Adam C. Siepel | Academic Influence

Adam C. Siepel's AcademicInfluence.com Rankings

Adam C. Siepel

Computer Science

#3590

World Rank

#3771

Historical Rank

#1338

USA Rank

Database

#7893

World Rank

#8216

Historical Rank

#1012

USA Rank

computer-science Degrees

Adam C. Siepel

Biology

#4615

World Rank

#6859

Historical Rank

#1695

USA Rank

Bioinformatics

#118

World Rank

#120

Historical Rank

#20

USA Rank

Evolutionary Biology

#197

World Rank

#218

Historical Rank

#67

USA Rank

Computational Biology

#352

World Rank

#354

Historical Rank

#45

USA Rank

biology Degrees

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Computer Science
Biology

Adam C. Siepel's Degrees

PhD Computer Science Stanford University
Bachelors Computer Science Stanford University

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Why Is Adam C. Siepel Influential?

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According to Wikipedia, Adam C. Siepel is an American computational biologist known for his research in comparative genomics and population genetics, particularly the development of statistical methods and software tools for identifying evolutionarily conserved sequences. Siepel is currently Chair of the Simons Center for Quantitative Biology and Professor in the Watson School for Biological Sciences at Cold Spring Harbor Laboratory.

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Adam C. Siepel's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007) (5196)
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. (2005) (3639)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution (2004) (2417)
The ENCODE (ENCyclopedia Of DNA Elements) Project (2004) (2194)
Detection of nonneutral substitution rates on mammalian phylogenies. (2010) (1815)
The UCSC Genome Browser Database: update 2006 (2005) (1691)
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome (2007) (1309)
A high-resolution map of human evolutionary constraint using 29 mammals (2011) (1081)
The UCSC genome browser database: update 2007 (2006) (929)
An RNA gene expressed during cortical development evolved rapidly in humans (2006) (861)
Comparative analyses of multi-species sequences from targeted genomic regions (2003) (666)
Comparative and demographic analysis of orang-utan genomes (2011) (545)
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006) (538)
Patterns of Positive Selection in Six Mammalian Genomes (2008) (538)
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014) (534)
Bayesian inference of ancient human demography from individual genome sequences (2011) (512)
A distal enhancer and an ultraconserved exon are derived from a novel retroposon (2006) (496)
Genome Sequencing Highlights the Dynamic Early History of Dogs (2014) (482)
Forces Shaping the Fastest Evolving Regions in the Human Genome (2006) (439)
A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells (2011) (411)
A Simple Genetic Architecture Underlies Morphological Variation in Dogs (2010) (403)
PHAST and RPHAST: phylogenetic analysis with space/time models (2011) (369)
Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. (2003) (366)
Widespread regulatory activity of vertebrate microRNA* species. (2011) (362)
Ancient gene flow from early modern humans into Eastern Neanderthals (2016) (339)
Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. (2013) (303)
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. (2007) (293)
Combining phylogenetic and hidden Markov models in biosequence analysis (2003) (274)
Genome-Wide Inference of Ancestral Recombination Graphs (2013) (251)
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data (2016) (241)
A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. (1995) (240)
New Methods for Detecting Lineage-Specific Selection (2006) (238)
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. (2007) (221)
Probabilities of Fitness Consequences for Point Mutations Across the Human Genome (2014) (217)
Genomic Analyses of Transcription Factor Binding, Histone Acetylation, and Gene Expression Reveal Mechanistically Distinct Classes of Estrogen-Regulated Promoters (2007) (199)
Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. (2013) (171)
Three Periods of Regulatory Innovation During Vertebrate Evolution (2011) (134)
The completion of the Mammalian Gene Collection (MGC). (2009) (132)
Phylogenetic Hidden Markov Models (2005) (124)
Genome-wide inference of natural selection on human transcription factor binding sites (2013) (117)
Identification of active transcriptional regulatory elements with GRO-seq (2015) (109)
Sequencing and Comparative Analysis of a Conserved Syntenic Segment in the Solanaceae (2008) (108)
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease (2014) (106)
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data (2002) (99)
Computational identification of evolutionarily conserved exons (2004) (98)
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources (2001) (89)
The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome (2011) (87)
Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs (2016) (82)
Finding an Optimal Inversion Median: Experimental Results (2001) (80)
GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters (2015) (79)
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence. (2011) (75)
A community-maintained standard library of population genetic models (2019) (72)
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes (2013) (69)
Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation (2015) (67)
Is a super-enhancer greater than the sum of its parts? (2016) (63)
Gene Regulation by CcpA and Catabolite Repression Explored by RNA-Seq in Streptococcus mutans (2013) (63)
Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines (2014) (62)
Computational screening of conserved genomic DNA in search of functional noncoding elements (2005) (61)
Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo (2012) (60)
Contrasting X-linked and autosomal diversity across 14 human populations. (2014) (58)
Phylogenomics of primates and their ancestral populations. (2009) (54)
Darwinian alchemy: Human genes from noncoding DNA. (2009) (53)
Dynamic evolution of regulatory element ensembles in primate CD4+ T cells (2018) (53)
Targeted discovery of novel human exons by comparative genomics. (2007) (52)
A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells (2011) (52)
Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph (2019) (52)
A simplified hillslope erosion model with vegetation elements for practical applications (2002) (51)
Comparative Genomic Analysis of the Streptococcus dysgalactiae Species Group: Gene Content, Molecular Adaptation, and Promoter Evolution (2011) (49)
Efficient approximations for learning phylogenetic HMM models from data (2004) (44)
Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila (2014) (40)
Replacing and additive horizontal gene transfer in Streptococcus. (2012) (40)
Positive selection on apoptosis related genes (2010) (40)
An Algorithm to Enumerate Sorting Reversals for Signed Permutations (2003) (37)
New genes often acquire male-specific functions but rarely become essential in Drosophila (2017) (37)
An integration platform for heterogeneous bioinformatics software components (2001) (37)
The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution (2013) (35)
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. (2018) (35)
Diverse modes of evolutionary emergence and flux of conserved microRNA clusters (2014) (35)
phastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP (2018) (34)
An algorithm to enumerate all sorting reversals (2002) (34)
Error and Error Mitigation in Low-Coverage Genome Assemblies (2011) (33)
Contrasting human X-linked and autosomal variation in population-scale whole genome sequencing (2011) (33)
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data (2019) (33)
Cis-regulatory elements and human evolution. (2014) (31)
Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus (2017) (30)
An algorithm to find all sorting reversals (2002) (28)
Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii) (2013) (27)
Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol (2017) (26)
The Genome Sequence DataBase (GSDB): improving data quality and data access (1998) (25)
Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps (2020) (24)
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences (2018) (22)
Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. (2008) (21)
Challenges in funding and developing genomic software: roots and remedies (2019) (20)
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease (2018) (20)
Exact Algorithms for the Reversal Median Problem (2001) (20)
The Genome Sequence DataBase: towards an integrated functional genomics resource (1999) (19)
An inferred fitness consequence map of the rice genome (2020) (18)
From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection. (2020) (17)
Reconstructing the Evolutionary History of Complex Human Gene Clusters (2008) (15)
Inference of Ancestral Recombination Graphs Using ARGweaver. (2020) (14)
Exploitation of a new staging area in the Dutch Wadden Sea by Greylag Geese Anser anser: the importance of food-plant dynamics (1999) (13)
Ecological profiles of large timber species (2004) (13)
Extreme purifying selection against point mutations in the human genome (2021) (12)
The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes (1997) (11)
What explains the distribution of rare and endemic West African plants (2004) (10)
Ecological profiles of rare and endemic species (2004) (9)
Reconstructing Histories of Complex Gene Clusters on a Phylogeny (2009) (9)
Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs (2013) (8)
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph (2021) (7)
Phylogenetic modeling of regulatory element turnover based on epigenomic data (2019) (6)
Phylogenetic modeling of regulatory element turnover based on epigenomic data. (2020) (6)
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters (2009) (6)
Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland (2021) (5)
A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data (2021) (5)
Erratum to Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells [Molecular Cell 50, (2013) 778] (2013) (4)
RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription (2022) (4)
Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution (2017) (3)
Bioinformatics for rice resources. (2007) (3)
A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes Supplementary Information : Text S 1 (2013) (3)
Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species (2022) (3)
Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus (2020) (3)
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells (2021) (3)
Accurate Identification of Active Transcriptional Regulatory Elements from Global Run-On and Sequencing Data (2014) (3)
A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants (2022) (2)
SIA: Selection Inference Using the Ancestral Recombination Graph (2021) (2)
Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells (2016) (2)
Long-read sequencing reveals rapid evolution of immunity- and cancer-related genes in bats (2020) (2)
Genome Browser 28-Way vertebrate alignment and conservation track in the UCSC (2007) (2)
How Much Information is Provided by Human Epigenomic Data? An Evolutionary View (2018) (1)
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells (2022) (1)
Circadian immunity, sunrise time and the seasonality of respiratory infections (2021) (1)
Resource A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells (2011) (1)
ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens (2019) (1)
A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants (2021) (1)
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny (2009) (1)
Patterns of positive selection on the mammalian tree Supplementary Material (2008) (1)
Faculty Opinions recommendation of Most "dark matter" transcripts are associated with known genes. (2010) (1)
Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data (2023) (1)
Author Correction: Comparative and demographic analysis of orang-utan genomes (2022) (1)
Expectation Maximization for Combined Phylogenetic and Hidden Markov Models Adam Siepel December (2002) (1)
Input file for the GPhoCS analysis. (2015) (0)
Comparative mammalian genomics: models of evolution and detection of functional elements (2005) (0)
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences (2018) (0)
Dynamic evolution of regulatory element ensembles in primate CD4+ T cells (2018) (0)
A Unified Model Describing The Architecture And Creation Of Promoters And Enhancers (2015) (0)
An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon (2005) (0)
Cis-regulatory Elements and Human Evolution (2014) (0)
Species distributions in West African forests (2004) (0)
Challenges in funding and developing genomic software: roots and remedies (2019) (0)
Tracking genes and finding mutations: finding genes for complex traits in the domestic dog (Canis familiaris) (2010) (0)
Bacterial population genomics and the agent of human tooth decay at the dawn of agriculture (2014) (0)
Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences (2019) (0)
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data (2021) (0)
S 9 Demographic Analysis Using G-PhoCS (2013) (0)
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data (2017) (0)
An inferred fitness consequence map of the rice genome (2020) (0)
Genome Browser, zoomed out to view all of human chromosome 21 in the May 2004 assembly (2011) (0)
Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences (2019) (0)
selection in six Mammalian genomes. (2008) (0)
Browser 28-Way vertebrate alignment and conservation track in the UCSC data (2007) (0)
Scikit-ribo Enables Accura te Estimation and Robust Modeling of Translation Dynamics at Codon Resolution Graphical (2018) (0)
Genome Browser zoomed in to base-level view, showing Base Position, Restriction Enzymes, sno/miRNA (2011) (0)
Erratum: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. (2019) (0)
ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens (2021) (0)
Cornell University Life Sciences Core Laboratories Center. (2011) (0)
Error and Error Mitigation in Low-Coverage Genomes (2011) (0)
(No) effect of oral ivermectin treatment of ponies on dung degradation in semi-natural pastures. A field study (2010) (0)
Generative Probabilistic Model for Detecting Selection on Dispersed Genomic Elements from Polymorphism and Divergence (2011) (0)
Mapping gene ﬂow between ancient hominins through demography-aware inference of the ancestral recombination graph: S1 Text (2020) (0)

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