Anthony Capra (John A Capra, John Capra, J A Capra)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 70

Top Topics

Convolutional Neural Network

Machine Learning

Age Related Macular Degeneration

Top Venues

bioRxiv : the preprint server for biology

Genome biology and evolution

Nature communications

Bioinformatics (Oxford, England)

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

Publications

Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L Koleske, Niklas Handin, Virginia M Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin M Brand, Finn D Wolfreys, Jia Yang, Jason E Gestwicki, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet, Kathleen M Giacomini
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature communications 15 (1) (2024)
Gabriella O Estevam, Edmond M Linossi, Jingyou Rao, Christian B Macdonald, Ashraya Ravikumar, Karson M Chrispens, Anthony Capra, Willow Coyote-Maestas, Harold Pimentel, Eric A Collisson, Natalia Jura, Brian K Shoichet
Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv : the preprint server for biology (2024)
Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L Koleske, Niklas Handin, Virginia M Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin M Brand, Finn D Wolfreys, Jia Yang, Jason E Gestwicki, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet, Kathleen M Giacomini
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature communications 15 (1) (2024)
Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L Koleske, Niklas Handin, Virginia M Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin M Brand, Finn D Wolfreys, Jia Yang, Jason E Gestwicki, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet, Kathleen M Giacomini
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature communications 15 (1) (2024)
Christopher W Moth, Jonathan H Sheehan, Abdullah Al Mamun, R Michael Sivley, Alican Gulsevin, David C Rinker, Anthony Capra, Jens Meiler
VUStruct: a compute pipeline for high throughput and personalized structural biology. bioRxiv : the preprint server for biology (2024)
Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L Koleske, Niklas Handin, Virginia M Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin M Brand, Finn D Wolfreys, Jia Yang, Jason E Gestwicki, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet, Kathleen M Giacomini
Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature communications 15 (1) (2024)
Grace D Ramey, Alice S Tang, Thanaphong Phongpreecha, Monica M Yang, Sarah R Woldemariam, Tomiko T Oskotsky, Thomas J Montine, Isabel Allen, Zachary A Miller, Nima Aghaeepour, Anthony Capra, Marina Sirota
Exposure to autoimmune disorders increases Alzheimer's disease risk in a multi-site electronic health record analysis. medRxiv : the preprint server for health sciences (2024)
Christopher W Moth, Jonathan H Sheehan, Abdullah Al Mamun, R Michael Sivley, Alican Gulsevin, David C Rinker, Anthony Capra, Jens Meiler
VUStruct: a compute pipeline for high throughput and personalized structural biology. bioRxiv : the preprint server for biology (2024)
Christopher W Moth, Jonathan H Sheehan, Abdullah Al Mamun, R Michael Sivley, Alican Gulsevin, David C Rinker, Anthony Capra, Jens Meiler
VUStruct: a compute pipeline for high throughput and personalized structural biology. bioRxiv : the preprint server for biology (2024)
Gabriella O Estevam, Edmond M Linossi, Jingyou Rao, Christian B Macdonald, Ashraya Ravikumar, Karson M Chrispens, Anthony Capra, Willow Coyote-Maestas, Harold Pimentel, Eric A Collisson, Natalia Jura, Brian K Shoichet
Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv : the preprint server for biology (2024)
Mary Lauren Benton, Douglas M Ruderfer, Anthony Capra
Cis-regulatory landscape size, constraint, and tissue-specificity associate with gene function and expression. Genome biology and evolution (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Erin N Gilbertson, Colin M Brand, Evonne McArthur, David C Rinker, Shuzhen Kuang, Katherine S Pollard, Anthony Capra
Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv : the preprint server for biology (2023)
Erin N Gilbertson, Colin M Brand, Evonne McArthur, David C Rinker, Shuzhen Kuang, Katherine S Pollard, Anthony Capra
Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv : the preprint server for biology (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Ayesha Muhammad, Maria E Calandranis, Bian Li, Tao Yang, Daniel J Blackwell, M Lorena Harvey, Jeremy E Smith, Ashli E Chew, Anthony Capra, Kenneth A Matreyek, Douglas M Fowler, Dan M Roden, Andrew M Glazer
High-throughput functional mapping of variants in an arrhythmia gene, KCNE1 , reveals novel biology. bioRxiv : the preprint server for biology (2023)
Erin N Gilbertson, Colin M Brand, Evonne McArthur, David C Rinker, Shuzhen Kuang, Katherine S Pollard, Anthony Capra
Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv : the preprint server for biology (2023)
Ayesha Muhammad, Maria E Calandranis, Bian Li, Tao Yang, Daniel J Blackwell, M Lorena Harvey, Jeremy E Smith, Ashli E Chew, Anthony Capra, Kenneth A Matreyek, Douglas M Fowler, Dan M Roden, Andrew M Glazer
High-throughput functional mapping of variants in an arrhythmia gene, KCNE1 , reveals novel biology. bioRxiv : the preprint server for biology (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, Justin Siemann, Douglas McMahon, Anthony Capra
Neanderthal Introgression Shaped Human Circadian Traits. bioRxiv : the preprint server for biology (2023)
Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn, Claudia Fontsere, Merve Ceylan, Megan L Koleske, Niklas Handin, Virginia M Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin M Brand, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet, Kathleen M Giacomini
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. bioRxiv : the preprint server for biology (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, Justin Siemann, Douglas McMahon, Anthony Capra
Neanderthal Introgression Shaped Human Circadian Traits. bioRxiv : the preprint server for biology (2023)
Jean M Costello, Hannah Takasuka, Jacquelyn Roger, Ophelia Yin, Alice S Tang, Tomiko T Oskotsky, Marina Sirota, Anthony Capra
Associations with spontaneous and indicated preterm birth in a densely phenotyped EHR cohort. medRxiv : the preprint server for health sciences (2023)
Tyler J Hansen, Sarah L Fong, Anthony Capra, Emily Hodges
Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans . bioRxiv : the preprint server for biology (2023)
Colin M Brand, Laura L Colbran, Anthony Capra
Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nature ecology & evolution (2023)
Erin N Gilbertson, Colin M Brand, Evonne McArthur, David C Rinker, Shuzhen Kuang, Katherine S Pollard, Anthony Capra
Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv : the preprint server for biology (2023)
Colin M Brand, Shuzhen Kuang, Erin N Gilbertson, Evonne McArthur, Katherine S Pollard, Timothy H Webster, Anthony Capra
Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. bioRxiv : the preprint server for biology (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Evonne McArthur, Lisa Bastarache, Anthony Capra
Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes. JAMIA open 6 (1) (2023)
Laura M Gunsalus, Evonne McArthur, Ketrin Gjoni, Shuzhen Kuang, Maureen Pittman, Anthony Capra, Katherine Pollard
Comparing chromatin contact maps at scale: methods and insights. Research square (2023)
Michelle Grunin, Sarah de Jong, Ellen L Palmer, Bowen Jin, David Rinker, Christopher Moth, Anthony Capra, Jonathan L Haines, William S Bush, Anneke I den Hollander, null null
Spatial Distribution of Missense Variants within Complement Proteins Associates with Age Related Macular Degeneration. medRxiv : the preprint server for health sciences (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Colin M Brand, Laura L Colbran, Anthony Capra
Resurrecting the alternative splicing landscape of archaic hominins using machine learning. Nature ecology & evolution (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Laura M Gunsalus, Evonne McArthur, Ketrin Gjoni, Shuzhen Kuang, Maureen Pittman, Anthony Capra, Katherine S Pollard
Comparing chromatin contact maps at scale: methods and insights. bioRxiv : the preprint server for biology (2023)
Evonne McArthur, Lisa Bastarache, Anthony Capra
Linking rare and common disease vocabularies by mapping between the human phenotype ontology and phecodes. JAMIA open 6 (1) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, David C Rinker, Justin K Siemann, Douglas G McMahon, Anthony Capra
Archaic Introgression Shaped Human Circadian Traits. Genome biology and evolution 15 (12) (2023)
Zachary Cutts, Sarah Patterson, Lenka Maliskova, Kimberly E Taylor, Chun Jimmie Ye, Maria Dall'Era, Jinoos Yazdany, Lindsey Criswell, Gabriela K Fragiadakis, Charles Langelier, Anthony Capra, Marina Sirota, Cristina M Lanata
Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. bioRxiv : the preprint server for biology (2023)
Ayesha Muhammad, Maria E Calandranis, Bian Li, Tao Yang, Daniel J Blackwell, M Lorena Harvey, Jeremy E Smith, Ashli E Chew, Anthony Capra, Kenneth A Matreyek, Douglas M Fowler, Dan M Roden, Andrew M Glazer
High-throughput functional mapping of variants in an arrhythmia gene, KCNE1 , reveals novel biology. bioRxiv : the preprint server for biology (2023)
Kathleen M Giacomini, Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn, Claudia Fontsere, Merve Ceylan, Megan Koleske, Niklas Handin, Virginia Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur O Zalevsky, Andrej Sali, Colin Brand, Anthony Capra, Per Artursson, John W Newman, Tomas Marques-Bonet
Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates. Research square (2023)
Tyler J Hansen, Sarah L Fong, Anthony Capra, Emily Hodges
Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans . bioRxiv : the preprint server for biology (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, Justin Siemann, Douglas McMahon, Anthony Capra
Neanderthal Introgression Shaped Human Circadian Traits. bioRxiv : the preprint server for biology (2023)
Keila Velazquez-Arcelay, Laura L Colbran, Evonne McArthur, Colin M Brand, Justin Siemann, Douglas McMahon, Anthony Capra
Neanderthal Introgression Shaped Human Circadian Traits. bioRxiv : the preprint server for biology (2023)
Abin Abraham, Abigail L Labella, Mary Lauren Benton, Antonis Rokas, Anthony Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics (Oxford, England) 39 (1) (2023)
Alexandra M Blee, Bian Li, Turner Pecen, Jens Meiler, Zachary D Nagel, Anthony Capra, Walter Jacob Chazin
An Active Learning Framework Improves Tumor Variant Interpretation. Cancer research 82 (15) (2022)
Maria Niarchou, Daniel E Gustavson, J Fah Sathirapongsasuti, Manuel Anglada-Tort, Else Eising, Eamonn Bell, Evonne McArthur, Peter Straub, null null, J Devin McAuley, Anthony Capra, Fredrik Ullén, Nicole Creanza, Miriam A Mosing, David A Hinds, Lea K Davis, Nori Jacoby, Reyna L Gordon
Genome-wide association study of musical beat synchronization demonstrates high polygenicity. Nature human behaviour 6 (9) (2022)
Laura L Colbran, Maya R Johnson, Iain Mathieson, Anthony Capra
Tracing the Evolution of Human Gene Regulation and Its Association with Shifts in Environment. Genome biology and evolution 13 (11) (2022)
Sarah L Fong, Anthony Capra
Modeling the Evolutionary Architectures of Transcribed Human Enhancer Sequences Reveals Distinct Origins, Functions, and Associations with Human Trait Variation. Molecular biology and evolution 38 (9) (2022)
Bowen Jin, Anthony Capra, Penelope Benchek, Nicholas Wheeler, Adam C Naj, Kara L Hamilton-Nelson, John J Farrell, Yuk Yee Leung, Brian Kunkle, Badri Vadarajan, Gerard D Schellenberg, Richard Mayeux, Li-San Wang, Lindsay A Farrer, Margaret A Pericak-Vance, Eden R Martin, Jonathan L Haines, Dana C Crawford, William S Bush
An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. Genome research 32 (4) (2022)
Mary Lauren Benton, Abin Abraham, Abigail Leavitt LaBella, Patrick Abbot, Antonis Rokas, Anthony Capra
The influence of evolutionary history on human health and disease. Nature reviews. Genetics 22 (5) (2021)
Evonne McArthur, David C Rinker, Anthony Capra
Quantifying the contribution of Neanderthal introgression to the heritability of complex traits. Nature communications 12 (1) (2021)
Cyndya A Shibao, Karen M Joos, John A Phillips, Joy D Cogan, John H Newman, Rizwan Hamid, Jens Meiler, Anthony Capra, Jonathan H Sheehan, Francesco Vetrini, Yaping Yang, Bonnie Black, Andre Diedrich, David Roberston, Italo Biaggioni
Familial Autonomic Ganglionopathy Caused by Rare CHRNA3 Genetic Variants. Neurology 97 (2) (2021)
Daniel R Tilden, Jonathan H Sheehan, John H Newman, Jens Meiler, Anthony Capra, Andrea Ramirez, Jill H Simmons, Kathryn McCrystal Dahir
Phenotypic Profiling in Subjects Heterozygous for 1 of 2 Rare Variants in the Hypophosphatasia Gene (ALPL). Journal of the Endocrine Society 4 (8) (2020)
Ling Chen, Anthony Capra
Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS computational biology 16 (11) (2020)
Abigail Leavitt LaBella, Abin Abraham, Yakov Pichkar, Sarah L Fong, Ge Zhang, Louis J Muglia, Patrick Abbot, Antonis Rokas, Anthony Capra
Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nature communications 11 (1) (2020)
David C Rinker, Corinne N Simonti, Evonne McArthur, Douglas Shaw, Emily Hodges, Anthony Capra
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations. Nature ecology & evolution 4 (10) (2020)
Lide Han, Xuefang Zhao, Mary Lauren Benton, Thaneer Perumal, Ryan L Collins, Gabriel E Hoffman, Jessica S Johnson, Laura Sloofman, Harold Z Wang, Matthew R Stone, null null, Kristen J Brennand, Harrison Brand, Solveig K Sieberts, Stefano Marenco, Mette A Peters, Barbara K Lipska, Panagiotis Roussos, Anthony Capra, Michael E Talkowski, Douglas M Ruderfer
Functional annotation of rare structural variation in the human brain. Nature communications 11 (1) (2020)
Bian Li, Yucheng T Yang, Anthony Capra, Mark B Gerstein
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS computational biology 16 (11) (2020)
M R Alexander, C T Schoeder, J A Brown, C D Smart, C Moth, J P Wikswo, Anthony Capra, J Meiler, W Chen, Meena S Madhur
Which animals are at risk? Predicting species susceptibility to Covid-19. bioRxiv : the preprint server for biology (2020)
Laura L Colbran, Ling Chen, Anthony Capra
Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity. Genetics 211 (4) (2019)
Laura L Colbran, Eric R Gamazon, Dan Zhou, Patrick Evans, Nancy J Cox, Anthony Capra
Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Nature ecology & evolution 3 (11) (2019)
Joanna Zhang, Corinne N Simonti, Anthony Capra
Genome-wide maps of distal gene regulatory enhancers active in the human placenta. PloS one 13 (12) (2018)
Ling Chen, Alexandra E Fish, Anthony Capra
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS computational biology 14 (10) (2018)
Patrick Abbot, Anthony Capra
What is a placental mammal anyway? eLife 6 (2017)