Phylogeny based discovery of regulatory elements (Q33244264)

24 July 2017

Phylogeny based discovery of regulatory elements (English)

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24 July 2017

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Justin C Fay

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Jason Gertz

object named as

Jason Gertz

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1

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author name string

Barak A Cohen

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3

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24 July 2017

22 May 2006

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24 July 2017

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24 July 2017

7

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24 July 2017

266

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https://scigraph.springernature.com/pub.10.1186/1471-2105-7-266

24 July 2017

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cites work

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Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics.

21 June 2018

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Fast and reliable prediction of noncoding RNAs

21 June 2018

1 reference

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A model of the statistical power of comparative genome sequence analysis

21 June 2018

1 reference

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PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Transcriptional regulatory code of a eukaryotic genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure

21 June 2018

1 reference

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WebLogo: A Sequence Logo Generator

21 June 2018

1 reference

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Combining phylogenetic data with co-regulated genes to identify regulatory motifs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Position specific variation in the rate of evolution in transcription factor binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

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

21 June 2018

1 reference

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Transcriptional regulatory networks in Saccharomyces cerevisiae

21 June 2018

1 reference

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rVista for comparative sequence-based discovery of functional transcription factor binding sites

21 June 2018

1 reference

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Noncoding RNA gene detection using comparative sequence analysis

21 June 2018

1 reference

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SGP-1: prediction and validation of homologous genes based on sequence alignments

21 June 2018

1 reference

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Integrating genomic homology into gene structure prediction.

21 June 2018

1 reference

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The TRANSFAC system on gene expression regulation.

21 June 2018

1 reference

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DNA binding sites: representation and discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

A genome-wide transcriptional analysis of the mitotic cell cycle

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

PAML: a program package for phylogenetic analysis by maximum likelihood

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Phylogenetic methods come of age: testing hypotheses in an evolutionary context

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

ERA, a novel cis-acting element required for autoregulation and ethanol repression of PDC1 transcription in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Evolutionary trees from DNA sequences: A maximum likelihood approach

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

An examination of the constancy of the rate of molecular evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

A probabilistic method to detect regulatory modules.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Algorithms for phylogenetic footprinting.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Statistical tests of models of DNA substitution.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1525002

Estimating synonymous and nonsynonymous substitution rates

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16716228

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-7-266

1 reference

24 July 2017

journals/bmcbi/GertzFC06

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

24 July 2017

1 reference

PubMed ID

16716228