Integrative annotation of variants from 1092 humans: application to cancer genomics (Q22065599)

7 February 2023

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Gerstein

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7 February 2023

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Tyler-Smith

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7 February 2023

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Beal

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7 February 2023

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Paul Flicek

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Flicek

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7 February 2023

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Donna Muzny

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Muzny

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7 February 2023

Cristina Sisu

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Cristina

Sisu

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7 February 2023

Jieming Chen

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Jieming

Chen

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7 February 2023

Jishnu Das

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Jishnu

Das

1 reference

7 February 2023

Yong Kong

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Yong

Kong

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7 February 2023

Tuuli Lappalainen

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Tuuli

Lappalainen

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7 February 2023

Vincenza Colonna

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Vincenza

Colonna

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7 February 2023

Alexej Abyzov

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Alexej

Abyzov

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7 February 2023

Andrea Sboner

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Andrea

Sboner

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7 February 2023

Tune H Pers

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Tune H

Pers

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7 February 2023

Laura Clarke

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Laura

Clarke

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7 February 2023

Javier Herrero

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Javier

Herrero

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7 February 2023

Mark A Rubin

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Mark A

Rubin

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7 February 2023

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Fiona Cunningham

Fiona

Cunningham

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7 February 2023

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Zeynep H Gümüs

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Suganthi Balasubramanian

object named as

Suganthi Balasubramanian

13

Suganthi

Balasubramanian

1 reference

7 February 2023

Daniel G MacArthur

33

Daniel G

MacArthur

1 reference

ORCID Public Data File 2021

7 February 2023

1 reference

Andrew G. Clark

1 reference

ORCID Public Data File 2021

Andrea Angius

1 reference

ORCID Public Data File 2021

41

Michael Wilson

Michael

Wilson

1 reference

7 February 2023

37

Graham R S Ritchie

Graham R S

Ritchie

1 reference

7 February 2023

24

Erik Garrison

Erik

Garrison

1 reference

7 February 2023

34

Gabor Marth

Gabor

Marth

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7 February 2023

42

Yali Xue

Yali

Xue

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7 February 2023

Emmanouil Dermitzakis

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Emmanouil T Dermitzakis

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Dermitzakis

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7 February 2023

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Xinmeng Jasmine

Mu

Xinmeng Jasmine Mu

1 reference

7 February 2023

1

Ekta

Khurana

Ekta Khurana

1 reference

7 February 2023

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Lucas

Lochovsky

Lucas Lochovsky

1 reference

7 February 2023

10

Arif

Harmanci

Arif Harmanci

1 reference

7 February 2023

15

Dimple

Chakravarty

Dimple Chakravarty

1 reference

7 February 2023

16

Daniel

Challis

Daniel Challis

1 reference

7 February 2023

23

Robert Fragoza

Robert

Fragoza

1 reference

7 February 2023

Yao Fu

2

Yao

Fu

1 reference

7 February 2023

Hyun Min Kang

5

Hyun Min

Kang

1 reference

7 February 2023

Yuan Chen

17

Yuan

Chen

1 reference

7 February 2023

Declan Clarke

18

Declan

Clarke

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7 February 2023

Uday S Evani

21

Uday S

Evani

1 reference

7 February 2023

Naoki Kitabayashi

28

Naoki

Kitabayashi

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7 February 2023

Kasper Lage

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Kasper

Lage

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7 February 2023

Vaja Liluashvili

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Vaja

Liluashvili

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7 February 2023

Steven M Lipkin

32

Steven M

Lipkin

1 reference

7 February 2023

Jeffrey A Rosenfeld

38

Jeffrey A

Rosenfeld

1 reference

7 February 2023

Xiaomu Wei

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Xiaomu

Wei

1 reference

7 February 2023

Fuli Yu

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Fuli

Yu

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7 February 2023

Haiyuan Yu

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Haiyuan

Yu

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An integrated map of genetic variation from 1,092 human genomes

7 February 2023

publication date

4 October 2013

0 references

language of work or name

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0 references

342

0 references

issue

6154

0 references

page(s)

1235587

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

An integrated encyclopedia of DNA elements in the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Comprehensive molecular characterization of human colon and rectal cancer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Mutational processes molding the genomes of 21 breast cancers

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

The genomic complexity of primary human prostate cancer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Mapping copy number variation by population-scale genome sequencing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

A map of human genome variation from population-scale sequencing

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

International network of cancer genome projects

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

The diploid genome sequence of an individual human

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Global variation in copy number in the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Mutations in lipid transporter ABCA12 in harlequin ichthyosis and functional recovery by corrective gene transfer

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Ultraconserved Elements in the Human Genome

19 March 2017

1 reference

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Integrated genomic analyses of ovarian carcinoma

19 March 2017

1 reference

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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Comprehensive genomic characterization of squamous cell lung cancers

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Natural selection has driven population differentiation in modern humans

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Uroporphyrinogen III synthase erythroid promoter mutations in adjacent GATA1 and CP2 elements cause congenital erythropoietic porphyria

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Positive selection at the protein network periphery: Evaluation in terms of structural constraints and cellular context

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Natural selection on genes that underlie human disease susceptibility

6 April 2017

1 reference

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

A census of human cancer genes

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

GENCODE: the reference human genome annotation for The ENCODE Project

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Statistical significance for genomewide studies

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

The accessible chromatin landscape of the human genome

22 April 2017

1 reference

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Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein

22 April 2017

1 reference

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p31comet blocks Mad2 activation through structural mimicry

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Identification of a MAD2-binding protein, CMT2, and its role in mitosis

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Towards a proteome-scale map of the human protein–protein interaction network

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Self-assembling protein microarrays

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

A novel high-throughput (HTP) cloning strategy for site-directed designed chimeragenesis and mutation using the Gateway cloning system

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

High-quality binary protein interaction map of the yeast interactome network

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

In-silico human genomics with GeneCards

22 April 2017

1 reference

https://api.crossref.org/works/10.1126/SCIENCE.1235587

A framework for variation discovery and genotyping using next-generation DNA sequencing data

22 April 2017

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Highly Recurrent TERT Promoter Mutations in Human Melanoma

22 April 2017

1 reference

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TERT promoter mutations in familial and sporadic melanoma

7 April 2017

1 reference

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Systematic localization of common disease-associated variation in regulatory DNA

7 April 2017

1 reference

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Architecture of the human regulatory network derived from ENCODE data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Personal omics profiling reveals dynamic molecular and medical phenotypes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Positive natural selection in the human lineage

7 April 2017

1 reference

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Evolutionary rate in the protein interaction network

7 April 2017

1 reference

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A systematic survey of loss-of-function variants in human protein-coding genes

7 April 2017

1 reference

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A census of human transcription factors: function, expression and evolution

22 April 2017

1 reference

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A human phenome-interactome network of protein complexes implicated in genetic disorders

22 April 2017

1 reference

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The mutational landscape of lethal castration-resistant prostate cancer

22 April 2017

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Punctuated evolution of prostate cancer genomes

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal

12 September 2017

1 reference

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Interpretation of genomic variants using a unified biological network approach

12 September 2017

1 reference

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Identifying recent adaptations in large-scale genomic data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Interpreting noncoding genetic variation in complex traits and human disease

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Personal and population genomics of human regulatory variation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Classic selective sweeps were rare in recent human evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Population differentiation as an indicator of recent positive selection in humans: an empirical evaluation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

The promise and reality of personal genomics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Analytical methods for inferring functional effects of single base pair substitutions in human cancers

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Consequences of mutations in the non-coding RMRP RNA in cartilage-hair hypoplasia

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

The Human Gene Mutation Database: 2008 update

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3947637

Evidence of abundant purifying selection in humans for recently acquired regulatory functions

30 May 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

DEG: a database of essential genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Null mutations in human and mouse orthologs frequently result in different phenotypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Fast and flexible simulation of DNA sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Demographic history and rare allele sharing among human populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Human genome ultraconserved elements are ultraselected

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

AlleleSeq: analysis of allele-specific expression and binding in a network framework

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Rare and common regulatory variation in population-scale sequenced human genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

HINT: High-quality protein interactomes and their applications in understanding human disease

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

The MIPS mammalian protein-protein interaction database

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Edgetic perturbation models of human inherited disorders

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587

Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1235587