PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny (Q21145693)

17 August 2022

2

Eric D Siggia

Eric D

Siggia

1 reference

17 August 2022

Rahul Siddharthan

1

Rahul

Siddharthan

1 reference

16477324

PLOS Computational Biology

17 August 2022

language of work or name

English

0 references

publication date

December 2005

0 references

published in

0 references

volume

1

0 references

issue

7

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page(s)

e67

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copyright license

Creative Commons Attribution 4.0 International

start time

9 December 2005

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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19 March 2017

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19 March 2017

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19 March 2017

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12 September 2017

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12 September 2017

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12 September 2017

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12 September 2017

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Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8.

12 September 2017

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12 September 2017

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A microarray-assisted screen for potential Hap1 and Rox1 target genes in Saccharomyces cerevisiae

12 September 2017

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An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

12 September 2017

1 reference

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Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics

12 September 2017

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The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Multiple DNA and protein sequence alignment based on segment-to-segment comparison

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

SMASHing regulatory sites in DNA by human-mouse sequence comparisons.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Sequence turnover and tandem repeats in cis-regulatory modules in drosophila

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

The C-terminal domain of SIN1 in yeast interacts with a protein that binds the URS1 region of the yeast HO gene.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Phylogenetic motif detection by expectation-maximization on evolutionary mixtures

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

A probabilistic method to detect regulatory modules

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Algorithms for phylogenetic footprinting

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

SCPD: a promoter database of the yeast Saccharomyces cerevisiae.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1309704

Copper-specific transcriptional repression of yeast genes encoding critical components in the copper transport pathway

29 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/16477324

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.0010067

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.0010067

1 reference

journals/ploscb/SiddharthanSN05

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

16477324

1 reference