Items where Community is "Siepel lab"

Paper

Ou, Shujun, Scheben, Armin, Collins, Tyler, Qiu, Yinjie, Seetharam, Arun S, Menard, Claire C, Manchanda, Nancy, Gent, Jonathan I, Schatz, Michael C, Anderson, Sarah N, Hufford, Matthew B, Hirsch, Candice N (September 2024) Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research. ISSN 1088-9051

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Grimanelli, Daniel, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2024) Teosinte Pollen Drive guides maize diversification and domestication by RNAi. Nature. ISSN 0028-0836 (Public Dataset)

Serio, Ryan N, Scheben, Armin, Lu, Billy, Gargiulo, Domenic V, Patruno, Lucrezia, Buckholtz, Caroline L, Chaffee, Ryan J, Jibilian, Megan C, Persaud, Steven G, Staklinski, Stephen J, Hassett, Rebecca, Brault, Lise M, Ramazzotti, Daniele, Barbieri, Christopher E, Siepel, Adam C, Nowak, Dawid G (July 2024) Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer. Cancer Discovery. ISSN 2159-8274

Zhai, Jingjing, Gokaslan, Aaron, Schiff, Yair, Berthel, Ana, Liu, Zong-Yan, Miller, Zachary R, Scheben, Armin, Stitzer, Michelle C, Romay, M Cinta, Buckler, Edward S, Kuleshov, Volodymyr (June 2024) Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. bioRxiv. (Public Dataset) (Submitted)

Xue, Alexander, Huang, Yi-Fei, Siepel, Adam (2024) Inferring polygenic negative selection underlying an individual trait as a distribution of fitness effects (DFEs) from GWAS summary statistics. bioRxiv. (Submitted)

Liu, Lingjie, Zhao, Yixin, Siepel, Adam (December 2023) DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv. (Submitted)

Wang, Kejun, Hua, Guoying, Li, Jingyi, Yang, Yu, Zhang, Chenxi, Yang, Lan, Hu, Xiaoyu, Scheben, Armin, Wu, Yanan, Gong, Ping, Zhang, Shuangjie, Fan, Yanfeng, Zeng, Tao, Lu, Lizhi, Gong, Yanzhang, Jiang, Ruirui, Sun, Guirong, Tian, Yadong, Kang, Xiangtao, Hu, Haifei, Li, Wenting (December 2023) Duck pan-genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution. iMeta, 3 (1). e154. ISSN 2770-5986 (Public Dataset)

Kuderna, Lukas FK, Ulirsch, Jacob C, Rashid, Sabrina, Ameen, Mohamed, Sundaram, Laksshman, Hickey, Glenn, Cox, Anthony J, Gao, Hong, Kumar, Arvind, Aguet, Francois, Christmas, Matthew J, Clawson, Hiram, Haeussler, Maximilian, Janiak, Mareike C, Kuhlwilm, Martin, Orkin, Joseph D, Bataillon, Thomas, Manu, Shivakumara, Valenzuela, Alejandro, Bergman, Juraj, Rouselle, Marjolaine, Silva, Felipe Ennes, Agueda, Lidia, Blanc, Julie, Gut, Marta, de Vries, Dorien, Goodhead, Ian, Harris, R Alan, Raveendran, Muthuswamy, Jensen, Axel, Chuma, Idriss S, Horvath, Julie E, Hvilsom, Christina, Juan, David, Frandsen, Peter, Schraiber, Joshua G, de Melo, Fabiano R, Bertuol, Fabrício, Byrne, Hazel, Sampaio, Iracilda, Farias, Izeni, Valsecchi, João, Messias, Malu, da Silva, Maria NF, Trivedi, Mihir, Rossi, Rogerio, Hrbek, Tomas, Andriaholinirina, Nicole, Rabarivola, Clément J, Zaramody, Alphonse, Jolly, Clifford J, Phillips-Conroy, Jane, Wilkerson, Gregory, Abee, Christian, Simmons, Joe H, Fernandez-Duque, Eduardo, Kanthaswamy, Sree, Shiferaw, Fekadu, Wu, Dongdong, Zhou, Long, Shao, Yong, Zhang, Guojie, Keyyu, Julius D, Knauf, Sascha, Le, Minh D, Lizano, Esther, Merker, Stefan, Navarro, Arcadi, Nadler, Tilo, Khor, Chiea Chuen, Lee, Jessica, Tan, Patrick, Lim, Weng Khong, Kitchener, Andrew C, Zinner, Dietmar, Gut, Ivo, Melin, Amanda D, Guschanski, Katerina, Schierup, Mikkel Heide, Beck, Robin MD, Karakikes, Ioannis, Wang, Kevin C, Umapathy, Govindhaswamy, Roos, Christian, Boubli, Jean P, Siepel, Adam, Kundaje, Anshul, Paten, Benedict, Lindblad-Toh, Kerstin, Rogers, Jeffrey, Marques Bonet, Tomas, Farh, Kyle Kai-How (November 2023) Identification of constrained sequence elements across 239 primate genomes. Nature. ISSN 0028-0836

Hu, Haifei, Scheben, Armin, Wang, Jian, Li, Fangping, Li, Chengdao, Edwards, David, Zhao, Junliang (November 2023) Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. Plant Biotechnology Journal. ISSN 1467-7644

Mo, Ziyi, Siepel, Adam (November 2023) Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. PLoS Genetics, 19 (11). e1011032. ISSN 1553-7390

Staklinski, Stephen J, Scheben, Armin, Siepel, Adam, Kilberg, Michael S (November 2023) Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification. bioRxiv. (Submitted)

Zhao, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam (October 2023) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Research. ISSN 0305-1048

Ortiz, Jenelys Ruiz, Lewis, Steven M, Ciccone, Michael F, Chatterjee, Deeptiman, Henry, Samantha, Siepel, Adam, Dos Santos, Camila O (September 2023) Single-cell transcription mapping of murine and human mammary organoids responses to female hormones. bioRxiv. (Public Dataset) (Submitted)

Yao, Min, Preall, Jonathan, Yeh, Johannes, Pappin, Darryl J, Cifani, Paolo, Zhao, Yixin, Shen, Sophia, Moresco, Philip, He, Brian, Patel, Hardik, Habowski, Amber N, King, Daniel A, Raphael, Kara L, Rishi, Arvind, Sejpal, Divyesh V, Weiss, Matthew, Tuveson, David, Fearon, Douglas T (September 2023) Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens. JCI Insight. e172449. ISSN 2379-3708 (Public Dataset)

Mo, Ziyi, Siepel, Adam (September 2023) Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data. bioRxiv. (Submitted)

Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel J, Schatz, Michael C, Simmons, Nancy B, Siepel, Adam, McCombie, W Richard (September 2023) Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution, 15 (9). ISSN 1759-6653 (Public Dataset)

Berube, Benjamin, Ernst, Evan, Cahn, Jonathan, Roche, Benjamin, de Santis Alves, Cristiane, Lynn, Jason, Scheben, Armin, Siepel, Adam, Ross-Ibarra, Jeffrey, Kermicle, Jerry, Martienssen, Robert A (August 2023) Teosinte Pollen Drive guides maize domestication and evolution by RNAi. bioRxiv. (Public Dataset) (Submitted)

Chang, Mario C, Staklinski, Stephen J, Malut, Vinay R, Pierre, Geraldine L, Kilberg, Michael S, Merritt, Matthew E (April 2023) Metabolomic Profiling of Asparagine Deprivation in Asparagine Synthetase Deficiency Patient-Derived Cells. Nutrients, 15 (8). p. 1938. ISSN 2072-6643

Staklinski, Stephen J, Chang, Mario C, Ahrens-Nicklas, Rebecca C, Kaur, Shagun, Stefanatos, Arianna K, Dudenhausen, Elizabeth E, Merritt, Matthew E, Kilberg, Michael S (March 2023) Characterizing asparagine synthetase deficiency variants in lymphoblastoid cell lines. JIMD Reports, 64 (2). pp. 167-179. ISSN 2192-8304

Lu, Guang-An, Zhang, Jinning, Zhao, Yixin, Chen, Qingjian, Lin, Pei, Tang, Tian, Tang, Zhixiong, Wen, Haijun, Liufu, Zhongqi, Wu, Chung-I (January 2023) Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Molecular Biology and Evolution, 40 (1). msad005. ISSN 0737-4038

Chang, Mario C, Staklinski, Stephen J, Merritt, Matthew E, Kilberg, Michael S (2023) A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. Biology Methods and Protocols, 8 (1). bpad026. ISSN 2396-8923

Campagna, Leonardo, Mo, Ziyi, Siepel, Adam, Uy, J Albert C (November 2022) Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species. Plos Genetics, 18 (11). e1010474. ISSN 1553-7390

Vranken, S, Scheben, A, Batley, J, Wernberg, T, Coleman, MA (October 2022) Genomic consequences and selection efficacy in sympatric sexual versus asexual kelps. Frontiers in Marine Science, 9. ISSN 2296-7745

Abuhashem, Abderhman, Chivu, Alexandra G, Zhao, Yixin, Rice, Edward J, Siepel, Adam, Danko, Charles G, Hadjantonakis, Anna-Katerina (August 2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes and Development. ISSN 0890-9369

Locke, Devin P, Hillier, LaDeana W, Warren, Wesley C, Worley, Kim C, Nazareth, Lynne V, Muzny, Donna M, Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T, Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D, Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A, Fulton, Robert S, Nelson, Joanne O, Magrini, Vincent, Pohl, Craig, Graves, Tina A, Markovic, Chris, Cree, Andy, Dinh, Huyen H, Hume, Jennifer, Kovar, Christie L, Fowler, Gerald R, Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P, Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M, Eichler, Evan E, White, Simon, Searle, Stephen, Vilella, Albert J, Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Della Valle, Giuliano, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K, Walker, Jerilyn A, Ullmer, Brygg, Batzer, Mark A, Smit, Arian FA, Hubley, Robert, Casola, Claudio, Schrider, Daniel R, Hahn, Matthew W, Quesada, Victor, Puente, Xose S, Ordoñez, Gonzalo R, López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S, Miller, Webb, Kosiol, Carolin, Lawson, Heather A, Taliwal, Vikas, Martins, André L, Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D, Gutenkunst, Ryan N, Mailund, Thomas, Dutheil, Julien Y, Hobolth, Asger, Schierup, Mikkel H, Ryder, Oliver A, Yoshinaga, Yuko, de Jong, Pieter J, Weinstock, George M, Rogers, Jeffrey, Mardis, Elaine R, Gibbs, Richard A, Wilson, Richard K (August 2022) Author Correction: Comparative and demographic analysis of orang-utan genomes. Nature, 608 (7924). E36. ISSN 0028-0836

Byrne, Dennis, Scheben, Armin, Scott, John K, Webber, Bruce L, Batchelor, Kathryn L, Severn-Ellis, Anita A, Gooden, Ben, Bell, Karen L (August 2022) Genomics reveals the history of a complex plant invasion and improves the management of a biological invasion from the South African-Australian biotic exchange. Ecology and Evolution, 12 (8). e9179. ISSN 2045-7758

Dukler, Noah, Mughal, Mehreen R, Ramani, Ritika, Huang, Yi-Fei, Siepel, Adam (July 2022) Extreme purifying selection against point mutations in the human genome. Nature Communications, 13 (1). p. 4312. ISSN 2041-1723

Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (April 2022) A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants. The Plant Genome. e20204. ISSN 1940-3372

Zhao, Yixin, Liu, Lingjie, Siepel, Adam (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. bioRxiv. (Submitted)

Siepel, Adam, Zhao, Yixin, Liu, Lingjie (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Research Square. (Submitted)

Abuhashem, Abderhman, Chivu, Alexandra, Zhao, Yixin, Rice, Edward, Siepel, Adam, Danko, Charles, Hadjantonakis, Anna-Katerina (2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. bioRxiv. (Submitted)

Hejase, Hussein A, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam (November 2021) A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph. Molecular Biology and Evolution. ISSN 0737-4038

Yuan, Yuxuan, Scheben, Armin, Edwards, David, Chan, Ting-Fung (November 2021) Towards haplotype studies in polyploid plants to assist breeding. Molecular Plant. ISSN 1674-2052

Hutton, Elizabeth R, Vakoc, Christopher R, Siepel, Adam (September 2021) ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens. Genome Biology, 22 (1). p. 278. ISSN 1474-760X

Dukler, Noah, Mughal, Mehreen, Ramani, Ritika, Huang, Yi-Fei, Siepel, Adam (September 2021) Extreme purifying selection against point mutations in the human genome. BioRxiv. (Unpublished)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Wolter, Felix, Schindele, Patrick, Beying, Natalja, Scheben, Armin, Puchta, Holger (August 2021) Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants. The Plant Cell. ISSN 1532-298X

Hu, Haifei, Scheben, Armin, Verpaalen, Brent, Tirnaz, Soodeh, Bayer, Philipp E, Hodel, Richard GJ, Batley, Jacqueline, Soltis, Douglas E, Soltis, Pamela S, Edwards, David (July 2021) Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. New Phytologist. ISSN 0028-646X

Wang, Kejun, Hu, Haifei, Tian, Yadong, Li, Jingyi, Scheben, Armin, Zhang, Chenxi, Li, Yiyi, Wu, Junfeng, Yang, Lan, Fan, Xuewei, Sun, Guirong, Li, Donghua, Zhang, Yanhua, Han, Ruili, Jiang, Ruirui, Huang, Hetian, Yan, Fengbin, Wang, Yanbin, Li, Zhuanjian, Li, Guoxi, Liu, Xiaojun, Li, Wenting, Edwards, David, Kang, Xiangtao (July 2021) The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Molecular Biology and Evolution. ISSN 0737-4038

Mehravi, Shaghayegh, Ranjbar, Gholam Ali, Mirzaghaderi, Ghader, Severn-Ellis, Anita Alice, Scheben, Armin, Edwards, David, Batley, Jacqueline (June 2021) De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing. Agronomy, 11 (7). p. 1342. ISSN 2073-4395

Hejase, Hussein, Mo, Ziyi, Campagna, Leonardo, Siepel, Adam (June 2021) SIA: Selection Inference Using the Ancestral Recombination Graph. BioRxiv. (Unpublished)

Wu, Yaoyao, Johnson, Lynn, Song, Baoxing, Romay, Cinta, Stitzer, Michelle, Siepel, Adam, Buckler, Edward, Scheben, Armin (June 2021) A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants. BioRxiv. (Unpublished)

Vranken, Sofie, Wernberg, Thomas, Scheben, Armin, Severn-Ellis, Anita, Batley, Jacqueline, Philipp, Bayer Emanuel, Edwards, David, Wheeler, David, Coleman, Melinda Ann (May 2021) Genotype-environment mismatch of kelp forests under climate change. Molecular Ecology. ISSN 0962-1083

Henry, Samantha, Trousdell, Marygrace C, Cyrill, Samantha L, Zhao, Yixin, Feigman, Mary J, Bouhuis, Julia M, Aylard, Dominik A, Siepel, Adam, Dos Santos, Camila O (May 2021) Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. Journal of Mammary Gland Biology and Neoplasia. ISSN 1083-3021

Zhao, Yixin, Lu, Guang-An, Yang, Hao, Lin, Pei, Liufu, Zhongqi, Tang, Tian, Xu, Jin (April 2021) Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. Molecular Biology and Evolution, 38 (4). pp. 1544-1553. ISSN 0737-4038

Mo, Ziyi, Scheben, Armin, Steinberg, Joshua, Siepel, Adam, Martienssen, Robert (March 2021) Circadian immunity, sunrise time and the seasonality of respiratory infections. medRxiv. (Unpublished)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)

Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward J, Chivu, Alexandra G, Krumholz, Katie, Danko, Charles G, Siepel, Adam (February 2021) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biology, 19 (1). p. 30. ISSN 1741-7007

Siepel, Adam (January 2021) A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data. bioRxiv. (Unpublished)

Hejase, H. A., Salman-Minkov, A., Campagna, L., Hubisz, M. J., Lovette, I. J., Gronau, I., Siepel, A. (December 2020) Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci U S A, 117 (48). pp. 30554-30565. ISSN 0027-8424 (Print)0027-8424

Scheben, Armin, Ramos, Olivia Mendivil, Kramer, Melissa, Goodwin, Sara, Oppenheim, Sara, Becker, Daniel, Schatz, Michael, Simmons, Nancy, Siepel, Adam, McCombie, Richard (September 2020) Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus. BioRxiv. (Unpublished)

Hubisz, M. J., Williams, A. L., Siepel, A. (August 2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet, 16 (8). e1008895. ISSN 1553-7390 (Print)1553-7390

Bayer, P. E., Golicz, A. A., Scheben, A., Batley, J., Edwards, D. (August 2020) Plant pan-genomes are the new reference. Nat Plants, 6 (8). pp. 914-920. ISSN 2055-0278

Adrion, JR, Cole, C. B., Dukler, N., Galloway, JG, Gladstein, AL, Gower, G, Kyriazis, CC, Ragsdale, AP, Tsambos, G, Baumdicker, F, Carlson, J., Cartwright, R. A., Durvasula, A, Gronau, I., Kim, BY, McKenzie, P, Messer, PW, Noskova, E, Ortega-Del Vecchyo, D., Racimo, F, Struck, TJ, Gravel, S, Gutenkunst, R. N., Lohmueller, K. E., Ralph, PL, Schrider, D. R., Siepel, A., Kelleher, J. E., Kern, A. D. (June 2020) A Community-Maintained Standard Library of Population Genetic Models. Elife, 9. ISSN 2050-084X (Electronic)2050-084X (Linking)

Xue, Alexander T, Hickerson, Michael J (May 2020) Comparative phylogeographic inference with genome-wide data from aggregated population pairs. Evolution, 74 (5). pp. 808-830. ISSN 0014-3820

Dukler, N., Huang, Y-F., Siepel, A. (March 2020) Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data. Mol Biol Evol, 37 (7). pp. 2137-2152. ISSN 0737-4038

Hejase, Hussein, Salman-Minkov, Ayelet, Campagna, Leonardo, Hubisz, Melissa, Lovette, Irby, Gronau, Ilan, Siepel, Adam (March 2020) Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. BioRxiv. (Unpublished)

Joly-Lopez, Z., Platts, A. E., Gulko, B., Choi, J. Y., Groen, S. C., Zhong, X., Siepel, A., Purugganan, M. D. (February 2020) An inferred fitness consequence map of the rice genome. Nat Plants, 6 (2). pp. 119-130. ISSN 2055-0278 (Public Dataset)

Hubisz, M., Siepel, A. (January 2020) Inference of Ancestral Recombination Graphs Using ARGweaver. Methods Mol Biol, 2090. pp. 231-266. ISSN 1064-3745

Hejase, H. A., Dukler, N., Siepel, A. (January 2020) From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection. Trends Genet. ISSN 0168-9525 (Print)0168-9525

Hutton, Elizabeth, Vakoc, Christopher, Siepel, Adam (December 2019) ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens. bioRxiv.

Dukler, Noah, Huang, Yi-Fei, Siepel, Adam (September 2019) Phylogenetic modeling of regulatory element turnover based on epigenomic data. BioRxiv. (Unpublished)

Siepel, A. (July 2019) Challenges in funding and developing genomic software: roots and remedies. Genome Biol, 20 (1). p. 147. ISSN 1474-7596

Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward, Chivu, Alexandra, Krumholz, Katie, Danko, Charles, Siepel, Adam (July 2019) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BioRxiv. (Unpublished)

Zhao, Y., Shen, X., Tang, T., Wu, C. I. (July 2019) Weak Regulation of Many Targets Is Cumulatively Powerful-A Reply to Seitz on microRNA Functionality. Mol Biol Evol, 36 (7). pp. 1598-1599. ISSN 0737-4038

Hubisz, Melissa, Williams, Amy, Siepel, Adam (June 2019) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. BioRxiv. (Unpublished)

Huang, Yi-Fei, Siepel, Adam (June 2019) Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. Genome Research, 29 (8). pp. 1310-1321. ISSN 10889051 (ISSN)

Mohammed, Jaaved, Flynt, Alex S, Panzarino, Alexandra M, Mondal, Md Mosharrof Hossain, DeCruz, Matthew, Siepel, Adam, Lai, Eric C (May 2019) Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Research, 29 (5). p. 881. ISSN 1088-9051

Gulko, B., Siepel, A. (February 2019) Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Gulko, B., Siepel, A. (December 2018) An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. Nat Genet, 51 (2). pp. 335-342. ISSN 1061-4036

Ramani, R., Krumholz, K., Huang, Y. F., Siepel, A. (November 2018) PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP. Bioinformatics, 35 (13). pp. 2320-2322. ISSN 1367-4803

Gulko, Brad, Siepel, Adam (May 2018) How Much Information is Provided by Human Epigenomic Data? An Evolutionary View. BioRxiv. (Unpublished)

Fang, Han, Huang, Yi-Fei, Radhakrishnan, Aditya, Siepel, Adam, Lyon, Gholson J., Schatz, Michael C. (February 2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Systems, 6 (2). pp. 180-191. ISSN 2405-4712

Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L., Siepel, A. (January 2018) Dynamic evolution of regulatory element ensembles in primate CD4(+) T cells. Nat Ecol Evol. pp. 1-12. ISSN 2397-334x

Mohammed, J., Flynt, A. S., Panzarino, A. M., Mondal, M. M. H., DeCruz, M., Siepel, A., Lai, E. C. (January 2018) Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res, 28 (1). pp. 52-65. ISSN 1088-9051

Dukler, N., Booth, G. T., Huang, Y. F., Tippens, N., Waters, C. T., Danko, C. G., Lis, J. T., Siepel, A. (November 2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. Genome Res, 27 (11). pp. 1816-1829. ISSN 1088-9051

Kondo, S., Vedanayagam, J., Mohammed, J., Eizadshenass, S., Kan, L., Pang, N., Aradhya, R., Siepel, A., Steinhauer, J., Lai, E. C. (September 2017) New genes often acquire male-specific functions but rarely become essential in Drosophila. Genes Dev, 31 (18). pp. 1841-1846. ISSN 0890-9369

Ramani, R., Megason, G., Schallheim, J., Karlson, C., Vijayakumar, V., Vijayakumar, S., Hicks, C. (April 2017) Integrative Analysis of MicroRNA-Mediated Gene Signatures and Pathways Modulating White Blood Cell Count in Childhood Acute Lymphoblastic Leukemia. Biomarker Insights, 12. p. 1177271917702895. ISSN 1177-2719

Huang, Y. F., Gulko, B., Siepel, A. (April 2017) Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet, 49 (4). pp. 618-624. ISSN 1061-4036

Dukler, Noah, Booth, Gregory, Huang, Yi-Fei, Tippens, Nathaniel, Danko, Charles, Lis, John, Siepel, Adam (March 2017) Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol. BioRxiv. (Unpublished)

Hicks, C., Ramani, R., Sartor, O., Bhalla, R., Miele, L., Dlamini, Z., Gumede, N. (March 2017) An integrative genomics approach for associating genome-wide association studies information with localized and metastatic prostate cancer phenotypes. Biomarker Insights, 12.

Dukler, N., Gulko, B., Huang, Y. F., Siepel, A. (December 2016) Is a super-enhancer greater than the sum of its parts? Nat Genet, 49 (1). pp. 2-3. ISSN 1546-1718 (Electronic)1061-4036 (Linking)

Freedman, A. H., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Davis, B. W., Gronau, I., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., Ramirez, O., Hormozdiari, F., Alkan, C., Vila, C., Squire, K., Geffen, E., Kusak, J., Boyko, A. R., Parker, H. G., Lee, C., Tadigotla, V., Siepel, A., Bustamante, C. D., Harkins, T. T., Nelson, S. F., Marques-Bonet, T., Ostrander, E. A., Wayne, R. K., Novembre, J. (March 2016) Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet, 12 (3). e1005851. ISSN 1553-7390

Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajkovic, D., Kucan, Z., Gusic, I., Marques-Bonet, T., Andres, A. M., Viola, B., Paabo, S., Meyer, M., Siepel, A., Castellano, S. (February 2016) Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, 530 (7591). pp. 429-433. ISSN 1476-4687 (Electronic)0028-0836 (Linking)

Campagna, L., Gronau, I., Silveira, L. F., Siepel, A., Lovette, I. J. (August 2015) Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation. Mol Ecol, 24 (16). pp. 4238-4251. ISSN 1365-294X (Electronic)0962-1083 (Linking)

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T., Siepel, A. (May 2015) Identification of active transcriptional regulatory elements from GRO-seq data. Nat Methods, 12 (5). pp. 433-8. ISSN 1548-7105 (Electronic)1548-7091 (Linking)

Fuda, N. J., Guertin, M. J., Sharma, S., Danko, C. G., Martins, A. L., Siepel, A., Lis, J. T. (March 2015) GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters. Plos Genetics, 11 (3). e1005108. ISSN 1553-7390

Gulko, B., Hubisz, M. J., Gronau, I., Siepel, A. (March 2015) A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nature Genetics, 47 (3). pp. 276-283. ISSN 1061-4036

Mohammed, J., Siepel, A., Lai, E. C. (December 2014) Diverse modes of evolutionary emergence and flux of conserved microRNA clusters. RNA, 20 (12). pp. 1850-1863. ISSN 13558382

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., Lis, J. T. (December 2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet, 46 (12). pp. 1311-20. ISSN 1061-4036

Siepel, A., Arbiza, L. (December 2014) Cis-regulatory elements and human evolution. Curr Opin Genet Dev, 29c. pp. 81-89. ISSN 0959-437x

Peng, X., Alfoldi, J., Gori, K., Eisfeld, A. J., Tyler, S. R., Tisoncik-Go, J., Brawand, D., Law, G. L., Skunca, N., Hatta, M., Gasper, D. J., Kelly, S. M., Chang, J., Thomas, M. J., Johnson, J., Berlin, A. M., Lara, M., Russell, P., Swofford, R., Turner-Maier, J., Young, S., Hourlier, T., Aken, B., Searle, S., Sun, X., Yi, Y., Suresh, M., Tumpey, T. M., Siepel, A., Wisely, S. M., Dessimoz, C., Kawaoka, Y., Birren, B. W., Lindblad-Toh, K., Di Palma, F., Engelhardt, J. F., Palermo, R. E., Katze, M. G. (December 2014) The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nat Biotechnol, 32 (12). pp. 1250-5. ISSN 1087-0156

Couger, M. B., Pipes, L., Squina, F., Prade, R., Siepel, A., Palermo, R., Katze, M. G., Mason, C. E., Blood, P. D. (September 2014) Enabling large-scale next-generation sequence assembly with Blacklight. Concurrency and computation : practice & experience, 26 (13). pp. 2157-2166. ISSN 1532-0626 (Print)1532-0626

Mohammed, J., Bortolamiol-Becet, D., Flynt, A. S., Gronau, I., Siepel, A., Lai, E. C. (August 2014) Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila. RNA, 20 (8). pp. 1195-209. ISSN 1355-8382

Wen, J., Mohammed, J., Bortolamiol-Becet, D., Tsai, H., Robine, N., Westholm, J. O., Ladewig, E., Dai, Q., Okamura, K., Flynt, A. S., Zhang, D., Andrews, J., Cherbas, L., Kaufman, T. C., Cherbas, P., Siepel, A., Lai, E. C. (July 2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research, 24 (7). pp. 1236-50. ISSN 1088-9051

Arbiza, L., Gottipati, S., Siepel, A., Keinan, A. (June 2014) Contrasting X-linked and autosomal diversity across 14 human populations. Am J Hum Genet, 94 (6). pp. 827-44. ISSN 0002-9297

Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M., Galaverni, M., Fan, Z., Marx, P., Lorente-Galdos, B., Beale, H., Ramirez, O., Hormozdiari, F., Alkan, C., Vila, C., Squire, K., Geffen, E., Kusak, J., Boyko, A. R., Parker, H. G., Lee, C., Tadigotla, V., Siepel, A., Bustamante, C. D., Harkins, T. T., Nelson, S. F., Ostrander, E. A., Marques-Bonet, T., Wayne, R. K., Novembre, J. (January 2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genetics, 10 (1). e1004016. ISSN 15537390 (ISSN)

Rasmussen, M. D., Hubisz, M. J., Gronau, I., Siepel, A. (2014) Genome-wide inference of ancestral recombination graphs. PLoS Genetics, 10 (5). e1004342. ISSN 15537390 (ISSN)

Mohammed, J., Flynt, A. S., Siepel, A., Lai, E. C. (September 2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA, 19 (9). pp. 1295-308. ISSN 1355-8382

Arbiza, L., Gronau, I., Aksoy, B. A., Hubisz, M. J., Gulko, B., Keinan, A., Siepel, A. (July 2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet, 45 (7). pp. 723-9. ISSN 1061-4036

Gronau, I., Arbiza, L., Mohammed, J., Siepel, A. (May 2013) Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. Mol Biol Evol, 30 (5). pp. 1159-71. ISSN 0737-4038

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., Kraus, W. L. (April 2013) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol Cell, 50 (2). pp. 212-22. ISSN 1097-2765

Cornejo, O. E., Lefebure, T., Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S. J., Burne, R. A., Siepel, A., Bustamante, C. D., Stanhope, M. J. (April 2013) Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol, 30 (4). pp. 881-93. ISSN 0737-4038

Zeng, L., Choi, S. C., Danko, C. G., Siepel, A., Stanhope, M. J., Burne, R. A. (2013) Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One, 8 (3). e60465. ISSN 1932-6203

Ma, X., Kelley, J. L., Eilertson, K., Musharoff, S., Degenhardt, J. D., Martins, A. L., Vinar, T., Kosiol, C., Siepel, A., Gutenkunst, R. N., Bustamante, C. D. (2013) Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii). PLoS One, 8 (10). e77175. ISSN 1932-6203

Capra, J. A., Hubisz, M. J., Kostka, D., Pollard, K. S., Siepel, A. (2013) A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genetics, 9 (8). e1003684. ISSN 15537390 (ISSN)

Choi, S. C., Rasmussen, M. D., Hubisz, M. J., Gronau, I., Stanhope, M. J., Siepel, A. (November 2012) Replacing and additive horizontal gene transfer in Streptococcus. Mol Biol Evol, 29 (11). pp. 3309-20. ISSN 0737-4038

Kostka, D., Hubisz, M. J., Siepel, A., Pollard, K. S. (March 2012) The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol, 29 (3). pp. 1047-57. ISSN 0737-4038

Guertin, M. J., Martins, A. L., Siepel, A., Lis, J. T. (2012) Accurate prediction of inducible transcription factor binding intensities in vivo. PLoS Genet, 8 (3). e1002610. ISSN 1553-7390

Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, L. D., Lowe, C. B., Holloway, A. K., Clamp, M., Gnerre, S., Alfoldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., Di Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, M. J., Jaffe, D. B., Jungreis, I., Kent, W. J., Kostka, D., Lara, M., Martins, A. L., Massingham, T., Moltke, I., Raney, B. J., Rasmussen, M. D., Robinson, J., Stark, A., Vilella, A. J., Wen, J., Xie, X., Zody, M. C., Baldwin, J., Bloom, T., Chin, C. W., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, K. C., Kovar, C. L., Muzny, D. M., Gibbs, R. A., Cree, A., Dihn, H. H., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, L. R., Nazareth, L. V., Okwuonu, G., Santibanez, J., Warren, W. C., Mardis, E. R., Weinstock, G. M., Wilson, R. K., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P., Sodergren, E., Birney, E., Margulies, E. H., Herrero, J., Green, E. D., Haussler, D., Siepel, A., Goldman, N., Pollard, K. S., Pedersen, J. S., Lander, E. S., Kellis, M. (October 2011) A high-resolution map of human evolutionary constraint using 29 mammals. Nature, 478 (7370). pp. 476-82. ISSN 0028-0836

Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., Siepel, A. (October 2011) Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 43 (10). pp. 1031-4. ISSN 1061-4036

Lowe, C. B., Kellis, M., Siepel, A., Raney, B. J., Clamp, M., Salama, S. R., Kingsley, D. M., Lindblad-Toh, K., Haussler, D. (August 2011) Three periods of regulatory innovation during vertebrate evolution. Science, 333 (6045). pp. 1019-24. ISSN 0036-8075

Gottipati, S., Arbiza, L., Siepel, A., Clark, A. G., Keinan, A. (August 2011) Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing. Nat Genet, 43 (8). pp. 741-3. ISSN 1061-4036

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T., Kraus, W. L. (May 2011) A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell, 145 (4). pp. 622-34. ISSN 0092-8674

Yang, J. S., Phillips, M. D., Betel, D., Mu, P., Ventura, A., Siepel, A. C., Chen, K. C., Lai, E. C. (February 2011) Widespread regulatory activity of vertebrate microRNA* species. Rna, 17 (2). pp. 312-26. ISSN 1355-8382

Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., Yang, S. P., Wang, Z., Chinwalla, A. T., Minx, P., Mitreva, M., Cook, L., Delehaunty, K. D., Fronick, C., Schmidt, H., Fulton, L. A., Fulton, R. S., Nelson, J. O., Magrini, V., Pohl, C., Graves, T. A., Markovic, C., Cree, A., Dinh, H. H., Hume, J., Kovar, C. L., Fowler, G. R., Lunter, G., Meader, S., Heger, A., Ponting, C. P., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J. M., Eichler, E. E., White, S., Searle, S., Vilella, A. J., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darre, F., Farre, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Della Valle, G., Purgato, S., Rocchi, M., Konkel, M. K., Walker, J. A., Ullmer, B., Batzer, M. A., Smit, A. F., Hubley, R., Casola, C., Schrider, D. R., Hahn, M. W., Quesada, V., Puente, X. S., Ordonez, G. R., Lopez-Otin, C., Vinar, T., Brejova, B., Ratan, A., Harris, R. S., Miller, W., Kosiol, C., Lawson, H. A., Taliwal, V., Martins, A. L., Siepel, A., Roychoudhury, A., Ma, X., Degenhardt, J., Bustamante, C. D., Gutenkunst, R. N., Mailund, T., Dutheil, J. Y., Hobolth, A., Schierup, M. H., Ryder, O. A., Yoshinaga, Y., de Jong, P. J., Weinstock, G. M., Rogers, J., Mardis, E. R., Gibbs, R. A. (January 2011) Comparative and demographic analysis of orang-utan genomes. Nature, 469 (7331). pp. 529-33. ISSN 0028-0836

Hubisz, M. J., Pollard, K. S., Siepel, A. (January 2011) PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform, 12 (1). pp. 41-51. ISSN 1467-5463

Suzuki, H., Lefebure, T., Hubisz, M. J., Pavinski Bitar, P., Lang, P., Siepel, A., Stanhope, M. J. (2011) Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol, 3. pp. 168-85. ISSN 1759-6653

Hubisz, M. J., Lin, M. F., Kellis, M., Siepel, A. (2011) Error and error mitigation in low-coverage genome assemblies. PLoS One, 6 (2). e17034. ISSN 1932-6203

Vinar, T., Brejova, B., Song, G., Siepel, A. (September 2010) Reconstructing histories of complex gene clusters on a phylogeny. J Comput Biol, 17 (9). pp. 1267-79. ISSN 1066-5277

da Fonseca, R. R., Kosiol, C., Vinar, T., Siepel, A., Nielsen, R. (February 2010) Positive selection on apoptosis related genes. FEBS Lett, 584 (3). pp. 469-76. ISSN 0014-5793

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., Siepel, A. (January 2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 20 (1). pp. 110-21. ISSN 1088-9051

Boyko, A. R., Quignon, P., Li, L., Schoenebeck, J. J., Degenhardt, J. D., Lohmueller, K. E., Zhao, K., Brisbin, A., Parker, H. G., vonHoldt, B. M., Cargill, M., Auton, A., Reynolds, A., Elkahloun, A. G., Castelhano, M., Mosher, D. S., Sutter, N. B., Johnson, G. S., Novembre, J., Hubisz, M. J., Siepel, A., Wayne, R. K., Bustamante, C. D., Ostrander, E. A. (2010) A simple genetic architecture underlies morphological variation in dogs. PLoS Biology, 8 (8). e1000451. ISSN 1544-9173

Temple, G., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Jang, W., Wagner, L., Shenmen, C. M., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., Phan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B. L., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C. L., Stevens, M., Wei, C., van Baren, M. J., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Jacob, H., Gruber, C. E., Smith, M. R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A. (December 2009) The completion of the Mammalian Gene Collection (MGC). Genome Research, 19 (12). pp. 2324-33. ISSN 1088-9051

Siepel, A. (November 2009) Phylogenomics of primates and their ancestral populations. Genome Res, 19 (11). pp. 1929-41. ISSN 1088-9051

Siepel, A. (October 2009) Darwinian alchemy: Human genes from noncoding DNA. Genome Res, 19 (10). pp. 1693-5. ISSN 1088-9051

Zhang, Y., Song, G., Vinar, T., Green, E. D., Siepel, A., Miller, W. (August 2009) Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol, 16 (8). pp. 1051-70. ISSN 1066-5277

Holloway, A. K., Begun, D. J., Siepel, A., Pollard, K. S. (October 2008) Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research, 18 (10). pp. 1592-601. ISSN 1088-9051

Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, J., Siepel, A., Tanksley, S. D. (September 2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180 (1). pp. 391-408. ISSN 0016-6731 (Print)0016-6731

Kosiol, C., Vinar, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., Siepel, A. (2008) Patterns of positive selection in six Mammalian genomes. Plos Genetics, 4 (8). e1000144. ISSN 1553-7390

Miller, W., Rosenbloom, K., Hardison, R. C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D. C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S. L., Nekrutenko, A., Giardine, B., Harris, R. S., Tyekucheva, S., Diekhans, M., Pringle, T. H., Murphy, W. J., Lesk, A., Weinstock, G. M., Lindblad-Toh, K., Gibbs, R. A., Lander, E. S., Siepel, A., Haussler, D., Kent, W. J. (December 2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research, 17 (12). pp. 1797-808. ISSN 1088-9051

Siepel, A., Diekhans, M., Brejova, B., Langton, L., Stevens, M., Comstock, C. L., Davis, C., Ewing, B., Oommen, S., Lau, C., Yu, H. C., Li, J., Roe, B. A., Green, P., Gerhard, D. S., Temple, G., Haussler, D., Brent, M. R. (December 2007) Targeted discovery of novel human exons by comparative genomics. Genome Res, 17 (12). pp. 1763-73. ISSN 1088-9051 (Print)1088-9051

Kininis, M., Chen, B. S., Diehl, A. G., Isaacs, G. D., Zhang, T., Siepel, A. C., Clark, A. G., Kraus, W. L. (July 2007) Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters. Mol Cell Biol, 27 (14). pp. 5090-104. ISSN 0270-7306 (Print)0270-7306

Margulies, E. H., Cooper, G. M., Asimenos, G., Thomas, D. J., Dewey, C. N., Siepel, A., Birney, E., Keefe, D., Schwartz, A. S., Hou, M., Taylor, J., Nikolaev, S., Montoya-Burgos, J. I., Loytynoja, A., Whelan, S., Pardi, F., Massingham, T., Brown, J. B., Bickel, P., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Stone, E. A., Rosenbloom, K. R., Kent, W. J., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V. V., Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Hinrichs, A., Trumbower, H., Clawson, H., Zweig, A., Kuhn, R. M., Barber, G., Harte, R., Karolchik, D., Field, M. A., Moore, R. A., Matthewson, C. A., Schein, J. E., Marra, M. A., Antonarakis, S. E., Batzoglou, S., Goldman, N., Hardison, R., Haussler, D., Miller, W., Pachter, L., Green, E. D., Sidow, A. (June 2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research, 17 (6). pp. 760-74. ISSN 1088-9051

Gibbs, R. A., Rogers, J., Katze, M. G., Bumgarner, R., Weinstock, G. M., Mardis, E. R., Remington, K. A., Strausberg, R. L., Venter, J. C., Wilson, R. K., Batzer, M. A., Bustamante, C. D., Eichler, E. E., Hahn, M. W., Hardison, R. C., Makova, K. D., Miller, W., Milosavljevic, A., Palermo, R. E., Siepel, A., Sikela, J. M., Attaway, T., Bell, S., Bernard, K. E., Buhay, C. J., Chandrabose, M. N., Dao, M., Davis, C., Delehaunty, K. D., Ding, Y., Dinh, H. H., Dugan-Rocha, S., Fulton, L. A., Gabisi, R. A., Garner, T. T., Godfrey, J., Hawes, A. C., Hernandez, J., Hines, S., Holder, M., Hume, J., Jhangiani, S. N., Joshi, V., Khan, Z. M., Kirkness, E. F., Cree, A., Fowler, R. G., Lee, S., Lewis, L. R., Li, Z., Liu, Y. S., Moore, S. M., Muzny, D., Nazareth, L. V., Ngo, D. N., Okwuonu, G. O., Pai, G., Parker, D., Paul, H. A., Pfannkoch, C., Pohl, C. S., Rogers, Y. H., Ruiz, S. J., Sabo, A., Santibanez, J., Schneider, B. W., Smith, S. M., Sodergren, E., Svatek, A. F., Utterback, T. R., Vattathil, S., Warren, W., White, C. S., Chinwalla, A. T., Feng, Y., Halpern, A. L., Hillier, L. W., Huang, X., Minx, P., Nelson, J. O., Pepin, K. H., Qin, X., Sutton, G. G., Venter, E., Walenz, B. P., Wallis, J. W., Worley, K. C., Yang, S. P., Jones, S. M., Marra, M. A., Rocchi, M., Schein, J. E., Baertsch, R., Clarke, L., Csuros, M., Glasscock, J., Harris, R. A., Havlak, P., Jackson, A. R., Jiang, H. (April 2007) Evolutionary and biomedical insights from the rhesus macaque genome. Science, 316 (5822). pp. 222-34. ISSN 0036-8075

Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., Sugnet, C. W., Stanke, M., Smith, K. E., Siepel, A., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pedersen, J. S., Hsu, F., Hinrichs, A. S., Harte, R. A., Diekhans, M., Clawson, H., Bejerano, G., Barber, G. P., Baertsch, R., Haussler, D., Kent, W. J. (January 2007) The UCSC genome browser database: update 2007. Nucleic Acids Res, 35 (Databa). D668-73. ISSN 0305-1048

Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., Boyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Siepel, A. C. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 (7146). pp. 799-816. ISSN 00280836 (ISSN)

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., Rosenbloom, K. R., Kent, J., Haussler, D. (October 2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet, 2 (10). e168. ISSN 1553-7390

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M. A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., Kern, A. D., Dehay, C., Igel, H., Ares, M., Vanderhaeghen, P., Haussler, D. (September 2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature, 443 (7108). pp. 167-72. ISSN 0028-0836

Bejerano, G., Lowe, C. B., Ahituv, N., King, B., Siepel, A., Salama, S. R., Rubin, E. M., Kent, W. J., Haussler, D. (May 2006) A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature, 441 (7089). pp. 87-90. ISSN 0028-0836

Pedersen, J. S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E. S., Kent, J., Miller, W., Haussler, D. (April 2006) Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol, 2 (4). e33. ISSN 1553-734x

Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., Sultan-Qurraie, A., Thomas, D. J., Trumbower, H., Weber, R. J., Weirauch, M., Zweig, A. S., Haussler, D., Kent, W. J. (January 2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res, 34 (Databa). D590-8. ISSN 0305-1048

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., Weinstock, G. M., Wilson, R. K., Gibbs, R. A., Kent, W. J., Miller, W., Haussler, D. (August 2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 15 (8). pp. 1034-50. ISSN 1088-9051 (Print)1088-9051

Bejerano, G., Siepel, A. C., Kent, W. J., Haussler, D. (July 2005) Computational screening of conserved genomic DNA in search of functional noncoding elements. Nat Methods, 2 (7). pp. 535-45. ISSN 1548-7091 (Print)1548-7091

International Chicken Genome SequencingConsortium, (December 2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018). pp. 695-716. ISSN 0028-0836

ENCODE Project Consortium (October 2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306 (5696). pp. 636-40. ISSN 0036-8075

International Human Genome Sequencing Consortium (October 2004) Finishing the euchromatic sequence of the human genome. Nature, 431 (7011). pp. 931-45. ISSN 0028-0836

Jojic, V., Jojic, N., Meek, C., Geiger, D., Siepel, A., Haussler, D., Heckerman, D. (August 2004) Efficient approximations for learning phylogenetic HMM models from data. Bioinformatics, 20 Sup. i161-8. ISSN 1367-4803

Siepel, A., Haussler, D. (March 2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol, 21 (3). pp. 468-88. ISSN 0737-4038 (Print)0737-4038

Siepel, A., Haussler, D. (2004) Combining phylogenetic and hidden Markov models in biosequence analysis. J Comput Biol, 11 (2-3). pp. 413-28. ISSN 1066-5277 (Print)1066-5277

Siepel, A., Haussler, D. (2004) Computational identification of evolutionarily conserved exons. Proceedings of the eighth annual international conference on Resaerch in computational molecular biology. pp. 177-186.

Thomas, J. W., Touchman, J. W., Blakesley, R. W., Bouffard, G. G., Beckstrom-Sternberg, S. M., Margulies, E. H., Blanchette, M., Siepel, A. C., Thomas, P. J., McDowell, J. C., Maskeri, B., Hansen, N. F., Schwartz, M. S., Weber, R. J., Kent, W. J., Karolchik, D., Bruen, T. C., Bevan, R., Cutler, D. J., Schwartz, S., Elnitski, L., Idol, J. R., Prasad, A. B., Lee-Lin, S. Q., Maduro, V. V., Summers, T. J., Portnoy, M. E., Dietrich, N. L., Akhter, N., Ayele, K., Benjamin, B., Cariaga, K., Brinkley, C. P., Brooks, S. Y., Granite, S., Guan, X., Gupta, J., Haghighi, P., Ho, S. L., Huang, M. C., Karlins, E., Laric, P. L., Legaspi, R., Lim, M. J., Maduro, Q. L., Masiello, C. A., Mastrian, S. D., McCloskey, J. C., Pearson, R., Stantripop, S., Tiongson, E. E., Tran, J. T., Tsurgeon, C., Vogt, J. L., Walker, M. A., Wetherby, K. D., Wiggins, L. S., Young, A. C., Zhang, L. H., Osoegawa, K., Zhu, B., Zhao, B., Shu, C. L., De Jong, P. J., Lawrence, C. E., Smit, A. F., Chakravarti, A., Haussler, D., Green, P., Miller, W., Green, E. D. (August 2003) Comparative analyses of multi-species sequences from targeted genomic regions. Nature, 424 (6950). pp. 788-93. ISSN 0028-0836

Siepel, A., Haussler, D. (2003) Combining phylogenetic and hidden Markov models in biosequence analysis. Proceedings of the seventh annual international conference on Research in computational molecular biology. pp. 277-286.

Siepel, A. C. (2003) An algorithm to enumerate sorting reversals for signed permutations. J Comput Biol, 10 (3-4). pp. 575-97. ISSN 1066-5277 (Print)1066-5277

Siepel, A. (2002) An algorithm to find all sorting reversals. Proceedings of the sixth annual international conference on Computational biology. pp. 281-290.

Siepel, A. C., Steenhuis, T. S., Rose, C. W., Parlange, J. Y., McIsaac, G. F. (2002) A simplified hillslope erosion model with vegetation elements for practical applications. Journal of Hydrology, 258 (1-4). pp. 111-121.

Siepel, A., Farmer, A., Tolopko, A., Zhuang, M., Mendes, P., Beavis, W., Sobral, B. (January 2001) ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinformatics, 17 (1). pp. 83-94. ISSN 1367-4803 (Print)1367-4803

Siepel, A. C., Tolopko, A. N., Farmer, A. D., Steadman, P. A., Schilkey, F. D., Perry, B. D., Beavis, W. D. (2001) An integration platform for heterogeneous bioinformatics software components. IBM Systems Journal, 40 (2). pp. 570-591.

Skupski, M. P., Booker, M., Farmer, A., Harpold, M., Huang, W., Inman, J., Kiphart, D., Kodira, C., Root, S., Schilkey, F., Schwertfeger, J., Siepel, A., Stamper, D., Thayer, N., Thompson, R., Wortman, J., Zhuang, J. J., Harger, C. (January 1999) The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Research, 27 (1). pp. 35-8. ISSN 0305-1048

Harger, C., Skupski, M., Bingham, J., Farmer, A., Hoisie, S., Hraber, P., Kiphart, D., Krakowski, L., McLeod, M., Schwertfeger, J., Seluja, G., Siepel, A., Singh, G., Stamper, D., Steadman, P., Thayer, N., Thompson, R., Wargo, P., Waugh, M., Zhuang, J. J., Schad, P. A. (January 1998) The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res, 26 (1). pp. 21-6. ISSN 0305-1048 (Print)0305-1048

Harger, C., Skupski, M., Allen, E., Clark, C., Crowley, D., Dickinson, E., Easley, D., Espinosa-Lujan, A., Farmer, A., Fields, C., Flores, L., Harris, L., Keen, G., Manning, M., McLeod, M., O'Neill, J., Pumilia, M., Reinert, R., Rider, D., Rohrlich, J., Romero, Y., Schwertfeger, J., Seluja, G., Siepel, A., Schad, P. A. (January 1997) The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res, 25 (1). pp. 18-23. ISSN 0305-1048 (Print)0305-1048

Siepel, A. C., Halpern, A. L., Macken, C., Korber, B. T. (November 1995) A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses, 11 (11). pp. 1413-6. ISSN 0889-2229 (Print)0889-2229

Book Section

Vinar, Tomas, Brejova, B., Song, Giltae, Siepel, Adam (2009) Reconstructing Histories of Complex Gene Clusters on a Phylogeny. In: Comparative Genomics. Lecture Notes in Computer Science, 5817 . Springer Berlin Heidelberg, pp. 150-163. ISBN 978-3-642-04743-5

Zhang, Yu, Song, Giltae, Vinar, Tomas, Green, EricD, Siepel, Adam, Miller, Webb (2008) Reconstructing the Evolutionary History of Complex Human Gene Clusters. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science, 4955 . Springer Berlin Heidelberg, pp. 29-49. ISBN 978-3-540-78838-6

Sobral, Bruno W. S., Mangalam, Harry, Siepel, Adam, Mendes, Pedro, Pecherer, Rob, McLaren, Graham (2007) Bioinformatics for Rice Resources. In: Novartis Foundation Symposium 236 - Rice Biotechnology: Improving Yield, Stress Tolerance and Grain Quality. John Wiley & Sons, Ltd., pp. 59-84. ISBN 9780470515778

Siepel, Adam, Pollard, Katherine, Haussler, David (2006) New Methods for Detecting Lineage-Specific Selection. In: Research in Computational Molecular Biology. Lecture Notes in Computer Science, 3909 . Springer Berlin Heidelberg, pp. 190-205. ISBN 978-3-540-33295-4

Siepel, Adam, Haussler, David (2005) Phylogenetic Hidden Markov Models. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health . Springer New York, pp. 325-351. ISBN 978-0-387-22333-9

Moret, Bernard, Siepel, Adam, Tang, Jijun, Liu, Tao (2002) Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2452 . Springer Berlin Heidelberg, pp. 521-536. ISBN 978-3-540-44211-0

Siepel, Adam, Moret, Bernard (2001) Finding an Optimal Inversion Median: Experimental Results. In: Algorithms in Bioinformatics. Lecture Notes in Computer Science, 2149 . Springer Berlin Heidelberg, pp. 189-203. ISBN 978-3-540-42516-8

Conference or Workshop Item

Nattestad, Maria, Ng, Karen, Goodwin, Sara, Baslan, Timour, Sedlazeck, Fritz, Gurtowski, James, Hutton, Elizabeth, Sundaravadanam, Yogi, Garvin, Tyler, Alford, Marley, Tseng, Elizabeth, Rescheneder, Philipp, Chin, Jason, Beck, Timothy, Kramer, Melissa, McPherson, John, Hicks, James, Schatz, Michael C, McCombie, William R (2016) Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using single molecule sequencing. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research, 2016 Apr 16-20, New Orleans, LA.

Thesis

Ziyi, Mo (January 2024) Scalable and robust deep-learning methods power evolutionary-genetic studies of biobank-scale population genomic data. PhD thesis, Cold Spring Harbor Laboratory.