Accurate, scalable cohort variant calls using DeepVariant and GLnexus
Yun, Taedong, Li, Helen, Chang, Pi-Chuan, Lin, Michael F, Carroll, Andrew, McLean, Cory Y
Published in Bioinformatics (05.04.2021)
Published in Bioinformatics (05.04.2021)
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An open resource for accurately benchmarking small variant and reference calls
Zook, Justin M., McDaniel, Jennifer, Olson, Nathan D., Wagner, Justin, Parikh, Hemang, Heaton, Haynes, Irvine, Sean A., Trigg, Len, Truty, Rebecca, McLean, Cory Y., De La Vega, Francisco M., Xiao, Chunlin, Sherry, Stephen, Salit, Marc
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Human-specific loss of regulatory DNA and the evolution of human-specific traits
Bejerano, Gill, Kingsley, David M, McLean, Cory Y, Reno, Philip L, Pollen, Alex A, Bassan, Abraham I, Capellini, Terence D, Guenther, Catherine, Indjeian, Vahan B, Lim, Xinhong, Menke, Douglas B, Schaar, Bruce T, Wenger, Aaron M
Published in Nature (London) (10.03.2011)
Published in Nature (London) (10.03.2011)
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DeepNull models non-linear covariate effects to improve phenotypic prediction and association power
McCaw, Zachary R., Colthurst, Thomas, Yun, Taedong, Furlotte, Nicholas A., Carroll, Andrew, Alipanahi, Babak, McLean, Cory Y., Hormozdiari, Farhad
Published in Nature communications (11.01.2022)
Published in Nature communications (11.01.2022)
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Longitudinal fundus imaging and its genome-wide association analysis provide evidence for a human retinal aging clock
Ahadi, Sara, Wilson, Kenneth A, Babenko, Boris, McLean, Cory Y, Bryant, Drew, Pritchard, Orion, Kumar, Ajay, Carrera, Enrique M, Lamy, Ricardo, Stewart, Jay M, Varadarajan, Avinash, Berndl, Marc, Kapahi, Pankaj, Bashir, Ali
Published in eLife (17.04.2023)
Published in eLife (17.04.2023)
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Predicting cardiovascular disease risk using photoplethysmography and deep learning
Weng, Wei-Hung, Baur, Sebastien, Daswani, Mayank, Chen, Christina, Harrell, Lauren, Kakarmath, Sujay, Jabara, Mariam, Behsaz, Babak, McLean, Cory Y, Matias, Yossi, Corrado, Greg S, Shetty, Shravya, Prabhakara, Shruthi, Liu, Yun, Danaei, Goodarz, Ardila, Diego
Published in PLOS global public health (2024)
Published in PLOS global public health (2024)
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Sequential regulatory activity prediction across chromosomes with convolutional neural networks
Kelley, David R, Reshef, Yakir A, Bileschi, Maxwell, Belanger, David, McLean, Cory Y, Snoek, Jasper
Published in Genome research (01.05.2018)
Published in Genome research (01.05.2018)
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A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae
Reno, Philip L, McLean, Cory Y, Hines, Jasmine E, Capellini, Terence D, Bejerano, Gill, Kingsley, David M
Published in PloS one (19.12.2013)
Published in PloS one (19.12.2013)
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A universal SNP and small-indel variant caller using deep neural networks
Poplin, Ryan, Chang, Pi-Chuan, Alexander, David, Schwartz, Scott, Colthurst, Thomas, Ku, Alexander, Newburger, Dan, Dijamco, Jojo, Nguyen, Nam, Afshar, Pegah T, Gross, Sam S, Dorfman, Lizzie, McLean, Cory Y, DePristo, Mark A
Published in Nature biotechnology (01.11.2018)
Published in Nature biotechnology (01.11.2018)
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GREAT improves functional interpretation of cis -regulatory regions
Bejerano, Gill, McLean, Cory Y, Bristor, Dave, Hiller, Michael, Clarke, Shoa L, Schaar, Bruce T, Lowe, Craig B, Wenger, Aaron M
Published in Nature biotechnology (01.05.2010)
Published in Nature biotechnology (01.05.2010)
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DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer
Baid, Gunjan, Cook, Daniel E., Shafin, Kishwar, Yun, Taedong, Llinares-López, Felipe, Berthet, Quentin, Belyaeva, Anastasiya, Töpfer, Armin, Wenger, Aaron M., Rowell, William J., Yang, Howard, Kolesnikov, Alexey, Ammar, Waleed, Vert, Jean-Philippe, Vaswani, Ashish, McLean, Cory Y., Nattestad, Maria, Chang, Pi-Chuan, Carroll, Andrew
Published in Nature biotechnology (01.02.2023)
Published in Nature biotechnology (01.02.2023)
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Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma
Johnson, Brett E., Mazor, Tali, Hong, Chibo, Barnes, Michael, Aihara, Koki, McLean, Cory Y., Fouse, Shaun D., Yamamoto, Shogo, Ueda, Hiroki, Tatsuno, Kenji, Asthana, Saurabh, Jalbert, Llewellyn E., Nelson, Sarah J., Bollen, Andrew W., Gustafson, W. Clay, Charron, Elise, Weiss, William A., Smirnov, Ivan V., Song, Jun S., Olshen, Adam B., Cha, Soonmee, Zhao, Yongjun, Moore, Richard A., Mungali, Andrew J., Jones, Steven J. M., Hirst, Martin, Marra, Marco A., Saito, Nobuhito, Aburatani, Hiroyuki, Mukasa, Akitake, Berger, Mitchel S., Chang, Susan M., Taylor, Barry S., Costello, Joseph F.
Published in Science (American Association for the Advancement of Science) (10.01.2014)
Published in Science (American Association for the Advancement of Science) (10.01.2014)
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Large-scale machine-learning-based phenotyping significantly improves genomic discovery for optic nerve head morphology
Alipanahi, Babak, Hormozdiari, Farhad, Behsaz, Babak, Cosentino, Justin, McCaw, Zachary R., Schorsch, Emanuel, Sculley, D., Dorfman, Elizabeth H., Foster, Paul J., Peng, Lily H., Phene, Sonia, Hammel, Naama, Carroll, Andrew, Khawaja, Anthony P., McLean, Cory Y.
Published in American journal of human genetics (01.07.2021)
Published in American journal of human genetics (01.07.2021)
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Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models
Cosentino, Justin, Behsaz, Babak, Alipanahi, Babak, McCaw, Zachary R., Hill, Davin, Schwantes-An, Tae-Hwi, Lai, Dongbing, Carroll, Andrew, Hobbs, Brian D., Cho, Michael H., McLean, Cory Y., Hormozdiari, Farhad
Published in Nature genetics (01.05.2023)
Published in Nature genetics (01.05.2023)
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Journal Article
GenomeWarp: an alignment-based variant coordinate transformation
McLean, Cory Y, Hwang, Yeongwoo, Poplin, Ryan, DePristo, Mark A
Published in Bioinformatics (01.11.2019)
Published in Bioinformatics (01.11.2019)
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Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction
Yun, Taedong, Cosentino, Justin, Behsaz, Babak, McCaw, Zachary R., Hill, Davin, Luben, Robert, Lai, Dongbing, Bates, John, Yang, Howard, Schwantes-An, Tae-Hwi, Zhou, Yuchen, Khawaja, Anthony P., Carroll, Andrew, Hobbs, Brian D., Cho, Michael H., McLean, Cory Y., Hormozdiari, Farhad
Published in Nature genetics (01.08.2024)
Published in Nature genetics (01.08.2024)
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Diagnosis of Parkinson's disease on the basis of clinical and genetic classification: a population-based modelling study
Nalls, Mike A, PhD, McLean, Cory Y, PhD, Rick, Jacqueline, PhD, Eberly, Shirley, MS, Hutten, Samantha J, PhD, Gwinn, Katrina, MD, Sutherland, Margaret, PhD, Martinez, Maria, PhD, Heutink, Peter, PhD, Williams, Nigel M, PhD, Hardy, John, PhD, Gasser, Thomas, MD, Brice, Alexis, MD, Price, T Ryan, MS, Nicolas, Aude, PhD, Keller, Margaux F, PhD, Molony, Cliona, PhD, Gibbs, J Raphael, MS, Chen-Plotkin, Alice, MD, Suh, Eunran, PhD, Letson, Christopher, BS, Fiandaca, Massimo S, MD, Mapstone, Mark, PhD, Federoff, Howard J, MD, Noyce, Alastair J, MRCP, Morris, Huw, MD, Van Deerlin, Vivianna M, MD, Weintraub, Daniel, MD, Zabetian, Cyrus, MD, Hernandez, Dena G, MS, Lesage, Suzanne, PhD, Mullins, Meghan, BA, Conley, Emily Drabant, PhD, Northover, Carrie A M, PhD, Frasier, Mark, PhD, Marek, Ken, MD, Day-Williams, Aaron G, PhD, Stone, David J, PhD, Ioannidis, John P A, Prof, Singleton, Andrew B, Dr
Published in Lancet neurology (01.10.2015)
Published in Lancet neurology (01.10.2015)
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PRISM offers a comprehensive genomic approach to transcription factor function prediction
Wenger, Aaron M, Clarke, Shoa L, Guturu, Harendra, Chen, Jenny, Schaar, Bruce T, McLean, Cory Y, Bejerano, Gill
Published in Genome research (01.05.2013)
Published in Genome research (01.05.2013)
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