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Challenges in funding and developing genomic software: roots and remedies

Genome Biology, 2019-07, Vol.20 (1), p.147-147, Article 147

Siepel, Adam

2019

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Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

Nature genetics, 2017-04, Vol.49 (4), p.618-624

2017

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Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data

PLoS genetics, 2023-11, Vol.19 (11), p.e1011032-e1011032

2023

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

Nature genetics, 2015-03, Vol.47 (3), p.276-283

2015

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Genome-wide inference of ancestral recombination graphs

PLoS genetics, 2014-05, Vol.10 (5), p.e1004342-e1004342

2014

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

Nature genetics, 2014-12, Vol.46 (12), p.1311-1320

2014

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Detection of nonneutral substitution rates on mammalian phylogenies

Genome research, 2010-01, Vol.20 (1), p.110-121

2010

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Widespread regulatory activity of vertebrate microRNA species

RNA (Cambridge), 2011-02, Vol.17 (2), p.312-326

2011

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

PLoS genetics, 2020-08, Vol.16 (8), p.e1008895-e1008895

2020

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The statistics of bulk segregant analysis using next generation sequencing

PLoS computational biology, 2011-11, Vol.7 (11), p.e1002255-e1002255

2011

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Extreme purifying selection against point mutations in the human genome

Nature communications, 2022-07, Vol.13 (1), p.4312-12, Article 4312

2022

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Genome sequencing highlights the dynamic early history of dogs

PLoS genetics, 2014-01, Vol.10 (1), p.e1004016-e1004016

2014

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

Molecular biology and evolution, 2013-05, Vol.30 (5), p.1159-1171

2013

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Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

American journal of human genetics, 2014-06, Vol.94 (6), p.827-844

2014

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Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

Proceedings of the National Academy of Sciences - PNAS, 2020-12, Vol.117 (48), p.30554-30565

2020

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Fast statistical alignment

PLoS computational biology, 2009-05, Vol.5 (5), p.e1000392-e1000392

2009

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

Molecular cell, 2013-04, Vol.50 (2), p.212-222

2013

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Identification of active transcriptional regulatory elements from GRO-seq data

Nature methods, 2015-05, Vol.12 (5), p.433-438

2015

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New Methods for Detecting Lineage-Specific Selection

Research in Computational Molecular Biology, p.190-205

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ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens

Genome Biology, 2021-09, Vol.22 (1), p.278-278, Article 278

2021

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Comparative and demographic analysis of orang-utan genomes

Nature (London), 2011-01, Vol.469 (7331), p.529-533

2011

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Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species

PLoS genetics, 2022-11, Vol.18 (11), p.e1010474-e1010474

2022

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

Genome research, 2005-08, Vol.15 (8), p.1034-1050

2005

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Patterns of positive selection in six Mammalian genomes

PLoS genetics, 2008-08, Vol.4 (8), p.e1000144-e1000144

2008

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Challenges in funding and developing genomic software: roots and remedies

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data

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

Genome-wide inference of ancestral recombination graphs

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

Detection of nonneutral substitution rates on mammalian phylogenies

Widespread regulatory activity of vertebrate microRNA species

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

The statistics of bulk segregant analysis using next generation sequencing

Extreme purifying selection against point mutations in the human genome

Genome sequencing highlights the dynamic early history of dogs

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

Contrasting X-Linked and Autosomal Diversity across 14 Human Populations

Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps

Fast statistical alignment

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

Identification of active transcriptional regulatory elements from GRO-seq data

New Methods for Detecting Lineage-Specific Selection

ACE: a probabilistic model for characterizing gene-level essentiality in CRISPR screens

A community-maintained standard library of population genetic models

Comparative and demographic analysis of orang-utan genomes

Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species

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

Patterns of positive selection in six Mammalian genomes

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