Adam C Siepel (Adam Siepel)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 31

Top Venues

bioRxiv : the preprint server for biology

Nature

Genome research

Genome biology

Cornell University

University of California, Santa Cruz (PHD)

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

Affiliation History

Cornell University

United States

Adjunct Professor :: Department of Biological Statistics and Computational Biology

Watson School of Biological Sciences, Cold Spring Harbor Laboratory

United States

Professor

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory

United States

Chair

Stony Brook University

United States

Adjunct Associate Proessor :: Department of Computer Science

Weill Cornell Medical College of Cornell University

United States

Adjunct Professor of Computational Genomics :: Institute for Computational Biomedicine

Cornell University

United States

Associate Professor (with tenure) :: Biological Statistics and Computational Biology

European Bioinformatics Institute (EBI)

United Kingdom

Visiting Scientist (during sabbatic leave from Cornell)

Churchill College, University of Cambridge

United Kingdom

Visiting By-Fellow in Residence (during sabbatic leave from Cornell)

Cornell University

United States

Assistant Professor :: Biological Statistics & Computational Biology

University of California Santa Cruz

United States

Graduate Student Researcher

National Center for Genome Resources (NCGR)

United States

Director of Information Technology (acting)

National Center for Genome Resources (NCGR)

United States

Software Development Group Leader

National Center for Genome Resources (NCGR)

United States

Bioinformatics Programmer

Los Alamos National Laboratory

United States

Graduate Research Assistant :: HIV Database Group

Education History

University of California, Santa Cruz

United States

PHD :: Computer Science

University of New Mexico

United States

MSC

Cornell University

United States

BSC :: Agriculural and Biological Engineering

Publications

Benjamin Berube, Evan Ernst, Jonathan Cahn, Benjamin Roche, Cristiane de Santis Alves, Jason Lynn, Armin Scheben, Daniel Grimanelli, Adam C Siepel, Jeffrey Ross-Ibarra, Jerry Kermicle, Robert A Martienssen
Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature (2024)
Ryan N Serio, Armin Scheben, Billy Lu, Domenic V Gargiulo, Lucrezia Patruno, Caroline L Buckholtz, Ryan J Chaffee, Megan C Jibilian, Steven G Persaud, Stephen J Staklinski, Rebecca Hassett, Lise M Brault, Daniele Ramazzotti, Christopher E Barbieri, Adam C Siepel, Dawid G Nowak
Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer. Cancer discovery (2024)
Benjamin Berube, Evan Ernst, Jonathan Cahn, Benjamin Roche, Cristiane de Santis Alves, Jason Lynn, Armin Scheben, Daniel Grimanelli, Adam C Siepel, Jeffrey Ross-Ibarra, Jerry Kermicle, Robert A Martienssen
Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature (2024)
Benjamin Berube, Evan Ernst, Jonathan Cahn, Benjamin Roche, Cristiane de Santis Alves, Jason Lynn, Armin Scheben, Daniel Grimanelli, Adam C Siepel, Jeffrey Ross-Ibarra, Jerry Kermicle, Robert A Martienssen
Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature (2024)
Lingjie Liu, Yixin Zhao, Adam C Siepel
DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv : the preprint server for biology (2023)
Stephen J Staklinski, Armin Scheben, Adam C Siepel, Michael S Kilberg
Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv : the preprint server for biology (2023)
Lingjie Liu, Yixin Zhao, Adam C Siepel
DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv : the preprint server for biology (2023)
Jenelys Ruiz Ortiz, Steven M Lewis, Michael F Ciccone, Deeptiman Chatterjee, Samantha Henry, Adam C Siepel, Camila Oresco Dos Santos
Single-cell transcription mapping of murine and human mammary organoids responses to female hormones. bioRxiv : the preprint server for biology (2023)
Lingjie Liu, Yixin Zhao, Adam C Siepel
DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv : the preprint server for biology (2023)
Ziyi Mo, Adam C Siepel
Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. bioRxiv : the preprint server for biology (2023)
Ziyi Mo, Adam C Siepel
Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. bioRxiv : the preprint server for biology (2023)
Yixin Zhao, Lingjie Liu, Rebecca Hassett, Adam C Siepel
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic acids research (2023)
Lukas F K Kuderna, Jacob C Ulirsch, Sabrina Rashid, Mohamed Ameen, Laksshman Sundaram, Glenn Hickey, Anthony J Cox, Hong Gao, Arvind Kumar, François Aguet, Matthew J Christmas, Hiram Clawson, Maximilian Haeussler, Mareike C Janiak, Martin Kuhlwilm, Joseph D Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes Silva, Lidia Agueda, Julie Marie Blanc, Marta Gut, Dorien de Vries, Ian B Goodhead, R Alan Harris, Muthuswamy Raveendran, Axel Jensen, Idriss S Chuma, Julie E Horvath, Christina Hvilsom, David Juan, Peter Frandsen, Joshua G Schraiber, Fabiano R de Melo, Fabrício Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Pires Farias, João Valsecchi do Amaral, Malu Messias, Maria N F da Silva, Mihir Trivedi, Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Clément J Rabarivola, Alphonse Zaramody, Clifford J Jolly, Jane Phillips-Conroy, Gregory K Wilkerson, Christian Abee, Joe H Simmons, Eduardo Fernández-Duque, Sree Kanthaswamy, Fekadu Shiferaw, Dong-Dong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D Keyyu, Sascha Knauf, Minh D Le, Esther Lizano, Stefan Merker, Arcadi Navarro, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Boon-Ooi Tan, Weng Khong Lim, Andrew C Kitchener, Dietmar Zinner, Ivo Glynne Gut, Amanda Dawn Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin M D Beck, Ioannis Karakikes, Kevin C Wang, Govindhaswamy Umapathy, Christian Roos, Jean Phillipe Boubli, Adam C Siepel, Anshul Kundaje, Benedict Paten, Kerstin Lindblad-Toh, Jeffrey Rogers, Tomas Marques-Bonet, Kyle Kai-How Farh
Identification of constrained sequence elements across 239 primate genomes. Nature (2023)
Armin Scheben, Olivia Mendivil Ramos, Melissa Kramer, Sara Goodwin, Sara J Oppenheim, Daniel J Becker, Michael C Schatz, Nancy B Simmons, Adam C Siepel, W Richard McCombie
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome biology and evolution 15 (9) (2023)
Benjamin Berube, Evan Ernst, Jonathan Cahn, Benjamin Roche, Cristiane de Santis Alves, Jason Lynn, Armin Scheben, Adam C Siepel, Jeffrey Ross-Ibarra, Jerry Kermicle, Rob Martienssen
Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv : the preprint server for biology (2023)
Ziyi Mo, Adam C Siepel
Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. PLoS genetics 19 (11) (2023)
Abderhman Abuhashem, Alexandra G Chivu, Yixin Zhao, Edward J Rice, Adam C Siepel, Charles G Danko, Anna-Katerina Hadjantonakis
RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes & development (2022)
Noah Dukler, Mehreen R Mughal, Ritika Ramani, Yi-Fei Huang, Adam C Siepel
Extreme purifying selection against point mutations in the human genome. Nature communications 13 (1) (2022)
Yaoyao Wu, Lynn Johnson, Baoxing Song, Maria Cinta Romay, Michelle C Stitzer, Adam C Siepel, Edward S Buckler, Armin Scheben
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The plant genome 15 (2) (2022)
Amit Blumberg, Yixin Zhao, Yi-Fei Huang, Noah Dukler, Edward J Rice, Alexandra G Chivu, Katie Krumholz, Charles G Danko, Adam C Siepel
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC biology 19 (1) (2021)
Ziyi Mo, Armin Scheben, Joshua Steinberg, Adam C Siepel, Robert A Martienssen
Circadian immunity, sunrise time and the seasonality of respiratory infections. medRxiv : the preprint server for health sciences (2021)
Hussein A Hejase, Ziyi Mo, Leonardo Campagna, Adam C Siepel
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph. Molecular biology and evolution (2021)
Elizabeth R Hutton, Christopher R Vakoc, Adam C Siepel
ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome biology 22 (1) (2021)
Jeffrey R Adrion, Christopher B Cole, Noah Dukler, Jared G Galloway, Ariella L Gladstein, Graham Gower, Christopher C Kyriazis, Aaron P Ragsdale, Georgia Tsambos, Franz Baumdicker, Jedidiah Carlson, Reed A Cartwright, Arun Durvasula, Zehavit Leibovich, Bernard Y Kim, Patrick McKenzie, Philipp W Messer, Ekaterina Noskova, Diego Ortega-Del Vecchyo, Fernando Racimo, Travis J Struck, Simon Gravel, Ryan N Gutenkunst, Kirk E Lohmueller, Peter L Ralph, Daniel R Schrider, Adam C Siepel, Jerome Kelleher, Andrew D Kern
A community-maintained standard library of population genetic models. eLife 9 (2020)
Hussein A Hejase, Ayelet Salman-Minkov, Leonardo Campagna, Melissa J Hubisz, Irby J Lovette, Zehavit Leibovich, Adam C Siepel
Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences of the United States of America 117 (48) (2020)
Melissa J Hubisz, Amy L Williams, Adam C Siepel
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS genetics 16 (8) (2020)
Adam C Siepel
Challenges in funding and developing genomic software: roots and remedies. Genome biology 20 (1) (2019)
Yi-Fei Huang, Adam C Siepel
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. Genome research 29 (8) (2019)
Charles G Danko, Lauren A Choate, Brooke A Marks, Edward J Rice, Zhong Wang, Tinyi Chu, Andre L Martins, Noah Dukler, Scott A Coonrod, Elia D Tait Wojno, John T Lis, W Lee Kraus, Adam C Siepel
Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nature ecology & evolution 2 (3) (2018)
Brad Gulko, Adam C Siepel
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nature genetics 51 (2) (2018)
Noah Dukler, Gregory T Booth, Yi-Fei Huang, Nathaniel Tippens, Colin T Waters, Charles G Danko, John T Lis, Adam C Siepel
Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome research 27 (11) (2017)

Adam C Siepel.css-eqlu8i{font-size:small;padding-left:4px;} (Adam Siepel)

Publication Activity (10 Years)

Top Topics

Top Venues

Adam C Siepel (Adam Siepel)