Single Cell Analysis Program (SCAP)
Single Cell Analysis Program (SCAP)
Program Publications
Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. | Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K | Nature biotechnology | 24213699 | Nat Biotechnol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24213699 |
| Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. | Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K | Nature biotechnology | 29227469 | Nat Biotechnol | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29227469 |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu Y, Zhang K | Nature reviews. Nephrology | 32221477 | Nat Rev Nephrol | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32221477 |
| Assessment of Single Cell RNA-Seq Normalization Methods. | Ding B, Zheng L, Wang W | G3 (Bethesda, Md.) | 28468817 | G3 (Bethesda) | 2017 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/28468817 |
| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K | Nature protocols | 34650278 | Nat Protoc | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34650278 |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | bioRxiv : the preprint server for biology | 37645998 | bioRxiv | 2023 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/37645998 |
| Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. | Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV | Nature methods | 26780092 | Nat Methods | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26780092 |
| Assessing characteristics of RNA amplification methods for single cell RNA sequencing. | Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, Nguyen JD, Salathia N, Shallcross J, Souaiaia T, Spaethling JM, Walker CP, Wang J, Wang K, Wang W, Wildberg A, Zheng L, Chow RH, Eberwine J, Knowles JA, Zhang K, Kim J | BMC genomics | 27881084 | BMC Genomics | 2016 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/27881084 |
| Normalization and noise reduction for single cell RNA-seq experiments. | Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, Wildberg A, Wang W | Bioinformatics (Oxford, England) | 25717193 | Bioinformatics | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/25717193 |
| Highly multiplexed subcellular RNA sequencing in situ. | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM | Science (New York, N.Y.) | 24578530 | Science | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/24578530 |
| Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. | Wu Y, Tamayo P, Zhang K | Cell systems | 30528274 | Cell Syst | 2018 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/30528274 |
| Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | Nature communications | 38509069 | Nat Commun | 2024 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/38509069 |
| Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM | Nature protocols | 25675209 | Nat Protoc | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25675209 |
| Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. | Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K | Science (New York, N.Y.) | 27339989 | Science | 2016 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/27339989 |
| Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. | Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B | Nature neuroscience | 29434377 | Nat Neurosci | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29434377 |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen S, Lake BB, Zhang K | Nature biotechnology | 31611697 | Nat Biotechnol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31611697 |
| A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. | Lake BB, Codeluppi S, Yung YC, Gao D, Chun J, Kharchenko PV, Linnarsson S, Zhang K | Scientific reports | 28729663 | Sci Rep | 2017 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/28729663 |
| Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. | Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J | Genome biology | 26056000 | Genome Biol | 2015 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/26056000 |
| Disparity in the quality of COVID-19 data reporting across India. | Vasudevan V, Gnanasekaran A, Sankar V, Vasudevan SA, Zou J | BMC public health | 34167499 | BMC Public Health | 2021 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/34167499 |
| Ensuring that biomedical AI benefits diverse populations. | Zou J, Schiebinger L | EBioMedicine | 33962897 | EBioMedicine | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33962897 |
| How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. | Wu E, Wu K, Daneshjou R, Ouyang D, Ho DE, Zou J | Nature medicine | 33820998 | Nat Med | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33820998 |
| Data valuation for medical imaging using Shapley value and application to a large-scale chest X-ray dataset. | Tang S, Ghorbani A, Yamashita R, Rehman S, Dunnmon JA, Zou J, Rubin DL | Scientific reports | 33863957 | Sci Rep | 2021 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/33863957 |
| Leveraging physiology and artificial intelligence to deliver advancements in health care. | Zhang A, Wu Z, Wu E, Wu M, Snyder MP, Zou J, Wu JC | Physiological reviews | 37104717 | Physiol Rev | 2023 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/37104717 |
| GPT detectors are biased against non-native English writers. | Liang W, Yuksekgonul M, Mao Y, Wu E, Zou J | Patterns (New York, N.Y.) | 37521038 | Patterns (N Y) | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37521038 |
| Cardiac regeneration based on mechanisms of cardiomyocyte proliferation and differentiation. | Senyo SE, Lee RT, Kühn B | Stem cell research | 25306390 | Stem Cell Res | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25306390 |
| Single-neuron isolation for RNA analysis using pipette capture and laser capture microdissection. | Lovatt D, Bell T, Eberwine J | Cold Spring Harbor protocols | 25561613 | Cold Spring Harb Protoc | 2015 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/25561613 |
| Single cell transcriptomics of noncoding RNAs and their cell-specificity. | Gawronski KAB, Kim J | Wiley interdisciplinary reviews. RNA | 28762653 | Wiley Interdiscip Rev RNA | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28762653 |
| Mechanisms of Cardiomyocyte Proliferation and Differentiation in Development and Regeneration. | Yester JW, Kühn B | Current cardiology reports | 28185170 | Curr Cardiol Rep | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28185170 |
| Cellular Deconstruction: Finding Meaning in Individual Cell Variation. | Eberwine J, Kim J | Trends in cell biology | 26410403 | Trends Cell Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26410403 |
| Integrating spatial gene expression and breast tumour morphology via deep learning. | He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J, Lundeberg J, Zou J | Nature biomedical engineering | 32572199 | Nat Biomed Eng | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32572199 |
| CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. | Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J | Nature communications | 37963886 | Nat Commun | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/37963886 |
| High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury. | Jeong H, Na YJ, Lee K, Kim YH, Lee Y, Kang M, Jiang BC, Yeom YI, Wu LJ, Gao YJ, Kim J, Oh SB | Pain | 26761385 | Pain | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26761385 |
| Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. | Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, Sul JY, Dmochowski IJ, Eberwine J | Nature methods | 24412976 | Nat Methods | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24412976 |
| Comprehensive analysis of 2.4 million patent-to-research citations maps the biomedical innovation and translation landscape. | Manjunath A, Li H, Song S, Zhang Z, Liu S, Kahrobai N, Gowda A, Seffens A, Zou J, Kumar I | Nature biotechnology | 34113042 | Nat Biotechnol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34113042 |
| Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. | Liu H, Zhang CH, Ammanamanchi N, Suresh S, Lewarchik C, Rao K, Uys GM, Han L, Abrial M, Yimlamai D, Ganapathy B, Guillermier C, Chen N, Khaladkar M, Spaethling J, Eberwine JH, Kim J, Walsh S, Choudhury S, Little K, Francis K, Sharma M, Viegas M, Bais A, Kostka D, Ding J, Bar-Joseph Z, Wu Y, Yechoor V, Moulik M, Johnson J, Weinberg J, Reyes-Múgica M, Steinhauser ML, Kühn B | Science translational medicine | 31597755 | Sci Transl Med | 2019 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/31597755 |
| Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. | Middleton SA, Eberwine J, Kim J | BMC biology | 30678683 | BMC Biol | 2019 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/30678683 |
| Shifting machine learning for healthcare from development to deployment and from models to data. | Zhang A, Xing L, Zou J, Wu JC | Nature biomedical engineering | 35788685 | Nat Biomed Eng | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35788685 |
| Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing. | Morris J, Na YJ, Zhu H, Lee JH, Giang H, Ulyanova AV, Baltuch GH, Brem S, Chen HI, Kung DK, Lucas TH, O'Rourke DM, Wolf JA, Grady MS, Sul JY, Kim J, Eberwine J | Cell reports | 29212019 | Cell Rep | 2017 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/29212019 |
| Antisense RNA amplification for target assessment of total mRNA from a single cell. | Morris J, Bell TJ, Buckley PT, Eberwine JH | Cold Spring Harbor protocols | 25368303 | Cold Spring Harb Protoc | 2014 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/25368303 |
| Muscling up the heart: a preadolescent cardiomyocyte proliferation contributes to heart growth. | Zhang CH, Kühn B | Circulation research | 25258401 | Circ Res | 2014 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/25258401 |
| Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. | Dueck H, Eberwine J, Kim J | BioEssays : news and reviews in molecular, cellular and developmental biology | 26625861 | Bioessays | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26625861 |
| Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics. | Spaethling JM, Na YJ, Lee J, Ulyanova AV, Baltuch GH, Bell TJ, Brem S, Chen HI, Dueck H, Fisher SA, Garcia MP, Khaladkar M, Kung DK, Lucas TH Jr, O'Rourke DM, Stefanik D, Wang J, Wolf JA, Bartfai T, Grady MS, Sul JY, Kim J, Eberwine JH | Cell reports | 28099855 | Cell Rep | 2017 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/28099855 |
| BABEL enables cross-modality translation between multiomic profiles at single-cell resolution. | Wu KE, Yost KE, Chang HY, Zou J | Proceedings of the National Academy of Sciences of the United States of America | 33827925 | Proc Natl Acad Sci U S A | 2021 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/33827925 |
| Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms: A Scoping Review. | Daneshjou R, Smith MP, Sun MD, Rotemberg V, Zou J | JAMA dermatology | 34550305 | JAMA Dermatol | 2021 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/34550305 |
| PIVOT: platform for interactive analysis and visualization of transcriptomics data. | Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J | BMC bioinformatics | 29304726 | BMC Bioinformatics | 2018 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/29304726 |
| RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. | Wu KE, Fazal FM, Parker KR, Zou J, Chang HY | Cell systems | 32673562 | Cell Syst | 2020 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/32673562 |
| DynaMorph: self-supervised learning of morphodynamic states of live cells. | Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB | Molecular biology of the cell | 35138913 | Mol Biol Cell | 2022 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/35138913 |
| The successes and future prospects of the linear antisense RNA amplification methodology. | Li J, Eberwine J | Nature protocols | 29599441 | Nat Protoc | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29599441 |
| GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT. | Chen Y, Zou J | bioRxiv : the preprint server for biology | 37905130 | bioRxiv | 2024 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/37905130 |
| Alveolar epithelial cell processing of nanoparticles activates autophagy and lysosomal exocytosis. | Sipos A, Kim KJ, Chow RH, Flodby P, Borok Z, Crandall ED | American journal of physiology. Lung cellular and molecular physiology | 29722567 | Am J Physiol Lung Cell Mol Physiol | 2018 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/29722567 |
| Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues. | Lin MY, Wang YL, Wu WL, Wolseley V, Tsai MT, Radic V, Thornton ME, Grubbs BH, Chow RH, Huang IC | Scientific reports | 29093521 | Sci Rep | 2017 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/29093521 |
| Altered adult neurogenesis and gliogenesis in patients with mesial temporal lobe epilepsy. | Ammothumkandy A, Ravina K, Wolseley V, Tartt AN, Yu PN, Corona L, Zhang N, Nune G, Kalayjian L, Mann JJ, Rosoklija GB, Arango V, Dwork AJ, Lee B, Smith JAD, Song D, Berger TW, Heck C, Chow RH, Boldrini M, Liu CY, Russin JJ, Bonaguidi MA | Nature neuroscience | 35383330 | Nat Neurosci | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35383330 |
| Direct measurement of bipolar cell responses to electrical stimulation in wholemount mouse retina. | Walston ST, Chow RH, Weiland JD | Journal of neural engineering | 29513646 | J Neural Eng | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29513646 |
| Human adult neurogenesis loss corresponds with cognitive decline during epilepsy progression. | Ammothumkandy A, Corona L, Ravina K, Wolseley V, Nelson J, Atai N, Abedi A, Jimenez N, Armacost M, D'Orazio LM, Zuverza-Chavarria V, Cayce A, McCleary C, Nune G, Kalayjian L, Lee DJ, Lee B, Chow RH, Heck C, Russin JJ, Liu CY, Smith JAD, Bonaguidi MA | Cell stem cell | 39642885 | Cell Stem Cell | 2025 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39642885 |
| Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp. | Kim JMH, Camarena A, Walker C, Lin MY, Wolseley V, Souaiaia T, Thornton M, Grubbs B, Chow RH, Evgrafov OV, Knowles JA | Scientific reports | 32029778 | Sci Rep | 2020 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/32029778 |
| Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model. | Lyon RC, Mezzano V, Wright AT, Pfeiffer E, Chuang J, Banares K, Castaneda A, Ouyang K, Cui L, Contu R, Gu Y, Evans SM, Omens JH, Peterson KL, McCulloch AD, Sheikh F | Human molecular genetics | 24108106 | Hum Mol Genet | 2014 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24108106 |
| 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 K, Deacon DC, Rao F, Schork AJ, Fung MM, Waalen J, Schork NJ, Nievergelt CM, Chi NC, O'Connor DT | Journal of the American College of Cardiology | 24140660 | J Am Coll Cardiol | 2014 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/24140660 |
| Regeneration: making muscle from hPSCs. | Zhu X, Fu L, Yi F, Liu GH, Ocampo A, Qu J, Izpisua Belmonte JC | Cell research | 25001388 | Cell Res | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25001388 |
| Mathematical approaches to modeling development and reprogramming. | Morris R, Sancho-Martinez I, Sharpee TO, Izpisua Belmonte JC | Proceedings of the National Academy of Sciences of the United States of America | 24706886 | Proc Natl Acad Sci U S A | 2014 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/24706886 |
| Modelling Fanconi anemia pathogenesis and therapeutics using integration-free patient-derived iPSCs. | Liu GH, Suzuki K, Li M, Qu J, Montserrat N, Tarantino C, Gu Y, Yi F, Xu X, Zhang W, Ruiz S, Plongthongkum N, Zhang K, Masuda S, Nivet E, Tsunekawa Y, Soligalla RD, Goebl A, Aizawa E, Kim NY, Kim J, Dubova I, Li Y, Ren R, Benner C, Del Sol A, Bueren J, Trujillo JP, Surralles J, Cappelli E, Dufour C, Esteban CR, Belmonte JCI | Nature communications | 24999918 | Nat Commun | 2014 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/24999918 |
| Purging and isolating pluripotent cells, "sweet" dreams become true? | Sancho-Martinez I, Nivet E, Izpisua Belmonte JC | Cell research | 22025252 | Cell Res | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22025252 |
| Conversion of human fibroblasts into monocyte-like progenitor cells. | Pulecio J, Nivet E, Sancho-Martinez I, Vitaloni M, Guenechea G, Xia Y, Kurian L, Dubova I, Bueren J, Laricchia-Robbio L, Belmonte JCI | Stem cells (Dayton, Ohio) | 25175072 | Stem Cells | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25175072 |
| Loss of IP3R-dependent Ca2+ signalling in thymocytes leads to aberrant development and acute lymphoblastic leukemia. | Ouyang K, Leandro Gomez-Amaro R, Stachura DL, Tang H, Peng X, Fang X, Traver D, Evans SM, Chen J | Nature communications | 25215520 | Nat Commun | 2014 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/25215520 |
| Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling. | Nariai N, Greenwald WW, DeBoever C, Li H, Frazer KA | Genetics | 29074555 | Genetics | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29074555 |
| In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). | D'Antonio-Chronowska A, D'Antonio M, Frazer KA | Bio-protocol | 33659414 | Bio Protoc | 2020 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/33659414 |
| Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. | D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA | eLife | 31746734 | Elife | 2019 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/31746734 |
| Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. | Kurian L, Aguirre A, Sancho-Martinez I, Benner C, Hishida T, Nguyen TB, Reddy P, Nivet E, Krause MN, Nelles DA, Esteban CR, Campistol JM, Yeo GW, Belmonte JCI | Circulation | 25739401 | Circulation | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25739401 |
| Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. | Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA | BMC bioinformatics | 28388874 | BMC Bioinformatics | 2017 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/28388874 |
| High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells. | D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, Frazer KA | Stem cell reports | 28410643 | Stem Cell Reports | 2017 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/28410643 |
| Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. | Moore-Morris T, Guimarães-Camboa N, Banerjee I, Zambon AC, Kisseleva T, Velayoudon A, Stallcup WB, Gu Y, Dalton ND, Cedenilla M, Gomez-Amaro R, Zhou B, Brenner DA, Peterson KL, Chen J, Evans SM | The Journal of clinical investigation | 24937432 | J Clin Invest | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24937432 |
| Enhancer release and retargeting activates disease-susceptibility genes. | Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG | Nature | 34040254 | Nature | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34040254 |
| In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. | D'Antonio M, Nguyen JP, Arthur TD, Matsui H, Donovan MKR, D'Antonio-Chronowska A, Frazer KA | PLoS computational biology | 35226669 | PLoS Comput Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35226669 |
| Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. | D'Antonio M, Nguyen JP, Arthur TD, iPSCORE Consortium, Matsui H, D'Antonio-Chronowska A, Frazer KA | Nature communications | 36854752 | Nat Commun | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36854752 |
| Reprogramming by lineage specifiers: blurring the lines between pluripotency and differentiation. | Sancho-Martinez I, Ocampo A, Izpisua Belmonte JC | Current opinion in genetics & development | 25461451 | Curr Opin Genet Dev | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25461451 |
| RE: stem cells loaded with multimechanistic oncolytic herpes simplex virus variants for brain tumor therapy. | Krause MN, Sancho-Martinez I, Izpisua Belmonte JC | Journal of the National Cancer Institute | 25473104 | J Natl Cancer Inst | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25473104 |
| In vivo activation of a conserved microRNA program induces mammalian heart regeneration. | Aguirre A, Montserrat N, Zacchigna S, Nivet E, Hishida T, Krause MN, Kurian L, Ocampo A, Vazquez-Ferrer E, Rodriguez-Esteban C, Kumar S, Moresco JJ, Yates JR 3rd, Campistol JM, Sancho-Martinez I, Giacca M, Izpisua Belmonte JC | Cell stem cell | 25517466 | Cell Stem Cell | 2014 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/25517466 |
| Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. | Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D'Antonio-Chronowska A, Berggren WT, Izpisua Belmonte JC, Frazer KA | Cell stem cell | 28388429 | Cell Stem Cell | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28388429 |
| Sorting out where fibroblasts come from. | Moore-Morris T, Tallquist MD, Evans SM | Circulation research | 25214570 | Circ Res | 2014 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/25214570 |
| Efficient delivery and functional expression of transfected modified mRNA in human embryonic stem cell-derived retinal pigmented epithelial cells. | Hansson ML, Albert S, González Somermeyer L, Peco R, Mejía-Ramírez E, Montserrat N, Izpisua Belmonte JC | The Journal of biological chemistry | 25555917 | J Biol Chem | 2015 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/25555917 |
| Establishment of human iPSC-based models for the study and targeting of glioma initiating cells. | Sancho-Martinez I, Nivet E, Xia Y, Hishida T, Aguirre A, Ocampo A, Ma L, Morey R, Krause MN, Zembrzycki A, Ansorge O, Vazquez-Ferrer E, Dubova I, Reddy P, Lam D, Hishida Y, Wu MZ, Esteban CR, O'Leary D, Wahl GM, Verma IM, Laurent LC, Izpisua Belmonte JC | Nature communications | 26899176 | Nat Commun | 2016 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/26899176 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie W, Ren B | Science (New York, N.Y.) | 23869010 | Science | 2013 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/23869010 |
| Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. | Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC | Protein & cell | 24474197 | Protein Cell | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24474197 |
| Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming. | Ruiz S, Gore A, Li Z, Panopoulos AD, Montserrat N, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Schöler HR, Zhang K, Izpisua Belmonte JC | Nature communications | 23340422 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23340422 |
| Evolutionary conservation of Nkx2.5 autoregulation in the second heart field. | Clark CD, Zhang B, Lee B, Evans SI, Lassar AB, Lee KH | Developmental biology | 23165293 | Dev Biol | 2013 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/23165293 |
| Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. | Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA | Stem cell research | 32442913 | Stem Cell Res | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32442913 |
| Unveiling Complexity and Multipotentiality of Early Heart Fields. | Zhang Q, Carlin D, Zhu F, Cattaneo P, Ideker T, Evans SM, Bloomekatz J, Chi NC | Circulation research | 34162224 | Circ Res | 2021 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/34162224 |
| Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics. | Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE, HipSci Consortium, iPSCORE consortium, Undiagnosed Diseases Network, PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O | Nature genetics | 33664507 | Nat Genet | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33664507 |
| Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits. | Benaglio P, D'Antonio-Chronowska A, Ma W, Yang F, Young Greenwald WW, Donovan MKR, DeBoever C, Li H, Drees F, Singhal S, Matsui H, van Setten J, Sotoodehnia N, Gaulton KJ, Smith EN, D'Antonio M, Rosenfeld MG, Frazer KA | Nature genetics | 31570892 | Nat Genet | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31570892 |
| Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. | Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK | Developmental cell | 37848026 | Dev Cell | 2023 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/37848026 |
| Human Variant in the Cardiac Troponin I Switch Domain Causes Diastolic Dysfunction in a Novel Mouse Model. | Silver E, Duran JM, Gunes BB, Fenwick AJ, Maisel S, Wang TM, Manso AM, Cruz MS, Gu Y, Fong J, Shathaya A, Chen C, Soto-Hermida A, Feng W, Cho Y, Bogomolovas J, Gelow JM, Masri A, Frazer KA, Ross RS, Chen J, Makarewich CA, Cammarato A, McCulloch AD, Bushway P, Adler ED | Journal of the American Heart Association | 41195779 | J Am Heart Assoc | 2025 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/41195779 |
| 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. | Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG, Frazer KA | Nature | 21307941 | Nature | 2011 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/21307941 |
| Cut and paste: restoring cellular function by gene correction. | Liu GH, Sancho-Martinez I, Izpisua Belmonte JC | Cell research | 22143565 | Cell Res | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22143565 |
| Distinction between two populations of islet-1-positive cells in hearts of different murine strains. | Khattar P, Friedrich FW, Bonne G, Carrier L, Eschenhagen T, Evans SM, Schwartz K, Fiszman MY, Vilquin JT | Stem cells and development | 20942609 | Stem Cells Dev | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20942609 |
| Generation of a drug-inducible reporter system to study cell reprogramming in human cells. | Ruiz S, Panopoulos AD, Montserrat N, Multon MC, Daury A, Rocher C, Spanakis E, Batchelder EM, Orsini C, Deleuze JF, Izpisua Belmonte JC | The Journal of biological chemistry | 23019325 | J Biol Chem | 2012 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/23019325 |
| iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. | Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA | Stem cell reports | 28410642 | Stem Cell Reports | 2017 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/28410642 |
| The 3D genome in transcriptional regulation and pluripotency. | Gorkin DU, Leung D, Ren B | Cell stem cell | 24905166 | Cell Stem Cell | 2014 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/24905166 |
| A cut above the rest: targeted genome editing technologies in human pluripotent stem cells. | Li M, Suzuki K, Kim NY, Liu GH, Izpisua Belmonte JC | The Journal of biological chemistry | 24362028 | J Biol Chem | 2014 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/24362028 |
| Efficient generation of human iPSCs by a synthetic self-replicative RNA. | Yoshioka N, Gros E, Li HR, Kumar S, Deacon DC, Maron C, Muotri AR, Chi NC, Fu XD, Yu BD, Dowdy SF | Cell stem cell | 23910086 | Cell Stem Cell | 2013 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/23910086 |
| Tissue specific requirements for WNT11 in developing outflow tract and dorsal mesenchymal protrusion. | van Vliet PP, Lin L, Boogerd CJ, Martin JF, Andelfinger G, Grossfeld PD, Evans SM | Developmental biology | 28669819 | Dev Biol | 2017 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/28669819 |
| In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE). | D'Antonio-Chronowska A, D'Antonio M, Frazer KA | Bio-protocol | 33654959 | Bio Protoc | 2019 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/33654959 |
| Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci. | Smith EN, D'Antonio-Chronowska A, Greenwald WW, Borja V, Aguiar LR, Pogue R, Matsui H, Benaglio P, Borooah S, D'Antonio M, Ayyagari R, Frazer KA | Stem cell reports | 31080113 | Stem Cell Reports | 2019 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/31080113 |
| Complex regulatory networks influence pluripotent cell state transitions in human iPSCs. | Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, iPSCORE Consortium, Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, Frazer KA | Nature communications | 38395976 | Nat Commun | 2024 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/38395976 |
| IFNγ activates an immune-like regulatory network in the cardiac vascular endothelium. | Arthur TD, Joshua IN, Nguyen JP, D'Antonio-Chronowska A, D'Antonio M, Frazer KA | Journal of molecular and cellular cardiology plus | 40104808 | J Mol Cell Cardiol Plus | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40104808 |
| 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 I, Zhang J, Moore-Morris T, Pfeiffer E, Buchholz KS, Liu A, Ouyang K, Stroud MJ, Gerace L, Evans SM, McCulloch A, Chen J | PLoS genetics | 24586179 | PLoS Genet | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24586179 |
| Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. | Suzuki K, Yu C, Qu J, Li M, Yao X, Yuan T, Goebl A, Tang S, Ren R, Aizawa E, Zhang F, Xu X, Soligalla RD, Chen F, Kim J, Kim NY, Liao HK, Benner C, Esteban CR, Jin Y, Liu GH, Li Y, Izpisua Belmonte JC | Cell stem cell | 24996168 | Cell Stem Cell | 2014 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/24996168 |
| Thymosin β4 is not required for embryonic viability or vascular development. | Banerjee I, Moore Morris T, Evans SM, Chen J | Circulation research | 23371905 | Circ Res | 2013 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/23371905 |
| The dawn of angiogenesis modeling: regenerating vasculature from human pluripotent stem cells. | Yi F, Qu J, Liu GH, Izpisua Belmonte JC | Cell research | 22964710 | Cell Res | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22964710 |
| Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. | Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, Plongthongkum N, Kumar S, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Kan NG, Schöler HR, Mercola M, Zhang K, Izpisua Belmonte JC | Proceedings of the National Academy of Sciences of the United States of America | 22991473 | Proc Natl Acad Sci U S A | 2012 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/22991473 |
| Beating in a dish: new hopes for cardiomyocyte regeneration. | Gu Y, Yi F, Liu GH, Izpisua Belmonte JC | Cell research | 23184058 | Cell Res | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23184058 |
| Coordination of heart and lung co-development by a multipotent cardiopulmonary progenitor. | Peng T, Tian Y, Boogerd CJ, Lu MM, Kadzik RS, Stewart KM, Evans SM, Morrisey EE | Nature | 23873040 | Nature | 2013 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/23873040 |
| HCN4 dynamically marks the first heart field and conduction system precursors. | Liang X, Wang G, Lin L, Lowe J, Zhang Q, Bu L, Chen Y, Chen J, Sun Y, Evans SM | Circulation research | 23743334 | Circ Res | 2013 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/23743334 |
| The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. | Panopoulos AD, Yanes O, Ruiz S, Kida YS, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua Belmonte JC | Cell research | 22064701 | Cell Res | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22064701 |
| Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. | Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED | Stem cells (Dayton, Ohio) | 25826782 | Stem Cells | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25826782 |
| Assessing the causal relationship between obesity and venous thromboembolism through a Mendelian Randomization study. | Lindström S, Germain M, Crous-Bou M, Smith EN, Morange PE, van Hylckama Vlieg A, de Haan HG, Chasman D, Ridker P, Brody J, de Andrade M, Heit JA, Tang W, DeVivo I, Grodstein F, Smith NL, Tregouet D, Kabrhel C, INVENT Consortium | Human genetics | 28528403 | Hum Genet | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28528403 |
| Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression. | Greenwald WW, Li H, Benaglio P, Jakubosky D, Matsui H, Schmitt A, Selvaraj S, D'Antonio M, D'Antonio-Chronowska A, Smith EN, Frazer KA | Nature communications | 30837461 | Nat Commun | 2019 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/30837461 |
| Association of Human iPSC Gene Signatures and X Chromosome Dosage with Two Distinct Cardiac Differentiation Trajectories. | D'Antonio-Chronowska A, Donovan MKR, Young Greenwald WW, Nguyen JP, Fujita K, Hashem S, Matsui H, Soncin F, Parast M, Ward MC, Coulet F, Smith EN, Adler E, D'Antonio M, Frazer KA | Stem cell reports | 31668852 | Stem Cell Reports | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31668852 |
| Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. | Veevers J, Farah EN, Corselli M, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, van Vliet P, Zhu M, Hegarty JM, Deacon DC, Grinstein JD, Dirschinger RJ, Frazer KA, Adler ED, Knowlton KU, Chi NC, Martin JC, Chen J, Evans SM | Stem cell reports | 30122443 | Stem Cell Reports | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30122443 |
| Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach. | D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D'Antonio-Chronowska A, Frazer KA | Cell reports | 30044985 | Cell Rep | 2018 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/30044985 |
| Correction to: Unveiling Complexity and Multipotentiality of Early Heart Fields. | Circulation research | 35239406 | Circ Res | 2022 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/35239406 | |
| Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. | DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA | Cell stem cell | 28388430 | Cell Stem Cell | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28388430 |
| Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants. | Arthur TD, Nguyen JP, Henson BA, D'Antonio-Chronowska A, Jaureguy J, Silva N, iPSCORE Consortium, Panopoulos AD, Izpisua Belmonte JC, D'Antonio M, McVicker G, Frazer KA | Cell genomics | 39986281 | Cell Genom | 2025 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/39986281 |
| Genetics of growth rate in induced pluripotent stem cells. | Lee BN, Taylor HJ, Cipriani F, Narisu N, Robertson CC, Swift AJ, Sinha N, Yan T, Bonnycastle LL, Dale N, Butt A, Parsaud H, Semrau S, NYSCF Global Stem Cell Array Team, GENESiPS Consortium, iPSCORE Consortium, Knowles JW, Carcamo-Orive I, D'Antonio-Chronowska A, Frazer KA, Biesecker LG, Noggle S, Erdos MR, Paull D, Collins FS, Taylor DL | bioRxiv : the preprint server for biology | 40631191 | bioRxiv | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40631191 |
| TACE/ADAM-17 phosphorylation by PKC-epsilon mediates premalignant changes in tobacco smoke-exposed lung cells. | Lemjabbar-Alaoui H, Sidhu SS, Mengistab A, Gallup M, Basbaum C | PloS one | 21423656 | PLoS One | 2011 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/21423656 |
| AceTree: a major update and case study in the long term maintenance of open-source scientific software. | Katzman B, Tang D, Santella A, Bao Z | BMC bioinformatics | 29618316 | BMC Bioinformatics | 2018 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/29618316 |
| Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model. | Santella A, Kovacevic I, Herndon LA, Hall DH, Du Z, Bao Z | Nucleic acids research | 26503254 | Nucleic Acids Res | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26503254 |
| WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration. | Santella A, Catena R, Kovacevic I, Shah P, Yu Z, Marquina-Solis J, Kumar A, Wu Y, Schaff J, Colón-Ramos D, Shroff H, Mohler WA, Bao Z | BMC bioinformatics | 26051157 | BMC Bioinformatics | 2015 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/26051157 |
| Irises: A practical tool for image-based analysis of cellular DNA content. | Vogel JL, Michaelson D, Santella A, Hubbard EJ, Bao Z | Worm | 25254149 | Worm | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25254149 |
| KIF1A/UNC-104 Transports ATG-9 to Regulate Neurodevelopment and Autophagy at Synapses. | Stavoe AK, Kargbo-Hill SE, Hall DH, Colón-Ramos DA | Developmental cell | 27396362 | Dev Cell | 2016 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/27396362 |
| Dual-view plane illumination microscopy for rapid and spatially isotropic imaging. | Kumar A, Wu Y, Christensen R, Chandris P, Gandler W, McCreedy E, Bokinsky A, Colón-Ramos DA, Bao Z, McAuliffe M, Rondeau G, Shroff H | Nature protocols | 25299154 | Nat Protoc | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25299154 |
| POS-1 Promotes Endo-mesoderm Development by Inhibiting the Cytoplasmic Polyadenylation of neg-1 mRNA. | Elewa A, Shirayama M, Kaymak E, Harrison PF, Powell DR, Du Z, Chute CD, Woolf H, Yi D, Ishidate T, Srinivasan J, Bao Z, Beilharz TH, Ryder SP, Mello CC | Developmental cell | 26096734 | Dev Cell | 2015 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/26096734 |
| Spatially isotropic four-dimensional imaging with dual-view plane illumination microscopy. | Wu Y, Wawrzusin P, Senseney J, Fischer RS, Christensen R, Santella A, York AG, Winter PW, Waterman CM, Bao Z, Colón-Ramos DA, McAuliffe M, Shroff H | Nature biotechnology | 24108093 | Nat Biotechnol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24108093 |
| Systematic quantification of developmental phenotypes at single-cell resolution during embryogenesis. | Moore JL, Du Z, Bao Z | Development (Cambridge, England) | 23861063 | Development | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23861063 |
| A semi-local neighborhood-based framework for probabilistic cell lineage tracing. | Santella A, Du Z, Bao Z | BMC bioinformatics | 24964866 | BMC Bioinformatics | 2014 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/24964866 |
| Cell cycle features of C. elegans germline stem/progenitor cells vary temporally and spatially. | Roy D, Michaelson D, Hochman T, Santella A, Bao Z, Goldberg JD, Hubbard EJA | Developmental biology | 26577869 | Dev Biol | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26577869 |
| C. elegans SoxB genes are dispensable for embryonic neurogenesis but required for terminal differentiation of specific neuron types. | Vidal B, Santella A, Serrano-Saiz E, Bao Z, Chuang CF, Hobert O | Development (Cambridge, England) | 26153233 | Development | 2015 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/26153233 |
| Visualizing Calcium Flux in Freely Moving Nematode Embryos. | Ardiel EL, Kumar A, Marbach J, Christensen R, Gupta R, Duncan W, Daniels JS, Stuurman N, Colón-Ramos D, Shroff H | Biophysical journal | 28494967 | Biophys J | 2017 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/28494967 |
| Using Stage- and Slit-Scanning to Improve Contrast and Optical Sectioning in Dual-View Inverted Light Sheet Microscopy (diSPIM). | Kumar A, Christensen R, Guo M, Chandris P, Duncan W, Wu Y, Santella A, Moyle M, Winter PW, Colón-Ramos D, Bao Z, Shroff H | The Biological bulletin | 27638693 | Biol Bull | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27638693 |
| E3 ubiquitin ligases promote progression of differentiation during C. elegans embryogenesis. | Du Z, He F, Yu Z, Bowerman B, Bao Z | Developmental biology | 25523393 | Dev Biol | 2015 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/25523393 |
| De novo inference of systems-level mechanistic models of development from live-imaging-based phenotype analysis. | Du Z, Santella A, He F, Tiongson M, Bao Z | Cell | 24439388 | Cell | 2014 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/24439388 |
| The Regulatory Landscape of Lineage Differentiation in a Metazoan Embryo. | Du Z, Santella A, He F, Shah PK, Kamikawa Y, Bao Z | Developmental cell | 26321128 | Dev Cell | 2015 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/26321128 |
| Untwisting the Caenorhabditis elegans embryo. | Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H | eLife | 26633880 | Elife | 2015 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/26633880 |
| An In Toto Approach to Dissecting Cellular Interactions in Complex Tissues. | Shah PK, Santella A, Jacobo A, Siletti K, Hudspeth AJ, Bao Z | Developmental cell | 29161596 | Dev Cell | 2017 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/29161596 |
| Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution. | Duncan LH, Moyle MW, Shao L, Sengupta T, Ikegami R, Kumar A, Guo M, Christensen R, Santella A, Bao Z, Shroff H, Mohler W, Colón-Ramos DA | Journal of visualized experiments : JoVE | 31233035 | J Vis Exp | 2019 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/31233035 |
| Crossword: a fully automated algorithm for the segmentation and quality control of protein microarray images. | Gierahn TM, Loginov D, Love JC | Journal of proteome research | 24417579 | J Proteome Res | 2014 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/24417579 |
| Single-cell technologies for monitoring immune systems. | Chattopadhyay PK, Gierahn TM, Roederer M, Love JC | Nature immunology | 24448570 | Nat Immunol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24448570 |
| Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. | Yamanaka YJ, Szeto GL, Gierahn TM, Forcier TL, Benedict KF, Brefo MS, Lauffenburger DA, Irvine DJ, Love JC | Analytical chemistry | 23205933 | Anal Chem | 2012 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/23205933 |
| Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. | Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH 2nd, Hughes TK, Love C, Shalek AK | Methods in molecular biology (Clifton, N.J.) | 31028635 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31028635 |
| Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. | Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK | Nature methods | 28192419 | Nat Methods | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28192419 |
| Tracking immune cells in vivo using magnetic resonance imaging. | Ahrens ET, Bulte JW | Nature reviews. Immunology | 24013185 | Nat Rev Immunol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24013185 |
| Astrocytes promote ethanol-induced enhancement of intracellular Ca(2+) signals through intercellular communication with neurons. | Kim HB, Morris J, Miyashiro K, Lehto T, Langel Ü, Eberwine J, Sul JY | iScience | 33997707 | iScience | 2021 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/33997707 |
| Astrocyte ethanol exposure reveals persistent and defined calcium response subtypes and associated gene signatures. | Kim HB, Lu Y, Oh SC, Morris J, Miyashiro K, Kim J, Eberwine J, Sul JY | The Journal of biological chemistry | 35716779 | J Biol Chem | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35716779 |
| Organization of Embryonic Morphogenesis via Mechanical Information. | Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O'Hern CS, Shattuck MD, Holley SA | Developmental cell | 31178400 | Dev Cell | 2019 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/31178400 |
| The tissue mechanics of vertebrate body elongation and segmentation. | McMillen P, Holley SA | Current opinion in genetics & development | 25796079 | Curr Opin Genet Dev | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25796079 |
| Integration of cell-cell and cell-ECM adhesion in vertebrate morphogenesis. | McMillen P, Holley SA | Current opinion in cell biology | 26189063 | Curr Opin Cell Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26189063 |
| Patterned Disordered Cell Motion Ensures Vertebral Column Symmetry. | Das D, Chatti V, Emonet T, Holley SA | Developmental cell | 28743003 | Dev Cell | 2017 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/28743003 |
| Acoustofluidic chemical waveform generator and switch. | Ahmed D, Muddana HS, Lu M, French JB, Ozcelik A, Fang Y, Butler PJ, Benkovic SJ, Manz A, Huang TJ | Analytical chemistry | 25405550 | Anal Chem | 2014 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/25405550 |
| Wave number-spiral acoustic tweezers for dynamic and reconfigurable manipulation of particles and cells. | Tian Z, Yang S, Huang PH, Wang Z, Zhang P, Gu Y, Bachman H, Chen C, Wu M, Xie Y, Huang TJ | Science advances | 31172021 | Sci Adv | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31172021 |
| Acoustofluidic actuation of in situ fabricated microrotors. | Kaynak M, Ozcelik A, Nama N, Nourhani A, Lammert PE, Crespi VH, Huang TJ | Lab on a chip | 27466140 | Lab Chip | 2016 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/27466140 |
| Acoustofluidic Rotational Manipulation of Cells and Organisms Using Oscillating Solid Structures. | Ozcelik A, Nama N, Huang PH, Kaynak M, McReynolds MR, Hanna-Rose W, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 27515787 | Small | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27515787 |
| Digital acoustofluidics enables contactless and programmable liquid handling. | Zhang SP, Lata J, Chen C, Mai J, Guo F, Tian Z, Ren L, Mao Z, Huang PH, Li P, Yang S, Huang TJ | Nature communications | 30050088 | Nat Commun | 2018 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/30050088 |
| Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. | Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE | Cell reports | 29117571 | Cell Rep | 2017 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/29117571 |
| Mixing high-viscosity fluids via acoustically driven bubbles. | Orbay S, Ozcelik A, Lata J, Kaynak M, Wu M, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 31588165 | J Micromech Microeng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/31588165 |
| Rotational manipulation of single cells and organisms using acoustic waves. | Ahmed D, Ozcelik A, Bojanala N, Nama N, Upadhyay A, Chen Y, Hanna-Rose W, Huang TJ | Nature communications | 27004764 | Nat Commun | 2016 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/27004764 |
| A high-throughput acoustic cell sorter. | Ren L, Chen Y, Li P, Mao Z, Huang PH, Rufo J, Guo F, Wang L, McCoy JP, Levine SJ, Huang TJ | Lab on a chip | 26289231 | Lab Chip | 2015 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/26289231 |
| Standing surface acoustic wave (SSAW)-based cell washing. | Li S, Ding X, Mao Z, Chen Y, Nama N, Guo F, Li P, Wang L, Cameron CE, Huang TJ | Lab on a chip | 25372273 | Lab Chip | 2015 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/25372273 |
| Experimental and numerical studies on standing surface acoustic wave microfluidics. | Mao Z, Xie Y, Guo F, Ren L, Huang PH, Chen Y, Rufo J, Costanzo F, Huang TJ | Lab on a chip | 26698361 | Lab Chip | 2016 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/26698361 |
| Three-dimensional manipulation of single cells using surface acoustic waves. | Guo F, Mao Z, Chen Y, Xie Z, Lata JP, Li P, Ren L, Liu J, Yang J, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 26811444 | Proc Natl Acad Sci U S A | 2016 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/26811444 |
| Acoustic streaming: an arbitrary Lagrangian-Eulerian perspective. | Nama N, Huang TJ, Costanzo F | Journal of fluid mechanics | 29051631 | J Fluid Mech | 2017 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/29051631 |
| Investigation of micromixing by acoustically oscillated sharp-edges. | Nama N, Huang PH, Huang TJ, Costanzo F | Biomicrofluidics | 27158292 | Biomicrofluidics | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27158292 |
| Acoustofluidic coating of particles and cells. | Ayan B, Ozcelik A, Bachman H, Tang SY, Xie Y, Wu M, Li P, Huang TJ | Lab on a chip | 27754503 | Lab Chip | 2016 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/27754503 |
| Hybrid Dielectric-loaded Nanoridge Plasmonic Waveguide for Low-Loss Light Transmission at the Subwavelength Scale. | Zhang B, Bian Y, Ren L, Guo F, Tang SY, Mao Z, Liu X, Sun J, Gong J, Guo X, Huang TJ | Scientific reports | 28091583 | Sci Rep | 2017 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/28091583 |
| Acoustic separation of circulating tumor cells. | Li P, Mao Z, Peng Z, Zhou L, Chen Y, Huang PH, Truica CI, Drabick JJ, El-Deiry WS, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25848039 | Proc Natl Acad Sci U S A | 2015 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/25848039 |
| A spatiotemporally controllable chemical gradient generator via acoustically oscillating sharp-edge structures. | Huang PH, Chan CY, Li P, Nama N, Xie Y, Wei CH, Chen Y, Ahmed D, Huang TJ | Lab on a chip | 26338516 | Lab Chip | 2015 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/26338516 |
| Reusable acoustic tweezers for disposable devices. | Guo F, Xie Y, Li S, Lata J, Ren L, Mao Z, Ren B, Wu M, Ozcelik A, Huang TJ | Lab on a chip | 26507411 | Lab Chip | 2015 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/26507411 |
| Acousto-plasmofluidics: Acoustic modulation of surface plasmon resonance in microfluidic systems. | Ahmed D, Peng X, Ozcelik A, Zheng Y, Huang TJ | AIP advances | 26421224 | AIP Adv | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26421224 |
| Probing Cell Deformability via Acoustically Actuated Bubbles. | Xie Y, Nama N, Li P, Mao Z, Huang PH, Zhao C, Costanzo F, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 26715211 | Small | 2016 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/26715211 |
| Circulating Tumor Cell Phenotyping via High-Throughput Acoustic Separation. | Wu M, Huang PH, Zhang R, Mao Z, Chen C, Kemeny G, Li P, Lee AV, Gyanchandani R, Armstrong AJ, Dao M, Suresh S, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 29968402 | Small | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29968402 |
| Numerical study of acoustophoretic motion of particles in a PDMS microchannel driven by surface acoustic waves. | Nama N, Barnkob R, Mao Z, Kähler CJ, Costanzo F, Huang TJ | Lab on a chip | 26001199 | Lab Chip | 2015 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/26001199 |
| Plasmofluidics: Merging Light and Fluids at the Micro-/Nanoscale. | Wang M, Zhao C, Miao X, Zhao Y, Rufo J, Liu YJ, Huang TJ, Zheng Y | Small (Weinheim an der Bergstrasse, Germany) | 26140612 | Small | 2015 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/26140612 |
| Exploring bubble oscillation and mass transfer enhancement in acoustic-assisted liquid-liquid extraction with a microfluidic device. | Xie Y, Chindam C, Nama N, Yang S, Lu M, Zhao Y, Mai JD, Costanzo F, Huang TJ | Scientific reports | 26223474 | Sci Rep | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26223474 |
| Rapid formation of size-controllable multicellular spheroids via 3D acoustic tweezers. | Chen K, Wu M, Guo F, Li P, Chan CY, Mao Z, Li S, Ren L, Zhang R, Huang TJ | Lab on a chip | 27327102 | Lab Chip | 2016 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/27327102 |
| On-Chip Production of Size-Controllable Liquid Metal Microdroplets Using Acoustic Waves. | Tang SY, Ayan B, Nama N, Bian Y, Lata JP, Guo X, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 27309129 | Small | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27309129 |
| Spatial colocalization and functional link of purinosomes with mitochondria. | French JB, Jones SA, Deng H, Pedley AM, Kim D, Chan CY, Hu H, Pugh RJ, Zhao H, Zhang Y, Huang TJ, Fang Y, Zhuang X, Benkovic SJ | Science (New York, N.Y.) | 26912862 | Science | 2016 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/26912862 |
| Acoustic actuation of bioinspired microswimmers. | Kaynak M, Ozcelik A, Nourhani A, Lammert PE, Crespi VH, Huang TJ | Lab on a chip | 27991641 | Lab Chip | 2017 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/27991641 |
| Surface Acoustic Waves Grant Superior Spatial Control of Cells Embedded in Hydrogel Fibers. | Lata JP, Guo F, Guo J, Huang PH, Yang J, Huang TJ | Advanced materials (Deerfield Beach, Fla.) | 27571239 | Adv Mater | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27571239 |
| Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves. | Guo F, Zhou W, Li P, Mao Z, Yennawar NH, French JB, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 25641793 | Small | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25641793 |
| Controlling cell-cell interactions using surface acoustic waves. | Guo F, Li P, French JB, Mao Z, Zhao H, Li S, Nama N, Fick JR, Benkovic SJ, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25535339 | Proc Natl Acad Sci U S A | 2015 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/25535339 |
| Acoustofluidic bacteria separation. | Li S, Ma F, Bachman H, Cameron CE, Zeng X, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 28798539 | J Micromech Microeng | 2017 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/28798539 |
| Standing Surface Acoustic Wave (SSAW)-Based Fluorescence-Activated Cell Sorter. | Ren L, Yang S, Zhang P, Qu Z, Mao Z, Huang PH, Chen Y, Wu M, Wang L, Li P, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 30168662 | Small | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30168662 |
| Acoustofluidic waveguides for localized control of acoustic wavefront in microfluidics. | Bian Y, Guo F, Yang S, Mao Z, Bachman H, Tang SY, Ren L, Zhang B, Gong J, Guo X, Huang TJ | Microfluidics and nanofluidics | 29358901 | Microfluid Nanofluidics | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29358901 |
| A sharp-edge-based acoustofluidic chemical signal generator. | Huang PH, Chan CY, Li P, Wang Y, Nama N, Bachman H, Huang TJ | Lab on a chip | 29668002 | Lab Chip | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29668002 |
| Acoustofluidic Fluorescence Activated Cell Sorter. | Nawaz AA, Chen Y, Nama N, Nissly RH, Ren L, Ozcelik A, Wang L, McCoy JP, Levine SJ, Huang TJ | Analytical chemistry | 26331909 | Anal Chem | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26331909 |
| Acoustic Actuation of in situ Fabricated Artificial Cilia. | Orbay S, Ozcelik A, Bachman H, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 30479458 | J Micromech Microeng | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30479458 |
| Acoustofluidic devices controlled by cell phones. | Bachman H, Huang PH, Zhao S, Yang S, Zhang P, Fu H, Huang TJ | Lab on a chip | 29302660 | Lab Chip | 2018 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/29302660 |
| Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. | Yang B, Chen X, Wang Y, Feng S, Pessino V, Stuurman N, Cho NH, Cheng KW, Lord SJ, Xu L, Xie D, Mullins RD, Leonetti MD, Huang B | Nature methods | 31061492 | Nat Methods | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31061492 |
| Imaging Specific Genomic DNA in Living Cells. | Chen B, Guan J, Huang B | Annual review of biophysics | 27145877 | Annu Rev Biophys | 2016 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/27145877 |
| Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. | Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B | Nucleic acids research | 26740581 | Nucleic Acids Res | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/26740581 |
| High-NA open-top selective-plane illumination microscopy for biological imaging. | Mcgorty R, Xie D, Huang B | Optics express | 28789271 | Opt Express | 2017 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/28789271 |
| Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans. | Kim J, Jimenez DS, Ragipani B, Zhang B, Street LA, Kramer M, Albritton SE, Winterkorn LH, Morao AK, Ercan S | eLife | 36331876 | Elife | 2022 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/36331876 |
| Versatile protein tagging in cells with split fluorescent protein. | Kamiyama D, Sekine S, Barsi-Rhyne B, Hu J, Chen B, Gilbert LA, Ishikawa H, Leonetti MD, Marshall WF, Weissman JS, Huang B | Nature communications | 26988139 | Nat Commun | 2016 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/26988139 |
| Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag. | Chen B, Zou W, Xu H, Liang Y, Huang B | Nature communications | 30498221 | Nat Commun | 2018 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/30498221 |
| Tracking Multiple Genomic Elements Using Correlative CRISPR Imaging and Sequential DNA FISH. | Guan J, Liu H, Shi X, Feng S, Huang B | Biophysical journal | 28355536 | Biophys J | 2017 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/28355536 |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A | PLoS genetics | 30625149 | PLoS Genet | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30625149 |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis IA, Gupte R, Raj A, Rouhanifard SH | Nature methods | 28604724 | Nat Methods | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28604724 |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons O, Raj A | Molecular cell | 27259209 | Mol Cell | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27259209 |
| Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? | Mellis IA, Raj A | Genome research | 26430156 | Genome Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26430156 |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR | Nature methods | 29941873 | Nat Methods | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29941873 |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A | Cell systems | 29454938 | Cell Syst | 2018 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/29454938 |
| ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A | Nature biotechnology | 30418432 | Nat Biotechnol | 2018 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/30418432 |
| Amendments: Author Correction: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A | Nature biotechnology | 30605160 | Nat Biotechnol | 2019 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/30605160 |
| The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. | Kotzin JJ, Spencer SP, McCright SJ, Kumar DBU, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CCD, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J | Nature | 27525555 | Nature | 2016 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/27525555 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA | Molecular cell | 27067601 | Mol Cell | 2016 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/27067601 |
| Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. | Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J | Immunity | 28930659 | Immunity | 2017 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/28930659 |
| A magnetic micropore chip for rapid (<1 hour) unbiased circulating tumor cell isolation and in situ RNA analysis. | Ko J, Bhagwat N, Yee SS, Black T, Redlinger C, Romeo J, O'Hara M, Raj A, Carpenter EL, Stanger BZ, Issadore D | Lab on a chip | 28809985 | Lab Chip | 2017 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/28809985 |
| Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. | Shaffer SM, Joshi RP, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE, Issadore D, Raj A | Lab on a chip | 26113495 | Lab Chip | 2015 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/26113495 |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A | Genes & development | 26944681 | Genes Dev | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26944681 |
| A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. | Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA | Genes & development | 27340175 | Genes Dev | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27340175 |
| Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. | Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A | Nature | 28607484 | Nature | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/28607484 |
| Sample Preparation and Analysis of Single Cells Using High Performance MALDI FTICR Mass Spectrometry. | Yang B, Tsui T, Caprioli RM, Norris JL | Methods in molecular biology (Clifton, N.J.) | 31565771 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/31565771 |
| Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation. | Yang B, Patterson NH, Tsui T, Caprioli RM, Norris JL | Journal of the American Society for Mass Spectrometry | 29536413 | J Am Soc Mass Spectrom | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29536413 |
| Candidate-based screening via gene modulation in human neurons and astrocytes implicates FERMT2 in Aβ and TAU proteostasis. | Sullivan SE, Liao M, Smith RV, White C, Lagomarsino VN, Xu J, Taga M, Bennett DA, De Jager PL, Young-Pearse TL | Human molecular genetics | 30371777 | Hum Mol Genet | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/30371777 |
| Cell-type Dependent Alzheimer's Disease Phenotypes: Probing the Biology of Selective Neuronal Vulnerability. | Muratore CR, Zhou C, Liao M, Fernandez MA, Taylor WM, Lagomarsino VN, Pearse RV 2nd, Rice HC, Negri JM, He A, Srikanth P, Callahan DG, Shin T, Zhou M, Bennett DA, Noggle S, Love JC, Selkoe DJ, Young-Pearse TL | Stem cell reports | 29153990 | Stem Cell Reports | 2017 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/29153990 |
| Modeling developmental neuropsychiatric disorders with iPSC technology: challenges and opportunities. | Young-Pearse TL, Morrow EM | Current opinion in neurobiology | 26517284 | Curr Opin Neurobiol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26517284 |
| Single-Cell Detection of Secreted Aβ and sAPPα from Human IPSC-Derived Neurons and Astrocytes. | Liao MC, Muratore CR, Gierahn TM, Sullivan SE, Srikanth P, De Jager PL, Love JC, Young-Pearse TL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26843653 | J Neurosci | 2016 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/26843653 |
| Induced pluripotent stem cells as a discovery tool for Alzheimer׳s disease. | Sullivan SE, Young-Pearse TL | Brain research | 26459988 | Brain Res | 2017 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26459988 |
| 3D Clumped Cell Segmentation Using Curvature Based Seeded Watershed. | Atta-Fosu T, Guo W, Jeter D, Mizutani CM, Stopczynski N, Sousa-Neves R | Journal of imaging | 28280723 | J Imaging | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28280723 |
| The nested embryonic dorsal domains of BMP-target genes are not scaled to size during the evolution of Drosophila species. | Chahda JS, Ambrosi P, Mizutani CM | Journal of experimental zoology. Part B, Molecular and developmental evolution | 35451554 | J Exp Zool B Mol Dev Evol | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35451554 |
| The epithelial polarity genes frazzled and GUK-holder adjust morphogen gradients to coordinate changes in cell position with cell fate specification. | Xue Y, Krishnan A, Chahda JS, Schweickart RA, Sousa-Neves R, Mizutani CM | PLoS biology | 36913435 | PLoS Biol | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36913435 |
| High-throughput genome editing and phenotyping facilitated by high resolution melting curve analysis. | Thomas HR, Percival SM, Yoder BK, Parant JM | PloS one | 25503746 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25503746 |
| Variations in dysfunction of sister chromatid cohesion in esco2 mutant zebrafish reflect the phenotypic diversity of Roberts syndrome. | Percival SM, Thomas HR, Amsterdam A, Carroll AJ, Lees JA, Yost HJ, Parant JM | Disease models & mechanisms | 26044958 | Dis Model Mech | 2015 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/26044958 |
| Approaches to Inactivate Genes in Zebrafish. | Parant JM, Yeh JR | Advances in experimental medicine and biology | 27165349 | Adv Exp Med Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27165349 |
| Observing Mitotic Division and Dynamics in a Live Zebrafish Embryo. | Percival SM, Parant JM | Journal of visualized experiments : JoVE | 27501381 | J Vis Exp | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27501381 |
| Single-cell tracking with PET using a novel trajectory reconstruction algorithm. | Lee KS, Kim TJ, Pratx G | IEEE transactions on medical imaging | 25423651 | IEEE Trans Med Imaging | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25423651 |
| Whole-body tracking of single cells via positron emission tomography. | Jung KO, Kim TJ, Yu JH, Rhee S, Zhao W, Ha B, Red-Horse K, Gambhir SS, Pratx G | Nature biomedical engineering | 32541917 | Nat Biomed Eng | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32541917 |
| Single-Cell Imaging Using Radioluminescence Microscopy Reveals Unexpected Binding Target for [18F]HFB. | Kiru L, Kim TJ, Shen B, Chin FT, Pratx G | Molecular imaging and biology | 29143174 | Mol Imaging Biol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29143174 |
| Evaluation of a BGO-Based PET System for Single-Cell Tracking Performance by Simulation and Phantom Studies. | Ouyang Y, Kim TJ, Pratx G | Molecular imaging | 27175009 | Mol Imaging | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27175009 |
| Altering metabolite distribution at Xenopus cleavage stages affects left-right gene expression asymmetries. | Onjiko RM, Nemes P, Moody SA | Genesis (New York, N.Y. : 2000) | 33826226 | Genesis | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33826226 |
| Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. | Onjiko RM, Moody SA, Nemes P | Proceedings of the National Academy of Sciences of the United States of America | 25941375 | Proc Natl Acad Sci U S A | 2015 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/25941375 |
| New-generation mass spectrometry expands the toolbox of cell and developmental biology. | Lombard-Banek C, Portero EP, Onjiko RM, Nemes P | Genesis (New York, N.Y. : 2000) | 28095647 | Genesis | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28095647 |
| Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos. | Onjiko RM, Portero EP, Moody SA, Nemes P | Journal of visualized experiments : JoVE | 29286491 | J Vis Exp | 2017 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/29286491 |
| Metabolic Comparison of Dorsal versus Ventral Cells Directly in the Live 8-cell Frog Embryo by Microprobe Single-cell CE-ESI-MS. | Onjiko RM, Plotnick DO, Moody SA, Nemes P | Analytical methods : advancing methods and applications | 29062391 | Anal Methods | 2017 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/29062391 |
| Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo. | Onjiko RM, Morris SE, Moody SA, Nemes P | The Analyst | 27004603 | Analyst | 2016 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/27004603 |
| In Situ Microprobe Single-Cell Capillary Electrophoresis Mass Spectrometry: Metabolic Reorganization in Single Differentiating Cells in the Live Vertebrate (Xenopus laevis) Embryo. | Onjiko RM, Portero EP, Moody SA, Nemes P | Analytical chemistry | 28434226 | Anal Chem | 2017 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/28434226 |
| Capillary Electrophoresis Electrospray Ionization Mass Spectrometry Reveals Metabolic Perturbations During Nematode Infection in Drosophila melanogaster. | Tuani YT, Ayon NJ, Onjiko RM, Choi SB, Yadav S, Eleftherianos I, Nemes P | Molecules (Basel, Switzerland) | 40363828 | Molecules | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40363828 |
| In Situ and In Vivo Molecular Analysis by Coherent Raman Scattering Microscopy. | Liao CS, Cheng JX | Annual review of analytical chemistry (Palo Alto, Calif.) | 27306307 | Annu Rev Anal Chem (Palo Alto Calif) | 2016 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/27306307 |
| Increased insular functional connectivity during repetitive negative thinking in major depression and healthy volunteers. | Edwards LS, Ganesan S, Tay J, Elliott ES, Misaki M, White EJ, Paulus MP, Guinjoan SM, Tsuchiyagaito A | Psychological medicine | 40936343 | Psychol Med | 2025 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/40936343 |
| Label-Free Imaging of Heme Dynamics in Living Organisms by Transient Absorption Microscopy. | Chen AJ, Yuan X, Li J, Dong P, Hamza I, Cheng JX | Analytical chemistry | 29401392 | Anal Chem | 2018 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/29401392 |
| Fingerprint Stimulated Raman Scattering Imaging Reveals Retinoid Coupling Lipid Metabolism and Survival. | Chen AJ, Li J, Jannasch A, Mutlu AS, Wang MC, Cheng JX | Chemphyschem : a European journal of chemical physics and physical chemistry | 29911339 | Chemphyschem | 2018 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/29911339 |
| Denoising Stimulated Raman Spectroscopic Images by Total Variation Minimization. | Liao CS, Choi JH, Zhang D, Chan SH, Cheng JX | The journal of physical chemistry. C, Nanomaterials and interfaces | 26955400 | J Phys Chem C Nanomater Interfaces | 2015 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26955400 |
| Identification of Neuronal Lineages in the Drosophila Peripheral Nervous System with a "Digital" Multi-spectral Lineage Tracing System. | Veling MW, Li Y, Veling MT, Litts C, Michki SN, Liu H, Ye B, Cai D | Cell reports | 31801091 | Cell Rep | 2019 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/31801091 |
| Prolonged mechanical stretch initiates intracellular calcium oscillations in human mesenchymal stem cells. | Kim TJ, Sun J, Lu S, Qi YX, Wang Y | PloS one | 25329052 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25329052 |
| Distinct mechanisms regulating mechanical force-induced Ca²⁺ signals at the plasma membrane and the ER in human MSCs. | Kim TJ, Joo C, Seong J, Vafabakhsh R, Botvinick EL, Berns MW, Palmer AE, Wang N, Ha T, Jakobsson E, Sun J, Wang Y | eLife | 25667984 | Elife | 2015 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/25667984 |
| Rapid and Localized Mechanical Stimulation and Adhesion Assay: TRPM7 Involvement in Calcium Signaling and Cell Adhesion. | Nishitani WS, Alencar AM, Wang Y | PloS one | 25946314 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25946314 |
| The antagonistic roles of PDGF and integrin αvβ3 in regulating ROS production at focal adhesions. | Lin LJ, Grimme JM, Sun J, Lu S, Gai L, Cropek DM, Wang Y | Biomaterials | 23465490 | Biomaterials | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23465490 |
| The role of mechanical tension on lipid raft dependent PDGF-induced TRPC6 activation. | Lei L, Lu S, Wang Y, Kim T, Mehta D, Wang Y | Biomaterials | 24397990 | Biomaterials | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24397990 |
| Distinct biophysical mechanisms of focal adhesion kinase mechanoactivation by different extracellular matrix proteins. | Seong J, Tajik A, Sun J, Guan JL, Humphries MJ, Craig SE, Shekaran A, García AJ, Lu S, Lin MZ, Wang N, Wang Y | Proceedings of the National Academy of Sciences of the United States of America | 24222685 | Proc Natl Acad Sci U S A | 2013 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/24222685 |
| Red-shifted fluorescent proteins monitor enzymatic activity in live HT-1080 cells with fluorescence lifetime imaging microscopy (FLIM). | Eichorst JP, Clegg RM, Wang Y | Journal of microscopy | 22971220 | J Microsc | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22971220 |
| The regulation of β-adrenergic receptor-mediated PKA activation by substrate stiffness via microtubule dynamics in human MSCs. | Kim TJ, Sun J, Lu S, Zhang J, Wang Y | Biomaterials | 24973298 | Biomaterials | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24973298 |
| Single-cell imaging of mechanotransduction in endothelial cells. | Lu S, Wang Y | Progress in molecular biology and translational science | 25081613 | Prog Mol Biol Transl Sci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25081613 |
| Genetically encoded fluorescent biosensors for live-cell imaging of MT1-MMP protease activity. | Ouyang M, Lu S, Wang Y | Methods in molecular biology (Clifton, N.J.) | 24052388 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24052388 |
| FRET imaging of calcium signaling in live cells in the microenvironment. | Qian T, Lu S, Ma H, Fang J, Zhong W, Wang Y | Integrative biology : quantitative biosciences from nano to macro | 23250282 | Integr Biol (Camb) | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23250282 |
| Mechanotransduction at focal adhesions: from physiology to cancer development. | Seong J, Wang N, Wang Y | Journal of cellular and molecular medicine | 23601032 | J Cell Mol Med | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23601032 |
| Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2. | Sun J, Lu S, Ouyang M, Lin LJ, Zhuo Y, Liu B, Chien S, Neel BG, Wang Y | Nature communications | 23792876 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23792876 |
| A FRET-Based Biosensor for Imaging SYK Activities in Living Cells. | Xiang X, Sun J, Wu J, He HT, Wang Y, Zhu C | Cellular and molecular bioengineering | 25541586 | Cell Mol Bioeng | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25541586 |
| Scalable microfluidics for single-cell RNA printing and sequencing. | Bose S, Wan Z, Carr A, Rizvi AH, Vieira G, Pe'er D, Sims PA | Genome biology | 26047807 | Genome Biol | 2015 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/26047807 |
| Single image super-resolution via an iterative reproducing kernel Hilbert space method. | Deng LJ, Guo W, Huang TZ | IEEE transactions on circuits and systems for video technology : a publication of the Circuits and Systems Society | 28603404 | IEEE Trans Circuits Syst Video Technol | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28603404 |
| Genetic analysis of mate discrimination in Drosophila simulans. | Chu Y, Yang E, Schinaman JM, Chahda JS, Sousa-Neves R | Evolution; international journal of organic evolution | 23888855 | Evolution | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23888855 |
| Modeling of the dorsal gradient across species reveals interaction between embryo morphology and Toll signaling pathway during evolution. | Ambrosi P, Chahda JS, Koslen HR, Chiel HJ, Mizutani CM | PLoS computational biology | 25165818 | PLoS Comput Biol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25165818 |
| Variation in the dorsal gradient distribution is a source for modified scaling of germ layers in Drosophila. | Chahda JS, Sousa-Neves R, Mizutani CM | Current biology : CB | 23583556 | Curr Biol | 2013 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/23583556 |
| The KRÜPPEL-like transcription factor DATILÓGRAFO is required in specific cholinergic neurons for sexual receptivity in Drosophila females. | Schinaman JM, Giesey RL, Mizutani CM, Lukacsovich T, Sousa-Neves R | PLoS biology | 25291190 | PLoS Biol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25291190 |
| Rational design and experimental evaluation of peptide ligands for the purification of adeno-associated viruses via affinity chromatography. | Shastry S, Chu W, Barbieri E, Greback-Clarke P, Smith WK, Cummings C, Minzoni A, Pancorbo J, Gilleskie G, Ritola K, Daniele MA, Johnson TF, Menegatti S | Biotechnology journal | 37728197 | Biotechnol J | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37728197 |
| Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. | Klein AM, Mazutis L, Akartuna I, Tallapragada N, Veres A, Li V, Peshkin L, Weitz DA, Kirschner MW | Cell | 26000487 | Cell | 2015 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/26000487 |
| Regulation of ribosomal RNA expression across the lifespan is fine-tuned by maternal diet before implantation. | Denisenko O, Lucas ES, Sun C, Watkins AJ, Mar D, Bomsztyk K, Fleming TP | Biochimica et biophysica acta | 27060415 | Biochim Biophys Acta | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27060415 |
| Epigenetic alterations in acute kidney injury. | Bomsztyk K, Denisenko O | Seminars in nephrology | 24011575 | Semin Nephrol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24011575 |
| Chromatin changes trigger laminin genes dysregulation in aging kidneys. | Denisenko O, Mar D, Trawczynski M, Bomsztyk K | Aging | 29846172 | Aging (Albany NY) | 2018 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/29846172 |
| Synchronous recruitment of epigenetic modifiers to endotoxin synergistically activated Tnf-α gene in acute kidney injury. | Bomsztyk K, Flanagin S, Mar D, Mikula M, Johnson A, Zager R, Denisenko O | PloS one | 23936185 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23936185 |
| Single cell epigenetic visualization assay. | Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, Denisenko O | Nucleic acids research | 33511400 | Nucleic Acids Res | 2021 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/33511400 |
| Mechanical regulation of stem-cell differentiation by the stretch-activated Piezo channel. | He L, Si G, Huang J, Samuel ADT, Perrimon N | Nature | 29414942 | Nature | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29414942 |
| Development of an optimized synthetic Notch receptor as an in vivo cell-cell contact sensor. | He L, Huang J, Perrimon N | Proceedings of the National Academy of Sciences of the United States of America | 28490499 | Proc Natl Acad Sci U S A | 2017 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/28490499 |
| Visualizing and manipulating temporal signaling dynamics with fluorescence-based tools. | Doupé DP, Perrimon N | Science signaling | 24692594 | Sci Signal | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24692594 |
| Spatial and temporal organization of signaling pathways. | Housden BE, Perrimon N | Trends in biochemical sciences | 25155749 | Trends Biochem Sci | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25155749 |
| In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer. | He L, Binari R, Huang J, Falo-Sanjuan J, Perrimon N | eLife | 31140975 | Elife | 2019 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/31140975 |
| A role for actomyosin contractility in Notch signaling. | Hunter GL, He L, Perrimon N, Charras G, Giniger E, Baum B | BMC biology | 30744634 | BMC Biol | 2019 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/30744634 |
| Mechanical Allostery: Evidence for a Force Requirement in the Proteolytic Activation of Notch. | Gordon WR, Zimmerman B, He L, Miles LJ, Huang J, Tiyanont K, McArthur DG, Aster JC, Perrimon N, Loparo JJ, Blacklow SC | Developmental cell | 26051539 | Dev Cell | 2015 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/26051539 |
| Organ injury accelerates stem cell differentiation by modulating a fate-transducing lateral inhibition circuit. | Sanders EN, Sun HT, Tabatabaee S, Lang CF, van Dijk SG, Su YH, Labott A, Idris J, He L, Marchetti M, Xie S, O'Brien LE | bioRxiv : the preprint server for biology | 39803552 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/39803552 |
| Diagnosis of prostate cancer by desorption electrospray ionization mass spectrometric imaging of small metabolites and lipids. | Banerjee S, Zare RN, Tibshirani RJ, Kunder CA, Nolley R, Fan R, Brooks JD, Sonn GA | Proceedings of the National Academy of Sciences of the United States of America | 28292895 | Proc Natl Acad Sci U S A | 2017 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/28292895 |
| Microdroplet fusion mass spectrometry for fast reaction kinetics. | Lee JK, Kim S, Nam HG, Zare RN | Proceedings of the National Academy of Sciences of the United States of America | 25775573 | Proc Natl Acad Sci U S A | 2015 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/25775573 |
| Acceleration of reaction in charged microdroplets. | Lee JK, Banerjee S, Nam HG, Zare RN | Quarterly reviews of biophysics | 26537403 | Q Rev Biophys | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26537403 |
| High-Resolution Live-Cell Imaging and Analysis by Laser Desorption/Ionization Droplet Delivery Mass Spectrometry. | Lee JK, Jansson ET, Nam HG, Zare RN | Analytical chemistry | 27110027 | Anal Chem | 2016 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/27110027 |
| Monitoring Enzymatic Reactions in Real Time Using Venturi Easy Ambient Sonic-Spray Ionization Mass Spectrometry. | Jansson ET, Dulay MT, Zare RN | Analytical chemistry | 27249533 | Anal Chem | 2016 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/27249533 |
| Microdroplet fusion mass spectrometry: accelerated kinetics of acid-induced chlorophyll demetallation. | Lee JK, Nam HG, Zare RN | Quarterly reviews of biophysics | 29233214 | Q Rev Biophys | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29233214 |
| High resolution laser mass spectrometry bioimaging. | Murray KK, Seneviratne CA, Ghorai S | Methods (San Diego, Calif.) | 26972785 | Methods | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/26972785 |
| Tip-enhanced laser ablation sample transfer for biomolecule mass spectrometry. | Ghorai S, Seneviratne CA, Murray KK | Journal of the American Society for Mass Spectrometry | 25287125 | J Am Soc Mass Spectrom | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25287125 |
| Compact and modular multicolour fluorescence detector for droplet microfluidics. | Cole RH, de Lange N, Gartner ZJ, Abate AR | Lab on a chip | 26032595 | Lab Chip | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26032595 |
| Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers. | Cole RH, Gartner ZJ, Abate AR | Journal of visualized experiments : JoVE | 27214249 | J Vis Exp | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/27214249 |
| PIWI proteins are essential for early Drosophila embryogenesis. | Mani SR, Megosh H, Lin H | Developmental biology | 24184635 | Dev Biol | 2014 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/24184635 |
| HistoMosaic Detecting KRAS G12V Mutation Across Colorectal Cancer Tissue Slices through in Situ PCR. | Raub CB, Lee CC, Shibata D, Taylor C, Kartalov E | Analytical chemistry | 26820161 | Anal Chem | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26820161 |
| Piwi Is a Key Regulator of Both Somatic and Germline Stem Cells in the Drosophila Testis. | Gonzalez J, Qi H, Liu N, Lin H | Cell reports | 26119740 | Cell Rep | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26119740 |
| Advanced targeted nanomedicine. | Pereira MC, Reshetnyak YK, Andreev OA | Journal of biotechnology | 25615945 | J Biotechnol | 2015 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/25615945 |
| Probe for the measurement of cell surface pH in vivo and ex vivo. | Anderson M, Moshnikova A, Engelman DM, Reshetnyak YK, Andreev OA | Proceedings of the National Academy of Sciences of the United States of America | 27382181 | Proc Natl Acad Sci U S A | 2016 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/27382181 |
| Targeting breast tumors with pH (low) insertion peptides. | Adochite RC, Moshnikova A, Carlin SD, Guerrieri RA, Andreev OA, Lewis JS, Reshetnyak YK | Molecular pharmaceutics | 25004202 | Mol Pharm | 2014 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/25004202 |
| Imaging Tumor Acidity: pH-Low Insertion Peptide Probe for Optoacoustic Tomography. | Reshetnyak YK | Clinical cancer research : an official journal of the American Association for Cancer Research | 26224874 | Clin Cancer Res | 2015 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/26224874 |
| pH dependent transfer of nano-pores into membrane of cancer cells to induce apoptosis. | Wijesinghe D, Arachchige MC, Lu A, Reshetnyak YK, Andreev OA | Scientific reports | 24356337 | Sci Rep | 2013 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/24356337 |
| Controlling lipid micelle stability using oligonucleotide headgroups. | Wilner SE, Sparks SE, Cowburn D, Girvin ME, Levy M | Journal of the American Chemical Society | 25634639 | J Am Chem Soc | 2015 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/25634639 |
| Probing endoplasmic reticulum dynamics using fluorescence imaging and photobleaching techniques. | Costantini L, Snapp E | Current protocols in cell biology | 24510787 | Curr Protoc Cell Biol | 2013 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/24510787 |
| T Cell Dynamic Activation and Functional Analysis in Nanoliter Droplet Microarray. | Sarkar S, Motwani V, Sabhachandani P, Cohen N, Konry T | Journal of clinical & cellular immunology | 26613065 | J Clin Cell Immunol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26613065 |
| Anti-myeloma activity and molecular logic operation by Natural Killer cells in microfluidic droplets. | Sarkar S, McKenney S, Sabhachandani P, Adler J, Hu X, Stroopinksy D, Rosenblatt J, Avigan D, Konry T | Sensors and actuators. B, Chemical | 31537955 | Sens Actuators B Chem | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/31537955 |
| 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 | 26686985 | Lab Chip | 2016 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/26686985 |
| 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 | 26456240 | Lab Chip | 2015 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/26456240 |
| Monovar: single-nucleotide variant detection in single cells. | Zafar H, Wang Y, Nakhleh L, Navin N, Chen K | Nature methods | 27088313 | Nat Methods | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27088313 |
| Clonal evolution in breast cancer revealed by single nucleus genome sequencing. | Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE | Nature | 25079324 | Nature | 2014 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/25079324 |
| Tumor evolution: Linear, branching, neutral or punctuated? | Davis A, Gao R, Navin N | Biochimica et biophysica acta. Reviews on cancer | 28110020 | Biochim Biophys Acta Rev Cancer | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28110020 |
| Punctuated copy number evolution and clonal stasis in triple-negative breast cancer. | Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE | Nature genetics | 27526321 | Nat Genet | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27526321 |
| BreakTrans: uncovering the genomic architecture of gene fusions. | Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L | Genome biology | 23972288 | Genome Biol | 2013 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/23972288 |
| SNES: single nucleus exome sequencing. | Leung ML, Wang Y, Waters J, Navin NE | Genome biology | 25853327 | Genome Biol | 2015 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/25853327 |
| Tumor evolution in response to chemotherapy: phenotype versus genotype. | Navin NE | Cell reports | 24529750 | Cell Rep | 2014 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/24529750 |
| Cancer genomics: one cell at a time. | Navin NE | Genome biology | 25222669 | Genome Biol | 2014 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/25222669 |
| Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations. | Malhotra A, Wang Y, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin NE | Genome medicine | 25729435 | Genome Med | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25729435 |
| Highly multiplexed targeted DNA sequencing from single nuclei. | Leung ML, Wang Y, Kim C, Gao R, Jiang J, Sei E, Navin NE | Nature protocols | 26741407 | Nat Protoc | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26741407 |
| Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq. | Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L, Yew CC, Waters JL, Leung ML, Rogers K, Rogers SM, McNoe LA, Selvanesan L, Navin N, Jenkins NA, Copeland NG, Mann MB | Nature biotechnology | 27479497 | Nat Biotechnol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27479497 |
| Optical clearing in collagen- and proteoglycan-rich osteochondral tissues. | Neu CP, Novak T, Gilliland KF, Marshall P, Calve S | Osteoarthritis and cartilage | 25454370 | Osteoarthritis Cartilage | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25454370 |
| Optical clearing in dense connective tissues to visualize cellular connectivity in situ. | Calve S, Ready A, Huppenbauer C, Main R, Neu CP | PloS one | 25581165 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25581165 |
| 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 DD, Famaey N, Vander Sloten J, Himmelreich U, Neu CP, Jonkers I | Osteoarthritis and cartilage | 30172835 | Osteoarthritis Cartilage | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30172835 |
| Functional assessment of strains around a full-thickness and critical sized articular cartilage defect under compressive loading using MRI. | Zevenbergen L, Gsell W, Chan DD, Vander Sloten J, Himmelreich U, Neu CP, Jonkers I | Osteoarthritis and cartilage | 30195045 | Osteoarthritis Cartilage | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30195045 |
| Intervertebral Disc Elastography to Relate Shear Modulus and Relaxometry in Compression and Bending. | Davis ZR, Gossett PC, Wilson RL, Kim W, Mei Y, Butz KD, Emery NC, Nauman EA, Avril S, Neu CP, Chan DD | bioRxiv : the preprint server for biology | 37732250 | bioRxiv | 2023 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/37732250 |
| Dissociated and Reconstituted Cartilage Microparticles in Densified Collagen Induce Local hMSC Differentiation. | Novak T, Seelbinder B, Twitchell CM, Voytik-Harbin SL Prof, Neu CP Prof | Advanced functional materials | 28824356 | Adv Funct Mater | 2016 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/28824356 |
| Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion. | Ghosh S, Scott AK, Seelbinder B, Barthold JE, Martin BMS, Kaonis S, Schneider SE, Henderson JT, Neu CP | Biophysical journal | 34800469 | Biophys J | 2022 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/34800469 |
| Comparison of intervertebral disc displacements measured under applied loading with MRI at 3.0 T and 9.4 T. | Chan DD, Gossett PC, Butz KD, Nauman EA, Neu CP | Journal of biomechanics | 24968943 | J Biomech | 2014 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/24968943 |
| Atomic force microscopy-coupled microcoils for cellular-scale nuclear magnetic resonance spectroscopy. | Mousoulis C, Maleki T, Ziaie B, Neu CP | Applied physics letters | 24719493 | Appl Phys Lett | 2013 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/24719493 |
| Single cell spectroscopy: noninvasive measures of small-scale structure and function. | Mousoulis C, Xu X, Reiter DA, Neu CP | Methods (San Diego, Calif.) | 23886910 | Methods | 2013 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/23886910 |
| Functional MRI can detect changes in intratissue strains in a full thickness and critical sized ovine cartilage defect model. | Chan DD, Cai L, Butz KD, Nauman EA, Dickerson DA, Jonkers I, Neu CP | Journal of biomechanics | 29169631 | J Biomech | 2018 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/29169631 |
| In Vivo Multiscale and Spatially-Dependent Biomechanics Reveals Differential Strain Transfer Hierarchy in Skeletal Muscle. | Ghosh S, Cimino JG, Scott AK, Damen FW, Phillips EH, Veress AI, Neu CP, Goergen CJ | ACS biomaterials science & engineering | 29276759 | ACS Biomater Sci Eng | 2017 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/29276759 |
| Single-cell and population NF-κB dynamic responses depend on lipopolysaccharide preparation. | Gutschow MV, Hughey JJ, Ruggero NA, Bajar BT, Valle SD, Covert MW | PloS one | 23301045 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23301045 |
| High-sensitivity measurements of multiple kinase activities in live single cells. | Regot S, Hughey JJ, Bajar BT, Carrasco S, Covert MW | Cell | 24949979 | Cell | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24949979 |
| Single-cell variation leads to population invariance in NF-κB signaling dynamics. | Hughey JJ, Gutschow MV, Bajar BT, Covert MW | Molecular biology of the cell | 25473117 | Mol Biol Cell | 2015 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/25473117 |
| Combinatorial processing of bacterial and host-derived innate immune stimuli at the single-cell level. | Gutschow MV, Mason JC, Lane KM, Maayan I, Hughey JJ, Bajar BT, Amatya DN, Valle SD, Covert MW | Molecular biology of the cell | 30462580 | Mol Biol Cell | 2019 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/30462580 |
| Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. | Kim DH, Marinov GK, Pepke S, Singer ZS, He P, Williams B, Schroth GP, Elowitz MB, Wold BJ | Cell stem cell | 25575081 | Cell Stem Cell | 2015 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/25575081 |
| Noncommutative Biology: Sequential Regulation of Complex Networks. | Letsou W, Cai L | PLoS computational biology | 27560383 | PLoS Comput Biol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27560383 |
| Molecular Time Sharing through Dynamic Pulsing in Single Cells. | Park J, Dies M, Lin Y, Hormoz S, Smith-Unna SE, Quinodoz S, Hernández-Jiménez MJ, Garcia-Ojalvo J, Locke JCW, Elowitz MB | Cell systems | 29454936 | Cell Syst | 2018 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/29454936 |
| In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. | Shah S, Lubeck E, Zhou W, Cai L | Neuron | 27764670 | Neuron | 2016 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/27764670 |
| Identification of a neural crest stem cell niche by Spatial Genomic Analysis. | Lignell A, Kerosuo L, Streichan SJ, Cai L, Bronner ME | Nature communications | 29184067 | Nat Commun | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/29184067 |
| Dynamics of epigenetic regulation at the single-cell level. | Bintu L, Yong J, Antebi YE, McCue K, Kazuki Y, Uno N, Oshimura M, Elowitz MB | Science (New York, N.Y.) | 26912859 | Science | 2016 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/26912859 |
| Dense transcript profiling in single cells by image correlation decoding. | Coskun AF, Cai L | Nature methods | 27271198 | Nat Methods | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27271198 |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L | Cell | 29887381 | Cell | 2018 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/29887381 |
| Tuning methylation-dependent silencing dynamics by synthetic modulation of CpG density. | Ma Y, Budde MW, Zhu J, Elowitz MB | bioRxiv : the preprint server for biology | 37398290 | bioRxiv | 2023 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/37398290 |
| Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. | Zhu Q, Shah S, Dries R, Cai L, Yuan GC | Nature biotechnology | 30371680 | Nat Biotechnol | 2018 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/30371680 |
| EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI). | Ma Y, Antebi Y | bioRxiv : the preprint server for biology | 37609189 | bioRxiv | 2023 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/37609189 |
| EasyFlow: An open-source, user-friendly cytometry analyzer with graphic user interface (GUI). | Ma Y, Eizenberg-Magar I, Antebi Y | PloS one | 39536028 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39536028 |
| Single-cell systems biology by super-resolution imaging and combinatorial labeling. | Lubeck E, Cai L | Nature methods | 22660740 | Nat Methods | 2012 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/22660740 |
| Single-cell phenotyping within transparent intact tissue through whole-body clearing. | Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, Shah S, Cai L, Gradinaru V | Cell | 25088144 | Cell | 2014 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/25088144 |
| Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. | Cutrale F, Trivedi V, Trinh LA, Chiu CL, Choi JM, Artiga MS, Fraser SE | Nature methods | 28068315 | Nat Methods | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28068315 |
| Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing. | Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, Lignell A, Choi HM, Gradinaru V, Pierce NA, Cai L | Development (Cambridge, England) | 27342713 | Development | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27342713 |
| Single-cell in situ RNA profiling by sequential hybridization. | Lubeck E, Coskun AF, Zhiyentayev T, Ahmad M, Cai L | Nature methods | 24681720 | Nat Methods | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24681720 |
| Eph-ephrin signaling modulated by polymerization and condensation of receptors. | Ojosnegros S, Cutrale F, Rodríguez D, Otterstrom JJ, Chiu CL, Hortigüela V, Tarantino C, Seriola A, Mieruszynski S, Martínez E, Lakadamyali M, Raya A, Fraser SE | Proceedings of the National Academy of Sciences of the United States of America | 29192024 | Proc Natl Acad Sci U S A | 2017 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/29192024 |
| Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. | Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S | Nature protocols | 30675035 | Nat Protoc | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30675035 |
| Dynamic heterogeneity and DNA methylation in embryonic stem cells. | Singer ZS, Yong J, Tischler J, Hackett JA, Altinok A, Surani MA, Cai L, Elowitz MB | Molecular cell | 25038413 | Mol Cell | 2014 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/25038413 |
| FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans. | Minor PJ, He TF, Sohn CH, Asthagiri AR, Sternberg PW | Development (Cambridge, England) | 23946444 | Development | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23946444 |
| Synthetic recording and in situ readout of lineage information in single cells. | Frieda KL, Linton JM, Hormoz S, Choi J, Chow KK, Singer ZS, Budde MW, Elowitz MB, Cai L | Nature | 27869821 | Nature | 2017 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/27869821 |
| Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. | Hormoz S, Singer ZS, Linton JM, Antebi YE, Shraiman BI, Elowitz MB | Cell systems | 27883889 | Cell Syst | 2016 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/27883889 |
| Profiling the transcriptome with RNA SPOTs. | Eng CL, Shah S, Thomassie J, Cai L | Nature methods | 29131163 | Nat Methods | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29131163 |
| Tuning Methylation-Dependent Silencing Dynamics by Synthetic Modulation of CpG Density. | Ma Y, Budde MW, Zhu J, Elowitz MB | ACS synthetic biology | 37572041 | ACS Synth Biol | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37572041 |
| In vivo robotics: the automation of neuroscience and other intact-system biological fields. | Kodandaramaiah SB, Boyden ES, Forest CR | Annals of the New York Academy of Sciences | 23841584 | Ann N Y Acad Sci | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23841584 |
| Nanotools for neuroscience and brain activity mapping. | Alivisatos AP, Andrews AM, Boyden ES, Chun M, Church GM, Deisseroth K, Donoghue JP, Fraser SE, Lippincott-Schwartz J, Looger LL, Masmanidis S, McEuen PL, Nurmikko AV, Park H, Peterka DS, Reid C, Roukes ML, Scherer A, Schnitzer M, Sejnowski TJ, Shepard KL, Tsao D, Turrigiano G, Weiss PS, Xu C, Yuste R, Zhuang X | ACS nano | 23514423 | ACS Nano | 2013 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/23514423 |
| Integration of autopatching with automated pipette and cell detection in vitro. | Wu 吴秋雨 Q, Kolb I, Callahan BM, Su Z, Stoy W, Kodandaramaiah SB, Neve R, Zeng H, Boyden ES, Forest CR, Chubykin AA | Journal of neurophysiology | 27385800 | J Neurophysiol | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27385800 |
| Advances in the automation of whole-cell patch clamp technology. | Suk HJ, Boyden ES, van Welie I | Journal of neuroscience methods | 31336060 | J Neurosci Methods | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31336060 |
| High-yield, automated intracellular electrophysiology in retinal pigment epithelia. | Lewallen CF, Wan Q, Maminishkis A, Stoy W, Kolb I, Hotaling N, Bharti K, Forest CR | Journal of neuroscience methods | 31562888 | J Neurosci Methods | 2019 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31562888 |
| Gamma frequency entrainment attenuates amyloid load and modifies microglia. | Iaccarino HF, Singer AC, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai LH | Nature | 27929004 | Nature | 2016 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/27929004 |
| Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions. | Lee TJ, Lewallen CF, Bumbarger DJ, Yunker PJ, Reid RC, Forest CR | Journal of colloid and interface science | 30041112 | J Colloid Interface Sci | 2018 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/30041112 |
| Shared and distinct transcriptomic cell types across neocortical areas. | Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H | Nature | 30382198 | Nature | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30382198 |
| A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. | Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES | Nature chemical biology | 29483642 | Nat Chem Biol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29483642 |
| Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics. | Lee TJ, Yip MC, Kumar A, Lewallen CF, Bumbarger DJ, Reid RC, Forest CR | eNeuro | 32094293 | eNeuro | 2020 Mar/Apr | https://www.ncbi.nlm.nih.gov/pubmed/32094293 |
| Closed-loop, ultraprecise, automated craniotomies. | Pak N, Siegle JH, Kinney JP, Denman DJ, Blanche TJ, Boyden ES | Journal of neurophysiology | 25855700 | J Neurophysiol | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/25855700 |
| Assembly and operation of the autopatcher for automated intracellular neural recording in vivo. | Kodandaramaiah SB, Holst GL, Wickersham IR, Singer AC, Franzesi GT, McKinnon ML, Forest CR, Boyden ES | Nature protocols | 26938115 | Nat Protoc | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26938115 |
| Mesoscale-duration activated states gate spiking in response to fast rises in membrane voltage in the awake brain. | Singer AC, Talei Franzesi G, Kodandaramaiah SB, Flores FJ, Cohen JD, Lee AK, Borgers C, Forest CR, Kopell NJ, Boyden ES | Journal of neurophysiology | 28566460 | J Neurophysiol | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28566460 |
| Cellular anatomy of the mouse primary motor cortex. | Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW | Nature | 34616071 | Nature | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34616071 |
| Deep learning-based real-time detection of neurons in brain slices for in vitro physiology. | Yip MC, Gonzalez MM, Valenta CR, Rowan MJM, Forest CR | Scientific reports | 33727679 | Sci Rep | 2021 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/33727679 |
| Screening channelrhodopsins using robotic intracellular electrophysiology and single cell sequencing. | Ehrlich S, VandeLoo AD, Badawy M, Gonzalez MM, Stockslager M, Yang A, Sinha S, Bracha S, Park D, Magondu B, Yang B, Boyden ES, Forest CR | bioRxiv : the preprint server for biology | 40894559 | bioRxiv | 2025 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/40894559 |
| Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues. | Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES | bioRxiv : the preprint server for biology | 38496681 | bioRxiv | 2024 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/38496681 |
| Patch-walking, a coordinated multi-pipette patch clamp for efficiently finding synaptic connections. | Yip MC, Gonzalez MM, Lewallen CF, Landry CR, Kolb I, Yang B, Stoy WM, Fong MF, Rowan MJM, Boyden ES, Forest CR | eLife | 39556439 | Elife | 2024 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/39556439 |
| SAMCell: Generalized Label-Free Biological Cell Segmentation with Segment Anything. | VandeLoo AD, Malta NJ, Aponte E, van Zyl C, Xu D, Forest CR | bioRxiv : the preprint server for biology | 39974978 | bioRxiv | 2025 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/39974978 |
| Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. | Suk HJ, van Welie I, Kodandaramaiah SB, Allen B, Forest CR, Boyden ES | Neuron | 28858614 | Neuron | 2017 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/28858614 |
| Optical method for automated measurement of glass micropipette tip geometry. | Stockslager MA, Capocasale CM, Holst GL, Simon MD, Li Y, McGruder DJ, Rousseau EB, Stoy WA, Sulchek T, Forest CR | Precision engineering | 27672230 | Precis Eng | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27672230 |
| Thermally multiplexed polymerase chain reaction. | Phaneuf CR, Pak N, Saunders DC, Holst GL, Birjiniuk J, Nagpal N, Culpepper S, Popler E, Shane AL, Jerris R, Forest CR | Biomicrofluidics | 26339317 | Biomicrofluidics | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26339317 |
| System for Rapid, Precise Modulation of Intraocular Pressure, toward Minimally-Invasive In Vivo Measurement of Intracranial Pressure. | Stockslager MA, Samuels BC, Allingham RR, Klesmith ZA, Schwaner SA, Forest CR, Ethier CR | PloS one | 26771837 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26771837 |
| Cell Membrane Tracking in Living Brain Tissue Using Differential Interference Contrast Microscopy. | Lee J, Kolb I, Forest CR, Rozell CJ | IEEE transactions on image processing : a publication of the IEEE Signal Processing Society | 29346099 | IEEE Trans Image Process | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29346099 |
| Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells. | Gouwens NW, Sorensen SA, Baftizadeh F, Budzillo A, Lee BR, Jarsky T, Alfiler L, Baker K, Barkan E, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Crichton K, Daigle TL, Dalley R, de Frates RA, Dee N, Desta T, Lee SD, Dotson N, Egdorf T, Ellingwood L, Enstrom R, Esposito L, Farrell C, Feng D, Fong O, Gala R, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Graybuck L, Gu H, Hadley K, Hawrylycz MJ, Henry AM, Hill D, Hupp M, Kebede S, Kim TK, Kim L, Kroll M, Lee C, Link KE, Mallory M, Mann R, Maxwell M, McGraw M, McMillen D, Mukora A, Ng L, Ng L, Ngo K, Nicovich PR, Oldre A, Park D, Peng H, Penn O, Pham T, Pom A, Popović Z, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Robertson M, Ronellenfitch K, Ruiz A, Sandman D, Smith K, Sulc J, Sunkin SM, Szafer A, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Ward K, Williams G, Zhou Z, Ting JT, Arkhipov A, Sümbül U, Lein ES, Koch C, Yao Z, Tasic B, Berg J, Murphy GJ, Zeng H | Cell | 33186530 | Cell | 2020 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/33186530 |
| Human neocortical expansion involves glutamatergic neuron diversification. | Berg J, Sorensen SA, Ting JT, Miller JA, Chartrand T, Buchin A, Bakken TE, Budzillo A, Dee N, Ding SL, Gouwens NW, Hodge RD, Kalmbach B, Lee C, Lee BR, Alfiler L, Baker K, Barkan E, Beller A, Berry K, Bertagnolli D, Bickley K, Bomben J, Braun T, Brouner K, Casper T, Chong P, Crichton K, Dalley R, de Frates R, Desta T, Lee SD, D'Orazi F, Dotson N, Egdorf T, Enstrom R, Farrell C, Feng D, Fong O, Furdan S, Galakhova AA, Gamlin C, Gary A, Glandon A, Goldy J, Gorham M, Goriounova NA, Gratiy S, Graybuck L, Gu H, Hadley K, Hansen N, Heistek TS, Henry AM, Heyer DB, Hill D, Hill C, Hupp M, Jarsky T, Kebede S, Keene L, Kim L, Kim MH, Kroll M, Latimer C, Levi BP, Link KE, Mallory M, Mann R, Marshall D, Maxwell M, McGraw M, McMillen D, Melief E, Mertens EJ, Mezei L, Mihut N, Mok S, Molnar G, Mukora A, Ng L, Ngo K, Nicovich PR, Nyhus J, Olah G, Oldre A, Omstead V, Ozsvar A, Park D, Peng H, Pham T, Pom CA, Potekhina L, Rajanbabu R, Ransford S, Reid D, Rimorin C, Ruiz A, Sandman D, Sulc J, Sunkin SM, Szafer A, Szemenyei V, Thomsen ER, Tieu M, Torkelson A, Trinh J, Tung H, Wakeman W, Waleboer F, Ward K, Wilbers R, Williams G, Yao Z, Yoon JG, Anastassiou C, Arkhipov A, Barzo P, Bernard A, Cobbs C, de Witt Hamer PC, Ellenbogen RG, Esposito L, Ferreira M, Gwinn RP, Hawrylycz MJ, Hof PR, Idema S, Jones AR, Keene CD, Ko AL, Murphy GJ, Ng L, Ojemann JG, Patel AP, Phillips JW, Silbergeld DL, Smith K, Tasic B, Yuste R, Segev I, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Koch C, Lein ES | Nature | 34616067 | Nature | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34616067 |
| Morphological diversity of single neurons in molecularly defined cell types. | Peng H, Xie P, Liu L, Kuang X, Wang Y, Qu L, Gong H, Jiang S, Li A, Ruan Z, Ding L, Yao Z, Chen C, Chen M, Daigle TL, Dalley R, Ding Z, Duan Y, Feiner A, He P, Hill C, Hirokawa KE, Hong G, Huang L, Kebede S, Kuo HC, Larsen R, Lesnar P, Li L, Li Q, Li X, Li Y, Li Y, Liu A, Lu D, Mok S, Ng L, Nguyen TN, Ouyang Q, Pan J, Shen E, Song Y, Sunkin SM, Tasic B, Veldman MB, Wakeman W, Wan W, Wang P, Wang Q, Wang T, Wang Y, Xiong F, Xiong W, Xu W, Ye M, Yin L, Yu Y, Yuan J, Yuan J, Yun Z, Zeng S, Zhang S, Zhao S, Zhao Z, Zhou Z, Huang ZJ, Esposito L, Hawrylycz MJ, Sorensen SA, Yang XW, Zheng Y, Gu Z, Xie W, Koch C, Luo Q, Harris JA, Wang Y, Zeng H | Nature | 34616072 | Nature | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34616072 |
| Autonomous patch-clamp robot for functional characterization of neurons in vivo: development and application to mouse visual cortex. | Holst GL, Stoy W, Yang B, Kolb I, Kodandaramaiah SB, Li L, Knoblich U, Zeng H, Haider B, Boyden ES, Forest CR | Journal of neurophysiology | 30969898 | J Neurophysiol | 2019 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/30969898 |
| Automated Intracellular Pharmacological Electrophysiology for Ligand-Gated Ionotropic Receptor and Pharmacology Screening. | Perszyk RE, Yip MC, McConnell OL, Wang ET, Jenkins A, Traynelis SF, Forest CR | Molecular pharmacology | 33958481 | Mol Pharmacol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33958481 |
| Classification of electrophysiological and morphological neuron types in the mouse visual cortex. | Gouwens NW, Sorensen SA, Berg J, Lee C, Jarsky T, Ting J, Sunkin SM, Feng D, Anastassiou CA, Barkan E, Bickley K, Blesie N, Braun T, Brouner K, Budzillo A, Caldejon S, Casper T, Castelli D, Chong P, Crichton K, Cuhaciyan C, Daigle TL, Dalley R, Dee N, Desta T, Ding SL, Dingman S, Doperalski A, Dotson N, Egdorf T, Fisher M, de Frates RA, Garren E, Garwood M, Gary A, Gaudreault N, Godfrey K, Gorham M, Gu H, Habel C, Hadley K, Harrington J, Harris JA, Henry A, Hill D, Josephsen S, Kebede S, Kim L, Kroll M, Lee B, Lemon T, Link KE, Liu X, Long B, Mann R, McGraw M, Mihalas S, Mukora A, Murphy GJ, Ng L, Ngo K, Nguyen TN, Nicovich PR, Oldre A, Park D, Parry S, Perkins J, Potekhina L, Reid D, Robertson M, Sandman D, Schroedter M, Slaughterbeck C, Soler-Llavina G, Sulc J, Szafer A, Tasic B, Taskin N, Teeter C, Thatra N, Tung H, Wakeman W, Williams G, Young R, Zhou Z, Farrell C, Peng H, Hawrylycz MJ, Lein E, Ng L, Arkhipov A, Bernard A, Phillips JW, Zeng H, Koch C | Nature neuroscience | 31209381 | Nat Neurosci | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31209381 |
| Automated in vivo patch-clamp evaluation of extracellular multielectrode array spike recording capability. | Allen BD, Moore-Kochlacs C, Bernstein JG, Kinney JP, Scholvin J, Seoane LF, Chronopoulos C, Lamantia C, Kodandaramaiah SB, Tegmark M, Boyden ES | Journal of neurophysiology | 29995597 | J Neurophysiol | 2018 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/29995597 |
| Patch-walking: Coordinated multi-pipette patch clamp for efficiently finding synaptic connections. | Yip MC, Gonzalez MM, Lewallen CF, Landry CR, Kolb I, Yang B, Stoy WM, Fong MF, Rowan MJM, Boyden ES, Forest CR | bioRxiv : the preprint server for biology | 39185225 | bioRxiv | 2024 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/39185225 |
| Method for Extracellular Electrochemical Impedance Spectroscopy on Epithelia. | Chien A, Lewallen CF, Khor H, Cegla AV, Guo R, McCarty NA, Bharti K, Forest CR | bioRxiv : the preprint server for biology | 41030979 | bioRxiv | 2025 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/41030979 |
| Noninvasive optical inhibition with a red-shifted microbial rhodopsin. | Chuong AS, Miri ML, Busskamp V, Matthews GA, Acker LC, Sørensen AT, Young A, Klapoetke NC, Henninger MA, Kodandaramaiah SB, Ogawa M, Ramanlal SB, Bandler RC, Allen BD, Forest CR, Chow BY, Han X, Lin Y, Tye KM, Roska B, Cardin JA, Boyden ES | Nature neuroscience | 24997763 | Nat Neurosci | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24997763 |
| Stress Enables Reinforcement-Elicited Serotonergic Consolidation of Fear Memory. | Baratta MV, Kodandaramaiah SB, Monahan PE, Yao J, Weber MD, Lin PA, Gisabella B, Petrossian N, Amat J, Kim K, Yang A, Forest CR, Boyden ES, Goosens KA | Biological psychiatry | 26248536 | Biol Psychiatry | 2016 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/26248536 |
| Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. | Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Levi B, Gray LT, Sorensen SA, Dolbeare T, Bertagnolli D, Goldy J, Shapovalova N, Parry S, Lee C, Smith K, Bernard A, Madisen L, Sunkin SM, Hawrylycz M, Koch C, Zeng H | Nature neuroscience | 26727548 | Nat Neurosci | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26727548 |
| A robot for high yield electrophysiology and morphology of single neurons in vivo. | Li L, Ouellette B, Stoy WA, Garren EJ, Daigle TL, Forest CR, Koch C, Zeng H | Nature communications | 28569837 | Nat Commun | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28569837 |
| Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. | Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu CC, English BP, Gao L, Martorell A, Suk HJ, Yoshida F, DeGennaro EM, Roossien DH, Gong G, Seneviratne U, Tannenbaum SR, Desimone R, Cai D, Boyden ES | Nature biotechnology | 27376584 | Nat Biotechnol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27376584 |
| Iterative expansion microscopy. | Chang JB, Chen F, Yoon YG, Jung EE, Babcock H, Kang JS, Asano S, Suk HJ, Pak N, Tillberg PW, Wassie AT, Cai D, Boyden ES | Nature methods | 28417997 | Nat Methods | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28417997 |
| Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording. | Harrison RR, Kolb I, Kodandaramaiah SB, Chubykin AA, Yang A, Bear MF, Boyden ES, Forest CR | Journal of neurophysiology | 25429119 | J Neurophysiol | 2015 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/25429119 |
| Cleaning patch-clamp pipettes for immediate reuse. | Kolb I, Stoy WA, Rousseau EB, Moody OA, Jenkins A, Forest CR | Scientific reports | 27725751 | Sci Rep | 2016 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/27725751 |
| Neuronal cell-type classification: challenges, opportunities and the path forward. | Zeng H, Sanes JR | Nature reviews. Neuroscience | 28775344 | Nat Rev Neurosci | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28775344 |
| A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. | Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H | Cell | 34004146 | Cell | 2021 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/34004146 |
| Machine Learning-Based Pipette Positional Correction for Automatic Patch Clamp In Vitro. | Gonzalez MM, Lewallen CF, Yip MC, Forest CR | eNeuro | 34312222 | eNeuro | 2021 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/34312222 |
| Method for Rapid Enzymatic Cleaning for Reuse of Patch Clamp Pipettes: Increasing Throughput by Eliminating Manual Pipette Replacement between Patch Clamp Attempts. | Landry CR, Yip MC, Kolb I, Stoy WA, Gonzalez MM, Forest CR | Bio-protocol | 34395724 | Bio Protoc | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/34395724 |
| Neuronal cell-subtype specificity of neural synchronization in mouse primary visual cortex. | Knoblich U, Huang L, Zeng H, Li L | Nature communications | 31182715 | Nat Commun | 2019 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/31182715 |
| Hierarchical organization of cortical and thalamic connectivity. | Harris JA, Mihalas S, Hirokawa KE, Whitesell JD, Choi H, Bernard A, Bohn P, Caldejon S, Casal L, Cho A, Feiner A, Feng D, Gaudreault N, Gerfen CR, Graddis N, Groblewski PA, Henry AM, Ho A, Howard R, Knox JE, Kuan L, Kuang X, Lecoq J, Lesnar P, Li Y, Luviano J, McConoughey S, Mortrud MT, Naeemi M, Ng L, Oh SW, Ouellette B, Shen E, Sorensen SA, Wakeman W, Wang Q, Wang Y, Williford A, Phillips JW, Jones AR, Koch C, Zeng H | Nature | 31666704 | Nature | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31666704 |
| PatcherBot: a single-cell electrophysiology robot for adherent cells and brain slices. | Kolb I, Landry CR, Yip MC, Lewallen CF, Stoy WA, Lee J, Felouzis A, Yang B, Boyden ES, Rozell CJ, Forest CR | Journal of neural engineering | 30970335 | J Neural Eng | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30970335 |
| Stabilization of Aliphatic Phosphines by Auxiliary Phosphine Sulfides Offers Zeptomolar Affinity and Unprecedented Selectivity for Probing Biological Cu(I). | Morgan MT, Yang B, Harankhedkar S, Nabatilan A, Bourassa D, McCallum AM, Sun F, Wu R, Forest CR, Fahrni CJ | Angewandte Chemie (International ed. in English) | 29885022 | Angew Chem Int Ed Engl | 2018 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/29885022 |
| Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging. | Piatkevich KD, Suk HJ, Kodandaramaiah SB, Yoshida F, DeGennaro EM, Drobizhev M, Hughes TE, Desimone R, Boyden ES, Verkhusha VV | Biophysical journal | 29017728 | Biophys J | 2017 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/29017728 |
| Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice. | Kolb I, Talei Franzesi G, Wang M, Kodandaramaiah SB, Forest CR, Boyden ES, Singer AC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 29279309 | J Neurosci | 2018 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/29279309 |
| Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. | Prevedel R, Yoon YG, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, Vaziri A | Nature methods | 24836920 | Nat Methods | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24836920 |
| Statistical analysis of molecular signal recording. | Glaser JI, Zamft BM, Marblestone AH, Moffitt JR, Tyo K, Boyden ES, Church G, Kording KP | PLoS computational biology | 23874187 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23874187 |
| Modeling and validation of autoinducer-mediated bacterial gene expression in microfluidic environments. | Austin CM, Stoy W, Su P, Harber MC, Bardill JP, Hammer BK, Forest CR | Biomicrofluidics | 25379076 | Biomicrofluidics | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/25379076 |
| Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. | Zhao Y, Bucur O, Irshad H, Chen F, Weins A, Stancu AL, Oh EY, DiStasio M, Torous V, Glass B, Stillman IE, Schnitt SJ, Beck AH, Boyden ES | Nature biotechnology | 28714966 | Nat Biotechnol | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28714966 |
| Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. | Suk HJ, van Welie I, Kodandaramaiah SB, Allen B, Forest CR, Boyden ES | Neuron | 28957673 | Neuron | 2017 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/28957673 |
| Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition. | Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH | Cell | 30879788 | Cell | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30879788 |
| Rapid Cortical Adaptation and the Role of Thalamic Synchrony during Wakefulness. | Wright NC, Borden PY, Liew YJ, Bolus MF, Stoy WM, Forest CR, Stanley GB | The Journal of neuroscience : the official journal of the Society for Neuroscience | 33986072 | J Neurosci | 2021 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/33986072 |
| Multi-neuron intracellular recording in vivo via interacting autopatching robots. | Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES, Forest CR | eLife | 29297466 | Elife | 2018 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/29297466 |
| Compensation of physiological motion enables high-yield whole-cell recording in vivo. | Stoy WM, Yang B, Kight A, Wright NC, Borden PY, Stanley GB, Forest CR | Journal of neuroscience methods | 33242530 | J Neurosci Methods | 2021 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/33242530 |
| Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice. | Veldman MB, Park CS, Eyermann CM, Zhang JY, Zuniga-Sanchez E, Hirano AA, Daigle TL, Foster NN, Zhu M, Langfelder P, Lopez IA, Brecha NC, Zipursky SL, Zeng H, Dong HW, Yang XW | Neuron | 32795398 | Neuron | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32795398 |
| Single-nucleus and single-cell transcriptomes compared in matched cortical cell types. | Bakken TE, Hodge RD, Miller JA, Yao Z, Nguyen TN, Aevermann B, Barkan E, Bertagnolli D, Casper T, Dee N, Garren E, Goldy J, Graybuck LT, Kroll M, Lasken RS, Lathia K, Parry S, Rimorin C, Scheuermann RH, Schork NJ, Shehata SI, Tieu M, Phillips JW, Bernard A, Smith KA, Zeng H, Lein ES, Tasic B | PloS one | 30586455 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30586455 |
| Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. | Jiang S, Wang Y, Liu L, Ding L, Ruan Z, Dong HW, Ascoli GA, Hawrylycz M, Zeng H, Peng H | Neuroinformatics | 35182359 | Neuroinformatics | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35182359 |
| A multimodal cell census and atlas of the mammalian primary motor cortex. | BRAIN Initiative Cell Census Network (BICCN) | Nature | 34616075 | Nature | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34616075 |
| A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve. | Caravaca AS, Tsaava T, Goldman L, Silverman H, Riggott G, Chavan SS, Bouton C, Tracey KJ, Desimone R, Boyden ES, Sohal HS, Olofsson PS | Journal of neural engineering | 28628030 | J Neural Eng | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28628030 |
| Electrophysiological and morphological characterization of single neurons in intact human brain organoids. | Landry CR, Yip MC, Zhou Y, Niu W, Wang Y, Yang B, Wen Z, Forest CR | Journal of neuroscience methods | 37236404 | J Neurosci Methods | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37236404 |
| Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues. | Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES | Nature communications | 39939319 | Nat Commun | 2025 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/39939319 |
| Method for Extracellular Electrochemical Impedance Spectroscopy on Epithelial Cell Monolayers. | Chien AJ, Lewallen CF, Khor H, Cegla AV, Guo R, Watson AL, Hatcher C, McCarty NA, Bharti K, Forest CR | Bio-protocol | 40657538 | Bio Protoc | 2025 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/40657538 |
| Connectomics of predicted Sst transcriptomic types in mouse visual cortex. | Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Joyce E, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu SC, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA | Nature | 40205210 | Nature | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40205210 |
| A shared neural ensemble links distinct contextual memories encoded close in time. | Cai DJ, Aharoni D, Shuman T, Shobe J, Biane J, Song W, Wei B, Veshkini M, La-Vu M, Lou J, Flores SE, Kim I, Sano Y, Zhou M, Baumgaertel K, Lavi A, Kamata M, Tuszynski M, Mayford M, Golshani P, Silva AJ | Nature | 27251287 | Nature | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27251287 |
| Elimination of dendritic spines with long-term memory is specific to active circuits. | Sanders J, Cowansage K, Baumgärtel K, Mayford M | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22956846 | J Neurosci | 2012 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/22956846 |
| Optogenetic reactivation of memory ensembles in the retrosplenial cortex induces systems consolidation. | de Sousa AF, Cowansage KK, Zutshi I, Cardozo LM, Yoo EJ, Leutgeb S, Mayford M | Proceedings of the National Academy of Sciences of the United States of America | 30877252 | Proc Natl Acad Sci U S A | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/30877252 |
| Exploring Memory Representations with Activity-Based Genetics. | Mayford M, Reijmers L | Cold Spring Harbor perspectives in biology | 26684182 | Cold Spring Harb Perspect Biol | 2015 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/26684182 |
| Direct reactivation of a coherent neocortical memory of context. | Cowansage KK, Shuman T, Dillingham BC, Chang A, Golshani P, Mayford M | Neuron | 25308330 | Neuron | 2014 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/25308330 |
| Synaptic potentiation of engram cells is necessary and sufficient for context fear memory. | M Cardozo L, de Sousa AF, Dillingham BC, Dang W, Job N, Yoo EJ, Ranamukhaarachchi SK, Yuan Q, Mayford M | Communications biology | 40467858 | Commun Biol | 2025 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/40467858 |
| Morphological effects on expression of growth differentiation factor 15 (GDF15), a marker of metastasis. | Aw Yong KM, Zeng Y, Vindivich D, Phillip JM, Wu PH, Wirtz D, Getzenberg RH | Journal of cellular physiology | 23996089 | J Cell Physiol | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23996089 |
| Focal adhesion size uniquely predicts cell migration. | Kim DH, Wirtz D | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23254340 | FASEB J | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23254340 |
| Multi-nucleated cells use ROS to induce breast cancer chemo-resistance in vitro and in vivo. | Parekh A, Das S, Parida S, Das CK, Dutta D, Mallick SK, Wu PH, Kumar BNP, Bharti R, Dey G, Banerjee K, Rajput S, Bharadwaj D, Pal I, Dey KK, Rajesh Y, Jena BC, Biswas A, Banik P, Pradhan AK, Das SK, Das AK, Dhara S, Fisher PB, Wirtz D, Mills GB, Mandal M | Oncogene | 29743594 | Oncogene | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29743594 |
| A robust nonlinear tissue-component discrimination method for computational pathology. | Sarnecki JS, Burns KH, Wood LD, Waters KM, Hruban RH, Wirtz D, Wu PH | Laboratory investigation; a journal of technical methods and pathology | 26779829 | Lab Invest | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26779829 |
| Nuclear lamin A/C harnesses the perinuclear apical actin cables to protect nuclear morphology. | Kim JK, Louhghalam A, Lee G, Schafer BW, Wirtz D, Kim DH | Nature communications | 29242553 | Nat Commun | 2017 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/29242553 |
| Local 3D matrix confinement determines division axis through cell shape. | He L, Chen W, Wu PH, Jimenez A, Wong BS, San A, Konstantopoulos K, Wirtz D | Oncotarget | 26515603 | Oncotarget | 2016 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/26515603 |
| Collective cancer cell invasion induced by coordinated contractile stresses. | Jimenez Valencia AM, Wu PH, Yogurtcu ON, Rao P, DiGiacomo J, Godet I, He L, Lee MH, Gilkes D, Sun SX, Wirtz D | Oncotarget | 26528856 | Oncotarget | 2015 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/26528856 |
| The Mechanobiology of Aging. | Phillip JM, Aifuwa I, Walston J, Wirtz D | Annual review of biomedical engineering | 26643020 | Annu Rev Biomed Eng | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26643020 |
| Statistical analysis of cell migration in 3D using the anisotropic persistent random walk model. | Wu PH, Giri A, Wirtz D | Nature protocols | 25719270 | Nat Protoc | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25719270 |
| MMSET/WHSC1 enhances DNA damage repair leading to an increase in resistance to chemotherapeutic agents. | Shah MY, Martinez-Garcia E, Phillip JM, Chambliss AB, Popovic R, Ezponda T, Small EC, Will C, Phillip MP, Neri P, Bahlis NJ, Wirtz D, Licht JD | Oncogene | 27109101 | Oncogene | 2016 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/27109101 |
| Normal mammary epithelial cells promote carcinoma basement membrane invasion by inducing microtubule-rich protrusions. | Lee MH, Wu PH, Gilkes D, Aifuwa I, Wirtz D | Oncotarget | 26334095 | Oncotarget | 2015 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/26334095 |
| Inhibition of Spleen Tyrosine Kinase Potentiates Paclitaxel-Induced Cytotoxicity in Ovarian Cancer Cells by Stabilizing Microtubules. | Yu Y, Gaillard S, Phillip JM, Huang TC, Pinto SM, Tessarollo NG, Zhang Z, Pandey A, Wirtz D, Ayhan A, Davidson B, Wang TL, Shih IeM | Cancer cell | 26096845 | Cancer Cell | 2015 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/26096845 |
| Small Extracellular Vesicles Promote Stiffness-mediated Metastasis. | Sneider A, Liu Y, Starich B, Du W, Nair PR, Marar C, Faqih N, Ciotti GE, Kim JH, Krishnan S, Ibrahim S, Igboko M, Locke A, Lewis DM, Hong H, Karl MN, Vij R, Russo GC, Gómez-de-Mariscal E, Habibi M, Muñoz-Barrutia A, Gu L, Eisinger-Mathason TSK, Wirtz D | Cancer research communications | 38630893 | Cancer Res Commun | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38630893 |
| Cytoskeletal tension induces the polarized architecture of the nucleus. | Kim DH, Wirtz D | Biomaterials | 25701041 | Biomaterials | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25701041 |
| COX-2 dependent regulation of mechanotransduction in human breast cancer cells. | Yoon AR, Stasinopoulos I, Kim JH, Yong HM, Kilic O, Wirtz D, Bhujwalla ZM, An SS | Cancer biology & therapy | 25701047 | Cancer Biol Ther | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25701047 |
| Senescent stromal cells induce cancer cell migration via inhibition of RhoA/ROCK/myosin-based cell contractility. | Aifuwa I, Giri A, Longe N, Lee SH, An SS, Wirtz D | Oncotarget | 26483365 | Oncotarget | 2015 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/26483365 |
| Inhibition of ovarian tumor cell invasiveness by targeting SYK in the tyrosine kinase signaling pathway. | Yu Y, Suryo Rahmanto Y, Lee MH, Wu PH, Phillip JM, Huang CH, Vitolo MI, Gaillard S, Martin SS, Wirtz D, Shih IM, Wang TL | Oncogene | 29643476 | Oncogene | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29643476 |
| Three-dimensional cell migration does not follow a random walk. | Wu PH, Giri A, Sun SX, Wirtz D | Proceedings of the National Academy of Sciences of the United States of America | 24594603 | Proc Natl Acad Sci U S A | 2014 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/24594603 |
| Deep learning identification of stiffness markers in breast cancer. | Sneider A, Kiemen A, Kim JH, Wu PH, Habibi M, White M, Phillip JM, Gu L, Wirtz D | Biomaterials | 35537336 | Biomaterials | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35537336 |
| Biophysical and biomolecular determination of cellular age in humans. | Phillip JM, Wu PH, Gilkes DM, Williams W, McGovern S, Daya J, Chen J, Aifuwa I, Lee JSH, Fan R, Walston J, Wirtz D | Nature biomedical engineering | 31372309 | Nat Biomed Eng | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31372309 |
| Recapitulation of molecular regulators of nuclear motion during cell migration. | Sneider A, Hah J, Wirtz D, Kim DH | Cell adhesion & migration | 30261154 | Cell Adh Migr | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30261154 |
| High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. | Lu Y, Chen JJ, Mu L, Xue Q, Wu Y, Wu PH, Li J, Vortmeyer AO, Miller-Jensen K, Wirtz D, Fan R | Analytical chemistry | 23339603 | Anal Chem | 2013 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/23339603 |
| Dimensional control of cancer cell migration. | Konstantopoulos K, Wu PH, Wirtz D | Biophysical journal | 23442847 | Biophys J | 2013 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/23442847 |
| Interstitial friction greatly impacts membrane mechanics. | Wirtz D | Biophysical journal | 23528079 | Biophys J | 2013 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/23528079 |
| Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration. | Jayatilaka H, Tyle P, Chen JJ, Kwak M, Ju J, Kim HJ, Lee JSH, Wu PH, Gilkes DM, Fan R, Wirtz D | Nature communications | 28548090 | Nat Commun | 2017 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/28548090 |
| Local mechanical response of cells to the controlled rotation of magnetic nanorods. | Castillo M, Ebensperger R, Wirtz D, Walczak M, Hurtado DE, Celedon A | Journal of biomedical materials research. Part B, Applied biomaterials | 24700696 | J Biomed Mater Res B Appl Biomater | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24700696 |
| Hypoxia and the extracellular matrix: drivers of tumour metastasis. | Gilkes DM, Semenza GL, Wirtz D | Nature reviews. Cancer | 24827502 | Nat Rev Cancer | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24827502 |
| Tight coupling between nucleus and cell migration through the perinuclear actin cap. | Kim DH, Cho S, Wirtz D | Journal of cell science | 24639463 | J Cell Sci | 2014 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/24639463 |
| Hypoxia-inducible factors mediate coordinated RhoA-ROCK1 expression and signaling in breast cancer cells. | Gilkes DM, Xiang L, Lee SJ, Chaturvedi P, Hubbi ME, Wirtz D, Semenza GL | Proceedings of the National Academy of Sciences of the United States of America | 24324133 | Proc Natl Acad Sci U S A | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24324133 |
| A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei. | Phillip JM, Han KS, Chen WC, Wirtz D, Wu PH | Nature protocols | 33424024 | Nat Protoc | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33424024 |
| Fractional re-distribution among cell motility states during ageing. | Phillip JM, Zamponi N, Phillip MP, Daya J, McGovern S, Williams W, Tschudi K, Jayatilaka H, Wu PH, Walston J, Wirtz D | Communications biology | 33469145 | Commun Biol | 2021 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/33469145 |
| Single-cell morphology encodes metastatic potential. | Wu PH, Gilkes DM, Phillip JM, Narkar A, Cheng TW, Marchand J, Lee MH, Li R, Wirtz D | Science advances | 32010778 | Sci Adv | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32010778 |
| A comparison of methods to assess cell mechanical properties. | Wu PH, Aroush DR, Asnacios A, Chen WC, Dokukin ME, Doss BL, Durand-Smet P, Ekpenyong A, Guck J, Guz NV, Janmey PA, Lee JSH, Moore NM, Ott A, Poh YC, Ros R, Sander M, Sokolov I, Staunton JR, Wang N, Whyte G, Wirtz D | Nature methods | 29915189 | Nat Methods | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29915189 |
| Tumor cell density regulates matrix metalloproteinases for enhanced migration. | Jayatilaka H, Umanzor FG, Shah V, Meirson T, Russo G, Starich B, Tyle P, Lee JSH, Khatau S, Gil-Henn H, Wirtz D | Oncotarget | 30220965 | Oncotarget | 2018 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/30220965 |
| Mammalian Cell Division in 3D Matrices via Quantitative Confocal Reflection Microscopy. | He L, Sneider A, Chen W, Karl M, Prasath V, Wu PH, Mattson G, Wirtz D | Journal of visualized experiments : JoVE | 29286363 | J Vis Exp | 2017 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/29286363 |
| Tumor proliferation and invasion are intrinsically coupled and unraveled through tunable spheroid and physics-based models. | Crawford AJ, Gomez-Cruz C, Russo GC, Huang W, Bhorkar I, Roy T, Muñoz-Barrutia A, Wirtz D, Garcia-Gonzalez D | Acta biomaterialia | 38160858 | Acta Biomater | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38160858 |
| Water permeation drives tumor cell migration in confined microenvironments. | Stroka KM, Jiang H, Chen SH, Tong Z, Wirtz D, Sun SX, Konstantopoulos K | Cell | 24726433 | Cell | 2014 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/24726433 |
| Nuclear envelope in nuclear positioning and cell migration. | Razafsky D, Wirtz D, Hodzic D | Advances in experimental medicine and biology | 24563361 | Adv Exp Med Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24563361 |
| Functional interplay between the cell cycle and cell phenotypes. | Chen WC, Wu PH, Phillip JM, Khatau SB, Choi JM, Dallas MR, Konstantopoulos K, Sun SX, Lee JS, Hodzic D, Wirtz D | Integrative biology : quantitative biosciences from nano to macro | 23319145 | Integr Biol (Camb) | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23319145 |
| Simultaneously defining cell phenotypes, cell cycle, and chromatin modifications at single-cell resolution. | Chambliss AB, Wu PH, Chen WC, Sun SX, Wirtz D | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23538711 | FASEB J | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23538711 |
| Switching from protease-independent to protease-dependent cancer cell invasion. | He L, Wirtz D | Biophysical journal | 25468324 | Biophys J | 2014 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/25468324 |
| Three-dimensional matrix fiber alignment modulates cell migration and MT1-MMP utility by spatially and temporally directing protrusions. | Fraley SI, Wu PH, He L, Feng Y, Krisnamurthy R, Longmore GD, Wirtz D | Scientific reports | 26423227 | Sci Rep | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26423227 |
| Evolution of cellular morpho-phenotypes in cancer metastasis. | Wu PH, Phillip JM, Khatau SB, Chen WC, Stirman J, Rosseel S, Tschudi K, Van Patten J, Wong M, Gupta S, Baras AS, Leek JT, Maitra A, Wirtz D | Scientific reports | 26675084 | Sci Rep | 2015 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/26675084 |
| EB1 and cytoplasmic dynein mediate protrusion dynamics for efficient 3-dimensional cell migration. | Jayatilaka H, Giri A, Karl M, Aifuwa I, Trenton NJ, Phillip JM, Khatau S, Wirtz D | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 29097501 | FASEB J | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29097501 |
| Universal artificial antigen presenting cells to selectively propagate T cells expressing chimeric antigen receptor independent of specificity. | Rushworth D, Jena B, Olivares S, Maiti S, Briggs N, Somanchi S, Dai J, Lee D, Cooper LJ | Journal of immunotherapy (Hagerstown, Md. : 1997) | 24714354 | J Immunother | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24714354 |
| Single-cell technologies for profiling T cells to enable monitoring of immunotherapies. | An X, Varadarajan N | Current opinion in chemical engineering | 31131208 | Curr Opin Chem Eng | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31131208 |
| Individual Motile CD4(+) T Cells Can Participate in Efficient Multikilling through Conjugation to Multiple Tumor Cells. | Liadi I, Singh H, Romain G, Rey-Villamizar N, Merouane A, Adolacion JR, Kebriaei P, Huls H, Qiu P, Roysam B, Cooper LJ, Varadarajan N | Cancer immunology research | 25711538 | Cancer Immunol Res | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25711538 |
| Constitutive Lck Activity Drives Sensitivity Differences between CD8+ Memory T Cell Subsets. | Moogk D, Zhong S, Yu Z, Liadi I, Rittase W, Fang V, Dougherty J, Perez-Garcia A, Osman I, Zhu C, Varadarajan N, Restifo NP, Frey AB, Krogsgaard M | Journal of immunology (Baltimore, Md. : 1950) | 27271569 | J Immunol | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27271569 |
| Multifaceted Role of BTLA in the Control of CD8(+) T-cell Fate after Antigen Encounter. | Ritthipichai K, Haymaker CL, Martinez M, Aschenbrenner A, Yi X, Zhang M, Kale C, Vence LM, Roszik J, Hailemichael Y, Overwijk WW, Varadarajan N, Nurieva R, Radvanyi LG, Hwu P, Bernatchez C | Clinical cancer research : an official journal of the American Association for Cancer Research | 28754817 | Clin Cancer Res | 2017 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/28754817 |
| Unmassked: Single-Cell Profiling of Immune Cell Populations in Tumors. | Varadarajan N | Molecular therapy : the journal of the American Society of Gene Therapy | 28684257 | Mol Ther | 2017 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/28684257 |
| Single-cell profiling of dynamic cytokine secretion and the phenotype of immune cells. | An X, Sendra VG, Liadi I, Ramesh B, Romain G, Haymaker C, Martinez-Paniagua M, Lu Y, Radvanyi LG, Roysam B, Varadarajan N | PloS one | 28837583 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28837583 |
| 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 A, Peyron I, Thaunat O, Dollinger C, Gilardin L, Sharma M, Wootla B, Rao DN, Padiolleau-Lefevre S, Boquet D, More A, Varadarajan N, Kaveri SV, Legendre C, Lacroix-Desmazes S | Journal of immunology (Baltimore, Md. : 1950) | 27067006 | J Immunol | 2016 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/27067006 |
| Tuning Sensitivity of CAR to EGFR Density Limits Recognition of Normal Tissue While Maintaining Potent Antitumor Activity. | Caruso HG, Hurton LV, Najjar A, Rushworth D, Ang S, Olivares S, Mi T, Switzer K, Singh H, Huls H, Lee DA, Heimberger AB, Champlin RE, Cooper LJ | Cancer research | 26330164 | Cancer Res | 2015 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/26330164 |
| Detection and isolation of auto-reactive human antibodies from primary B cells. | Sendra VG, Lie A, Romain G, Agarwal SK, Varadarajan N | Methods (San Diego, Calif.) | 23811296 | Methods | 2013 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/23811296 |
| Manufacture of clinical-grade CD19-specific T cells stably expressing chimeric antigen receptor using Sleeping Beauty system and artificial antigen presenting cells. | Singh H, Figliola MJ, Dawson MJ, Olivares S, Zhang L, Yang G, Maiti S, Manuri P, Senyukov V, Jena B, Kebriaei P, Champlin RE, Huls H, Cooper LJ | PloS one | 23741305 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23741305 |
| Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4(+) T cells. | Rath JA, Bajwa G, Carreres B, Hoyer E, Gruber I, Martínez-Paniagua MA, Yu YR, Nouraee N, Sadeghi F, Wu M, Wang T, Hebeisen M, Rufer N, Varadarajan N, Ho PC, Brenner MK, Gfeller D, Arber C | Science advances | 32923584 | Sci Adv | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32923584 |
| Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins. | Ramesh B, Sendra VG, Cirino PC, Varadarajan N | The Journal of biological chemistry | 23019324 | J Biol Chem | 2012 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/23019324 |
| Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING). | Merouane A, Rey-Villamizar N, Lu Y, Liadi I, Romain G, Lu J, Singh H, Cooper LJ, Varadarajan N, Roysam B | Bioinformatics (Oxford, England) | 26059718 | Bioinformatics | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26059718 |
| TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids. | Lu H, Li J, Martinez-Paniagua MA, Bandey IN, Amritkar A, Singh H, Mayerich D, Varadarajan N, Roysam B | Bioinformatics (Oxford, England) | 30084956 | Bioinformatics | 2019 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/30084956 |
| CAR T-cells that target acute B-lineage leukemia irrespective of CD19 expression. | Fousek K, Watanabe J, Joseph SK, George A, An X, Byrd TT, Morris JS, Luong A, Martínez-Paniagua MA, Sanber K, Navai SA, Gad AZ, Salsman VS, Mathew PR, Kim HN, Wagner DL, Brunetti L, Jang A, Baker ML, Varadarajan N, Hegde M, Kim YM, Heisterkamp N, Abdel-Azim H, Ahmed N | Leukemia | 32205861 | Leukemia | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32205861 |
| Quantitative high-throughput single-cell cytotoxicity assay for T cells. | Liadi I, Roszik J, Romain G, Cooper LJ, Varadarajan N | Journal of visualized experiments : JoVE | 23407457 | J Vis Exp | 2013 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/23407457 |
| Antibody Fc engineering improves frequency and promotes kinetic boosting of serial killing mediated by NK cells. | Romain G, Senyukov V, Rey-Villamizar N, Merouane A, Kelton W, Liadi I, Mahendra A, Charab W, Georgiou G, Roysam B, Lee DA, Varadarajan N | Blood | 25232058 | Blood | 2014 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/25232058 |
| Functional enrichment by direct plasmid recovery after fluorescence activated cell sorting. | Ramesh B, Frei CS, Cirino PC, Varadarajan N | BioTechniques | 26345509 | Biotechniques | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26345509 |
| Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA-Sequencing. | Mahendra A, Yang X, Abnouf S, Adolacion JRT, Park D, Soomro S, Roszik J, Coarfa C, Romain G, Wanzeck K, Bridges SL Jr, Aggarwal A, Qiu P, Agarwal SK, Mohan C, Varadarajan N | Arthritis & rheumatology (Hoboken, N.J.) | 30407753 | Arthritis Rheumatol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30407753 |
| A microfluidic assay for the quantification of the metastatic propensity of breast cancer specimens. | Yankaskas CL, Thompson KN, Paul CD, Vitolo MI, Mistriotis P, Mahendra A, Bajpai VK, Shea DJ, Manto KM, Chai AC, Varadarajan N, Kontrogianni-Konstantopoulos A, Martin SS, Konstantopoulos K | Nature biomedical engineering | 31061459 | Nat Biomed Eng | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31061459 |
| IgG Fc domains that bind C1q but not effector Fcγ receptors delineate the importance of complement-mediated effector functions. | Lee CH, Romain G, Yan W, Watanabe M, Charab W, Todorova B, Lee J, Triplett K, Donkor M, Lungu OI, Lux A, Marshall N, Lindorfer MA, Goff OR, Balbino B, Kang TH, Tanno H, Delidakis G, Alford C, Taylor RP, Nimmerjahn F, Varadarajan N, Bruhns P, Zhang YJ, Georgiou G | Nature immunology | 28604720 | Nat Immunol | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28604720 |
| Excess PLAC8 promotes an unconventional ERK2-dependent EMT in colon cancer. | Li C, Ma H, Wang Y, Cao Z, Graves-Deal R, Powell AE, Starchenko A, Ayers GD, Washington MK, Kamath V, Desai K, Gerdes MJ, Solnica-Krezel L, Coffey RJ | The Journal of clinical investigation | 24691442 | J Clin Invest | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24691442 |
| A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo. | Yang YP, Ma H, Starchenko A, Huh WJ, Li W, Hickman FE, Zhang Q, Franklin JL, Mortlock DP, Fuhrmann S, Carter BD, Ihrie RA, Coffey RJ | Cell reports | 28494873 | Cell Rep | 2017 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/28494873 |
| Understanding heterogeneous tumor microenvironment in metastatic melanoma. | Yan Y, Leontovich AA, Gerdes MJ, Desai K, Dong J, Sood A, Santamaria-Pang A, Mansfield AS, Chadwick C, Zhang R, Nevala WK, Flotte TJ, Ginty F, Markovic SN | PloS one | 31166985 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31166985 |
| Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. | Herring CA, Banerjee A, McKinley ET, Simmons AJ, Ping J, Roland JT, Franklin JL, Liu Q, Gerdes MJ, Coffey RJ, Lau KS | Cell systems | 29153838 | Cell Syst | 2018 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/29153838 |
| Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo. | Simmons AJ, Banerjee A, McKinley ET, Scurrah CR, Herring CA, Gewin LS, Masuzaki R, Karp SJ, Franklin JL, Gerdes MJ, Irish JM, Coffey RJ, Lau KS | Molecular systems biology | 26519361 | Mol Syst Biol | 2015 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/26519361 |
| Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks. | Simmons AJ, Scurrah CR, McKinley ET, Herring CA, Irish JM, Washington MK, Coffey RJ, Lau KS | Science signaling | 27729552 | Sci Signal | 2016 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/27729552 |
| Optimized multiplex immunofluorescence single-cell analysis reveals tuft cell heterogeneity. | McKinley ET, Sui Y, Al-Kofahi Y, Millis BA, Tyska MJ, Roland JT, Santamaria-Pang A, Ohland CL, Jobin C, Franklin JL, Lau KS, Gerdes MJ, Coffey RJ | JCI insight | 28570279 | JCI Insight | 2017 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/28570279 |
| Transcriptional expression of myelin basic protein in oligodendrocytes depends on functional syntaxin 4: a potential correlation with autocrine signaling. | Bijlard M, Klunder B, de Jonge JC, Nomden A, Tyagi S, de Vries H, Hoekstra D, Baron W | Molecular and cellular biology | 25512606 | Mol Cell Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25512606 |
| Imaging the Architecture of Granulomas Induced by Mycobacterium tuberculosis Infection with Single-molecule Fluorescence In Situ Hybridization. | Kumar R, Kolloli A, Subbian S, Kaushal D, Shi L, Tyagi S | Journal of immunology (Baltimore, Md. : 1950) | 38912840 | J Immunol | 2024 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/38912840 |
| Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status. | Vir P, Arrigucci R, Lakehal K, Davidow AL, Pine R, Tyagi S, Bushkin Y, Lardizabal A, Gennaro ML | PloS one | 26658491 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26658491 |
| Development of an Interferon-Gamma Release Assay (IGRA) to Aid Diagnosis of Histoplasmosis. | Datta K, LaRue R, Permpalung N, Das S, Zhang S, Mehta Steinke S, Bushkin Y, Nosanchuk JD, Marr KA | Journal of clinical microbiology | 36190260 | J Clin Microbiol | 2022 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/36190260 |
| Reduction in gene expression noise by targeted increase in accessibility at gene loci. | Fraser LCR, Dikdan RJ, Dey S, Singh A, Tyagi S | Proceedings of the National Academy of Sciences of the United States of America | 34625470 | Proc Natl Acad Sci U S A | 2021 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/34625470 |
| SuperSelective primer pairs for sensitive detection of rare somatic mutations. | Kramer FR, Vargas DY | Scientific reports | 34789731 | Sci Rep | 2021 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/34789731 |
| High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules. | Marras SAE, Bushkin Y, Tyagi S | Proceedings of the National Academy of Sciences of the United States of America | 31221755 | Proc Natl Acad Sci U S A | 2019 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/31221755 |
| Modulations of Homeostatic ACE2, CD147, GRP78 Pathways Correlate with Vascular and Endothelial Performance Markers during Pulmonary SARS-CoV-2 Infection. | Nisa A, Kumar R, Ramasamy S, Kolloli A, Olejnik J, Jalloh S, Gummuluru S, Subbian S, Bushkin Y | Cells | 38474396 | Cells | 2024 Feb 29 | https://www.ncbi.nlm.nih.gov/pubmed/38474396 |
| Single-cell analysis shows that paracrine signaling by first responder cells shapes the interferon-β response to viral infection. | Patil S, Fribourg M, Ge Y, Batish M, Tyagi S, Hayot F, Sealfon SC | Science signaling | 25670204 | Sci Signal | 2015 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/25670204 |
| Tuning noise in gene expression. | Tyagi S | Molecular systems biology | 25943344 | Mol Syst Biol | 2015 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/25943344 |
| CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. | Jalloh S, Olejnik J, Berrigan J, Nisa A, Suder EL, Akiyama H, Lei M, Tyagi S, Bushkin Y, Mühlberger E, Gummuluru S | bioRxiv : the preprint server for biology | 35378756 | bioRxiv | 2022 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/35378756 |
| Active Tuberculosis Is Characterized by Highly Differentiated Effector Memory Th1 Cells. | Arrigucci R, Lakehal K, Vir P, Handler D, Davidow AL, Herrera R, Estrada-Guzmán JD, Bushkin Y, Tyagi S, Lardizabal AA, Gennaro ML | Frontiers in immunology | 30283456 | Front Immunol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30283456 |
| Spermatid cyst polarization in Drosophila depends upon apkc and the CPEB family translational regulator orb2. | Xu S, Tyagi S, Schedl P | PLoS genetics | 24830287 | PLoS Genet | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24830287 |
| Fusion FISH imaging: single-molecule detection of gene fusion transcripts in situ. | Markey FB, Ruezinsky W, Tyagi S, Batish M | PloS one | 24675777 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24675777 |
| Barriers to transmission of transcriptional noise in a c-fos c-jun pathway. | Shah K, Tyagi S | Molecular systems biology | 24022005 | Mol Syst Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24022005 |
| Profiling T cell activation using single-molecule fluorescence in situ hybridization and flow cytometry. | Bushkin Y, Radford F, Pine R, Lardizabal A, Mangura BT, Gennaro ML, Tyagi S | Journal of immunology (Baltimore, Md. : 1950) | 25505292 | J Immunol | 2015 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/25505292 |
| CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses. | Jalloh S, Olejnik J, Berrigan J, Nisa A, Suder EL, Akiyama H, Lei M, Ramaswamy S, Tyagi S, Bushkin Y, Mühlberger E, Gummuluru S | PLoS pathogens | 36279285 | PLoS Pathog | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36279285 |
| Flow Cytometric Characterization of Antigen-Specific T Cells Based on RNA and Its Advantages in Detecting Infections and Immunological Disorders. | Radford F, Tyagi S, Gennaro ML, Pine R, Bushkin Y | Critical reviews in immunology | 28605344 | Crit Rev Immunol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28605344 |
| FISH-Flow, a protocol for the concurrent detection of mRNA and protein in single cells using fluorescence in situ hybridization and flow cytometry. | Arrigucci R, Bushkin Y, Radford F, Lakehal K, Vir P, Pine R, Martin D, Sugarman J, Zhao Y, Yap GS, Lardizabal AA, Tyagi S, Gennaro ML | Nature protocols | 28518171 | Nat Protoc | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28518171 |
| A New Interleukin-13 Amino-Coated Gadolinium Metallofullerene Nanoparticle for Targeted MRI Detection of Glioblastoma Tumor Cells. | Li T, Murphy S, Kiselev B, Bakshi KS, Zhang J, Eltahir A, Zhang Y, Chen Y, Zhu J, Davis RM, Madsen LA, Morris JR, Karolyi DR, LaConte SM, Sheng Z, Dorn HC | Journal of the American Chemical Society | 26022213 | J Am Chem Soc | 2015 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/26022213 |
| 21st century neurobehavioral theories of decision making in addiction: Review and evaluation. | Bickel WK, Mellis AM, Snider SE, Athamneh LN, Stein JS, Pope DA | Pharmacology, biochemistry, and behavior | 28942119 | Pharmacol Biochem Behav | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28942119 |
| Molecular mechanisms of experience-dependent plasticity in visual cortex. | Tropea D, Van Wart A, Sur M | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 18977729 | Philos Trans R Soc Lond B Biol Sci | 2009 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/18977729 |
| The origin and implementation of the Broadening Experiences in Scientific Training programs: an NIH common fund initiative. | Meyers FJ, Mathur A, Fuhrmann CN, O'Brien TC, Wefes I, Labosky PA, Duncan DS, August A, Feig A, Gould KL, Friedlander MJ, Schaffer CB, Van Wart A, Chalkley R | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 26432783 | FASEB J | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26432783 |
| Correction to "A New Interleukin-13 Amino-Coated Gadolinium Metallofullerene Nanoparticle for Targeted MRI Detection of Glioblastoma Tumor Cells". | Li T, Murphy S, Kiselev B, Bakshi KS, Zhang J, Eltahir A, Zhang Y, Chen Y, Zhu J, Davis RM, Madsen LA, Morris JR, Karolyi DR, LaConte SM, Sheng Z, Dorn HC | Journal of the American Chemical Society | 26820231 | J Am Chem Soc | 2016 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/26820231 |
| A cross-institutional analysis of the effects of broadening trainee professional development on research productivity. | Brandt PD, Sturzenegger Varvayanis S, Baas T, Bolgioni AF, Alder J, Petrie KA, Dominguez I, Brown AM, Stayart CA, Singh H, Van Wart A, Chow CS, Mathur A, Schreiber BM, Fruman DA, Bowden B, Wiesen CA, Golightly YM, Holmquist CE, Arneman D, Hall JD, Hyman LE, Gould KL, Chalkley R, Brennwald PJ, Layton RL | PLoS biology | 34264929 | PLoS Biol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34264929 |
| Applying Experiential Learning to Career Development Training for Biomedical Graduate Students and Postdocs: Perspectives on Program Development and Design. | Van Wart A, O'Brien TC, Varvayanis S, Alder J, Greenier J, Layton RL, Stayart CA, Wefes I, Brady AE | CBE life sciences education | 32822277 | CBE Life Sci Educ | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32822277 |
| Transforming training to reflect the workforce. | Mathur A, Meyers FJ, Chalkley R, O'Brien TC, Fuhrmann CN | Science translational medicine | 25925677 | Sci Transl Med | 2015 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/25925677 |
| Exposure to multiple career pathways by biomedical doctoral students at a public research university. | Mathur A, Chow CS, Feig AL, Kenaga H, Moldenhauer JA, Muthunayake NS, Ouellett ML, Pence LE, Straub V | PloS one | 29933412 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29933412 |
| Mastery of Transferrable Skills by Doctoral Scholars: Visualization using Digital Micro-credentialing. | Mathur A, Wood ME, Cano A | Change | 31656316 | Change | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/31656316 |
| Using Longitudinal Data on Career Outcomes to Promote Improvements and Diversity in Graduate Education. | Feig AL, Robinson L, Yan S, Byrd M, Mathur A | Change | 28804143 | Change | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28804143 |
| Visualization of gender, race, citizenship and academic performance in association with career outcomes of 15-year biomedical doctoral alumni at a public research university. | Mathur A, Cano A, Kohl M, Muthunayake NS, Vaidyanathan P, Wood ME, Ziyad M | PloS one | 29771987 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29771987 |
| Evolution of a Functional Taxonomy of Career Pathways for Biomedical Trainees. | Mathur A, Brandt P, Chalkley R, Daniel L, Labosky P, Stayart C, Meyers F | Journal of clinical and translational science | 30364657 | J Clin Transl Sci | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30364657 |
| Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States. | Chatterjee D, Nogueira AT, Wefes I, Chalkley R, Sturzenegger Varvayanis S, Fuhrmann CN, Varadarajan J, Jacob GA, Gaines CH, Hubbard NM, Chaudhary S, Layton RL | PloS one | 38507371 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38507371 |
| Career self-efficacy disparities in underrepresented biomedical scientist trainees. | Chatterjee D, Jacob GA, Varvayanis SS, Wefes I, Chalkley R, Nogueira AT, Fuhrmann CN, Varadarajan J, Hubbard NM, Gaines CH, Layton RL, Chaudhary S | PloS one | 36857379 | PLoS One | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36857379 |
| The "new normal": Adapting doctoral trainee career preparation for broad career paths in science. | St Clair R, Hutto T, MacBeth C, Newstetter W, McCarty NA, Melkers J | PloS one | 28542304 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28542304 |
| Applying inter-rater reliability to improve consistency in classifying PhD career outcomes. | Stayart CA, Brandt PD, Brown AM, Dahl T, Layton RL, Petrie KA, Flores-Kim EN, Peña CG, Fuhrmann CN, Monsalve GC | F1000Research | 32089837 | F1000Res | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32089837 |
| Faculty perceptions and knowledge of career development of trainees in biomedical science: What do we (think we) know? | Watts SW, Chatterjee D, Rojewski JW, Shoshkes Reiss C, Baas T, Gould KL, Brown AM, Chalkley R, Brandt P, Wefes I, Hyman L, Ford JK | PloS one | 30699144 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30699144 |
| Institutional Training Opportunities for PhD Students in Laboratory Medicine: An Unmet Career Development Need? | Colby JM, Wheeler FC, Petrie KA, Gould KL, Schmitz JE | The journal of applied laboratory medicine | 32445389 | J Appl Lab Med | 2020 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/32445389 |
| Survey of checkpoints along the pathway to diverse biomedical research faculty. | Meyers LC, Brown AM, Moneta-Koehler L, Chalkley R | PloS one | 29338019 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29338019 |
| From goal to outcome: Analyzing the progression of biomedical sciences PhD careers in a longitudinal study using an expanded taxonomy. | Brown AM, Meyers LC, Varadarajan J, Ward NJ, Cartailler JP, Chalkley RG, Gould KL, Petrie KA | FASEB bioAdvances | 37936923 | FASEB Bioadv | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37936923 |
| Principles and Strategies for Effective Teaching: A Workshop for Pre- and Postdoctoral Trainees in the Biomedical Sciences. | Hartley LM, Ferrara MJ, Handelsman MM, Rutebemberwa A, Wefes I | Journal of microbiology & biology education | 31890073 | J Microbiol Biol Educ | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31890073 |
| Enhancing Graduate and Postdoctoral Education To Create a Sustainable Biomedical Workforce. | Fuhrmann CN | Human gene therapy | 27762630 | Hum Gene Ther | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27762630 |
| Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action. | Silva EA, Des Jarlais C, Lindstaedt B, Rotman E, Watkins ES | PLoS biology | 27152650 | PLoS Biol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27152650 |
