Nature Search

An inferred fitness consequence map of the rice genome

A map of fitness consequence scores is generated for 246 rice genome region classes inferred from nine functional genomic and epigenomic datasets, which illuminates the evolutionary forces associated with genome diversity and guides crop breeding.

Zoé Joly-Lopez
Adrian E. Platts
Michael D. Purugganan
Research10 Feb 2020
Nature Plants

Volume: 6, P: 119-130
Publisher Correction: An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

Brad Gulko
Adam Siepel
Amendments and Corrections20 Feb 2019
Nature Genetics

Volume: 51, P: 577
Bayesian inference of ancient human demography from individual genome sequences

Adam Siepel and colleagues estimate key parameters for ancient human demography using a Bayesian analysis of the whole-genome sequences of six individuals from diverse populations. They present new methods for coalescent-based inference of demographic parameters as well as a custom pipeline for genotype inference.

Ilan Gronau
Melissa J Hubisz
Adam Siepel
Research18 Sept 2011
Nature Genetics

Volume: 43, P: 1031-1034
Is a super-enhancer greater than the sum of its parts?

Noah Dukler
Brad Gulko
Adam Siepel
Correspondence28 Dec 2016
Nature Genetics

Volume: 49, P: 2-3
An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences

FitCons2 is a new framework that simultaneously clusters genomic sites by epigenomic features and evaluates the strength of natural selection on these sites. FitCons2 scores are used to generate fitness–consequence maps for 115 human cell types.

Brad Gulko
Adam Siepel
Research17 Dec 2018
Nature Genetics

Volume: 51, P: 335-342
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

Adam Siepel and colleagues report a new computational method, LINSIGHT, that combines evolutionary conservation and functional genomic information to predict the fitness consequences of noncoding mutations in the human genome. They use LINSIGHT to show that fitness consequences of enhancer mutations depend on tissue and cell type specificity and promoter constraints.

Yi-Fei Huang
Brad Gulko
Adam Siepel
Research13 Mar 2017
Nature Genetics

Volume: 49, P: 618-624
Genome-wide inference of natural selection on human transcription factor binding sites

Adam Siepel and colleagues find that natural selection has exerted a significant influence on transcription factor binding sites in the human lineage using a new probabilistic method, INSIGHT. They analyzed whole-genome sequences from 54 individuals, as well as from several non-human primates, combined with chromatin immunoprecipitation and sequencing data sets to identify transcription factor binding sites and evidence of selection.

Leonardo Arbiza
Ilan Gronau
Adam Siepel
Research09 Jun 2013
Nature Genetics

Volume: 45, P: 723-729
A method for calculating probabilities of fitness consequences for point mutations across the human genome

Adam Siepel and colleagues develop a statistical method, fitCons, which combines comparative and functional genomic data to estimate the probability that a point mutation will influence fitness. They generate fitCons scores for three human cell types from ENCODE data sets and demonstrate improved prediction power for cis regulatory elements in comparison to conventional conservation-based scores.

Brad Gulko
Melissa J Hubisz
Adam Siepel
Research19 Jan 2015
Nature Genetics

Volume: 47, P: 276-283

Search

Filter By:

Search

Quick links