Andrew Carroll

Publication Activity (10 Years)

Years Active: 2020-2024
Publications (10 Years): 33

Top Topics

High Throughput

Convolutional Neural Network

Genome Wide Association Study

Top Venues

bioRxiv : the preprint server for biology

Nature genetics

medRxiv : the preprint server for health sciences

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Yuchen Zhou, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction. Nature genetics (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Jimin Park, Daniel E Cook, Pi-Chuan Chang, Alexey Kolesnikov, Lucas Brambrink, Juan Carlos Mier, Joshua Gardner, Brandy McNulty, Samuel Sacco, Ayse Keskus, Asher Bryant, Tanveer Ahmad, Jyoti Shetty, Yongmei Zhao, Bao Tran, Giuseppe Narzisi, Adrienne Helland, Byunggil Yoo, Irina Pushel, Lisa A Lansdon, Chengpeng Bi, Adam Walter, Margaret Gibson, Tomi Pastinen, Midhat S Farooqi, Nicolas Robine, Karen H Miga, Andrew Carroll, Mikhail Kolmogorov, Benedict Paten, Kishwar Shafin
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies. bioRxiv : the preprint server for biology (2024)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Yuchen Zhou, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction. Nature genetics (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Yuchen Zhou, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction. Nature genetics 56 (8) (2024)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Yuchen Zhou, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction. Nature genetics 56 (8) (2024)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized pangenome references. Nature methods (2024)
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Lucas Brambrink, Brandy McNulty, John E Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. Nature communications 15 (1) (2024)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Yuchen Zhou, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning on high-dimensional clinical data improves genomic discovery and prediction. Nature genetics 56 (8) (2024)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning improves genomic discovery for lung function and respiratory disease prediction. medRxiv : the preprint server for health sciences (2023)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning improves genomic discovery for lung function and respiratory disease prediction. medRxiv : the preprint server for health sciences (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Justin Cosentino, Babak Behsaz, Babak Alipanahi, Zachary Ryan McCaw, Davin Hill, Tae-Hwi Schwantes-An, Dongbing Lai, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Inference of chronic obstructive pulmonary disease with deep learning on raw spirograms identifies new genetic loci and improves risk models. Nature genetics (2023)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning improves genomic discovery for lung function and respiratory disease prediction. medRxiv : the preprint server for health sciences (2023)
Taedong Yun, Justin Cosentino, Babak Behsaz, Zachary Ryan McCaw, Davin Hill, Robert N Luben, Dongbing Lai, John Bates, Howard Yang, Tae-Hwi Schwantes-An, Anthony P Khawaja, Andrew Carroll, Brian D Hobbs, Michael H Cho, Cory Y McLean, Farhad Hormozdiari
Unsupervised representation learning improves genomic discovery for lung function and respiratory disease prediction. medRxiv : the preprint server for health sciences (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Alexey Kolesnikov, Daniel E Cook, Maria Nattestad, Brandy McNulty, John E Gorzynski, Sneha D Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Local read haplotagging enables accurate long-read small variant calling. bioRxiv : the preprint server for biology (2023)
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee Eddie Loh, Patrick Masterson, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara Potapova, Arang Rhie, Joana L Rocha, Fedor D Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven Jared Solar, Jessica M Storer, Peter H Sudmant, Sweetalana, Alex Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary Alfano Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv : the preprint server for biology (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Jouni Sirén, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M Eizenga, Adam M Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten
Personalized Pangenome References. bioRxiv : the preprint server for biology (2023)
Daniel E Cook, Aarti Venkat, Dennis Yelizarov, Yannick Pouliot, Pi-Chuan Chang, Andrew Carroll, Francisco M De La Vega
A deep-learning-based RNA-seq germline variant caller. Bioinformatics advances 3 (1) (2023)
Charles Markello, Charles Huang, Alex Rodriguez, Andrew Carroll, Pi-Chuan Chang, Jordan M Eizenga, Thomas Markello, David Haussler, Benedict Paten
A complete pedigree-based graph workflow for rare candidate variant analysis. Genome research 32 (5) (2022)
John E Gorzynski, Sneha D Goenka, Kishwar Shafin, Tanner D Jensen, Dianna G Fisk, Megan E Grove, Elizabeth Spiteri, Trevor Pesout, Jean Monlong, Jonathan A Bernstein, Scott R Ceresnak, Pi-Chuan Chang, Jeffrey W Christle, Henry ChubbW, Kyla Dunn, Daniel R Garalde, Joseph Guillory, Maura R Z Ruzhnikov, Chris Wright, Courtney J Wusthoff, Katherine Xiong, Seth A Hollander, Gerald J Berry, Miten Jain, Fritz J Sedlazeck, Andrew Carroll, Benedict Paten, Euan A Ashley
Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic Shock. Circulation. Genomic and precision medicine 15 (2) (2022)
Zachary Ryan McCaw, Thomas Colthurst, Taedong Yun, Nicholas A Furlotte, Andrew Carroll, Babak Alipanahi, Cory Y McLean, Farhad Hormozdiari
DeepNull models non-linear covariate effects to improve phenotypic prediction and association power. Nature communications 13 (1) (2022)
Gunjan Baid, Daniel E Cook, Kishwar Shafin, Taedong Yun, Felipe Llinares-López, Quentin Berthet, Anastasiya Belyaeva, Armin Töpfer, Aaron M Wenger, William J Rowell, Howard Yang, Alexey Kolesnikov, Waleed Ammar, Jean-Philippe Vert, Ashish Vaswani, Cory Y McLean, Maria Nattestad, Pi-Chuan Chang, Andrew Carroll
DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nature biotechnology (2022)
John E Gorzynski, Sneha D Goenka, Kishwar Shafin, Tanner D Jensen, Dianna G Fisk, Megan E Grove, Elizabeth Spiteri, Trevor Pesout, Jean Monlong, Gunjan Baid, Jonathan A Bernstein, Scott Ceresnak, Pi-Chuan Chang, Jeffrey W Christle, Henry ChubbW, Karen P Dalton, Kyla Dunn, Daniel R Garalde, Joseph Guillory, Joshua W Knowles, Alexey Kolesnikov, Michael Ma, Tia Moscarello, Maria Nattestad, Marco Perez, Maura R Z Ruzhnikov, Mehrzad Samadi, Ankit Setia, Chris Wright, Courtney J Wusthoff, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J Sedlazeck, Andrew Carroll, Benedict Paten, Euan A Ashley
Ultrarapid Nanopore Genome Sequencing in a Critical Care Setting. The New England journal of medicine 386 (7) (2022)
Sneha D Goenka, John E Gorzynski, Kishwar Shafin, Dianna G Fisk, Trevor Pesout, Tanner D Jensen, Jean Monlong, Pi-Chuan Chang, Gunjan Baid, Jonathan A Bernstein, Jeffrey W Christle, Karen P Dalton, Daniel R Garalde, Megan E Grove, Joseph Guillory, Alexey Kolesnikov, Maria Nattestad, Maura R Z Ruzhnikov, Mehrzad Samadi, Ankit Sethia, Elizabeth Spiteri, Christopher J Wright, Katherine Xiong, Tong Zhu, Miten Jain, Fritz J Sedlazeck, Andrew Carroll, Benedict Paten, Euan A Ashley
Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nature biotechnology 40 (7) (2022)
Kishwar Shafin, Trevor Pesout, Pi-Chuan Chang, Maria Nattestad, Alexey Kolesnikov, Sidharth Goel, Gunjan Baid, Mikhail Kolmogorov, Jordan M Eizenga, Karen H Miga, Paolo Carnevali, Miten Jain, Andrew Carroll, Benedict Paten
Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nature methods 18 (11) (2021)
Jouni Sirén, Jean Monlong, Xian Chang, Adam M Novak, Jordan M Eizenga, Charles Markello, Jonas A Sibbesen, Glenn Hickey, Pi-Chuan Chang, Andrew Carroll, Namrata Gupta, Stacey Gabriel, Thomas W Blackwell, Aakrosh Ratan, Kent D Taylor, Stephen S Rich, Jerome I Rotter, David Haussler, Erik Garrison, Benedict Paten
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes. Science (New York, N.Y.) 374 (6574) (2021)
Jared Oâ Connell, Taedong Yun, Meghan Moreno, Helen Li, Nadia Litterman, Alexey Kolesnikov, Elizabeth Noblin, Pi-Chuan Chang, Anjali Shastri, Elizabeth H Dorfman, Suyash S Shringarpure, null null, Adam Auton, Andrew Carroll, Cory Y McLean
A population-specific reference panel for improved genotype imputation in African Americans. Communications biology 4 (1) (2021)
Lesley M Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher Mark Watson, Christos Proukakis, Wayne E Clarke, Naoki Nariai, Eric T Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M Wenger, Marc L Salit, Justin M Zook
A crowdsourced set of curated structural variants for the human genome. PLoS computational biology 16 (6) (2020)