Single Cell Analysis Program (SCAP)
Single Cell Analysis Program (SCAP)
Program Publications
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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 |
|---|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Ensuring that biomedical AI benefits diverse populations. | Zou J, Schiebinger L | EBioMedicine | 33962897 | EBioMedicine | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33962897 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Epigenomic analysis of multilineage differentiation of human embryonic stem cells. | Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B | Cell | 23664764 | Cell | 2013 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/23664764 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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