Comprehensive single-cell transcriptional profiling of a multicellular organism
Cao, Junyue, Packer, Jonathan S., Ramani, Vijay, Cusanovich, Darren A., Huynh, Chau, Daza, Riza, Qiu, Xiaojie, Lee, Choli, Furlan, Scott N., Steemers, Frank J., Adey, Andrew, Waterston, Robert H., Trapnell, Cole, Shendure, Jay
Published in Science (American Association for the Advancement of Science) (18.08.2017)
Published in Science (American Association for the Advancement of Science) (18.08.2017)
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Journal Article
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
Cusanovich, Darren A., Hill, Andrew J., Aghamirzaie, Delasa, Daza, Riza M., Pliner, Hannah A., Berletch, Joel B., Filippova, Galina N., Huang, Xingfan, Christiansen, Lena, DeWitt, William S., Lee, Choli, Regalado, Samuel G., Read, David F., Steemers, Frank J., Disteche, Christine M., Trapnell, Cole, Shendure, Jay
Published in Cell (23.08.2018)
Published in Cell (23.08.2018)
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Journal Article
CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions
Gasperini, Molly, Findlay, Gregory M., McKenna, Aaron, Milbank, Jennifer H., Lee, Choli, Zhang, Melissa D., Cusanovich, Darren A., Shendure, Jay
Published in American journal of human genetics (03.08.2017)
Published in American journal of human genetics (03.08.2017)
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Journal Article
Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations
O’Roak, Brian J., Vives, Laura, Girirajan, Santhosh, Karakoc, Emre, Krumm, Niklas, Coe, Bradley P., Levy, Roie, Ko, Arthur, Lee, Choli, Smith, Joshua D., Turner, Emily H., Stanaway, Ian B., Vernot, Benjamin, Malig, Maika, Baker, Carl, Reilly, Beau, Akey, Joshua M., Borenstein, Elhanan, Rieder, Mark J., Nickerson, Deborah A., Bernier, Raphael, Shendure, Jay, Eichler, Evan E.
Published in Nature (London) (10.05.2012)
Published in Nature (London) (10.05.2012)
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Journal Article
Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations
O'Roak, Brian J, Deriziotis, Pelagia, Lee, Choli, Vives, Laura, Schwartz, Jerrod J, Girirajan, Santhosh, Karakoc, Emre, MacKenzie, Alexandra P, Ng, Sarah B, Baker, Carl, Rieder, Mark J, Nickerson, Deborah A, Bernier, Raphael, Fisher, Simon E, Shendure, Jay, Eichler, Evan E
Published in Nature genetics (01.06.2011)
Published in Nature genetics (01.06.2011)
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Journal Article
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
Pe'er, Dana, Shendure, Jay, Patwardhan, Rupali P, Litvin, Oren, Lee, Choli, Young, David L
Published in Nature biotechnology (01.12.2009)
Published in Nature biotechnology (01.12.2009)
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Journal Article
Targeted capture and massively parallel sequencing of 12 human exomes
Ng, Sarah B, Shendure, Jay, Turner, Emily H, Robertson, Peggy D, Flygare, Steven D, Bigham, Abigail W, Lee, Choli, Shaffer, Tristan, Wong, Michelle, Bhattacharjee, Arindam, Eichler, Evan E, Bamshad, Michael, Nickerson, Deborah A
Published in Nature (London) (10.09.2009)
Published in Nature (London) (10.09.2009)
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Journal Article
Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders
O'Roak, Brian J., Vives, Laura, Fu, Wenqing, Egertson, Jarrett D., Stanaway, Ian B., Phelps, Ian G., Carvill, Gemma, Kumar, Akash, Lee, Choli, Ankenman, Katy, Munson, Jeff, Hiatt, Joseph B., Turner, Emily H., Levy, Roie, O'Day, Diana R., Krumm, Niklas, Coe, Bradley P., Martin, Beth K., Borenstein, Elhanan, Nickerson, Deborah A., Mefford, Heather C., Doherty, Dan, Akey, Joshua M., Bernier, Raphael, Eichler, Evan E., Shendure, Jay
Published in Science (American Association for the Advancement of Science) (21.12.2012)
Published in Science (American Association for the Advancement of Science) (21.12.2012)
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Journal Article
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
Ma, Wenxiu, Ay, Ferhat, Lee, Choli, Gulsoy, Gunhan, Deng, Xinxian, Cook, Savannah, Hesson, Jennifer, Cavanaugh, Christopher, Ware, Carol B, Krumm, Anton, Shendure, Jay, Blau, Carl Anthony, Disteche, Christine M, Noble, William S, Duan, Zhijun
Published in Nature methods (01.01.2015)
Published in Nature methods (01.01.2015)
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Journal Article
Massively parallel functional dissection of mammalian enhancers in vivo
Patwardhan, Rupali P, Hiatt, Joseph B, Witten, Daniela M, Kim, Mee J, Smith, Robin P, May, Dalit, Lee, Choli, Andrie, Jennifer M, Lee, Su-In, Cooper, Gregory M, Ahituv, Nadav, Pennacchio, Len A, Shendure, Jay
Published in Nature biotechnology (01.03.2012)
Published in Nature biotechnology (01.03.2012)
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Journal Article
A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
Roach, David J, Burton, Joshua N, Lee, Choli, Stackhouse, Bethany, Butler-Wu, Susan M, Cookson, Brad T, Shendure, Jay, Salipante, Stephen J
Published in PLoS genetics (01.07.2015)
Published in PLoS genetics (01.07.2015)
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Journal Article
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data
Kim, Hyeon-Jin, Yardimci, Galip Gürkan, Bonora, Giancarlo, Ramani, Vijay, Liu, Jie, Qiu, Ruolan, Lee, Choli, Hesson, Jennifer, Ware, Carol B, Shendure, Jay, Duan, Zhijun, Noble, William Stafford
Published in PLoS computational biology (18.09.2020)
Published in PLoS computational biology (18.09.2020)
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Journal Article
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
Salipante, Stephen J, Roach, David J, Kitzman, Jacob O, Snyder, Matthew W, Stackhouse, Bethany, Butler-Wu, Susan M, Lee, Choli, Cookson, Brad T, Shendure, Jay
Published in Genome research (01.01.2015)
Published in Genome research (01.01.2015)
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Journal Article
Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers
Kumar, Akash, White, Thomas A, MacKenzie, Alexandra P, Clegg, Nigel, Lee, Choli, Dumpit, Ruth F, Coleman, Ilsa, Ng, Sarah B, Salipante, Stephen J, Rieder, Mark J, Nickerson, Deborah A, Corey, Eva, Lange, Paul H, Morrissey, Colm, Vessella, Robert L, Nelson, Peter S, Shendure, Jay
Published in Proceedings of the National Academy of Sciences - PNAS (11.10.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (11.10.2011)
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Journal Article
Parallel, tag-directed assembly of locally derived short sequence reads
Hiatt, Joseph B, Shendure, Jay, Patwardhan, Rupali P, Turner, Emily H, Lee, Choli
Published in Nature methods (01.02.2010)
Published in Nature methods (01.02.2010)
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Journal Article
Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation
Bonora, Giancarlo, Ramani, Vijay, Singh, Ritambhara, Fang, He, Jackson, Dana L, Srivatsan, Sanjay, Qiu, Ruolan, Lee, Choli, Trapnell, Cole, Shendure, Jay, Duan, Zhijun, Deng, Xinxian, Noble, William S, Disteche, Christine M
Published in Genome Biology (27.09.2021)
Published in Genome Biology (27.09.2021)
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Journal Article
Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes
Kumar, Akash, Boyle, Evan A, Tokita, Mari, Mikheev, Andrei M, Sanger, Michelle C, Girard, Emily, Silber, John R, Gonzalez-Cuyar, Luis F, Hiatt, Joseph B, Adey, Andrew, Lee, Choli, Kitzman, Jacob O, Born, Donald E, Silbergeld, Daniel L, Olson, James M, Rostomily, Robert C, Shendure, Jay
Published in Genome biology (03.12.2014)
Published in Genome biology (03.12.2014)
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Journal Article
Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma
Campbell, Catarina D, Mohajeri, Kiana, Malig, Maika, Hormozdiari, Fereydoun, Nelson, Benjamin, Du, Gaixin, Patterson, Kristen M, Eng, Celeste, Torgerson, Dara G, Hu, Donglei, Herman, Catherine, Chong, Jessica X, Ko, Arthur, O'Roak, Brian J, Krumm, Niklas, Vives, Laura, Lee, Choli, Roth, Lindsey A, Rodriguez-Cintron, William, Rodriguez-Santana, Jose, Brigino-Buenaventura, Emerita, Davis, Adam, Meade, Kelley, LeNoir, Michael A, Thyne, Shannon, Jackson, Daniel J, Gern, James E, Lemanske, Jr, Robert F, Shendure, Jay, Abney, Mark, Burchard, Esteban G, Ober, Carole, Eichler, Evan E
Published in PloS one (12.08.2014)
Published in PloS one (12.08.2014)
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Journal Article
Correction: A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota
Roach, David J, Burton, Joshua N, Lee, Choli, Stackhouse, Bethany, Butler-Wu, Susan M, Cookson, Brad T, Shendure, Jay, Salipante, Stephen J
Published in PLoS genetics (01.04.2017)
Published in PLoS genetics (01.04.2017)
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Journal Article
Whole genome prediction for preimplantation genetic diagnosis
Kumar, Akash, Ryan, Allison, Kitzman, Jacob O, Wemmer, Nina, Snyder, Matthew W, Sigurjonsson, Styrmir, Lee, Choli, Banjevic, Milena, Zarutskie, Paul W, Lewis, Alexandra P, Shendure, Jay, Rabinowitz, Matthew
Published in Genome medicine (08.04.2015)
Published in Genome medicine (08.04.2015)
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