List of works - Adam C. Siepel

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences

scientific article

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

scientific article (publication date: 4 May 2006)

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

scientific article

A method for calculating probabilities of fitness consequences for point mutations across the human genome

scientific article

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

scientific article

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

scientific article published on 5 May 2011

A simple genetic architecture underlies morphological variation in dogs

scientific article

A simplified hillslope erosion model with vegetation elements for practical applications

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

scientific article published on 26 June 2008

Accurate prediction of inducible transcription factor binding intensities in vivo

scientific article

Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila

scientific article published on 18 June 2014

An RNA gene expressed during cortical development evolved rapidly in humans

scientific article

An algorithm to enumerate sorting reversals for signed permutations

scientific article

An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

article

An inferred fitness consequence map of the rice genome

scientific article published on 10 February 2020

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

scientific article

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

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

scientific article

Ancient gene flow from early modern humans into Eastern Neanderthals

scientific article

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Bayesian inference of ancient human demography from individual genome sequences

scientific article (publication date: 18 September 2011)

Bioinformatics for rice resources

scientific article

Challenges in funding and developing genomic software: roots and remedies

scientific article published on 29 July 2019

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

scientific article published on 15 February 2021

Cis-regulatory elements and human evolution

scientific article published on 16 September 2014

Combining phylogenetic and hidden Markov models in biosequence analysis

scientific article published in January 2004

Combining phylogenetic and hidden Markov models in biosequence analysis

scholarly article published 2003

Comparative analyses of multi-species sequences from targeted genomic regions

scientific article (publication date: 14 August 2003)

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution

scientific article

Computational identification of evolutionarily conserved exons

Computational screening of conserved genomic DNA in search of functional noncoding elements

scientific article published in July 2005

Contrasting X-linked and autosomal diversity across 14 human populations

scientific article

Darwinian alchemy: Human genes from noncoding DNA

scientific article

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

scientific article

Detection of nonneutral substitution rates on mammalian phylogenies

scientific article published on 26 October 2009

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

scientific article

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

scientific article

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

scientific article

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.

scientific article

Efficient approximations for learning phylogenetic HMM models from data

scientific article

Enabling large-scale next-generation sequence assembly with Blacklight

scientific article

Error and error mitigation in low-coverage genome assemblies

scientific article

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease

scientific article published on 27 June 2019

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans ⬇️

scientific article published on 10 December 2012

Evolutionary history reconstruction for Mammalian complex gene clusters

scientific article

Forces shaping the fastest evolving regions in the human genome

scientific article

From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection

scientific article published on 15 January 2020

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters

scientific article published on 27 March 2015

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans

scientific article

Genome sequencing highlights the dynamic early history of dogs

scientific article published in January 2014

Genome-wide inference of ancestral recombination graphs

scientific article

Genome-wide inference of natural selection on human transcription factor binding sites

scientific article

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters

scientific article published on 21 May 2007

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and classification of conserved RNA secondary structures in the human genome

scientific article

Identification of active transcriptional regulatory elements from GRO-seq data

scientific article

Inference of Ancestral Recombination Graphs Using ARGweaver

scientific article published on 01 January 2020

Inference of natural selection from interspersed genomic elements based on polymorphism and divergence

scientific article published on 05 February 2013

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

scientific article published on 06 August 2020

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

article

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

scientific article published on 12 October 2017

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

New Methods for Detecting Lineage-Specific Selection

PHAST and RPHAST: phylogenetic analysis with space/time models

scientific article

Patterns of positive selection in six Mammalian genomes

scientific article

Phylogenetic Hidden Markov Models

article

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

scientific article

Phylogenomics of primates and their ancestral populations

scientific article (publication date: November 2009)

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

scientific article (publication date: 2013)

Positive selection on apoptosis related genes

scientific article published on 22 December 2009

Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

scientific article published on 01 March 2019

Reconstructing Histories of Complex Gene Clusters on a Phylogeny

article

Reconstructing histories of complex gene clusters on a phylogeny

scientific article published in September 2010

Reconstructing the Evolutionary History of Complex Human Gene Clusters

article

Replacing and additive horizontal gene transfer in Streptococcus

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae

scientific article (publication date: September 2008)

Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells

scientific article published on 21 March 2013

Targeted discovery of novel human exons by comparative genomics

scientific article

The Genome Sequence DataBase (GSDB): improving data quality and data access

scientific article

The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes

scientific article

The Genome Sequence DataBase: towards an integrated functional genomics resource

scientific article

The UCSC Genome Browser Database: update 2006

scientific article

The UCSC genome browser database: update 2007.

scientific article

The completion of the Mammalian Gene Collection (MGC).

scientific article published on 18 September 2009

The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease

scientific article (publication date: December 2014)

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

scientific article published on 23 July 2013

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

scientific article

Three periods of regulatory innovation during vertebrate evolution ⬇️

scientific article

Widespread regulatory activity of vertebrate microRNA* species

scientific article

List of works by Adam C. Siepel

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences

A distal enhancer and an ultraconserved exon are derived from a novel retroposon

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

A method for calculating probabilities of fitness consequences for point mutations across the human genome

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

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

A simple genetic architecture underlies morphological variation in dogs

A simplified hillslope erosion model with vegetation elements for practical applications

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

Accurate prediction of inducible transcription factor binding intensities in vivo

Adaptive evolution of testis-specific, recently evolved, clustered miRNAs in Drosophila

An RNA gene expressed during cortical development evolved rapidly in humans

An algorithm to enumerate sorting reversals for signed permutations

An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

An inferred fitness consequence map of the rice genome

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

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

Ancient gene flow from early modern humans into Eastern Neanderthals

Author Correction: Comparative and demographic analysis of orang-utan genomes

Bayesian inference of ancient human demography from individual genome sequences

Bioinformatics for rice resources

Challenges in funding and developing genomic software: roots and remedies

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Cis-regulatory elements and human evolution

Combining phylogenetic and hidden Markov models in biosequence analysis

Combining phylogenetic and hidden Markov models in biosequence analysis

Comparative analyses of multi-species sequences from targeted genomic regions

Comparative and demographic analysis of orang-utan genomes

Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution

Computational identification of evolutionarily conserved exons

Computational screening of conserved genomic DNA in search of functional noncoding elements

Contrasting X-linked and autosomal diversity across 14 human populations

Darwinian alchemy: Human genes from noncoding DNA

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs

Detection of nonneutral substitution rates on mammalian phylogenies

Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Diverse modes of evolutionary emergence and flux of conserved microRNA clusters

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.

Efficient approximations for learning phylogenetic HMM models from data

Enabling large-scale next-generation sequence assembly with Blacklight

Error and error mitigation in low-coverage genome assemblies

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease

Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans ⬇️

Evolutionary history reconstruction for Mammalian complex gene clusters

Forces shaping the fastest evolving regions in the human genome

From Summary Statistics to Gene Trees: Methods for Inferring Positive Selection

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters

Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans

Genome sequencing highlights the dynamic early history of dogs

Genome-wide inference of ancestral recombination graphs

Genome-wide inference of natural selection on human transcription factor binding sites

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters

ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Identification and classification of conserved RNA secondary structures in the human genome

Identification of active transcriptional regulatory elements from GRO-seq data

Inference of Ancestral Recombination Graphs Using ARGweaver

Inference of natural selection from interspersed genomic elements based on polymorphism and divergence

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

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

New Methods for Detecting Lineage-Specific Selection

PHAST and RPHAST: phylogenetic analysis with space/time models

Patterns of positive selection in six Mammalian genomes

Phylogenetic Hidden Markov Models

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

Phylogenomics of primates and their ancestral populations

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus and Pongo abelii)

Positive selection on apoptosis related genes

Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

Reconstructing Histories of Complex Gene Clusters on a Phylogeny

Reconstructing histories of complex gene clusters on a phylogeny