Siepel, Adam

Detection of nonneutral substitution rates on mammalian phylogenies

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research

Genomics and Phylogenetic StudiesEvolution and Genetic Dynamics

Cited by 2,353

Evolutionary and biomedical insights from the rhesus macaque genome.

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., et al. (2007) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,403

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,108

An RNA gene expressed during cortical development evolved rapidly in humans

Pollard, K. S., Salama, S. R., Lambert, N., Lambot, M.-A., Coppens, S., Pedersen, J. S., Katzman, S., King, B., Onodera, C., Siepel, A., et al. (2006) · Nature

Neurogenesis and neuroplasticity mechanismsGenetics and Neurodevelopmental Disorders

Cited by 1,005

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

Core, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., & Lis, J. T. (2014) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 693

Genome sequencing highlights the dynamic early history of dogs

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., et al. (2014) · PLoS Genetics

Human-Animal Interaction StudiesGenetic diversity and population structure

Cited by 624

Ancient gene flow from early modern humans into Eastern Neanderthals

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., et al. (2016) · Nature

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 577

Patterns of Positive Selection in Six Mammalian Genomes

Kosiol, C., Vinař, T., da Fonseca, R. R., Hubisz, M. J., Bustamante, C. D., Nielsen, R., & Siepel, A. (2008) · PLoS Genetics

Evolution and Genetic DynamicsGenomics and Phylogenetic Studies

Cited by 576

Forces shaping the fastest evolving regions in the human genome

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 511

PHAST and RPHAST: phylogenetic analysis with space/time models

Hubisz, M. J., Pollard, K. S., & Siepel, A. (2011) · Briefings in Bioinformatics

Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical Research

Cited by 490

Genome-Wide Inference of Ancestral Recombination Graphs

Rasmussen, M. D., Hubisz, M. J., Gronau, I., & Siepel, A. (2014) · PLoS Genetics

Genomics and Phylogenetic StudiesForensic and Genetic Research

Cited by 371

Widespread regulatory activity of vertebrate microRNA* species

Yang, J.-S., Phillips, M. D., Betel, D., Mu, P., Ventura, A., Siepel, A. C., Chen, K. C., & Lai, E. C. (2011) · RNA

MicroRNA in disease regulationPlant Molecular Biology Research

Cited by 360

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A., & Kraus, W. L. (2013) · Molecular Cell

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 333

Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans

Cornejo, O. E., Lefébure, T., Pavinski Bitar, P. D., Lang, P., Richards, V. P., Eilertson, K., Do, T., Beighton, D., Zeng, L., Ahn, S.-J., et al. (2013) · Molecular Biology and Evolution

Oral microbiology and periodontitis researchGenomics and Phylogenetic Studies

Cited by 198

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

Hubisz, M. J., Williams, A. L., & Siepel, A. (2020) · PLOS Genetics

Pleistocene-Era Hominins and ArchaeologyForensic and Genetic Research

Cited by 130

Demographically-based evaluation of genomic regions under selection in domestic dogs

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., et al. (2016) · PLoS Genetics

Genetic and phenotypic traits in livestockHuman-Animal Interaction Studies

Cited by 104

The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome

Kostka, D., Hubisz, M. J., Siepel, A., & Pollard, K. S. (2012) · Molecular Biology and Evolution

Evolution and Genetic DynamicsGenomics and Phylogenetic Studies

Cited by 102

Is a super-enhancer greater than the sum of its parts?

Dukler, N., Gulko, B., Huang, Y.-F., & Siepel, A. (2017) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 79

A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes

Capra, J. A., Hubisz, M. J., Kostka, D., Pollard, K. S., & Siepel, A. (2013) · PLoS Genetics

Evolution and Genetic DynamicsChromosomal and Genetic Variations

Cited by 77

Positive selection on apoptosis related genes

da Fonseca, R. R., Kosiol, C., Vinař, T., Siepel, A., & Nielsen, R. (2010) · FEBS Letters

Evolution and Genetic DynamicsCell death mechanisms and regulation

Cited by 42

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

Wu, Y., Johnson, L., Song, B., Romay, C., Stitzer, M., Siepel, A., Buckler, E., & Scheben, A. (2022) · The Plant Genome

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 10