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

B Gulko, A Siepel - Nature genetics, 2019 - nature.com
Here we ask the question “How much information do epigenomic datasets provide about
human genomic function?” We consider nine epigenomic features across 115 cell types and …

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

B Gulko, MJ Hubisz, I Gronau, A Siepel - Nature genetics, 2015 - nature.com
We describe a new computational method for estimating the probability that a point mutation
at each position in a genome will influence fitness. These'fitness consequence'(fitCons) …

The missing diversity in human epigenomic studies

CE Breeze, S Beck, SI Berndt, N Franceschini - Nature genetics, 2022 - nature.com
The missing diversity in human epigenomic studies | Nature Genetics Skip to main content
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Genome-wide inference of natural selection on human transcription factor binding sites

L Arbiza, I Gronau, BA Aksoy, MJ Hubisz, B Gulko… - Nature …, 2013 - nature.com
For decades, it has been hypothesized that gene regulation has had a central role in human
evolution, yet much remains unknown about the genome-wide impact of regulatory …

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

YF Huang, A Siepel - Genome Research, 2019 - genome.cshlp.org
A central challenge in human genomics is to understand the cellular, evolutionary, and
clinical significance of genetic variants. Here, we introduce a unified population-genetic and …

Mutational load and the functional fraction of the human genome

B Galeota-Sprung, P Sniegowski… - Genome biology and …, 2020 - academic.oup.com
The fraction of the human genome that is functional is a question of both evolutionary and
practical importance. Studies of sequence divergence have suggested that the functional …

Potential energy landscapes identify the information-theoretic nature of the epigenome

G Jenkinson, E Pujadas, J Goutsias, AP Feinberg - Nature genetics, 2017 - nature.com
Epigenetics is the study of biochemical modifications carrying information independent of
DNA sequence, which are heritable through cell division. In 1940, Waddington coined the …

The sequences of 150,119 genomes in the UK Biobank

BV Halldorsson, HP Eggertsson, KHS Moore… - Nature, 2022 - nature.com
Detailed knowledge of how diversity in the sequence of the human genome affects
phenotypic diversity depends on a comprehensive and reliable characterization of both …

Genome-wide signals of positive selection in human evolution

D Enard, PW Messer, DA Petrov - Genome research, 2014 - genome.cshlp.org
The role of positive selection in human evolution remains controversial. On the one hand,
scans for positive selection have identified hundreds of candidate loci, and the genome …

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

DL Goode, GM Cooper, J Schmutz, M Dickson… - Genome …, 2010 - genome.cshlp.org
Here, we demonstrate how comparative sequence analysis facilitates genome-wide base-
pair-level interpretation of individual genetic variation and address two questions of …