(Q35840707)

10 August 2017

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

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10 August 2017

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6

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10 August 2017

7

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10 August 2017

56

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10 August 2017

Stilianos Antonarakis

69

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10 August 2017

71

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10 August 2017

14

Ari Löytynoja

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Michele Clamp

49

Michele Clamp

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Donna Karolchik

63

Donna Karolchik

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Kerstin Lindblad-Toh

54

Kerstin Lindblad-Toh

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Damian Keefe

8

Damian Keefe

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David Haussler

73

David Haussler

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Heather Trumbower

57

Heather Trumbower

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Tim Massingham

17

Tim Massingham

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Sante Gnerre

51

Sante Gnerre

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Abel Ureta-Vidal

22

Abel Ureta-Vidal

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Ian Holmes

20

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Ross Hardison

72

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Lior Pachter

75

Lior Pachter

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Galt Barber

61

Galt Barber

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Erica Sodergren

39

Erica Sodergren

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Tina Graves

45

Tina Graves

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Eric Lander

55

Eric S Lander

1 reference

10 August 2017

George M Weinstock

43

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Juan I. Montoya-Burgos

13

Juan I Montoya-Burgos

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10 August 2017

23

Benedict Paten

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10 August 2017

58

Hiram Clawson

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10 August 2017

76

Eric D Green

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10 August 2017

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Webb Miller

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10 August 2017

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James C Mullikin

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10 August 2017

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Ann Zweig

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10 August 2017

47

Elaine R Mardis

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10 August 2017

25

Kate R Rosenbloom

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10 August 2017

5

Colin N Dewey

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10 August 2017

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W James Kent

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10 August 2017

11

James Taylor

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10 August 2017

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Donna M Muzny

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10 August 2017

70

Serafim Batzoglou

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10 August 2017

48

Richard K Wilson

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10 August 2017

41

Kim C Worley

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10 August 2017

12

Sergey Nikolaev

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10 August 2017

68

Marco A Marra

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10 August 2017

3

George Asimenos

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10 August 2017

27

Gerard G Bouffard

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10 August 2017

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Xiaobin Guan

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10 August 2017

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Jacquelyn R Idol

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10 August 2017

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Valerie V B Maduro

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10 August 2017

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Baishali Maskeri

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10 August 2017

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Robert W Blakesley

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10 August 2017

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Jacqueline E Schein

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10 August 2017

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Robert M Kuhn

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10 August 2017

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Rachel Harte

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10 August 2017

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Peter Bickel

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10 August 2017

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James Cuff

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1

Elliott H Margulies

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10 August 2017

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Nancy F Hansen

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10 August 2017

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Huaiyang Jiang

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10 August 2017

44

Richard A Gibbs

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10 August 2017

Gregory M Cooper

2

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10 August 2017

Daryl J Thomas

4

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10 August 2017

Ariel S Schwartz

9

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10 August 2017

Minmei Hou

10

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10 August 2017

Simon Whelan

15

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10 August 2017

Fabio Pardi

16

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10 August 2017

James B Brown

18

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10 August 2017

Eric A Stone

24

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10 August 2017

Jennifer C McDowell

33

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10 August 2017

Morgan Park

34

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10 August 2017

Pamela J Thomas

35

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10 August 2017

Alice C Young

36

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10 August 2017

David A Wheeler

40

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10 August 2017

Robert Fulton

46

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10 August 2017

David B Jaffe

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10 August 2017

Jean L Chang

53

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10 August 2017

Matthew A Field

64

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10 August 2017

Richard A Moore

65

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10 August 2017

Carrie A Matthewson

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10 August 2017

Arend Sidow

77

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10 August 2017

1 June 2007

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10 August 2017

760-774

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10 August 2017

6

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

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Using genomic data to unravel the root of the placental mammal phylogeny

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Early history of mammals is elucidated with the ENCODE multiple species sequencing data

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

A "silent" polymorphism in the MDR1 gene changes substrate specificity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Genetics. SNPs, silent but not invisible.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

The ENCODE Project at UC Santa Cruz

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

In vivo enhancer analysis of human conserved non-coding sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

XRate: a fast prototyping, training and annotation tool for phylo-grammars

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

A large family of ancient repeat elements in the human genome is under strong selection

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Genome sequence, comparative analysis and haplotype structure of the domestic dog

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Initial sequence of the chimpanzee genome and comparison with the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Trade-offs in detecting evolutionarily constrained sequence by comparative genomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Distribution and intensity of constraint in mammalian genomic sequence

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

ProbCons: Probabilistic consistency-based multiple sequence alignment

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Assessing computational tools for the discovery of transcription factor binding sites

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Highly conserved non-coding sequences are associated with vertebrate development

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

The ENCODE (ENCyclopedia Of DNA Elements) Project

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Finishing the euchromatic sequence of the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

An intermediate grade of finished genomic sequence suitable for comparative analyses

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Recent advances in Drosophila genomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Aligning multiple genomic sequences with the threaded blockset aligner

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

MAVID: constrained ancestral alignment of multiple sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Characterization of evolutionary rates and constraints in three Mammalian genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

MUSCLE: multiple sequence alignment with high accuracy and high throughput

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Versatile and open software for comparing large genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

An abundance of bidirectional promoters in the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Comparative genomic analysis as a tool for biological discovery

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Identification and characterization of multi-species conserved sequences

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Genomic regulatory regions: insights from comparative sequence analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Mutation rate variation in the mammalian genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Scanning Human Gene Deserts for Long-Range Enhancers

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Comparative analyses of multi-species sequences from targeted genomic regions

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Sequencing and comparison of yeast species to identify genes and regulatory elements

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

A vision for the future of genomics research

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Phylogenetic shadowing of primate sequences to find functional regions of the human genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Origin of a substantial fraction of human regulatory sequences from transposable elements

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Human-mouse alignments with BLASTZ

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

The UCSC Genome Browser Database

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Initial sequencing and comparative analysis of the mouse genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

The human genome browser at UCSC

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

BLAT—The BLAST-Like Alignment Tool

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Resolution of the early placental mammal radiation using Bayesian phylogenetics

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Conserved noncoding sequences are reliable guides to regulatory elements.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

T-Coffee: A novel method for fast and accurate multiple sequence alignment

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Evidence for stabilizing selection in a eukaryotic enhancer element.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Prediction of complete gene structures in human genomic DNA

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Evolutionary trees from DNA sequences: A maximum likelihood approach

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Detecting highly conserved regions of the human genome by multispecies sequence comparisons.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Conserved noncoding sequences are selectively constrained and not mutation cold spots

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891336

Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes

14 November 2018

1 reference

12 December 2020

SABmark--a benchmark for sequence alignment that covers the entire known fold space

1 reference

12 December 2020

Orthology, paralogy and proposed classification for paralog subtypes

1 reference

12 December 2020

Transposable elements are found in a large number of human protein-coding genes

1 reference

12 December 2020

Identifiers

DOI

10.1101/GR.6034307

1 reference

10 August 2017

1 reference

10 August 2017

1 reference