hui; Gee, James C; Kim, Yongsoo; Chung, Kwanghun; Yang, X William; Peng, Hanchuan; Luo, Qingming; Mitra, Partha P; Zador, Anthony M; Zeng, Hongkui; Ascoli, Giorgio A; Josh Huang, Z; Osten, Pavel; Harris, Julie A; Dong, Hong-Wei | Nature | 2021 10 | 34616071 | |
| Human neocortical expansion involves glutamatergic neuron diversification. | Berg, Jim; Sorensen, Staci A; Ting, Jonathan T; Miller, Jeremy A; Chartrand, Thomas; Buchin, Anatoly; Bakken, Trygve E; Budzillo, Agata; Dee, Nick; Ding, Song-Lin; Gouwens, Nathan W; Hodge, Rebecca D; Kalmbach, Brian; Lee, Changkyu; Lee, Brian R; Alfiler, Lauren; Baker, Katherine; Barkan, Eliza; Beller, Allison; Berry, Kyla; Bertagnolli, Darren; Bickley, Kris; Bomben, Jasmine; Braun, Thomas; Brouner, Krissy; Casper, Tamara; Chong, Peter; Crichton, Kirsten; Dalley, Rachel; de Frates, Rebecca; Desta, Tsega; Lee, Samuel Dingman; D'Orazi, Florence; Dotson, Nadezhda; Egdorf, Tom; Enstrom, Rachel; Farrell, Colin; Feng, David; Fong, Olivia; Furdan, Szabina; Galakhova, Anna A; Gamlin, Clare; Gary, Amanda; Glandon, Alexandra; Goldy, Jeff; Gorham, Melissa; Goriounova, Natalia A; Gratiy, Sergey; Graybuck, Lucas; Gu, Hong; Hadley, Kristen; Hansen, Nathan; Heistek, Tim S; Henry, Alex M; Heyer, Djai B; Hill, DiJon; Hill, Chris; Hupp, Madie; Jarsky, Tim; Kebede, Sara; Keene, Lisa; Kim, Lisa; Kim, Mean-Hwan; Kroll, Matthew; Latimer, Caitlin; Levi, Boaz P; Link, Katherine E; Mallory, Matthew; Mann, Rusty; Marshall, Desiree; Maxwell, Michelle; McGraw, Medea; McMillen, Delissa; Melief, Erica; Mertens, Eline J; Mezei, Leona; Mihut, Norbert; Mok, Stephanie; Molnar, Gabor; Mukora, Alice; Ng, Lindsay; Ngo, Kiet; Nicovich, Philip R; Nyhus, Julie; Olah, Gaspar; Oldre, Aaron; Omstead, Victoria; Ozsvar, Attila; Park, Daniel; Peng, Hanchuan; Pham, Trangthanh; Pom, Christina A; Potekhina, Lydia; Rajanbabu, Ramkumar; Ransford, Shea; Reid, David; Rimorin, Christine; Ruiz, Augustin; Sandman, David; Sulc, Josef; Sunkin, Susan M; Szafer, Aaron; Szemenyei, Viktor; Thomsen, Elliot R; Tieu, Michael; Torkelson, Amy; Trinh, Jessica; Tung, Herman; Wakeman, Wayne; Waleboer, Femke; Ward, Katelyn; Wilbers, René; Williams, Grace; Yao, Zizhen; Yoon, Jae-Geun; Anastassiou, Costas; Arkhipov, Anton; Barzo, Pal; Bernard, Amy; Cobbs, Charles; de Witt Hamer, Philip C; Ellenbogen, Richard G; Esposito, Luke; Ferreira, Manuel; Gwinn, Ryder P; Hawrylycz, Michael J; Hof, Patrick R; Idema, Sander; Jones, Allan R; Keene, C Dirk; Ko, Andrew L; Murphy, Gabe J; Ng, Lydia; Ojemann, Jeffrey G; Patel, Anoop P; Phillips, John W; Silbergeld, Daniel L; Smith, Kimberly; Tasic, Bosiljka; Yuste, Rafael; Segev, Idan; de Kock, Christiaan P J; Mansvelder, Huibert D; Tamas, Gabor; Zeng, Hongkui; Koch, Christof; Lein, Ed S | Nature | 2021 10 | 34616067 | |
| Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms: A Scoping Review. | Daneshjou, Roxana; Smith, Mary P; Sun, Mary D; Rotemberg, Veronica; Zou, James | JAMA dermatology | 2021 11 01 | 34550305 | |
| Machine Learning-Based Pipette Positional Correction for Automatic Patch Clamp In Vitro. | Gonzalez, Mercedes M; Lewallen, Colby F; Yip, Mighten C; Forest, Craig R | eNeuro | 2021 Jul-Aug | 34312222 | |
| A cross-institutional analysis of the effects of broadening trainee professional development on research productivity. | Brandt, Patrick D; Sturzenegger Varvayanis, Susi; Baas, Tracey; Bolgioni, Amanda F; Alder, Janet; Petrie, Kimberly A; Dominguez, Isabel; Brown, Abigail M; Stayart, C Abigail; Singh, Harinder; Van Wart, Audra; Chow, Christine S; Mathur, Ambika; Schreiber, Barbara M; Fruman, David A; Bowden, Brent; Wiesen, Christopher A; Golightly, Yvonne M; Holmquist, Chris E; Arneman, Daniel; Hall, Joshua D; Hyman, Linda E; Gould, Kathleen L; Chalkley, Roger; Brennwald, Patrick J; Layton, Rebekah L | PLoS biology | 2021 Jul | 34264929 | |
| Disparity in the quality of COVID-19 data reporting across India. | Vasudevan, Varun; Gnanasekaran, Abeynaya; Sankar, Varsha; Vasudevan, Siddarth A; Zou, James | BMC public health | 2021 06 24 | 34167499 | |
| Unveiling Complexity and Multipotentiality of Early Heart Fields. | Zhang, Qingquan; Carlin, Daniel; Zhu, Fugui; Cattaneo, Paola; Ideker, Trey; Evans, Sylvia M; Bloomekatz, Joshua; Chi, Neil C | Circulation research | 2021 Aug 06 | 34162224 | |
| Comprehensive analysis of 2.4 million patent-to-research citations maps the biomedical innovation and translation landscape. | Manjunath, Anoop; Li, Hongyu; Song, Shuchen; Zhang, Zhixing; Liu, Shu; Kahrobai, Nathan; Gowda, Arya; Seffens, Angelina; Zou, James; Kumar, Ishan | Nature biotechnology | 2021 06 | 34113042 | |
| A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. | Yao, Zizhen; van Velthoven, Cindy T J; Nguyen, Thuc Nghi; Goldy, Jeff; Sedeno-Cortes, Adriana E; Baftizadeh, Fahimeh; Bertagnolli, Darren; Casper, Tamara; Chiang, Megan; Crichton, Kirsten; Ding, Song-Lin; Fong, Olivia; Garren, Emma; Glandon, Alexandra; Gouwens, Nathan W; Gray, James; Graybuck, Lucas T; Hawrylycz, Michael J; Hirschstein, Daniel; Kroll, Matthew; Lathia, Kanan; Lee, Changkyu; Levi, Boaz; McMillen, Delissa; Mok, Stephanie; Pham, Thanh; Ren, Qingzhong; Rimorin, Christine; Shapovalova, Nadiya; Sulc, Josef; Sunkin, Susan M; Tieu, Michael; Torkelson, Amy; Tung, Herman; Ward, Katelyn; Dee, Nick; Smith, Kimberly A; Tasic, Bosiljka; Zeng, Hongkui | Cell | 2021 Jun 10 | 34004146 | |
| Astrocytes promote ethanol-induced enhancement of intracellular Ca2+ signals through intercellular communication with neurons. | Kim, Hyun-Bum; Morris, Jacqueline; Miyashiro, Kevin; Lehto, Tõnis; Langel, Ülo; Eberwine, James; Sul, Jai-Yoon | iScience | 2021 May 21 | 33997707 | |
| Rapid Cortical Adaptation and the Role of Thalamic Synchrony during Wakefulness. | Wright, Nathaniel C; Borden, Peter Y; Liew, Yi Juin; Bolus, Michael F; Stoy, William M; Forest, Craig R; Stanley, Garrett B | The Journal of neuroscience : the official journal of the Society for Neuroscience | 2021 06 23 | 33986072 | |
| Ensuring that biomedical AI benefits diverse populations. | Zou, James; Schiebinger, Londa | EBioMedicine | 2021 May | 33962897 | |
| Automated Intracellular Pharmacological Electrophysiology for Ligand-Gated Ionotropic Receptor and Pharmacology Screening. | Perszyk, Riley E; Yip, Mighten C; McConnell, Ona L; Wang, Eric T; Jenkins, Andrew; Traynelis, Stephen F; Forest, Craig R | Molecular pharmacology | 2021 07 | 33958481 | |
| Data valuation for medical imaging using Shapley value and application to a large-scale chest X-ray dataset. | Tang, Siyi; Ghorbani, Amirata; Yamashita, Rikiya; Rehman, Sameer; Dunnmon, Jared A; Zou, James; Rubin, Daniel L | Scientific reports | 2021 04 16 | 33863957 | |
| BABEL enables cross-modality translation between multiomic profiles at single-cell resolution. | Wu, Kevin E; Yost, Kathryn E; Chang, Howard Y; Zou, James | Proceedings of the National Academy of Sciences of the United States of America | 2021 04 13 | 33827925 | |
| Altering metabolite distribution at Xenopus cleavage stages affects left-right gene expression asymmetries. | Onjiko, Rosemary M; Nemes, Peter; Moody, Sally A | Genesis (New York, N.Y. : 2000) | 2021 06 | 33826226 | |
| How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. | Wu, Eric; Wu, Kevin; Daneshjou, Roxana; Ouyang, David; Ho, Daniel E; Zou, James | Nature medicine | 2021 04 | 33820998 | |
| Deep learning-based real-time detection of neurons in brain slices for in vitro physiology. | Yip, Mighten C; Gonzalez, Mercedes M; Valenta, Christopher R; Rowan, Matthew J M; Forest, Craig R | Scientific reports | 2021 Mar 16 | 33727679 | |
| Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. | Bonder, Marc Jan; Smail, Craig; Gloudemans, Michael J; Frésard, Laure; Jakubosky, David; D'Antonio, Matteo; Li, Xin; Ferraro, Nicole M; Carcamo-Orive, Ivan; Mirauta, Bogdan; Seaton, Daniel D; Cai, Na; Vakili, Dara; Horta, Danilo; Zhao, Chunli; Zastrow, Diane B; Bonner, Devon E; HipSci Consortium; iPSCORE consortium; Undiagnosed Diseases Network; PhLiPS consortium; Wheeler, Matthew T; Kilpinen, Helena; Knowles, Joshua W; Smith, Erin N; Frazer, Kelly A; Montgomery, Stephen B; Stegle, Oliver | Nature genetics | 2021 03 | 33664507 | |
| In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). | D'Antonio-Chronowska, Agnieszka; D'Antonio, Matteo; Frazer, Kelly A | Bio-protocol | 2020 Sep 20 | 33659414 | |
| In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE). | D'Antonio-Chronowska, Agnieszka; D'Antonio, Matteo; Frazer, Kelly A | Bio-protocol | 2019 Dec 20 | 33654959 | |
| Single cell epigenetic visualization assay. | Kint, Sam; Van Criekinge, Wim; Vandekerckhove, Linos; De Vos, Winnok H; Bomsztyk, Karol; Krause, Diane S; Denisenko, Oleg | Nucleic acids research | 2021 May 07 | 33511400 | |
| Fractional re-distribution among cell motility states during ageing. | Phillip, Jude M; Zamponi, Nahuel; Phillip, Madonna P; Daya, Jena; McGovern, Shaun; Williams, Wadsworth; Tschudi, Katherine; Jayatilaka, Hasini; Wu, Pei-Hsun; Walston, Jeremy; Wirtz, Denis | Communications biology | 2021 Jan 19 | 33469145 | |
| A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei. | Phillip, Jude M; Han, Kyu-Sang; Chen, Wei-Chiang; Wirtz, Denis; Wu, Pei-Hsun | Nature protocols | 2021 02 | 33424024 | |
| Compensation of physiological motion enables high-yield whole-cell recording in vivo. | Stoy, William M; Yang, Bo; Kight, Ali; Wright, Nathaniel C; Borden, Peter Y; Stanley, Garrett B; Forest, Craig R | Journal of neuroscience methods | 2021 Jan 15 | 33242530 | |
| Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. | Gouwens, Nathan W; Sorensen, Staci A; Baftizadeh, Fahimeh; Budzillo, Agata; Lee, Brian R; Jarsky, Tim; Alfiler, Lauren; Baker, Katherine; Barkan, Eliza; Berry, Kyla; Bertagnolli, Darren; Bickley, Kris; Bomben, Jasmine; Braun, Thomas; Brouner, Krissy; Casper, Tamara; Crichton, Kirsten; Daigle, Tanya L; Dalley, Rachel; de Frates, Rebecca A; Dee, Nick; Desta, Tsega; Lee, Samuel Dingman; Dotson, Nadezhda; Egdorf, Tom; Ellingwood, Lauren; Enstrom, Rachel; Esposito, Luke; Farrell, Colin; Feng, David; Fong, Olivia; Gala, Rohan; Gamlin, Clare; Gary, Amanda; Glandon, Alexandra; Goldy, Jeff; Gorham, Melissa; Graybuck, Lucas; Gu, Hong; Hadley, Kristen; Hawrylycz, Michael J; Henry, Alex M; Hill, DiJon; Hupp, Madie; Kebede, Sara; Kim, Tae Kyung; Kim, Lisa; Kroll, Matthew; Lee, Changkyu; Link, Katherine E; Mallory, Matthew; Mann, Rusty; Maxwell, Michelle; McGraw, Medea; McMillen, Delissa; Mukora, Alice; Ng, Lindsay; Ng, Lydia; Ngo, Kiet; Nicovich, Philip R; Oldre, Aaron; Park, Daniel; Peng, Hanchuan; Penn, Osnat; Pham, Thanh; Pom, Alice; Popovi?, Zoran; Potekhina, Lydia; Rajanbabu, Ramkumar; Ransford, Shea; Reid, David; Rimorin, Christine; Robertson, Miranda; Ronellenfitch, Kara; Ruiz, Augustin; Sandman, David; Smith, Kimberly; Sulc, Josef; Sunkin, Susan M; Szafer, Aaron; Tieu, Michael; Torkelson, Amy; Trinh, Jessica; Tung, Herman; Wakeman, Wayne; Ward, Katelyn; Williams, Grace; Zhou, Zhi; Ting, Jonathan T; Arkhipov, Anton; Sümbül, Uygar; Lein, Ed S; Koch, Christof; Yao, Zizhen; Tasic, Bosiljka; Berg, Jim; Murphy, Gabe J; Zeng, Hongkui | Cell. | 2020 Nov 12; | 33186530 | |
| Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4+ T cells. | Rath, Jan A; Bajwa, Gagan; Carreres, Benoit; Hoyer, Elisabeth; Gruber, Isabelle; Martínez-Paniagua, Melisa A; Yu, Yi-Ru; Nouraee, Nazila; Sadeghi, Fatemeh; Wu, Mengfen; Wang, Tao; Hebeisen, Michael; Rufer, Nathalie; Varadarajan, Navin; Ho, Ping-Chih; Brenner, Malcolm K; Gfeller, David; Arber, Caroline | Science advances | 2020 07 | 32923584 | |
| Applying Experiential Learning to Career Development Training for Biomedical Graduate Students and Postdocs: Perspectives on Program Development and Design. | Van Wart, Audra; O'Brien, Theresa C; Varvayanis, Susi; Alder, Janet; Greenier, Jennifer; Layton, Rebekah L; Stayart, C Abigail; Wefes, Inge; Brady, Ashley E | CBE life sciences education. | 2020 09; | 32822277 | |
| Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice. | Veldman, Matthew B; Park, Chang Sin; Eyermann, Charles M; Zhang, Jason Y; Zuniga-Sanchez, Elizabeth; Hirano, Arlene A; Daigle, Tanya L; Foster, Nicholas N; Zhu, Muye; Langfelder, Peter; Lopez, Ivan A; Brecha, Nicholas C; Zipursky, S Lawrence; Zeng, Hongkui; Dong, Hong-Wei; Yang, X William | Neuron | 2020 10 14 | 32795398 | |
| RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. | Wu, Kevin E; Fazal, Furqan M; Parker, Kevin R; Zou, James; Chang, Howard Y | Cell systems. | 2020 07 22; | 32673562 | |
| Integrating spatial gene expression and breast tumour morphology via deep learning. | He, Bryan; Bergenstråhle, Ludvig; Stenbeck, Linnea; Abid, Abubakar; Andersson, Alma; Borg, Åke; Maaskola, Jonas; Lundeberg, Joakim; Zou, James | Nature biomedical engineering. | 2020 08; | 32572199 | |
| Whole-body tracking of single cells via positron emission tomography. | Jung, Kyung Oh; Kim, Tae Jin; Yu, Jung Ho; Rhee, Siyeon; Zhao, Wei; Ha, Byunghang; Red-Horse, Kristy; Gambhir, Sanjiv Sam; Pratx, Guillem | Nature biomedical engineering. | 2020 Aug; | 32541917 | |
| Institutional Training Opportunities for PhD Students in Laboratory Medicine: An Unmet Career Development Need? | Colby, Jennifer M; Wheeler, Ferrin C; Petrie, Kimberly A; Gould, Kathleen L; Schmitz, Jonathan E | The journal of applied laboratory medicine. | 2020 03 01; | 32445389 | |
| Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. | Kanchan, Kanika; Iyer, Kruthika; Yanek, Lisa R; Carcamo-Orive, Ivan; Taub, Margaret A; Malley, Claire; Baldwin, Kristin; Becker, Lewis C; Broeckel, Ulrich; Cheng, Linzhao; Cowan, Chad; D'Antonio, Matteo; Frazer, Kelly A; Quertermous, Thomas; Mostoslavsky, Gustavo; Murphy, George; Rabinovitch, Marlene; Rader, Daniel J; Steinberg, Martin H; Topol, Eric; Yang, Wenli; Knowles, Joshua W; Jaquish, Cashell E; Ruczinski, Ingo; Mathias, Rasika A | Stem cell research. | 2020 07; | 32442913 | |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu, Yan; Zhang, Kun | Nature reviews. Nephrology. | 2020 07; | 32221477 | |
| CAR T-cells that target acute B-lineage leukemia irrespective of CD19 expression. | Fousek, Kristen; Watanabe, Junji; Joseph, Sujith K; George, Ann; An, Xingyue; Byrd, Tiara T; Morris, Jessica S; Luong, Annie; Martínez-Paniagua, Melisa A; Sanber, Khaled; Navai, Shoba A; Gad, Ahmed Z; Salsman, Vita S; Mathew, Pretty R; Kim, Hye Na; Wagner, Dimitrios L; Brunetti, Lorenzo; Jang, Albert; Baker, Matthew L; Varadarajan, Navin; Hegde, Meenakshi; Kim, Yong-Mi; Heisterkamp, Nora; Abdel-Azim, Hisham; Ahmed, Nabil | Leukemia. | 2020 Mar 24; | 32205861 | |
| Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics. | Lee, Timothy J; Yip, Mighten C; Kumar, Aditi; Lewallen, Colby F; Bumbarger, Daniel J; Reid, R Clay; Forest, Craig R | eNeuro. | 2020 Mar/Apr; | 32094293 | |
| Applying inter-rater reliability to improve consistency in classifying PhD career outcomes. | Stayart, C Abigail; Brandt, Patrick D; Brown, Abigail M; Dahl, Tamara; Layton, Rebekah L; Petrie, Kimberly A; Flores-Kim, Emma N; Peña, Christopher G; Fuhrmann, Cynthia N; Monsalve, Gabriela C | F1000Research. | 2020; | 32089837 | |
| Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants. | Donovan, Margaret K R; D'Antonio-Chronowska, Agnieszka; D'Antonio, Matteo; Frazer, Kelly A | Nature communications. | 2020 02 19; | 32075962 | |
| Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp. | Kim, Jae Mun Hugo; Camarena, Adrian; Walker, Christopher; Lin, Ming Yi; Wolseley, Victoria; Souaiaia, Tade; Thornton, Matthew; Grubbs, Brendan; Chow, Robert H; Evgrafov, Oleg V; Knowles, James A | Scientific reports. | 2020 Feb 06; | 32029778 | |
| Single-cell morphology encodes metastatic potential. | Wu, Pei-Hsun; Gilkes, Daniele M; Phillip, Jude M; Narkar, Akshay; Cheng, Thomas Wen-Tao; Marchand, Jorge; Lee, Meng-Horng; Li, Rong; Wirtz, Denis | Science advances. | 2020 01; | 32010778 | |
| Principles and Strategies for Effective Teaching: A Workshop for Pre- and Postdoctoral Trainees in the Biomedical Sciences. | Hartley, Laurel M; Ferrara, Michael J; Handelsman, Mitchell M; Rutebemberwa, Alleluiah; Wefes, Inge | Journal of microbiology & biology education. | 2019; | 31890073 | |
| Identification of Neuronal Lineages in the Drosophila Peripheral Nervous System with a ''Digital'' Multi-spectral Lineage Tracing System. | Veling, Macy W; Li, Ye; Veling, Mike T; Litts, Christopher; Michki, Nigel; Liu, Hao; Ye, Bing; Cai, Dawen | Cell reports. | 2019 Dec 03; | 31801091 | |
| Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. | D'Antonio, Matteo; Reyna, Joaquin; Jakubosky, David; Donovan, Margaret Kr; Bonder, Marc-Jan; Matsui, Hiroko; Stegle, Oliver; Nariai, Naoki; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | eLife | 2019 11 20 | 31746734 | |
| Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories. | D'Antonio-Chronowska, Agnieszka; Donovan, Margaret K R; Young Greenwald, William W; Nguyen, Jennifer Phuong; Fujita, Kyohei; Hashem, Sherin; Matsui, Hiroko; Soncin, Francesca; Parast, Mana; Ward, Michelle C; Coulet, Florence; Smith, Erin N; Adler, Eric; D'Antonio, Matteo; Frazer, Kelly A | Stem cell reports. | 2019 11 12; | 31668852 | |
| Hierarchical organization of cortical and thalamic connectivity. | Harris, Julie A; Mihalas, Stefan; Hirokawa, Karla E; Whitesell, Jennifer D; Choi, Hannah; Bernard, Amy; Bohn, Phillip; Caldejon, Shiella; Casal, Linzy; Cho, Andrew; Feiner, Aaron; Feng, David; Gaudreault, Nathalie; Gerfen, Charles R; Graddis, Nile; Groblewski, Peter A; Henry, Alex M; Ho, Anh; Howard, Robert; Knox, Joseph E; Kuan, Leonard; Kuang, Xiuli; Lecoq, Jerome; Lesnar, Phil; Li, Yaoyao; Luviano, Jennifer; McConoughey, Stephen; Mortrud, Marty T; Naeemi, Maitham; Ng, Lydia; Oh, Seung Wook; Ouellette, Benjamin; Shen, Elise; Sorensen, Staci A; Wakeman, Wayne; Wang, Quanxin; Wang, Yun; Williford, Ali; Phillips, John W; Jones, Allan R; Koch, Christof; Zeng, Hongkui | Nature | 2019 11 | 31666704 | |
| Mastery of Transferrable Skills by Doctoral Scholars: Visualization using Digital Micro-credentialing. | Mathur, Ambika; Wood, Mary E; Cano, Annmarie | Change. | 2018; | 31656316 | |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen, Song; Lake, Blue B; Zhang, Kun | Nature biotechnology. | 2019 12; | 31611697 | |
| Control of cytokinesis by ?-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. | Liu, Honghai; Zhang, Cheng-Hai; Ammanamanchi, Niyatie; Suresh, Sangita; Lewarchik, Christopher; Rao, Krithika; Uys, Gerrida M; Han, Lu; Abrial, Maryline; Yimlamai, Dean; Ganapathy, Balakrishnan; Guillermier, Christelle; Chen, Nathalie; Khaladkar, Mugdha; Spaethling, Jennifer; Eberwine, James H; Kim, Junhyong; Walsh, Stuart; Choudhury, Sangita; Little, Kathryn; Francis, Kimberly; Sharma, Mahesh; Viegas, Melita; Bais, Abha; Kostka, Dennis; Ding, Jun; Bar-Joseph, Ziv; Wu, Yijen; Yechoor, Vijay; Moulik, Mousumi; Johnson, Jennifer; Weinberg, Jacqueline; Reyes-Múgica, Miguel; Steinhauser, Matthew L; Kühn, Bernhard | Science translational medicine. | 2019 Oct 09; | 31597755 | |
| Mixing high-viscosity fluids via acoustically driven bubbles. | Orbay, Sinem; Ozcelik, Adem; Lata, James; Kaynak, Murat; Wu, Mengxi; Huang, Tony Jun | Journal of micromechanics and microengineering : structures, devices, and systems. | 2017; | 31588165 | |
| Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. | Benaglio, Paola; D'Antonio-Chronowska, Agnieszka; Ma, Wubin; Yang, Feng; Young Greenwald, William W; Donovan, Margaret K R; DeBoever, Christopher; Li, He; Drees, Frauke; Singhal, Sanghamitra; Matsui, Hiroko; van Setten, Jessica; Sotoodehnia, Nona; Gaulton, Kyle J; Smith, Erin N; D'Antonio, Matteo; Rosenfeld, Michael G; Frazer, Kelly A | Nature genetics. | 2019 10; | 31570892 | |
| Sample Preparation and Analysis of Single Cells Using High Performance MALDI FTICR Mass Spectrometry. | Yang, Bo; Tsui, Tina; Caprioli, Richard M; Norris, Jeremy L | Methods in molecular biology (Clifton, N.J.). | 2020; | 31565771 | |
| High-yield, automated intracellular electrophysiology in retinal pigment epithelia. | Lewallen, Colby F; Wan, Qin; Maminishkis, Arvydas; Stoy, William; Kolb, Ilya; Hotaling, Nathan; Bharti, Kapil; Forest, Craig R | Journal of neuroscience methods. | 2019 12 01; | 31562888 | |
| Anti-myeloma activity and molecular logic operation by Natural Killer cells in microfluidic droplets. | Sarkar, Saheli; McKenney, Seamus; Sabhachandani, Pooja; Adler, James; Hu, Xiaozhe; Stroopinksy, Dina; Rosenblatt, Jacalyn; Avigan, David; Konry, Tania | Sensors and actuators. B, Chemical. | 2019 Mar 01; | 31537955 | |
| Biophysical and biomolecular determination of cellular age in humans. | Phillip, Jude M; Wu, Pei-Hsun; Gilkes, Daniele M; Williams, Wadsworth; McGovern, Shaun; Daya, Jena; Chen, Jonathan; Aifuwa, Ivie; Lee, Jerry S H; Fan, Rong; Walston, Jeremy; Wirtz, Denis | Nature biomedical engineering. | 2017 Jul; | 31372309 | |
| Advances in the automation of whole-cell patch clamp technology. | Suk, Ho-Jun; Boyden, Edward S; van Welie, Ingrid | Journal of neuroscience methods. | 2019 10 01; | 31336060 | |
| Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution. | Duncan, Leighton H; Moyle, Mark W; Shao, Lin; Sengupta, Titas; Ikegami, Richard; Kumar, Abhishek; Guo, Min; Christensen, Ryan; Santella, Anthony; Bao, Zhirong; Shroff, Hari; Mohler, William; Colón-Ramos, Daniel A | Journal of visualized experiments : JoVE. | 2019 06 06; | 31233035 | |
| High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. | Marras, Salvatore A E; Bushkin, Yuri; Tyagi, Sanjay | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Jul 09; | 31221755 | |
| Classification of electrophysiological and morphological neuron types in the mouse visual cortex. | Gouwens, Nathan W; Sorensen, Staci A; Berg, Jim; Lee, Changkyu; Jarsky, Tim; Ting, Jonathan; Sunkin, Susan M; Feng, David; Anastassiou, Costas A; Barkan, Eliza; Bickley, Kris; Blesie, Nicole; Braun, Thomas; Brouner, Krissy; Budzillo, Agata; Caldejon, Shiella; Casper, Tamara; Castelli, Dan; Chong, Peter; Crichton, Kirsten; Cuhaciyan, Christine; Daigle, Tanya L; Dalley, Rachel; Dee, Nick; Desta, Tsega; Ding, Song-Lin; Dingman, Samuel; Doperalski, Alyse; Dotson, Nadezhda; Egdorf, Tom; Fisher, Michael; de Frates, Rebecca A; Garren, Emma; Garwood, Marissa; Gary, Amanda; Gaudreault, Nathalie; Godfrey, Keith; Gorham, Melissa; Gu, Hong; Habel, Caroline; Hadley, Kristen; Harrington, James; Harris, Julie A; Henry, Alex; Hill, DiJon; Josephsen, Sam; Kebede, Sara; Kim, Lisa; Kroll, Matthew; Lee, Brian; Lemon, Tracy; Link, Katherine E; Liu, Xiaoxiao; Long, Brian; Mann, Rusty; McGraw, Medea; Mihalas, Stefan; Mukora, Alice; Murphy, Gabe J; Ng, Lindsay; Ngo, Kiet; Nguyen, Thuc Nghi; Nicovich, Philip R; Oldre, Aaron; Park, Daniel; Parry, Sheana; Perkins, Jed; Potekhina, Lydia; Reid, David; Robertson, Miranda; Sandman, David; Schroedter, Martin; Slaughterbeck, Cliff; Soler-Llavina, Gilberto; Sulc, Josef; Szafer, Aaron; Tasic, Bosiljka; Taskin, Naz; Teeter, Corinne; Thatra, Nivretta; Tung, Herman; Wakeman, Wayne; Williams, Grace; Young, Rob; Zhou, Zhi; Farrell, Colin; Peng, Hanchuan; Hawrylycz, Michael J; Lein, Ed; Ng, Lydia; Arkhipov, Anton; Bernard, Amy; Phillips, John W; Zeng, Hongkui; Koch, Christof | Nature neuroscience | 2019 07 | 31209381 | |
| Neuronal cell-subtype specificity of neural synchronization in mouse primary visual cortex. | Knoblich, Ulf; Huang, Lawrence; Zeng, Hongkui; Li, Lu | Nature communications | 2019 06 10 | 31182715 | |
| Organization of Embryonic Morphogenesis via Mechanical Information. | Das, Dipjyoti; Jülich, Dörthe; Schwendinger-Schreck, Jamie; Guillon, Emilie; Lawton, Andrew K; Dray, Nicolas; Emonet, Thierry; O'Hern, Corey S; Shattuck, Mark D; Holley, Scott A | Developmental cell. | 2019 Jun 17; | 31178400 | |
| Understanding heterogeneous tumor microenvironment in metastatic melanoma. | Yan, Yiyi; Leontovich, Alexey A; Gerdes, Michael J; Desai, Keyur; Dong, Jinhong; Sood, Anup; Santamaria-Pang, Alberto; Mansfield, Aaron S; Chadwick, Chrystal; Zhang, Rong; Nevala, Wendy K; Flotte, Thomas J; Ginty, Fiona; Markovic, Svetomir N | PloS one. | 2019; | 31166985 | |
| In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer. | He, Li; Binari, Richard; Huang, Jiuhong; Falo-Sanjuan, Julia; Perrimon, Norbert | eLife. | 2019 May 29; | 31140975 | |
| Single-cell technologies for profiling T cells to enable monitoring of immunotherapies. | An, Xingyue; Varadarajan, Navin | Current opinion in chemical engineering. | 2018 Mar; | 31131208 | |
| Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci. | Smith, Erin N; D'Antonio-Chronowska, Agnieszka; Greenwald, William W; Borja, Victor; Aguiar, Lana R; Pogue, Robert; Matsui, Hiroko; Benaglio, Paola; Borooah, Shyamanga; D'Antonio, Matteo; Ayyagari, Radha; Frazer, Kelly A | Stem cell reports. | 2019 Jun 11; | 31080113 | |
| Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. | Yang, Bin; Chen, Xingye; Wang, Yina; Feng, Siyu; Pessino, Veronica; Stuurman, Nico; Cho, Nathan H; Cheng, Karen W; Lord, Samuel J; Xu, Linfeng; Xie, Dan; Mullins, R Dyche; Leonetti, Manuel D; Huang, Bo | Nature methods. | 2019 06; | 31061492 | |
| A microfluidic assay for the quantification of the metastatic propensity of breast cancer specimens. | Yankaskas, Christopher L; Thompson, Keyata N; Paul, Colin D; Vitolo, Michele I; Mistriotis, Panagiotis; Mahendra, Ankit; Bajpai, Vivek K; Shea, Daniel J; Manto, Kristen M; Chai, Andreas C; Varadarajan, Navin; Kontrogianni-Konstantopoulos, Aikaterini; Martin, Stuart S; Konstantopoulos, Konstantinos | Nature biomedical engineering. | 2019 Jun; | 31061459 | |
| Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. | Aicher, Toby P; Carroll, Shaina; Raddi, Gianmarco; Gierahn, Todd; Wadsworth 2nd, Marc H; Hughes, Travis K; Love, Chris; Shalek, Alex K | Methods in molecular biology (Clifton, N.J.). | 2019; | 31028635 | |
| PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices. | Kolb, Ilya; Landry, Corey R; Yip, Mighten C; Lewallen, Colby F; Stoy, William A; Lee, John; Felouzis, Amanda; Yang, Bo; Boyden, Edward S; Rozell, Christopher J; Forest, Craig R | Journal of neural engineering. | 2019 08; | 30970335 | |
| Autonomous patch-clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex. | Holst, Gregory L; Stoy, William; Yang, Bo; Kolb, Ilya; Kodandaramaiah, Suhasa B; Li, Lu; Knoblich, Ulf; Zeng, Hongkui; Haider, Bilal; Boyden, Edward S; Forest, Craig R | Journal of neurophysiology. | 2019 Jun 01; | 30969898 | |
| Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition. | Martorell, Anthony J; Paulson, Abigail L; Suk, Ho-Jun; Abdurrob, Fatema; Drummond, Gabrielle T; Guan, Webster; Young, Jennie Z; Kim, David Nam-Woo; Kritskiy, Oleg; Barker, Scarlett J; Mangena, Vamsi; Prince, Stephanie M; Brown, Emery N; Chung, Kwanghun; Boyden, Edward S; Singer, Annabelle C; Tsai, Li-Huei | Cell. | 2019 Apr 04; | 30879788 | |
| Optogenetic reactivation of memory ensembles in the retrosplenial cortex induces systems consolidation. | de Sousa, André F; Cowansage, Kiriana K; Zutshi, Ipshita; Cardozo, Leonardo M; Yoo, Eun J; Leutgeb, Stefan; Mayford, Mark | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Apr 23; | 30877252 | |
| Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. | Greenwald, William W; Li, He; Benaglio, Paola; Jakubosky, David; Matsui, Hiroko; Schmitt, Anthony; Selvaraj, Siddarth; D'Antonio, Matteo; D'Antonio-Chronowska, Agnieszka; Smith, Erin N; Frazer, Kelly A | Nature communications. | 2019 03 05; | 30837461 | |
| A role for actomyosin contractility in Notch signaling. | Hunter, Ginger L; He, Li; Perrimon, Norbert; Charras, Guillaume; Giniger, Edward; Baum, Buzz | BMC biology. | 2019 02 11; | 30744634 | |
| Faculty perceptions and knowledge of career development of trainees in biomedical science: What do we (think we) know? | Watts, Stephanie W; Chatterjee, Deepshikha; Rojewski, Julie W; Shoshkes Reiss, Carol; Baas, Tracey; Gould, Kathleen L; Brown, Abigail M; Chalkley, Roger; Brandt, Patrick; Wefes, Inge; Hyman, Linda; Ford, J Kevin | PloS one. | 2019; | 30699144 | |
| Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. | Middleton, Sarah A; Eberwine, James; Kim, Junhyong | BMC biology. | 2019 01 24; | 30678683 | |
| Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. | Cutrale, Francesco; Rodriguez, Daniel; Hortigüela, Verónica; Chiu, Chi-Li; Otterstrom, Jason; Mieruszynski, Stephen; Seriola, Anna; Larrañaga, Enara; Raya, Angel; Lakadamyali, Melike; Fraser, Scott E; Martinez, Elena; Ojosnegros, Samuel | Nature protocols | 2019 02 | 30675035 | |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, Arjun | PLoS genetics. | 2019 01; | 30625149 | |
| Amendments: Author Correction: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, Arjun | Nature biotechnology. | 2019 01 03; | 30605160 | |
| Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. | Bakken, Trygve E; Hodge, Rebecca D; Miller, Jeremy A; Yao, Zizhen; Nguyen, Thuc Nghi; Aevermann, Brian; Barkan, Eliza; Bertagnolli, Darren; Casper, Tamara; Dee, Nick; Garren, Emma; Goldy, Jeff; Graybuck, Lucas T; Kroll, Matthew; Lasken, Roger S; Lathia, Kanan; Parry, Sheana; Rimorin, Christine; Scheuermann, Richard H; Schork, Nicholas J; Shehata, Soraya I; Tieu, Michael; Phillips, John W; Bernard, Amy; Smith, Kimberly A; Zeng, Hongkui; Lein, Ed S; Tasic, Bosiljka | PloS one | 2018 | 30586455 | |
| Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. | Wu, Yan; Tamayo, Pablo; Zhang, Kun | Cell systems. | 2018 12 26; | 30528274 | |
| Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag. | Chen, Baohui; Zou, Wei; Xu, Haiyue; Liang, Ying; Huang, Bo | Nature communications. | 2018 Nov 29; | 30498221 | |
| Acoustic Actuation of in situ Fabricated Artificial Cilia. | Orbay, Sinem; Ozcelik, Adem; Bachman, Hunter; Huang, Tony Jun | Journal of micromechanics and microengineering : structures, devices, and systems. | 2018 Feb; | 30479458 | |
| Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level. | Gutschow, Miriam V; Mason, John C; Lane, Keara M; Maayan, Inbal; Hughey, Jacob J; Bajar, Bryce T; Amatya, Debha N; Valle, Sean D; Covert, Markus W | Molecular biology of the cell. | 2019 01 15; | 30462580 | |
| ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard, Sara H; Mellis, Ian A; Dunagin, Margaret; Bayatpour, Sareh; Jiang, Connie L; Dardani, Ian; Symmons, Orsolya; Emert, Benjamin; Torre, Eduardo; Cote, Allison; Sullivan, Alessandra; Stamatoyannopoulos, John A; Raj, Arjun | Nature biotechnology. | 2018 Nov 12; | 30418432 | |
| Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA-Sequencing. | Mahendra, Ankit; Yang, Xingyu; Abnouf, Shaza; Adolacion, Jay R T; Park, Daechan; Soomro, Sanam; Roszik, Jason; Coarfa, Cristian; Romain, Gabrielle; Wanzeck, Keith; Bridges Jr, S Louis; Aggarwal, Amita; Qiu, Peng; Agarwal, Sandeep K; Mohan, Chandra; Varadarajan, Navin | Arthritis & rheumatology (Hoboken, N.J.). | 2019 Apr; | 30407753 | |
| Shared and distinct transcriptomic cell types across neocortical areas. | Tasic, Bosiljka; Yao, Zizhen; Graybuck, Lucas T; Smith, Kimberly A; Nguyen, Thuc Nghi; Bertagnolli, Darren; Goldy, Jeff; Garren, Emma; Economo, Michael N; Viswanathan, Sarada; Penn, Osnat; Bakken, Trygve; Menon, Vilas; Miller, Jeremy; Fong, Olivia; Hirokawa, Karla E; Lathia, Kanan; Rimorin, Christine; Tieu, Michael; Larsen, Rachael; Casper, Tamara; Barkan, Eliza; Kroll, Matthew; Parry, Sheana; Shapovalova, Nadiya V; Hirschstein, Daniel; Pendergraft, Julie; Sullivan, Heather A; Kim, Tae Kyung; Szafer, Aaron; Dee, Nick; Groblewski, Peter; Wickersham, Ian; Cetin, Ali; Harris, Julie A; Levi, Boaz P; Sunkin, Susan M; Madisen, Linda; Daigle, Tanya L; Looger, Loren; Bernard, Amy; Phillips, John; Lein, Ed; Hawrylycz, Michael; Svoboda, Karel; Jones, Allan R; Koch, Christof; Zeng, Hongkui | Nature. | 2018 11; | 30382198 | |
| Candidate-based screening via gene modulation in human neurons and astrocytes implicates FERMT2 in A? and TAU proteostasis. | Sullivan, Sarah E; Liao, Meichen; Smith, Robert V; White, Charles; Lagomarsino, Valentina N; Xu, Jishu; Taga, Mariko; Bennett, David A; De Jager, Philip L; Young-Pearse, Tracy L | Human molecular genetics. | 2019 Mar 01; | 30371777 | |
| Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu, Qian; Shah, Sheel; Dries, Ruben; Cai, Long; Yuan, Guo-Cheng | Nature biotechnology. | 2018 Oct 29; | 30371680 | |
| Evolution of a Functional Taxonomy of Career Pathways for Biomedical Trainees. | Mathur, Ambika; Brandt, P; Chalkley, R; Daniel, L; Labosky, P; Stayart, C; Meyers, F | Journal of clinical and translational science. | 2018 Apr; | 30364657 | |
| Active Tuberculosis Is Characterized by Highly Differentiated Effector Memory Th1 Cells. | Arrigucci, Riccardo; Lakehal, Karim; Vir, Pooja; Handler, Deborah; Davidow, Amy L; Herrera, Rosa; Estrada-Guzmán, Julia Dolores; Bushkin, Yuri; Tyagi, Sanjay; Lardizabal, Alfred A; Gennaro, Maria Laura | Frontiers in immunology. | 2018; | 30283456 | |
| Recapitulation of molecular regulators of nuclear motion during cell migration. | Sneider, Alexandra; Hah, Jungwon; Wirtz, Denis; Kim, Dong-Hwee | Cell adhesion & migration. | 2019 12; | 30261154 | |
| Tumor cell density regulates matrix metalloproteinases for enhanced migration. | Jayatilaka, Hasini; Umanzor, Fatima G; Shah, Vishwesh; Meirson, Tomer; Russo, Gabriella; Starich, Bartholomew; Tyle, Pranay; Lee, Jerry S H; Khatau, Shyam; Gil-Henn, Hava; Wirtz, Denis | Oncotarget. | 2018 Aug 24; | 30220965 | |
| Functional assessment of strains around a full-thickness and critical sized articular cartilage defect under compressive loading using MRI. | Zevenbergen, L; Gsell, W; Chan, D D; Vander Sloten, J; Himmelreich, U; Neu, C P; Jonkers, I | Osteoarthritis and cartilage. | 2018 12; | 30195045 | |
| Cartilage-on-cartilage contact: effect of compressive loading on tissue deformations and structural integrity of bovine articular cartilage. | Zevenbergen, L; Gsell, W; Cai, L; Chan, D D; Famaey, N; Vander Sloten, J; Himmelreich, U; Neu, C P; Jonkers, I | Osteoarthritis and cartilage. | 2018 12; | 30172835 | |
| Standing Surface Acoustic Wave (SSAW)-Based Fluorescence-Activated Cell Sorter. | Ren, Liqiang; Yang, Shujie; Zhang, Peiran; Qu, Zhiguo; Mao, Zhangming; Huang, Po-Hsun; Chen, Yuchao; Wu, Mengxi; Wang, Lin; Li, Peng; Huang, Tony Jun | Small (Weinheim an der Bergstrasse, Germany). | 2018 10; | 30168662 | |
| Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. | Veevers, Jennifer; Farah, Elie N; Corselli, Mirko; Witty, Alec D; Palomares, Karina; Vidal, Jason G; Emre, Nil; Carson, Christian T; Ouyang, Kunfu; Liu, Canzhao; van Vliet, Patrick; Zhu, Maggie; Hegarty, Jeffrey M; Deacon, Dekker C; Grinstein, Jonathan D; Dirschinger, Ralf J; Frazer, Kelly A; Adler, Eric D; Knowlton, Kirk U; Chi, Neil C; Martin, Jody C; Chen, Ju; Evans, Sylvia M | Stem cell reports. | 2018 09 11; | 30122443 | |
| TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids. | Lu, Hengyang; Li, Jiabing; Martinez-Paniagua, Melisa A; Bandey, Irfan N; Amritkar, Amit; Singh, Harjeet; Mayerich, David; Varadarajan, Navin; Roysam, Badrinath | Bioinformatics (Oxford, England). | 2019 02 15; | 30084956 | |
| Digital acoustofluidics enables contactless and programmable liquid handling. | Zhang, Steven Peiran; Lata, James; Chen, Chuyi; Mai, John; Guo, Feng; Tian, Zhenhua; Ren, Liqiang; Mao, Zhangming; Huang, Po-Hsun; Li, Peng; Yang, Shujie; Huang, Tony Jun | Nature communications. | 2018 07 26; | 30050088 | |
| Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach. | D'Antonio, Matteo; Benaglio, Paola; Jakubosky, David; Greenwald, William W; Matsui, Hiroko; Donovan, Margaret K R; Li, He; Smith, Erin N; D'Antonio-Chronowska, Agnieszka; Frazer, Kelly A | Cell reports. | 2018 07 24; | 30044985 | |
| Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions. | Lee, Timothy J; Lewallen, Colby F; Bumbarger, Daniel J; Yunker, Peter J; Reid, R Clay; Forest, Craig R | Journal of colloid and interface science. | 2018 Dec 01; | 30041112 | |
| Automated in vivo patch-clamp evaluation of extracellular multielectrode array spike recording capability. | Allen, Brian D; Moore-Kochlacs, Caroline; Bernstein, Jacob G; Kinney, Justin P; Scholvin, Jorg; Seoane, Luís F; Chronopoulos, Chris; Lamantia, Charlie; Kodandaramaiah, Suhasa B; Tegmark, Max; Boyden, Edward S | Journal of neurophysiology. | 2018 11 01; | 29995597 | |
| Circulating Tumor Cell Phenotyping via High-Throughput Acoustic Separation. | Wu, Mengxi; Huang, Po-Hsun; Zhang, Rui; Mao, Zhangming; Chen, Chuyi; Kemeny, Gabor; Li, Peng; Lee, Adrian V; Gyanchandani, Rekha; Armstrong, Andrew J; Dao, Ming; Suresh, Subra; Huang, Tony Jun | Small (Weinheim an der Bergstrasse, Germany). | 2018 08; | 29968402 | |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang, Mo; Wang, Jingshu; Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Bonasio, Roberto; Murray, John I; Raj, Arjun; Li, Mingyao; Zhang, Nancy R | Nature methods. | 2018 Jul; | 29941873 | |
| Exposure to multiple career pathways by biomedical doctoral students at a public research university. | Mathur, Ambika; Chow, Christine S; Feig, Andrew L; Kenaga, Heidi; Moldenhauer, Judith A; Muthunayake, Nisansala S; Ouellett, Mathew L; Pence, Laura E; Straub, Victoria | PloS one. | 2018; | 29933412 | |
| A comparison of methods to assess cell mechanical properties. | Wu, Pei-Hsun; Aroush, Dikla Raz-Ben; Asnacios, Atef; Chen, Wei-Chiang; Dokukin, Maxim E; Doss, Bryant L; Durand-Smet, Pauline; Ekpenyong, Andrew; Guck, Jochen; Guz, Nataliia V; Janmey, Paul A; Lee, Jerry S H; Moore, Nicole M; Ott, Albrecht; Poh, Yeh-Chuin; Ros, Robert; Sander, Mathias; Sokolov, Igor; Staunton, Jack R; Wang, Ning; Whyte, Graeme; Wirtz, Denis | Nature methods. | 2018 07; | 29915189 | |
| Fingerprint Stimulated Raman Scattering Imaging Reveals Retinoid Coupling Lipid Metabolism and Survival. | Chen, Andy J; Li, Junjie; Jannasch, Amber; Mutlu, Ayse Sena; Wang, Meng C; Cheng, Ji-Xin | Chemphyschem : a European journal of chemical physics and physical chemistry. | 2018 10 05; | 29911339 | |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah, Sheel; Takei, Yodai; Zhou, Wen; Lubeck, Eric; Yun, Jina; Eng, Chee-Huat Linus; Koulena, Noushin; Cronin, Christopher; Karp, Christoph; Liaw, Eric J; Amin, Mina; Cai, Long | Cell. | 2018 May 31; | 29887381 | |
| Stabilization of Aliphatic Phosphines by Auxiliary Phosphine Sulfides Offers Zeptomolar Affinity and Unprecedented Selectivity for Probing Biological CuI. | Morgan, M Thomas; Yang, Bo; Harankhedkar, Shefali; Nabatilan, Arielle; Bourassa, Daisy; McCallum, Adam M; Sun, Fangxu; Wu, Ronghu; Forest, Craig R; Fahrni, Christoph J | Angewandte Chemie (International ed. in English). | 2018 Jun 08; | 29885022 | |
| Chromatin changes trigger laminin genes dysregulation in aging kidneys. | Denisenko, Oleg; Mar, Daniel; Trawczynski, Matthew; Bomsztyk, Karol | Aging. | 2018 05 29; | 29846172 | |
| Multi-nucleated cells use ROS to induce breast cancer chemo-resistance in vitro and in vivo. | Parekh, Aditya; Das, Subhayan; Parida, Sheetal; Das, Chandan Kanta; Dutta, Debabrata; Mallick, Sanjaya K; Wu, Pei-Hsun; Kumar, B N Prashanth; Bharti, Rashmi; Dey, Goutam; Banerjee, Kacoli; Rajput, Shashi; Bharadwaj, Deblina; Pal, Ipsita; Dey, Kaushik Kumar; Rajesh, Yetirajam; Jena, Bikash Chandra; Biswas, Angana; Banik, Payel; Pradhan, Anjan K; Das, Swadesh K; Das, Amit Kumar; Dhara, Santanu; Fisher, Paul B; Wirtz, Denis; Mills, Gordon B; Mandal, Mahitosh | Oncogene. | 2018 08; | 29743594 | |
| Alveolar epithelial cell processing of nanoparticles activates autophagy and lysosomal exocytosis. | Sipos, Arnold; Kim, Kwang-Jin; Chow, Robert H; Flodby, Per; Borok, Zea; Crandall, Edward D | American journal of physiology. Lung cellular and molecular physiology. | 2018 08 01; | 29722567 | |
| A sharp-edge-based acoustofluidic chemical signal generator. | Huang, Po-Hsun; Chan, Chung Yu; Li, Peng; Wang, Yuqi; Nama, Nitesh; Bachman, Hunter; Huang, Tony Jun | Lab on a chip. | 2018 05 15; | 29668002 | |
| Inhibition of ovarian tumor cell invasiveness by targeting SYK in the tyrosine kinase signaling pathway. | Yu, Yu; Suryo Rahmanto, Yohan; Lee, Meng-Horng; Wu, Pei-Hsun; Phillip, Jude M; Huang, Chuan-Hsiang; Vitolo, Michele I; Gaillard, Stephanie; Martin, Stuart S; Wirtz, Denis; Shih, Ie-Ming; Wang, Tian-Li | Oncogene. | 2018 07; | 29643476 | |
| AceTree: a major update and case study in the long term maintenance of open-source scientific software. | Katzman, Braden; Tang, Doris; Santella, Anthony; Bao, Zhirong | BMC bioinformatics. | 2018 Apr 04; | 29618316 | |
| The successes and future prospects of the linear antisense RNA amplification methodology. | Li, Jifen; Eberwine, James | Nature protocols. | 2018 05; | 29599441 | |
| Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation. | Yang, Bo; Patterson, Nathan Heath; Tsui, Tina; Caprioli, Richard M; Norris, Jeremy L | Journal of the American Society for Mass Spectrometry. | 2018 Mar 13; | 29536413 | |
| Direct measurement of bipolar cell responses to electrical stimulation in wholemount mouse retina. | Walston, Steven T; Chow, Robert H; Weiland, James D | Journal of neural engineering. | 2018 08; | 29513646 | |
| A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. | Piatkevich, Kiryl D; Jung, Erica E; Straub, Christoph; Linghu, Changyang; Park, Demian; Suk, Ho-Jun; Hochbaum, Daniel R; Goodwin, Daniel; Pnevmatikakis, Eftychios; Pak, Nikita; Kawashima, Takashi; Yang, Chao-Tsung; Rhoades, Jeffrey L; Shemesh, Or; Asano, Shoh; Yoon, Young-Gyu; Freifeld, Limor; Saulnier, Jessica L; Riegler, Clemens; Engert, Florian; Hughes, Thom; Drobizhev, Mikhail; Szabo, Balint; Ahrens, Misha B; Flavell, Steven W; Sabatini, Bernardo L; Boyden, Edward S | Nature chemical biology. | 2018 Apr; | 29483642 | |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre, Eduardo; Dueck, Hannah; Shaffer, Sydney; Gospocic, Janko; Gupte, Rohit; Bonasio, Roberto; Kim, Junhyong; Murray, John; Raj, Arjun | Cell systems. | 2018 Feb 28; | 29454938 | |
| Molecular Time Sharing through Dynamic Pulsing in Single Cells. | Park, Jin; Dies, Marta; Lin, Yihan; Hormoz, Sahand; Smith-Unna, Stephanie E; Quinodoz, Sofia; Hernández-Jiménez, María Jesús; Garcia-Ojalvo, Jordi; Locke, James C W; Elowitz, Michael B | Cell systems. | 2018 Feb 28; | 29454936 | |
| Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. | Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing | Nature neuroscience. | 2018 Mar; | 29434377 | |
| Mechanical regulation of stem-cell differentiation by the stretch-activated Piezo channel. | He, Li; Si, Guangwei; Huang, Jiuhong; Samuel, Aravinthan D T; Perrimon, Norbert | Nature. | 2018 03 01; | 29414942 | |
| Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy. | Chen, Andy Jing; Yuan, Xiaojing; Li, Junjie; Dong, Puting; Hamza, Iqbal; Cheng, Ji-Xin | Analytical chemistry. | 2018 03 06; | 29401392 | |
| Acoustofluidic waveguides for localized control of acoustic wavefront in microfluidics. | Bian, Yusheng; Guo, Feng; Yang, Shujie; Mao, Zhangming; Bachman, Hunter; Tang, Shi-Yang; Ren, Liqiang; Zhang, Bin; Gong, Jianying; Guo, Xiasheng; Huang, Tony Jun | Microfluidics and nanofluidics. | 2017 Aug; | 29358901 | |
| Cell Membrane Tracking in Living Brain Tissue Using Differential Interference Contrast Microscopy. | Lee, John; Kolb, Ilya; Forest, Craig R; Rozell, Christopher J | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society. | 2018 Apr; | 29346099 | |
| Survey of checkpoints along the pathway to diverse biomedical research faculty. | Meyers, Lindsay C; Brown, Abigail M; Moneta-Koehler, Liane; Chalkley, Roger | PloS one. | 2018; | 29338019 | |
| Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. | Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A | Development (Cambridge, England). | 2018 01 08; | 29311262 | |
| PIVOT: platform for interactive analysis and visualization of transcriptomics data. | Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong | BMC bioinformatics. | 2018 Jan 05; | 29304726 | |
| Acoustofluidic devices controlled by cell phones. | Bachman, Hunter; Huang, Po-Hsun; Zhao, Shuaiguo; Yang, Shujie; Zhang, Peiran; Fu, Hai; Huang, Tony Jun | Lab on a chip. | 2018 Jan 30; | 29302660 | |
| Multi-neuron intracellular recording in vivo via interacting autopatching robots. | Kodandaramaiah, Suhasa B; Flores, Francisco J; Holst, Gregory L; Singer, Annabelle C; Han, Xue; Brown, Emery N; Boyden, Edward S; Forest, Craig R | eLife. | 2018 01 03; | 29297466 | |
| Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos. | Onjiko, Rosemary M; Portero, Erika P; Moody, Sally A; Nemes, Peter | Journal of visualized experiments : JoVE. | 2017 Dec 22; | 29286491 | |
| Mammalian Cell Division in 3D Matrices via Quantitative Confocal Reflection Microscopy. | He, Lijuan; Sneider, Alexandra; Chen, Weitong; Karl, Michelle; Prasath, Vishnu; Wu, Pei-Hsun; Mattson, Gunnar; Wirtz, Denis | Journal of visualized experiments : JoVE. | 2017 11 29; | 29286363 | |
| Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice. | Kolb, Ilya; Talei Franzesi, Giovanni; Wang, Michael; Kodandaramaiah, Suhasa B; Forest, Craig R; Boyden, Edward S; Singer, Annabelle C | The Journal of neuroscience : the official journal of the Society for Neuroscience. | 2018 Feb 14; | 29279309 | |
| In Vivo Multiscale and Spatially-Dependent Biomechanics Reveals Differential Strain Transfer Hierarchy in Skeletal Muscle. | Ghosh, Soham; Cimino, James G; Scott, Adrienne K; Damen, Frederick W; Phillips, Evan H; Veress, Alexander I; Neu, Corey P; Goergen, Craig J | ACS biomaterials science & engineering. | 2017 Nov 13; | 29276759 | |
| Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology. | Kim, Jeong-Ki; Louhghalam, Arghavan; Lee, Geonhui; Schafer, Benjamin W; Wirtz, Denis; Kim, Dong-Hwee | Nature communications. | 2017 Dec 14; | 29242553 | |
| Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation. | Lee, Jae Kyoo; Nam, Hong Gil; Zare, Richard N | Quarterly reviews of biophysics. | 2017 01; | 29233214 | |
| Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. | Lake, Blue B; Chen, Song; Sos, Brandon C; Fan, Jean; Kaeser, Gwendolyn E; Yung, Yun C; Duong, Thu E; Gao, Derek; Chun, Jerold; Kharchenko, Peter V; Zhang, Kun | Nature biotechnology. | 2018 Jan; | 29227469 | |
| Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing. | Morris, Jacqueline; Na, Young-Ji; Zhu, Hua; Lee, Jae-Hee; Giang, Hoa; Ulyanova, Alexandra V; Baltuch, Gordon H; Brem, Steven; Chen, H Isaac; Kung, David K; Lucas, Timothy H; O'Rourke, Donald M; Wolf, John A; Grady, M Sean; Sul, Jai-Yoon; Kim, Junhyong; Eb | Cell reports. | 2017 Dec 05; | 29212019 | |
| Eph-ephrin signaling modulated by polymerization and condensation of receptors. | Ojosnegros, Samuel; Cutrale, Francesco; Rodríguez, Daniel; Otterstrom, Jason J; Chiu, Chi Li; Hortigüela, Verónica; Tarantino, Carolina; Seriola, Anna; Mieruszynski, Stephen; Martínez, Elena; Lakadamyali, Melike; Raya, Angel; Fraser, Scott E | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Dec 12; | 29192024 | |
| Identification of a neural crest stem cell niche by Spatial Genomic Analysis. | Lignell, Antti; Kerosuo, Laura; Streichan, Sebastian J; Cai, Long; Bronner, Marianne E | Nature communications. | 2017 Nov 28; | 29184067 | |
| Functional MRI can detect changes in intratissue strains in a full thickness and critical sized ovine cartilage defect model. | Chan, Deva D; Cai, Luyao; Butz, Kent D; Nauman, Eric A; Dickerson, Darryl A; Jonkers, Ilse; Neu, Corey P | Journal of biomechanics. | 2018 01 03; | 29169631 | |
| An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues. | Shah, Pavak Kirit; Santella, Anthony; Jacobo, Adrian; Siletti, Kimberly; Hudspeth, A J; Bao, Zhirong | Developmental cell. | 2017 Nov 20; | 29161596 | |
| Cell-type Dependent Alzheimer's Disease Phenotypes: Probing the Biology of Selective Neuronal Vulnerability. | Muratore, Christina R; Zhou, Constance; Liao, Meichen; Fernandez, Marty A; Taylor, Walter M; Lagomarsino, Valentina N; Pearse 2nd, Richard V; Rice, Heather C; Negri, Joseph M; He, Amy; Srikanth, Priya; Callahan, Dana G; Shin, Taehwan; Zhou, Monica; Bennett, David A; Noggle, Scott; Love, J Christopher; Selkoe, Dennis J; Young-Pearse, Tracy L | Stem cell reports. | 2017 12 12; | 29153990 | |
| Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. | Herring, Charles A; Banerjee, Amrita; McKinley, Eliot T; Simmons, Alan J; Ping, Jie; Roland, Joseph T; Franklin, Jeffrey L; Liu, Qi; Gerdes, Michael J; Coffey, Robert J; Lau, Ken S | Cell systems. | 2017 Nov 07; | 29153838 | |
| Single-Cell Imaging Using Radioluminescence Microscopy Reveals Unexpected Binding Target for [18F]HFB. | Kiru, Louise; Kim, Tae Jin; Shen, Bin; Chin, Frederick T; Pratx, Guillem | Molecular imaging and biology. | 2018 06; | 29143174 | |
| Profiling the transcriptome with RNA SPOTs. | Eng, Chee-Huat Linus; Shah, Sheel; Thomassie, Julian; Cai, Long | Nature methods. | 2017 Dec; | 29131163 | |
| Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. | Guo, Feng; Li, Sixing; Caglar, Mehmet Umut; Mao, Zhangming; Liu, Wu; Woodman, Andrew; Arnold, Jamie J; Wilke, Claus O; Huang, Tony Jun; Cameron, Craig E | Cell reports. | 2017 Nov 07; | 29117571 | |
| EB1 and cytoplasmic dynein mediate protrusion dynamics for efficient 3-dimensional cell migration. | Jayatilaka, Hasini; Giri, Anjil; Karl, Michelle; Aifuwa, Ivie; Trenton, Nicholaus J; Phillip, Jude M; Khatau, Shyam; Wirtz, Denis | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2018 03; | 29097501 | |
| Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues. | Lin, Ming-Yi; Wang, Yi-Ling; Wu, Wan-Lin; Wolseley, Victoria; Tsai, Ming-Ting; Radic, Vladimir; Thornton, Matthew E; Grubbs, Brendan H; Chow, Robert H; Huang, I-Chueh | Scientific reports. | 2017 Nov 01; | 29093521 | |
| Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. | Nariai, Naoki; Greenwald, William W; DeBoever, Christopher; Li, He; Frazer, Kelly A | Genetics. | 2017 12; | 29074555 | |
| Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. | Onjiko, Rosemary M; Plotnick, David O; Moody, Sally A; Nemes, Peter | Analytical methods : advancing methods and applications. | 2017 Sep 14; | 29062391 | |
| Acoustic streaming: an arbitrary Lagrangian-Eulerian perspective. | Nama, Nitesh; Huang, Tony Jun; Costanzo, Francesco | Journal 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 V | Biophysical journal. | 2017 Nov 21; | 29017728 | |
| Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. | Suk, Ho-Jun; van Welie, Ingrid; Kodandaramaiah, Suhasa B; Allen, Brian; Forest, Craig R; Boyden, Edward S | Neuron. | 2017 Sep 27; | 28957673 | |
| 21st century neurobehavioral theories of decision making in addiction: Review and evaluation. | Bickel, Warren K; Mellis, Alexandra M; Snider, Sarah E; Athamneh, Liqa N; Stein, Jeffrey S; Pope, Derek A | Pharmacology, biochemistry, and behavior. | 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, Jorge | Immunity. | 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 S | Neuron. | 2017 Aug 30; | 28858614 | |
| Single-cell profiling of dynamic cytokine secretion and the phenotype of immune cells. | An, Xingyue; Sendra, Victor G; Liadi, Ivan; Ramesh, Balakrishnan; Romain, Gabrielle; Haymaker, Cara; Martinez-Paniagua, Melisa; Lu, Yanbin; Radvanyi, Laszlo G; Roysam, Badrinath; Varadarajan, Navin | PloS one. | 2017; | 28837583 | |
| Dissociated and Reconstituted Cartilage Microparticles in Densified Collagen Induce Local hMSC Differentiation. | Novak, Tyler; Seelbinder, Benjamin; Twitchell, Celina M; Voytik-Harbin Prof, Sherry L; Neu Prof, Corey P | Advanced functional materials. | 2016 Aug 09; | 28824356 | |
| A magnetic micropore chip for rapid ( | Ko, Jina; Bhagwat, Neha; Yee, Stephanie S; Black, Taylor; Redlinger, Colleen; Romeo, Janae; O'Hara, Mark; Raj, Arjun; Carpenter, Erica L; Stanger, Ben Z; Issadore, David | Lab on a chip. | 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, Ambika | Change. | 2016; | 28804143 | |
| Acoustofluidic bacteria separation. | Li, Sixing; Ma, Fen; Bachman, Hunter; Cameron, Craig E; Zeng, Xiangqun; Huang, Tony Jun | Journal of micromechanics and microengineering : structures, devices, and systems. | 2017 Jan 01; | 28798539 | |
| High-NA open-top selective-plane illumination microscopy for biological imaging. | Mcgorty, Ryan; Xie, Dan; Huang, Bo | Optics express. | 2017 Jul 24; | 28789271 | |
| Neuronal cell-type classification: challenges, opportunities and the path forward. | Zeng, Hongkui; Sanes, Joshua R | Nature reviews. Neuroscience | 2017 Sep | 28775344 | |
| Single cell transcriptomics of noncoding RNAs and their cell-specificity. | Gawronski, Katerina A B; Kim, Junhyong | Wiley 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, Chantale | Clinical cancer research : an official journal of the American Association for Cancer Research. | 2017 Jul 28; | 28754817 | |
| Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry. | Das, Dipjyoti; Chatti, Veena; Emonet, Thierry; Holley, Scott A | Developmental cell. | 2017 07 24; | 28743003 | |
| A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. | Lake, Blue B; Codeluppi, Simone; Yung, Yun C; Gao, Derek; Chun, Jerold; Kharchenko, Peter V; Linnarsson, Sten; Zhang, Kun | Scientific reports. | 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 S | Nature biotechnology. | 2017 Aug; | 28714966 | |
| Unmassked: Single-Cell Profiling of Immune Cell Populations in Tumors. | Varadarajan, Navin | Molecular therapy : the journal of the American Society of Gene Therapy. | 2017 Aug 02; | 28684257 | |
| Tissue specific requirements for WNT11 in developing outflow tract and dorsal mesenchymal protrusion. | van Vliet, Patrick P; Lin, Lizhu; Boogerd, Cornelis J; Martin, James F; Andelfinger, Gregor; Grossfeld, Paul D; Evans, Sylvia M | Developmental biology. | 2017 09 01; | 28669819 | |
| A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve. | Caravaca, A S; Tsaava, T; Goldman, L; Silverman, H; Riggott, G; Chavan, S S; Bouton, C; Tracey, K J; Desimone, R; Boyden, E S; Sohal, H S; Olofsson, P S | Journal of neural engineering. | 2017 12; | 28628030 | |
| Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. | Shaffer, Sydney M; Dunagin, Margaret C; Torborg, Stefan R; Torre, Eduardo A; Emert, Benjamin; Krepler, Clemens; Beqiri, Marilda; Sproesser, Katrin; Brafford, Patricia A; Xiao, Min; Eggan, Elliott; Anastopoulos, Ioannis N; Vargas-Garcia, Cesar A; Singh, Abhyudai; Nathanson, Katherine L; Herlyn, Meenhard; Raj, Arjun | Nature. | ; | 28607484 | |
| Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. | Radford, Felix; Tyagi, Sanjay; Gennaro, Maria Laura; Pine, Richard; Bushkin, Yuri | Critical reviews in immunology. | 2016; | 28605344 | |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis, Ian A; Gupte, Rohit; Raj, Arjun; Rouhanifard, Sara H | Nature methods. | 2017 Jun 12; | 28604724 | |
| IgG Fc domains that bind C1q but not effector Fc? receptors delineate the importance of complement-mediated effector functions. | Lee, Chang-Han; Romain, Gabrielle; Yan, Wupeng; Watanabe, Makiko; Charab, Wissam; Todorova, Biliana; Lee, Jiwon; Triplett, Kendra; Donkor, Moses; Lungu, Oana I; Lux, Anja; Marshall, Nicholas; Lindorfer, Margaret A; Goff, Odile Richard-Le; Balbino, Bianca; Kang, Tae Hyun; Tanno, Hidetaka; Delidakis, George; Alford, Corrine; Taylor, Ronald P; Nimmerjahn, Falk; Varadarajan, Navin; Bruhns, Pierre; Zhang, Yan Jessie; Georgiou, George | Nature immunology. | 2017 Aug; | 28604720 | |
| Single image super-resolution via an iterative reproducing kernel Hilbert space method. | Deng, Liang-Jian; Guo, Weihong; Huang, Ting-Zhu | IEEE transactions on circuits and systems for video technology : a publication of the Circuits and Systems Society. | 2016 Nov; | 28603404 | |
| Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity. | McKinley, Eliot T; Sui, Yunxia; Al-Kofahi, Yousef; Millis, Bryan A; Tyska, Matthew J; Roland, Joseph T; Santamaria-Pang, Alberto; Ohland, Christina L; Jobin, Christian; Franklin, Jeffrey L; Lau, Ken S; Gerdes, Michael J; Coffey, Robert J | JCI insight. | 2017 Jun 02; | 28570279 | |
| A robot for high yield electrophysiology and morphology of single neurons in vivo. | Li, Lu; Ouellette, Benjamin; Stoy, William A; Garren, Emma J; Daigle, Tanya L; Forest, Craig R; Koch, Christof; Zeng, Hongkui | Nature communications. | 2017 Jun 01; | 28569837 | |
| Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain. | Singer, Annabelle C; Talei Franzesi, Giovanni; Kodandaramaiah, Suhasa B; Flores, Francisco J; Cohen, Jeremy D; Lee, Albert K; Börgers, Christoph; Forest, Craig R; Kopell, Nancy J; Boyden, Edward S | Journal of neurophysiology. | 2017 May 31; | 28566460 | |
| Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration. | Jayatilaka, Hasini; Tyle, Pranay; Chen, Jonathan J; Kwak, Minsuk; Ju, Julia; Kim, Hyun Ji; Lee, Jerry S H; Wu, Pei-Hsun; Gilkes, Daniele M; Fan, Rong; Wirtz, Denis | Nature communications. | 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, Julia | PloS 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 Consortium | Human 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 Laura | Nature protocols. | 2017 Jun; | 28518171 | |
| Visualizing Calcium Flux in Freely Moving Nematode Embryos. | Ardiel, Evan L; Kumar, Abhishek; Marbach, Joseph; Christensen, Ryan; Gupta, Rishi; Duncan, William; Daniels, Jonathan S; Stuurman, Nico; Colón-Ramos, Daniel; Shroff, Hari | Biophysical journal. | 2017 May 09; | 28494967 | |
| A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo. | Yang, Yu-Ping; Ma, Haiting; Starchenko, Alina; Huh, Won Jae; Li, Wei; Hickman, F Edward; Zhang, Qin; Franklin, Jeffrey L; Mortlock, Douglas P; Fuhrmann, Sabine; Carter, Bruce D; Ihrie, Rebecca A; Coffey, Robert J | Cell reports. | 2017 May 09; | 28494873 | |
| Development of an optimized synthetic Notch receptor as an in vivo cell-cell contact sensor. | He, Li; Huang, Jiuhong; Perrimon, Norbert | Proceedings of the National Academy of Sciences of the United States of America. | 2017 05 23; | 28490499 | |
| Assessment of Single Cell RNA-Seq Normalization Methods. | Ding, Bo; Zheng, Lina; Wang, Wei | G3 (Bethesda, Md.). | 2017 Jul 05; | 28468817 | |
| In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry: Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo. | Onjiko, Rosemary M; Portero, Erika P; Moody, Sally A; Nemes, Peter | Analytical chemistry. | 2017 Jul 05; | 28434226 | |
| Iterative expansion microscopy. | Chang, Jae-Byum; Chen, Fei; Yoon, Young-Gyu; Jung, Erica E; Babcock, Hazen; Kang, Jeong Seuk; Asano, Shoh; Suk, Ho-Jun; Pak, Nikita; Tillberg, Paul W; Wassie, Asmamaw T; Cai, Dawen; Boyden, Edward S | Nature methods. | 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 A | Stem 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 A | Stem cell reports. | 2017 Apr 11; | 28410642 | |
| High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. | D'Antonio, Matteo; Woodruff, Grace; Nathanson, Jason L; D'Antonio-Chronowska, Agnieszka; Arias, Angelo; Matsui, Hiroko; Williams, Roy; Herrera, Cheryl; Reyna, Sol M; Yeo, Gene W; Goldstein, Lawrence S B; Panopoulos, Athanasia D; Frazer, Kelly A | Stem cell reports. | 2017 Apr 04; | 28392217 | |
| iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. | Panopoulos, Athanasia D; D'Antonio, Matteo; Benaglio, Paola; Williams, Roy; Hashem, Sherin I; Schuldt, Bernhard M; DeBoever, Christopher; Arias, Angelo D; Garcia, Melvin; Nelson, Bradley C; Harismendy, Olivier; Jakubosky, David A; Donovan, Margaret K R; Greenwald, William W; Farnam, KathyJean; Cook, Megan; Borja, Victor; Miller, Carl A; Grinstein, Jonathan D; Drees, Frauke; Okubo, Jonathan; Diffenderfer, Kenneth E; Hishida, Yuriko; Modesto, Veronica; Dargitz, Carl T; Feiring, Rachel; Zhao, Chang; Aguirre, Aitor; McGarry, Thomas J; Matsui, Hiroko; Li, He; Reyna, Joaquin; Rao, Fangwen; O'Connor, Daniel T; Yeo, Gene W; Evans, Sylvia M; Chi, Neil C; Jepsen, Kristen; Nariai, Naoki; Müller, Franz-Josef; Goldstein, Lawrence S B; Izpisua Belmonte, Juan Carlos; Adler, Eric; Loring, Jeanne F; Berggren, W Travis; D'Antonio-Chronowska, Agnieszka; Smith, Erin N; Frazer, Kelly A | Stem cell reports. | 2017 Apr 03; | 28392216 | |
| 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 A | BMC 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 A | Cell 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 A | Cell stem cell. | 2017 Apr 06; | 28388429 | |
| Tracking Multiple Genomic Elements Using Correlative CRISPR Imaging and Sequential DNA FISH. | Guan, Juan; Liu, Harrison; Shi, Xiaoyu; Feng, Siyu; Huang, Bo | Biophysical journal. | 2017 Mar 28; | 28355536 | |
| 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 A | Proceedings 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, Rui | Journal 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 K | Nature methods. | 2017 Apr; | 28192419 | |
| Mechanisms of Cardiomyocyte Proliferation and Differentiation in Development and Regeneration. | Yester, Jessie Wettig; Kühn, Bernhard | Current cardiology reports. | 2017 Feb; | 28185170 | |
| Tumor evolution: Linear, branching, neutral or punctuated? | Davis, Alexander; Gao, Ruli; Navin, Nicholas | Biochimica 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 H | Cell 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, Peter | Genesis (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 Jun | Scientific reports. | 2017 Jan 16; | 28091583 | |
| Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. | Cutrale, Francesco; Trivedi, Vikas; Trinh, Le A; Chiu, Chi-Li; Choi, John M; Artiga, Marcela S; Fraser, Scott E | Nature methods. | 2017 02; | 28068315 | |
| Acoustic actuation of bioinspired microswimmers. | Kaynak, Murat; Ozcelik, Adem; Nourhani, Amir; Lammert, Paul E; Crespi, Vincent H; Huang, Tony Jun | Lab 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-Huei | Nature. | 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 B | Cell 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, Junhyong | BMC genomics. | 2016 Nov 24; | 27881084 | |
| Synthetic recording and in situ readout of lineage information in single cells. | Frieda, Kirsten L; Linton, James M; Hormoz, Sahand; Choi, Joonhyuk; Chow, Ke-Huan K; Singer, Zakary S; Budde, Mark W; Elowitz, Michael B; Cai, Long | Nature. | 2017 01 05; | 27869821 | |
| In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. | Shah, Sheel; Lubeck, Eric; Zhou, Wen; Cai, Long | Neuron. | 2016 Oct 19; | 27764670 | |
| Enhancing Graduate and Postdoctoral Education To Create a Sustainable Biomedical Workforce. | Fuhrmann, Cynthia N | Human 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 Jun | Lab 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 S | Science 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 R | Scientific 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 R | Precision 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, Hari | The Biological bulletin. | 2016 Aug; | 27638693 | |
| Surface Acoustic Waves Grant Superior Spatial Control of Cells Embedded in Hydrogel Fibers. | Lata, James P; Guo, Feng; Guo, Jinshan; Huang, Po-Hsun; Yang, Jian; Huang, Tony Jun | Advanced materials (Deerfield Beach, Fla.). | 2016 Oct; | 27571239 | |
| Noncommutative Biology: Sequential Regulation of Complex Networks. | Letsou, William; Cai, Long | PLoS computational biology. | 2016 08; | 27560383 | |
| 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 E | Nature 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, Jorge | Nature. | 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 Jun | Small (Weinheim an der Bergstrasse, Germany). | 2016 Oct; | 27515787 | |
| Observing Mitotic Division and Dynamics in a Live Zebrafish Embryo. | Percival, Stefanie M; Parant, John M | Journal of visualized experiments : JoVE. | 2016 07 15; | 27501381 | |
| 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 B | Nature 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 Jun | Lab 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 A | Developmental 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 A | Journal 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 A | Proceedings 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, Long | Development (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 A | Genes & 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, Kun | Science (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 Jun | Lab on a chip. | 2016 Jul 5; | 27327102 | |
| On-Chip Production of Size-Controllable Liquid Metal Microdroplets Using Acoustic Waves. | Tang, Shi-Yang; Ayan, Bugra; Nama, Nitesh; Bian, Yusheng; Lata, James P; Guo, Xiasheng; Huang, Tony Jun | Small (Weinheim an der Bergstrasse, Germany). | 2016 Jul; | 27309129 | |
| In Situ and In Vivo Molecular Analysis by Coherent Raman Scattering Microscopy. | Liao, Chien-Sheng; Cheng, Ji-Xin | Annual 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, Michelle | Journal of immunology (Baltimore, Md. : 1950). | 2016 Jul 15; | 27271569 | |
| Dense transcript profiling in single cells by image correlation decoding. | Coskun, Ahmet F; Cai, Long | Nature methods. | 2016 Aug; | 27271198 | |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons, Orsolya; Raj, Arjun | Molecular 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 J | Nature. | 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 N | Analytical chemistry. | 2016 Jun 21; | 27249533 | |
| Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers. | Cole, Russell H; Gartner, Zev J; Abate, Adam R | Journal 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, Guillem | Molecular imaging. | 2016; | 27175009 | |
| Approaches to Inactivate Genes in Zebrafish. | Parant, John M; Yeh, Jing-Ruey Joanna | Advances in experimental medicine and biology. | 2016; | 27165349 | |
| Investigation of micromixing by acoustically oscillated sharp-edges. | Nama, Nitesh; Huang, Po-Hsun; Huang, Tony Jun; Costanzo, Francesco | Biomicrofluidics. | 2016 Mar; | 27158292 | |
| Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action. | Silva, Elizabeth A; Des Jarlais, Christine; Lindstaedt, Bill; Rotman, Erik; Watkins, Elizabeth S | PLoS biology | 2016 May | e1002458 | 27152650 |
| Imaging Specific Genomic DNA in Living Cells. | Chen, Baohui; Guan, Juan; Huang, Bo | Annual 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 N | Analytical chemistry. | 2016 May 17; | 27110027 | |
| MMSET/WHSC1 enhances DNA damage repair leading to an increase in resistance to chemotherapeutic agents. | Shah, M Y; Martinez-Garcia, E; Phillip, J M; Chambliss, A B; Popovic, R; Ezponda, T; Small, E C; Will, C; Phillip, M P; Neri, P; Bahlis, N J; Wirtz, D; Licht, J D | Oncogene. | 2016 11 10; | 27109101 | |
| Monovar: single-nucleotide variant detection in single cells. | Zafar, Hamim; Wang, Yong; Nakhleh, Luay; Navin, Nicholas; Chen, Ken | Nature methods. | ; | 27088313 | |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA. | Molecular Cell | 2016 April 5 | V:62 P:1-11 | 27067601 |
| 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, Sébastien | Journal 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 P | Biochimica 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 Jun | Nature 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, Peter | The 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, Bo | Nature communications. | 2016; | 26988139 | |
| High resolution laser mass spectrometry bioimaging. | Murray, Kermit K; Seneviratne, Chinthaka A; Ghorai, Suman | Methods (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-Xin | The 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, Arjun | Genes & 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 S | Nature 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 J | Science (New York, N.Y.). | 2016 Feb 12; | 733-7 | 26912862 |
| 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 B | Science (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 Carlos | Nature 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 L | The Journal of neuroscience : the official journal of the Society for Neuroscience. | 2016 Feb 3; | 1730-46 | 26843653 |
| Correction to "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 C | Journal of the American Chemical Society | 2016 Feb 10 | 1723 | 26820231 |
| 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, Emil | Analytical 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 Jun | Proceedings 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 V | Nature methods. | 2016 Mar; | 241-4 | 26780092 |
| 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-Hsun | Laboratory 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 Ross | PloS 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 Bae | Pain. | 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 E | Nature 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, Bo | Nucleic 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, Hongkui | Nature 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 Jun | Small (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 Jun | Lab 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, T | Lab on a chip. | 2016 Jan 26; | 497-505 | 26686985 |
| Exploring Memory Representations with Activity-Based Genetics. | Mayford, Mark; Reijmers, Leon | Cold Spring Harbor perspectives in biology. | 2015 Dec 18; | 26684182 | |
| Evolution of cellular morpho-phenotypes in cancer metastasis. | Wu, Pei-Hsun; Phillip, Jude M; Khatau, Shyam B; Chen, Wei-Chiang; Stirman, Jeffrey; Rosseel, Sophie; Tschudi, Katherine; Van Patten, Joshua; Wong, Michael; Gupta, Sonal; Baras, Alexander S; Leek, Jeffrey T; Maitra, Anirban; Wirtz, Denis | Scientific reports. | 2015 Dec 17; | 26675084 | |
| 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 Laura | PloS one. | 2015; | 26658491 | |
| The Mechanobiology of Aging. | Phillip, Jude M; Aifuwa, Ivie; Walston, Jeremy; Wirtz, Denis | Annual 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, Hari | eLife. | 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, Junhyong | BioEssays : 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, Tania | Journal 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 Albert | Developmental biology. | 2016 Jan 1; | 261-71 | 26577869 |
| Acceleration of reaction in charged microdroplets. | Lee, Jae Kyoo; Banerjee, Shibdas; Nam, Hong Gil; Zare, Richard N | Quarterly 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, Denis | Oncotarget. | 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 S | Molecular systems biology. | 2015 Oct; | 835 | 26519361 |
| Modeling developmental neuropsychiatric disorders with iPSC technology: challenges and opportunities. | Young-Pearse, Tracy L; Morrow, Eric M | Current opinion in neurobiology. | 2016 Feb; | 66-73 | 26517284 |
| 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, Denis | Oncotarget. | 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 Jun | Lab on a chip. | 2015 Dec 21; | 4517-23 | 26507411 |
| 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, Zhirong | Nucleic 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, Denis | Oncotarget. | 2015 Oct 13; | 30516-31 | 26483365 |
| Induced pluripotent stem cells as a discovery tool for Alzheimer?s disease. | Sullivan, Sarah E; Young-Pearse, Tracy L | Brain 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, T | Lab on a chip. | 2015 Dec 7; | 4441-50 | 26456240 |
| 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. Chalkley | The FASEB Journal | 2015 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, Arjun | Genome research. | 2015 Oct; | 1466-72 | 26430156 |
| 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, Denis | Scientific reports. | 2015; | 14580 | 26423227 |
| Acousto-plasmofluidics: Acoustic modulation of surface plasmon resonance in microfluidic systems. | Ahmed, Daniel; Peng, Xiaolei; Ozcelik, Adem; Zheng, Yuebing; Huang, Tony Jun | AIP advances. | 2015 Sep; | 26421224 | |
| Cellular Deconstruction: Finding Meaning in Individual Cell Variation. | Eberwine, James; Kim, Junhyong | Trends in cell biology. | 2015 Oct; | 569-78 | 26410403 |
| Functional enrichment by direct plasmid recovery after fluorescence activated cell sorting. | Ramesh, Balakrishnan; Frei, Christopher S; Cirino, Patrick C; Varadarajan, Navin | BioTechniques. | 2015 Sep; | 157-61 | 26345509 |
| 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 R | Biomicrofluidics. | 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 Jun | Lab on a chip. | 2015 Nov 7; | 4166-76 | 26338516 |
| 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, Denis | Oncotarget. | 2015 Oct 20; | 32634-45 | 26334095 |
| 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 Jun | Analytical 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 N | Cancer research. | 2015 Sep 1; | 3505-18 | 26330164 |
| The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo. | Du, Zhuo; Santella, Anthony; He, Fei; Shah, Pavak K; Kamikawa, Yuko; Bao, Zhirong | Developmental cell. | 2015 Sep 14; | 592-607 | 26321128 |
| 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 Jun | Lab on a chip. | 2015 Oct 7; | 3870-9 | 26289231 |
| 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 A | Biological psychiatry. | 2016 May 15; | 26248536 | |
| Imaging Tumor Acidity: pH-Low Insertion Peptide Probe for Optoacoustic Tomography. | Reshetnyak, Yana K | Clinical 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 Jun | Scientific reports. | 2015; | 12572 | 26223474 |
| Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis. | McMillen, Patrick; Holley, Scott A | Current opinion in cell biology. | 2015 Oct; | 48-53 | 26189063 |
| 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, Oliver | Development (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, Yuebing | Small (Weinheim an der Bergstrasse, Germany). | 2015 Sep 16; | 4423-44 | 26140612 |
| Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis. | Gonzalez, Jacob; Qi, Hongying; Liu, Na; Lin, Haifan | Cell reports. | 2015 Jul 7; | 150-61 | 26119740 |
| 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, Arjun | Lab on a chip. | 2015 Aug 7; | 3170-82 | 26113495 |
| 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-Ming | Cancer cell. | 2015 Jul 13; | 82-96 | 26096845 |
| 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 C | Developmental 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, Badrinath | Bioinformatics (Oxford, England). | 2015 Oct 1; | 3189-97 | 26059718 |
| 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, Junhyong | Genome biology. | 2015; | 122 | 26056000 |
| 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 C | Developmental cell. | 2015 Jun 22; | 729-36 | 26051539 |
| 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, Zhirong | BMC bioinformatics. | 2015; | 189 | 26051157 |
| 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 A | Genome biology. | 2015; | 120 | 26047807 |
| 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 M | Disease models & mechanisms. | 2015 Aug 1; | 941-55 | 26044958 |
| Compact and modular multicolour fluorescence detector for droplet microfluidics. | Cole, Russell H; de Lange, Niek; Gartner, Zev J; Abate, Adam R | Lab on a chip. | 2015 Jul 7; | 2754-8 | 26032595 |
| 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 C | Journal of the American Chemical Society. | 2015 Jun 24; | 7881-8 | 26022213 |
| 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 Jun | Lab on a chip. | 2015 Jun 21; | 2700-9 | 26001199 |
| 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 W | Cell. | 2015 May 21; | 1187-201 | 26000487 |
| Rapid and Localized Mechanical Stimulation and Adhesion Assay: TRPM7 Involvement in Calcium Signaling and Cell Adhesion. | Nishitani, Wagner Shin; Alencar, Adriano Mesquita; Wang, Yingxiao | PloS one. | 2015; | e0126440 | 25946314 |
| Tuning noise in gene expression. | Tyagi, Sanjay | Molecular systems biology. | 2015 May; | 805 | 25943344 |
| Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. | Onjiko, Rosemary M; Moody, Sally A; Nemes, Peter | Proceedings of the National Academy of Sciences of the United States of America. | 2015 May 26; | 6545-50 | 25941375 |
| Transforming training to reflect the workforce. | Mathur, Ambika; Meyers, Frederick J; Chalkley, Roger; O'Brien, Theresa C; Fuhrmann, Cynthia N | Science translational medicine. | 2015 Apr 29; | 285ed4 | 25925677 |
| Closed-loop, ultraprecise, automated craniotomies. | Pak, Nikita; Siegle, Joshua H; Kinney, Justin P; Denman, Daniel J; Blanche, Timothy J; Boyden, Edward S | Journal of neurophysiology. | 2015 Jun 1; | 3943-53 | 25855700 |
| SNES: single nucleus exome sequencing. | Leung, Marco L; Wang, Yong; Waters, Jill; Navin, Nicholas E | Genome biology. | 2015; | 55 | 25853327 |
| 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 Jun | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Apr 21; | 4970-5 | 25848039 |
| 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, Bernhard | Science translational medicine. | 2015 Apr 1; | 281ra45 | 25834111 |
| 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; | 2343-50 | 25826782 |
| The tissue mechanics of vertebrate body elongation and segmentation. | McMillen, Patrick; Holley, Scott A | Current opinion in genetics & development. | 2015 Jun; | 106-11 | 25796079 |
| Microdroplet fusion mass spectrometry for fast reaction kinetics. | Lee, Jae Kyoo; Kim, Samuel; Nam, Hong Gil; Zare, Richard N | Proceedings 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 Belmon | Circulation. | 2015 Apr 7; | 1278-90 | 25739401 |
| 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 E | Genome medicine. | 2015; | 6 | 25729435 |
| Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model. | Wu, Pei-Hsun; Giri, Anjil; Wirtz, Denis | Nature protocols. | 2015 Mar; | 517-27 | 25719270 |
| 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, Wei | Bioinformatics (Oxford, England). | 2015 Jul 1; | 2225-7 | 25717193 |
| 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, Navin | Cancer immunology research. | 2015 May; | 473-82 | 25711538 |
| 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 S | Cancer biology & therapy. | 2015; | 430-7 | 25701047 |
| Cytoskeletal tension induces the polarized architecture of the nucleus. | Kim, Dong-Hwee; Wirtz, Denis | Biomaterials. | 2015 Apr; | 161-72 | 25701041 |
| 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 M | Nature protocols. | 2015 Mar; | 442-58 | 25675209 |
| 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 C | Science signaling. | 2015 Feb 10; | ra16 | 25670204 |
| 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, Yingxiao | eLife. | 2015; | e04876 | 25667984 |
| 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 Jun | Small (Weinheim an der Bergstrasse, Germany). | 2015 Jun; | 2733-7 | 25641793 |
| Controlling lipid micelle stability using oligonucleotide headgroups. | Wilner, Samantha E; Sparks, Samuel E; Cowburn, David; Girvin, Mark E; Levy, Matthew | Journal of the American Chemical Society. | 2015 Feb 18; | 2171-4 | 25634639 |
| Advanced targeted nanomedicine. | Arachchige, Mohan C M; Reshetnyak, Yana K; Andreev, Oleg A | Journal of biotechnology. | 2015 May 20; | 88-97 | 25615945 |
| Optical clearing in dense connective tissues to visualize cellular connectivity in situ. | Calve, Sarah; Ready, Andrew; Huppenbauer, Christopher; Main, Russell; Neu, Corey P | PloS one. | 2015; | e0116662 | 25581165 |
| 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 J | Cell stem cell. | 2015 Jan 8; | 88-101 | 25575081 |
| Single-neuron isolation for RNA analysis using pipette capture and laser capture microdissection. | Lovatt, Ditte; Bell, Thomas; Eberwine, James | Cold Spring Harbor protocols. | 2015 Jan; | pdb.prot072439 | 25561613 |
| 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 Carlos | The Journal of biological chemistry. | 2015 Feb 27; | 5661-72 | 25555917 |
| 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 Jun | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Jan 6; | 43-8 | 25535339 |
| E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. | Du, Zhuo; He, Fei; Yu, Zidong; Bowerman, Bruce; Bao, Zhirong | Developmental biology. | 2015 Feb 15; | 267-79 | 25523393 |
| 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, J | Cell stem cell. | 2014 Nov 6; | 589-604 | 25517466 |
| 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, Wia | Molecular and cellular biology. | 2015 Feb; | 675-87 | 25512606 |
| 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, Sanjay | Journal of immunology (Baltimore, Md. : 1950). | 2015 Jan 15; | 836-41 | 25505292 |
| High-throughput genome editing and phenotyping facilitated by high resolution melting curve analysis. | Thomas, Holly R; Percival, Stefanie M; Yoder, Bradley K; Parant, John M | PloS one. | 2014; | e114632 | 25503746 |
| Single-cell variation leads to population invariance in NF-*B signaling dynamics. | Hughey, Jacob J; Gutschow, Miriam V; Bajar, Bryce T; Covert, Markus W | Molecular biology of the cell. | 2015 Feb 1; | 583-90 | 25473117 |
| RE: stem cells loaded with multimechanistic oncolytic herpes simplex virus variants for brain tumor therapy. | Krause, Marie N; Sancho-Martinez, Ignacio; Izpisua Belmonte, Juan Carlos | Journal of the National Cancer Institute. | 2015 Jan; | 368 | 25473104 |
| Switching from protease-independent to protease-dependent cancer cell invasion. | He, Lijuan; Wirtz, Denis | Biophysical journal. | 2014 Dec 2; | 2484-5 | 25468324 |
| Reprogramming by lineage specifiers: blurring the lines between pluripotency and differentiation. | Sancho-Martinez, Ignacio; Ocampo, Alejandro; Izpisua Belmonte, Juan Carlos | Current opinion in genetics & development. | 2014 Oct; | 57-63 | 25461451 |
| Optical clearing in collagen- and proteoglycan-rich osteochondral tissues. | Neu, C P; Novak, T; Gilliland, K F; Marshall, P; Calve, S | Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society. | 2015 Mar; | 405-13 | 25454370 |
| 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 R | Journal of neurophysiology. | 2015 Feb 15; | 1275-82 | 25429119 |
| Single-cell tracking with PET using a novel trajectory reconstruction algorithm. | Lee, Keum Sil; Kim, Tae Jin; Pratx, Guillem | IEEE transactions on medical imaging. | 2015 Apr; | 994-1003 | 25423651 |
| 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 Jun | Analytical chemistry. | 2014 Dec 2; | 11803-10 | 25405550 |
| Modeling and validation of autoinducer-mediated bacterial gene expression in microfluidic environments. | Austin, Caitlin M; Stoy, William; Su, Peter; Harber, Marie C; Bardill, J Patrick; Hammer, Brian K; Forest, Craig R | Biomicrofluidics. | 2014 May; | 25379076 | |
| 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 Jun | Lab on a chip. | 2015 Jan 7; | 331-8 | 25372273 |
| Antisense RNA amplification for target assessment of total mRNA from a single cell. | Morris, Jacqueline; Bell, Thomas J; Buckley, Peter T; Eberwine, James H | Cold Spring Harbor protocols. | 2014 Nov 03; | 25368303 | |
| Prolonged mechanical stretch initiates intracellular calcium oscillations in human mesenchymal stem cells. | Kim, Tae-Jin; Sun, Jie; Lu, Shaoying; Qi, Ying-Xin; Wang, Yingxiao | PloS one. | 2014; | e109378 | 25329052 |
| Direct reactivation of a coherent neocortical memory of context. | Cowansage, Kiriana K; Shuman, Tristan; Dillingham, Blythe C; Chang, Allene; Golshani, Peyman; Mayford, Mark | Neuron. | 2014 Oct 22; | 25308330 | |
| Cardiac regeneration based on mechanisms of cardiomyocyte proliferation and differentiation. | Senyo, Samuel E; Lee, Richard T; Kuhn, Bernhard | Stem cell research. | 2014 Nov; | 532-41 | 25306390 |
| 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, Hari | Nature protocols. | 2014 Nov; | 2555-73 | 25299154 |
| 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, Rui | PLoS biology. | 2014 Oct; | e1001964 | 25291190 |
| Tip-enhanced laser ablation sample transfer for biomolecule mass spectrometry. | Ghorai, Suman; Seneviratne, Chinthaka A; Murray, Kermit K | Journal of the American Society for Mass Spectrometry. | 2015 Jan; | 63-70 | 25287125 |
| Functional imaging in OA: role of imaging in the evaluation of tissue biomechanics. | Neu, C P | Osteoarthritis and cartilage / OARS, Osteoarthritis Research Society. | 2014 Oct; | 1349-59 | 25278049 |
| Muscling up the heart: a preadolescent cardiomyocyte proliferation contributes to heart growth. | Zhang, Cheng-Hai; Kuhn, Bernhard | Circulation research. | 2014 Sep 26; | 690-2 | 25258401 |
| Irises: A practical tool for image-based analysis of cellular DNA content. | Vogel, Julia L Moore; Michaelson, David; Santella, Anthony; Hubbard, E Jane Albert; Bao, Zhirong | Worm. | 2014; | 25254149 | |
| 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, Navin | Blood. | 2014 Nov 20; | 3241-9 | 25232058 |
| Cancer genomics: one cell at a time. | Navin, Nicholas E | Genome biology. | 2014; | 452 | 25222669 |
| 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, Ju | Nature communications. | 2014 Sep 12; | 25215520 | |
| Sorting out where fibroblasts come from. | Moore-Morris, Thomas; Tallquist, Michelle D; Evans, Sylvia M | Circulation research. | 2014 Sep 12; | 602-4 | 25214570 |
| 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 Carlos | Stem cells (Dayton, Ohio). | 2014 Nov; | 2923-38 | 25175072 |
| 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 Mieko | PLoS computational biology. | 2014 Aug; | e1003807 | 25165818 |
| Spatial and temporal organization of signaling pathways. | Housden, Benjamin E; Perrimon, Norbert | Trends in biochemical sciences. | 2014 Oct; | 457-64 | 25155749 |
| Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing. | Yang, Bin; Treweek, Jennifer B; Kulkarni, Rajan P; Deverman, Benjamin E; Chen, Chun-Kan; Lubeck, Eric; Shah, Sheel; Cai, Long; Gradinaru, Viviana | Cell | 2014 Aug 14 | 945-58 | 25088144 |
| Single-cell imaging of mechanotransduction in endothelial cells. | Lu, Shaoying; Wang, Yingxiao | Progress in molecular biology and translational science. | 2014; | 25081613 | |
| Clonal evolution in breast cancer revealed by single nucleus genome sequencing. | Wang, Yong; Waters, Jill; Leung, Marco L; Unruh, Anna; Roh, Whijae; Shi, Xiuqing; Chen, Ken; Scheet, Paul; Vattathil, Selina; Liang, Han; Multani, Asha; Zhang, Hong; Zhao, Rui; Michor, Franziska; Meric-Bernstam, Funda; Navin, Nicholas E | Nature | 2014 Aug 14 | 155-60 | 25079324 |
| Dynamic heterogeneity and DNA methylation in embryonic stem cells. | Singer, Zakary S; Yong, John; Tischler, Julia; Hackett, Jamie A; Altinok, Alphan; Surani, M Azim; Cai, Long; Elowitz, Michael B | Molecular cell. | 2014 Jul 17; | 319-31 | 25038413 |
| Targeting breast tumors with pH (low) insertion peptides. | Adochite, Ramona-Cosmina; Moshnikova, Anna; Carlin, Sean D; Guerrieri, Renato A; Andreev, Oleg A; Lewis, Jason S; Reshetnyak, Yana K | Molecular pharmaceutics. | 2014 Aug 4; | 2896-905 | 25004202 |
| Regeneration: making muscle from hPSCs. | Zhu, Xiping; Fu, Lina; Yi, Fei; Liu, Guang-Hui; Ocampo, Alejandro; Qu, Jing; Izpisua Belmonte, Juan Carlos | Cell research. | 2014 Oct; | 1159-61 | 25001388 |
| 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; | 4330 | 24999918 |
| Noninvasive optical inhibition with a red-shifted microbial rhodopsin. | Chuong, Amy S; Miri, Mitra L; Busskamp, Volker; Matthews, Gillian A C; Acker, Leah C; Sorensen, Andreas T; Young, Andrew; Klapoetke, Nathan C; Henninger, Mike A; Kodandaramaiah, Suhasa B; Ogawa, Masaaki; Ramanlal, Shreshtha B; Bandler, Rachel C; Allen, Br | Nature neuroscience | 2014 Aug | 1123-9 | 24997763 |
| Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. | Suzuki, Keiichiro; Yu, Chang; Qu, Jing; Li, Mo; Yao, Xiaotian; Yuan, Tingting; Goebl, April; Tang, Senwei; Ren, Ruotong; Aizawa, Emi; Zhang, Fan; Xu, Xiuling; Soligalla, Rupa Devi; Chen, Feng; Kim, Jessica; Kim, Na Young; Liao, Hsin-Kai; Benner, Chris; Es | Cell stem cell. | 2014 Jul 3; | 31-6 | 24996168 |
| The regulation of *-adrenergic receptor-mediated PKA activation by substrate stiffness via microtubule dynamics in human MSCs. | Kim, Tae-Jin; Sun, Jie; Lu, Shaoying; Zhang, Jin; Wang, Yingxiao | Biomaterials | 2014 Jun 24 | NULL | 24973298 |
| Comparison of intervertebral disc displacements measured under applied loading with MRI at 3.0 T and 9.4 T. | Chan, Deva D; Gossett, Paull C; Butz, Kent D; Nauman, Eric A; Neu, Corey P | Journal of biomechanics. | 2014 Aug 22; | 2801-6 | 24968943 |
| A semi-local neighborhood-based framework for probabilistic cell lineage tracing. | Santella, Anthony; Du, Zhuo; Bao, Zhirong | BMC bioinformatics. | 2014; | 217 | 24964866 |
| High-sensitivity measurements of multiple kinase activities in live single cells. | Regot, Sergi; Hughey, Jacob J; Bajar, Bryce T; Carrasco, Silvia; Covert, Markus W | Cell | 2014 Jun 19 | 1724-34 | 24949979 |
| Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. | Moore-Morris, Thomas; Guimaraes-Camboa, Nuno; Banerjee, Indroneal; Zambon, Alexander C; Kisseleva, Tatiana; Velayoudon, Aurelie; Stallcup, William B; Gu, Yusu; Dalton, Nancy D; Cedenilla, Marta; Gomez-Amaro, Rafael; Zhou, Bin; Brenner, David A; Peterson, | The Journal of clinical investigation | 2014 Jul 1 | 2921-34 | 24937432 |
| The 3D Genome in Transcriptional Regulation and Pluripotency. | Gorkin, David U; Leung, Danny; Ren, Bing | Cell stem cell | 2014 Jun 5 | 762-775 | 24905166 |
| Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. | Prevedel, Robert; Yoon, Young-Gyu; Hoffmann, Maximilian; Pak, Nikita; Wetzstein, Gordon; Kato, Saul; Schrodel, Tina; Raskar, Ramesh; Zimmer, Manuel; Boyden, Edward S; Vaziri, Alipasha | Nature methods | 2014 May 18 | NULL | 24836920 |
| Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2. | Xu, Shuwa; Tyagi, Sanjay; Schedl, Paul | PLoS genetics | 2014 May | e1004380 | 24830287 |
| Hypoxia and the extracellular matrix: drivers of tumour metastasis. | Gilkes, Daniele M; Semenza, Gregg L; Wirtz, Denis | Nature reviews. Cancer. | 2014 Jun; | 430-9 | 24827502 |
| Genetic characteristics and pathogenic mechanisms of periodontal pathogens. | Amano, A; Chen, C; Honma, K; Li, C; Settem, R P; Sharma, A | Advances in dental research | 2014 May | 15-22 | 24736700 |
| Water permeation drives tumor cell migration in confined microenvironments. | Stroka, Kimberly M; Jiang, Hongyuan; Chen, Shih-Hsun; Tong, Ziqiu; Wirtz, Denis; Sun, Sean X; Konstantopoulos, Konstantinos | Cell | 2014 Apr 24 | 611-23 | 24726433 |
| Atomic force microscopy-coupled microcoils for cellular-scale nuclear magnetic resonance spectroscopy. | Mousoulis, Charilaos; Maleki, Teimour; Ziaie, Babak; Neu, Corey P | Applied physics letters. | 2013 Apr 08; | 24719493 | |
| Universal artificial antigen presenting cells to selectively propagate T cells expressing chimeric antigen receptor independent of specificity. | Rushworth, David; Jena, Bipulendu; Olivares, Simon; Maiti, Sourindra; Briggs, Neima; Somanchi, Srinivas; Dai, Jianliang; Lee, Dean; Cooper, Laurence J N | Journal of immunotherapy (Hagerstown, Md. : 1997) | 2014 May | 204-13 | 24714354 |
| Mathematical approaches to modeling development and reprogramming. | Morris, Rob; Sancho-Martinez, Ignacio; Sharpee, Tatyana O; Izpisua Belmonte, Juan Carlos | Proceedings of the National Academy of Sciences of the United States of America. | 2014 Apr 8; | 5076-82 | 24706886 |
| Local mechanical response of cells to the controlled rotation of magnetic nanorods. | Castillo, Matias; Ebensperger, Roberto; Wirtz, Denis; Walczak, Magdalena; Hurtado, Daniel E; Celedon, Alfredo | Journal of biomedical materials research. Part B, Applied biomaterials. | 2014 Nov; | 1779-85 | 24700696 |
| Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. | Doupé, David P; Perrimon, Norbert | Science signaling. | 2014 Apr 1; | re1 | 24692594 |
| Excess PLAC8 promotes an unconventional ERK2-dependent EMT in colon cancer. | Li, Cunxi; Ma, Haiting; Wang, Yang; Cao, Zheng; Graves-Deal, Ramona; Powell, Anne E; Starchenko, Alina; Ayers, Gregory D; Washington, Mary Kay; Kamath, Vidya; Desai, Keyur; Gerdes, Michael J; Solnica-Krezel, Lila; Coffey, Robert J | The Journal of clinical investigation | 2014 Apr 1 | NULL | 24691442 |
| Single-cell in situ RNA profiling by sequential hybridization. | Lubeck, Eric; Coskun, Ahmet F; Zhiyentayev, Timur; Ahmad, Mubhij; Cai, Long | Nature methods | 2014 Apr | 360-1 | 24681720 |
| Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ. | Markey, Fatu Badiane; Ruezinsky, William; Tyagi, Sanjay; Batish, Mona | PloS one | 2014 | e93488 | 24675777 |
| Tight coupling between nucleus and cell migration through the perinuclear actin cap. | Kim, Dong-Hwee; Cho, Sangkyun; Wirtz, Denis | Journal of cell science | 2014 Jun 1 | 2528-41 | 24639463 |
| Three-dimensional cell migration does not follow a random walk. | Wu, Pei-Hsun; Giri, Anjil; Sun, Sean X; Wirtz, Denis | Proceedings of the National Academy of Sciences of the United States of America | 2014 Mar 18 | 3949-54 | 24594603 |
| Targeted ablation of nesprin 1 and nesprin 2 from murine myocardium results in cardiomyopathy, altered nuclear morphology and inhibition of the biomechanical gene response. | Banerjee, Indroneal; Zhang, Jianlin; Moore-Morris, Thomas; Pfeiffer, Emily; Buchholz, Kyle S; Liu, Ao; Ouyang, Kunfu; Stroud, Matthew J; Gerace, Larry; Evans, Sylvia M; McCulloch, Andrew; Chen, Ju | PLoS genetics. | 2014 Feb; | e1004114 | 24586179 |
| 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 21 | 1360-3 | 24578530 |
| Nuclear envelope in nuclear positioning and cell migration. | Razafsky, David; Wirtz, Denis; Hodzic, Didier | Advances in experimental medicine and biology. | 2014; | 471-90 | 24563361 |
| The cytolethal distending toxin of Aggregatibacter actinomycetemcomitans inhibits macrophage phagocytosis and subverts cytokine production. | Ando-Suguimoto, Ellen Sayuri; da Silva, Maike Paulino; Kawamoto, Dione; Chen, Casey; DiRienzo, Joseph M; Mayer, Marcia Pinto Alves | Cytokine | 2014 Mar | 46-53 | 24548424 |
| A markerless protocol for genetic analysis of Aggregatibacter actinomycetemcomitans. | Cheng, Ya-An; Jee, Jason; Hsu, Genie; Huang, Yanyan; Chen, Casey; Lin, Chun-Pin | Journal of the Formosan Medical Association = Taiwan yi zhi | 2014 Feb | 114-23 | 24530245 |
| Tumor evolution in response to chemotherapy: phenotype versus genotype. | Navin, Nicholas E | Cell reports | 2014 Feb 13 | 417-9 | 24529750 |
| Probing Endoplasmic Reticulum Dynamics using Fluorescence Imaging and Photobleaching Techniques. | Costantini, Lindsey; Snapp, Erik | Current protocols in cell biology / editorial board, Juan S. Bonifacino ... [et al.] | 2013 | 21.7.1-21.7.29 | 24510787 |
| Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. | Gu, Ying; Liu, Guang-Hui; Plongthongkum, Nongluk; Benner, Christopher; Yi, Fei; Qu, Jing; Suzuki, Keiichiro; Yang, Jiping; Zhang, Weiqi; Li, Mo; Montserrat, Nuria; Crespo, Isaac; Del Sol, Antonio; Esteban, Concepcion Rodriguez; Zhang, Kun; Izpisua Belmont | Protein & cell. | 2014 Jan; | 59-68 | 24474197 |
| Single-cell technologies for monitoring immune systems. | Chattopadhyay, Pratip K; Gierahn, Todd M; Roederer, Mario; Love, J Christopher | Nature immunology | 2014 Feb | 128-35 | 24448570 |
| De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. | Du, Zhuo; Santella, Anthony; He, Fei; Tiongson, Michael; Bao, Zhirong | Cell | 2014 Jan 16 | 359-72 | 24439388 |
| Crossword: A Fully Automated Algorithm for the Segmentation and Quality Control of Protein Microarray Images. | Gierahn, Todd M; Loginov, Denis; Love, J Christopher | Journal of proteome research | 2014 Jan 24 | NULL | 24417579 |
| Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. | Lovatt, Ditte; Ruble, Brittani K; Lee, Jaehee; Dueck, Hannah; Kim, Tae Kyung; Fisher, Stephen; Francis, Chantal; Spaethling, Jennifer M; Wolf, John A; Grady, M Sean; Ulyanova, Alexandra V; Yeldell, Sean B; Griepenburg, Julianne C; Buckley, Peter T; Kim, J | Nature methods | 2014 Feb | 190-6 | 24412976 |
| The role of mechanical tension on lipid raft dependent PDGF-induced TRPC6 activation. | Lei, Lei; Lu, Shaoying; Wang, Yi; Kim, Taejin; Mehta, Dolly; Wang, Yingxiao | Biomaterials | 2014 Mar | 2868-77 | 24397990 |
| A cut above the rest: targeted genome editing technologies in human pluripotent stem cells. | Li, Mo; Suzuki, Keiichiro; Kim, Na Young; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos | The Journal of biological chemistry. | 2014 Feb 21; | 4594-9 | 24362028 |
| pH dependent transfer of nano-pores into membrane of cancer cells to induce apoptosis. | Wijesinghe, Dayanjali; Arachchige, Mohan C M; Lu, Andrew; Reshetnyak, Yana K; Andreev, Oleg A | Scientific reports | 2013 | 3560 | 24356337 |
| Hypoxia-inducible factors mediate coordinated RhoA-ROCK1 expression and signaling in breast cancer cells. | Gilkes, Daniele M; Xiang, Lisha; Lee, Sun Joo; Chaturvedi, Pallavi; Hubbi, Maimon E; Wirtz, Denis; Semenza, Gregg L | Proceedings of the National Academy of Sciences of the United States of America. | 2014 Jan 21; | E384-93 | 24324133 |
| Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins. | Seong, Jihye; Tajik, Arash; Sun, Jie; Guan, Jun-Lin; Humphries, Martin J; Craig, Susan E; Shekaran, Asha; Garcia, Andres J; Lu, Shaoying; Lin, Michael Z; Wang, Ning; Wang, Yingxiao | Proceedings of the National Academy of Sciences of the United States of America | 2013 Nov 26 | 19372-7 | 24222685 |
| Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. | Gole, Jeff; Gore, Athurva; Richards, Andrew; Chiu, Yu-Jui; Fung, Ho-Lim; Bushman, Diane; Chiang, Hsin-I; Chun, Jerold; Lo, Yu-Hwa; Zhang, Kun | Nature biotechnology | 2013 Dec | 1126-32 | 24213699 |
| PIWI proteins are essential for early Drosophila embryogenesis. | Mani, Sneha Ramesh; Megosh, Heather; Lin, Haifan | Developmental biology | 2013 Oct 31 | NULL | 24184635 |
| PIWI proteins are essential for early Drosophila embryogenesis. | Mani, Sneha Ramesh; Megosh, Heather; Lin, Haifan | Developmental biology | 2014 Jan 15 | 340-9 | 24184635 |
| Human heart rate: heritability of resting and stress values in twin pairs, and influence of genetic variation in the adrenergic pathway at a microribonucleic acid (microrna) motif in the 3'-UTR of cytochrome b561 [corrected]. | Zhang, Kuixing; Deacon, Dekker C; Rao, Fangwen; Schork, Andrew J; Fung, Maple M; Waalen, Jill; Schork, Nicholas J; Nievergelt, Caroline M; Chi, Neil C; O'Connor, Daniel T | Journal of the American College of Cardiology. | 2014 Feb 4; | 358-68 | 24140660 |
| Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model. | Lyon, Robert C; Mezzano, Valeria; Wright, Adam T; Pfeiffer, Emily; Chuang, Joyce; Banares, Katherine; Castaneda, Allan; Ouyang, Kunfu; Cui, Li; Contu, Riccardo; Gu, Yusu; Evans, Sylvia M; Omens, Jeffrey H; Peterson, Kirk L; McCulloch, Andrew D; Sheikh, Fa | Human molecular genetics. | 2014 Mar 1; | 1134-50 | 24108106 |
| Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. | Wu, Yicong; Wawrzusin, Peter; Senseney, Justin; Fischer, Robert S; Christensen, Ryan; Santella, Anthony; York, Andrew G; Winter, Peter W; Waterman, Clare M; Bao, Zhirong; Colon-Ramos, Daniel A; McAuliffe, Matthew; Shroff, Hari | Nature biotechnology | 2013 Nov | 1032-8 | 24108093 |
| Genetically encoded fluorescent biosensors for live-cell imaging of MT1-MMP protease activity. | Ouyang, Mingxing; Lu, Shaoying; Wang, Yingxiao | Methods in molecular biology (Clifton, N.J.). | 2014; | 24052388 | |
| Barriers to transmission of transcriptional noise in a c-fos c-jun pathway. | Shah, Khyati; Tyagi, Sanjay | Molecular systems biology | 2013 | 687 | 24022005 |
| Tracking immune cells in vivo using magnetic resonance imaging. | Ahrens, Eric T; Bulte, Jeff W M | Nature reviews. Immunology. | 2013 Oct; | 24013185 | |
| Epigenetic alterations in acute kidney injury. | Bomsztyk, Karol; Denisenko, Oleg | Seminars in nephrology | 2013 Jul | 327-40 | 24011575 |
| Morphological effects on expression of growth differentiation factor 15 (GDF15), a marker of metastasis. | Aw Yong, Koh Meng; Zeng, Yu; Vindivich, Donald; Phillip, Jude M; Wu, Pei-Hsun; Wirtz, Denis; Getzenberg, Robert H | Journal of cellular physiology. | 2014 Mar; | 362-73 | 23996089 |
| BreakTrans: uncovering the genomic architecture of gene fusions. | Chen, Ken; Navin, Nicholas E; Wang, Yong; Schmidt, Heather K; Wallis, John W; Niu, Beifang; Fan, Xian; Zhao, Hao; McLellan, Michael D; Hoadley, Katherine A; Mardis, Elaine R; Ley, Timothy J; Perou, Charles M; Wilson, Richard K; Ding, Li | Genome biology. | 2013; | R87 | 23972288 |
| FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans. | Minor, Paul J; He, Ting-Fang; Sohn, Chang Ho; Asthagiri, Anand R; Sternberg, Paul W | Development (Cambridge, England) | 2013 Sep | 3882-91 | 23946444 |
| Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-? gene in acute kidney injury. | Bomsztyk, Karol; Flanagin, Steve; Mar, Daniel; Mikula, Michal; Johnson, Ali; Zager, Richard; Denisenko, Oleg | PloS one. | 2013; | 23936185 | |
| Efficient generation of human iPSCs by a synthetic self-replicative RNA. | Yoshioka, Naohisa; Gros, Edwige; Li, Hai-Ri; Kumar, Shantanu; Deacon, Dekker C; Maron, Cornelia; Muotri, Alysson R; Chi, Neil C; Fu, Xiang-Dong; Yu, Benjamin D; Dowdy, Steven F | Cell stem cell. | 2013 Aug 1; | 246-54 | 23910086 |
| Genetic analysis of mate discrimination in Drosophila simulans. | Chu, Y; Yang, E; Schinaman, J M; Chahda, J S; Sousa-Neves, R | Evolution; international journal of organic evolution | 2013 Aug | 2335-47 | 23888855 |
| Single cell spectroscopy: Noninvasive measures of small-scale structure and function. | Mousoulis, Charilaos; Xu, Xin; Reiter, David A; Neu, Corey P | Methods (San Diego, Calif.) | 2013 Jul 22 | NULL | 23886910 |
| Statistical analysis of molecular signal recording. | Glaser, Joshua I; Zamft, Bradley M; Marblestone, Adam H; Moffitt, Jeffrey R; Tyo, Keith; Boyden, Edward S; Church, George; Kording, Konrad P | PLoS computational biology | 2013 Jul | e1003145 | 23874187 |
| Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor. | Peng, Tien; Tian, Ying; Boogerd, Cornelis J; Lu, Min Min; Kadzik, Rachel S; Stewart, Kathleen M; Evans, Sylvia M; Morrisey, Edward E | Nature | 2013 Aug 29 | 589-92 | 23873040 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie, Wei; Ren, Bing | Science (New York, N.Y.) | 2013 Jul 19 | 245-7 | 23869010 |
| Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis. | Moore, Julia L; Du, Zhuo; Bao, Zhirong | Development (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 R | Annals of the New York Academy of Sciences | 2013 Dec | 63-71 | 23841584 |
| In vivo robotics: the automation of neuroscience and other intact-system biological fields. | Kodandaramaiah, Suhasa B; Boyden, Edward S; Forest, Craig R | Annals of the New York Academy of Sciences | 2013 Jul 10 | NULL | 23841584 |
| Detection and isolation of auto-reactive human antibodies from primary B cells. | Sendra, Victor G; Lie, Anthony; Romain, Gabrielle; Agarwal, Sandeep K; Varadarajan, Navin | Methods (San Diego, Calif.) | 2013 Jun 26 | NULL | 23811296 |
| Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2. | Sun, Jie; Lu, Shaoying; Ouyang, Mingxing; Lin, Li-Jung; Zhuo, Yue; Liu, Bo; Chien, Shu; Neel, Benjamin G; Wang, Yingxiao | Nature communications | 2013 Jun 24 | 2037 | 23792876 |
| HCN4 dynamically marks the first heart field and conduction system precursors. | Liang, Xingqun; Wang, Gang; Lin, Lizhu; Lowe, Jennifer; Zhang, Qingquan; Bu, Lei; Chen, Yihan; Chen, Ju; Sun, Yunfu; Evans, Sylvia M | Circulation research | 2013 Aug 2 | 399-407 | 23743334 |
| Manufacture of clinical-grade CD19-specific T cells stably expressing chimeric antigen receptor using Sleeping Beauty system and artificial antigen presenting cells. | Singh, Harjeet; Figliola, Matthew J; Dawson, Margaret J; Olivares, Simon; Zhang, Ling; Yang, Ge; Maiti, Sourindra; Manuri, Pallavi; Senyukov, Vladimir; Jena, Bipulendu; Kebriaei, Partow; Champlin, Richard E; Huls, Helen; Cooper, Laurence J N | PloS one | 2013 | e64138 | 23741305 |
| Single-cell transcriptomics for drug target discovery. | Spaethling, Jennifer M; Eberwine, James H | Current opinion in pharmacology. | 2013 Oct; | 786-90 | 23725882 |
| Epigenomic analysis of multilineage differentiation of human embryonic stem cells. | Xie, Wei; Schultz, Matthew D; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W; Tian, Shulan; Hawkins, R David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; N | Cell | 2013 May 23 | 1134-48 | 23664764 |
| Mechanotransduction at focal adhesions: from physiology to cancer development. | Seong, Jihye; Wang, Ning; Wang, Yingxiao | Journal of cellular and molecular medicine | 2013 May | 597-604 | 23601032 |
| Variation in the dorsal gradient distribution is a source for modified scaling of germ layers in Drosophila. | Chahda, Juan Sebastian; Sousa-Neves, Rui; Mizutani, Claudia Mieko | Current biology : CB | 2013 Apr 22 | 710-6 | 23583556 |
| Simultaneously defining cell phenotypes, cell cycle, and chromatin modifications at single-cell resolution. | Chambliss, Allison B; Wu, Pei-Hsun; Chen, Wei-Chiang; Sun, Sean X; Wirtz, Denis | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2013 Jul | 2667-76 | 23538711 |
| Interstitial friction greatly impacts membrane mechanics. | Wirtz, Denis | Biophysical journal | 2013 Mar 19 | 1217-8 | 23528079 |
| Nanotools for neuroscience and brain activity mapping. | Alivisatos, A Paul; Andrews, Anne M; Boyden, Edward S; Chun, Miyoung; Church, George M; Deisseroth, Karl; Donoghue, John P; Fraser, Scott E; Lippincott-Schwartz, Jennifer; Looger, Loren L; Masmanidis, Sotiris; McEuen, Paul L; Nurmikko, Arto V; Park, Hongk | ACS nano | 2013 Mar 26 | 1850-66 | 23514423 |
| The antagonistic roles of PDGF and integrin ýývýý3 in regulating ROS production at focal adhesions. | Lin, Li-Jung; Grimme, Jill M; Sun, Jie; Lu, Shaoying; Gai, Lisa; Cropek, Donald M; Wang, Yingxiao | Biomaterials | 2013 May | 3807-15 | 23465490 |
| Dimensional control of cancer cell migration. | Konstantopoulos, Konstantinos; Wu, Pei-Hsun; Wirtz, Denis | Biophysical journal | 2013 Jan 22 | 279-80 | 23442847 |
| Quantitative high-throughput single-cell cytotoxicity assay for T cells. | Liadi, Ivan; Roszik, Jason; Romain, Gabrielle; Cooper, Laurence J N; Varadarajan, Navin | Journal of visualized experiments : JoVE | 2013 | e50058 | 23407457 |
| Thymosin *4 is not required for embryonic viability or vascular development. | Banerjee, Indroneal; Moore Morris, Thomas; Evans, Sylvia M; Chen, Ju | Circulation research. | 2013 Feb 1; | e25-8 | 23371905 |
| Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming. | Ruiz, Sergio; Gore, Athurva; Li, Zhe; Panopoulos, Athanasia D; Montserrat, Nuria; Fung, Ho-Lim; Giorgetti, Alessandra; Bilic, Josipa; Batchelder, Erika M; Zaehres, Holm; Scholer, Hans R; Zhang, Kun; Izpisua Belmonte, Juan Carlos | Nature communications. | 2013; | 1382 | 23340422 |
| High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. | Lu, Yao; Chen, Jonathan J; Mu, Luye; Xue, Qiong; Wu, Yu; Wu, Pei-Hsun; Li, Jie; Vortmeyer, Alexander O; Miller-Jensen, Kathryn; Wirtz, Denis; Fan, Rong | Analytical chemistry | 2013 Feb 19 | 2548-56 | 23339603 |
| Functional interplay between the cell cycle and cell phenotypes. | Chen, Wei-Chiang; Wu, Pei-Hsun; Phillip, Jude M; Khatau, Shyam B; Choi, Jae Min; Dallas, Matthew R; Konstantopoulos, Konstantinos; Sun, Sean X; Lee, Jerry S H; Hodzic, Didier; Wirtz, Denis | Integrative biology : quantitative biosciences from nano to macro | 2013 Mar | 523-34 | 23319145 |
| Single-cell and population NF-ýýB dynamic responses depend on lipopolysaccharide preparation. | Gutschow, Miriam V; Hughey, Jacob J; Ruggero, Nicholas A; Bajar, Bryce T; Valle, Sean D; Covert, Markus W | PloS one | 2013 | e53222 | 23301045 |
| Focal adhesion size uniquely predicts cell migration. | Kim, Dong-Hwee; Wirtz, Denis | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2013 Apr | 1351-61 | 23254340 |
| FRET imaging of calcium signaling in live cells in the microenvironment. | Qian, Tongcheng; Lu, Shaoying; Ma, Hongwei; Fang, Jing; Zhong, Wenxuan; Wang, Yingxiao | Integrative biology : quantitative biosciences from nano to macro | 2013 Jan 28 | 431-8 | 23250282 |
| Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. | Yamanaka, Yvonne J; Szeto, Gregory L; Gierahn, Todd M; Forcier, Talitha L; Benedict, Kelly F; Brefo, Mavis S N; Lauffenburger, Douglas A; Irvine, Darrell J; Love, J Christopher | Analytical chemistry | 2012 Dec 18 | 10531-6 | 23205933 |
| Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans. | Huang, Y; Kittichotirat, W; Mayer, M P A; Hall, R; Bumgarner, R; Chen, C | Molecular oral microbiology | 2013 Feb | 17-Jan | 23194436 |
| Beating in a dish: new hopes for cardiomyocyte regeneration. | Gu, Ying; Yi, Fei; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos | Cell research. | 2013 Mar; | 314-6 | 23184058 |
| Evolutionary conservation of Nkx2.5 autoregulation in the second heart field. | Clark, Christopher D; Zhang, Boding; Lee, Benjamin; Evans, Samuel I; Lassar, Andrew B; Lee, Kyu-Ho | Developmental biology. | 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 E | Journal of bacteriology | 2013 Jan | 156-66 | 23104812 |
| Generation of a drug-inducible reporter system to study cell reprogramming in human cells. | Ruiz, Sergio; Panopoulos, Athanasia D; Montserrat, Nuria; Multon, Marie-Christine; Daury, Aurelie; Rocher, Corinne; Spanakis, Emmanuel; Batchelder, Erika M; Orsini, Cecile; Deleuze, Jean-Francois; Izpisua Belmonte, Juan Carlos | The Journal of biological chemistry. | 2012 Nov 23; | 40767-78 | 23019325 |
| Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins. | Ramesh, Balakrishnan; Sendra, Victor G; Cirino, Patrick C; Varadarajan, Navin | The Journal of biological chemistry. | 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 Carlos | Proceedings 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, Y | Journal of microscopy | 2012 Oct | 77-89 | 22971220 |
| The dawn of angiogenesis modeling: regenerating vasculature from human pluripotent stem cells. | Yi, Fei; Qu, Jing; Liu, Guang-Hui; Izpisua Belmonte, Juan Carlos | Cell research. | 2013 Jan; | 5-Mar | 22964710 |
| Elimination of dendritic spines with long-term memory is specific to active circuits. | Sanders, Jeff; Cowansage, Kiriana; Baumgartel, Karsten; Mayford, Mark | The Journal of neuroscience : the official journal of the Society for Neuroscience | 2012 Sep 5 | 12570-8 | 22956846 |
| Single-cell systems biology by super-resolution imaging and combinatorial labeling. | Lubeck, Eric; Cai, Long | Nature methods | 2012 Jul | 743-8 | 22660740 |
| Genome sequence of a serotype b non-JP2 aggregatibacter actinomycetemcomitans strain, ANH9381, from a periodontally healthy individual. | Chen, Casey; Kittichotirat, Weerayuth; Chen, Weizhen; Downey, Jennifer S; Bumgarner, Roger | Journal of bacteriology | 2012 Apr | 1837 | 22408240 |
| Cut and paste: restoring cellular function by gene correction. | Liu, Guang-Hui; Sancho-Martinez, Ignacio; Izpisua Belmonte, Juan Carlos | Cell 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 Belm | Cell research. | 2012 Jan; | 168-77 | 22064701 |
| TACE/ADAM-17 phosphorylation by PKC-epsilon mediates premalignant changes in tobacco smoke-exposed lung cells. | Lemjabbar-Alaoui, Hassan; Sidhu, Sukhvinder S; Mengistab, Aklilu; Gallup, Marianne; Basbaum, Carol | PloS one. | 2011 Mar 15; | 21423656 | |
| Distinction between two populations of islet-1-positive cells in hearts of different murine strains. | Khattar, Patricia; Friedrich, Felix W; Bonne, Gisèle; Carrier, Lucie; Eschenhagen, Thomas; Evans, Sylvia M; Schwartz, Ketty; Fiszman, Marc Y; Vilquin, Jean-Thomas | Stem cells and development. | 2011 06; | 20942609 | |
| Molecular mechanisms of experience-dependent plasticity in visual cortex. | Tropea, Daniela; Van Wart, Audra; Sur, Mriganka | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 2009 Feb 12 | 18977729 |