(Q24801531)

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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

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Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura (English)

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Drosophila melanogaster

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Drosophila pseudoobscura

object named as

Drosophila pseudoobscura

1 reference

based on heuristic

inferred from title

Michael B. Eisen

6

object named as

Michael B Eisen

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Benjamin P Berman

object named as

Benjamin P Berman

1

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Steven Salzberg

object named as

Steven L Salzberg

4

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Susan E. Celniker

7

object named as

Susan E Celniker

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author name string

Barret D Pfeiffer

2

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Todd R Laverty

3

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Gerald M Rubin

5

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language of work or name

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publication date

2004

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5

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R61

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9

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https://scigraph.springernature.com/pub.10.1186/gb-2004-5-9-r61

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Benchmarking tools for the alignment of functional noncoding DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Conservation of regulatory elements between two species of Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Comparative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Systematic determination of patterns of gene expression during Drosophila embryogenesis

1 reference

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7 April 2017

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Human-mouse alignments with BLASTZ

1 reference

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7 April 2017

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

1 reference

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7 April 2017

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7 April 2017

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

1 reference

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7 April 2017

Initial sequencing and analysis of the human genome

1 reference

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7 April 2017

Regulation of even-skipped stripe 2 in the Drosophila embryo

1 reference

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7 April 2017

Initial sequencing and comparative analysis of the mouse genome

1 reference

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7 April 2017

The Sequence of the Human Genome

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7 April 2017

The genome sequence of Drosophila melanogaster

1 reference

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7 April 2017

Genome sequence of the nematode C. elegans: a platform for investigating biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Alignment of whole genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Mutations affecting segment number and polarity in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

A gene complex controlling segmentation in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Transcription regulation and animal diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

VISTA : visualizing global DNA sequence alignments of arbitrary length

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

A whole-genome assembly of Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

7 April 2017

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Long-range enhancer-promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Distinguishing regulatory DNA from neutral sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Decoding cis-regulatory DNAs in the Drosophila genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

SCORE: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. Site clustering over random expectation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Profiling patterned transcripts in Drosophila embryos

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Dorsal gradient networks in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Transcriptional regulation in Drosophila: the post-genome challenge

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Detection of cis-element clusters in higher eukaryotic DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Selection intensity against deleterious mutations in RNA secondary structures and rate of compensatory nucleotide substitutions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

A predictive model for regulatory sequences directing liver-specific transcription.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Genomic strategies to identify mammalian regulatory sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Evidence for stabilizing selection in a eukaryotic enhancer element.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Complex regulatory region mediating tailless expression in early embryonic patterning and brain development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Distinct parasegmental and imaginal enhancers and the establishment of the expression pattern of the Ubx gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

New heat shock puffs and beta-galactosidase activity resulting from transformation of Drosophila with an hsp70-lacZ hybrid gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Chromosomal walking and jumping to isolate DNA from the Ace and rosy loci and the bithorax complex in Drosophila melanogaster

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Inferring the number of evolutionary events from DNA coding sequence differences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

The correct activation of Antennapedia and bithorax complex genes requires the fushi tarazu gene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Autoregulatory and gap gene response elements of the even-skipped promoter of Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

The bx region enhancer, a distant cis-control element of the Drosophila Ubx gene and its regulation by hunchback and other segmentation genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

cis-acting control elements for Krüppel expression in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

The hardwiring of development: organization and function of genomic regulatory systems.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 September 2017

Expression, regulation and function of the homeobox gene empty spiracles in brain and ventral nerve cord development of Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Identification of regulatory regions which confer muscle-specific gene expression.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

A statistical model for locating regulatory regions in genomic DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Control elements of the Drosophila segmentation gene fushi tarazu.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Vectors for Drosophila P-element-mediated transformation and tissue culture transfection.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Regulation of segment polarity genes in the Drosophila blastoderm by fushi tarazu and even skipped

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Krüppel requirement for knirps enhancement reflects overlapping gap gene activities in the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Gradients of Krüppel and knirps gene products direct pair-rule gene stripe patterning in the posterior region of the Drosophila embryo

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

The Drosophila segmentation gene runt has an extended cis-regulatory region that is required for vital expression at other stages of development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

30 May 2018

Expected rates and modes of evolution of enhancer sequences.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Specification of neuropeptide cell identity by the integration of retrograde BMP signaling and a combinatorial transcription factor code.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Coevolution in bicoid-dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Rapid restructuring of bicoid-dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

The FlyBase database of the Drosophila genome projects and community literature.

1 reference

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28 November 2018

odd-skipped is expressed in multiple tissues during Drosophila embryogenesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Microarray analysis of Drosophila development during metamorphosis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

The even-skipped locus is contained in a 16-kb chromatin domain.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Concentration-dependent patterning by an ectopic expression domain of the Drosophila gap gene knirps.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

The role of a Drosophila POU homeo domain gene in the specification of neural precursor cell identity in the developing embryonic central nervous system.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Non-periodic cues generate seven ftz stripes in the Drosophila embryo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Regulation of the Drosophila segmentation gene hunchback by two maternal morphogenetic centres

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=522868

28 November 2018

Using the TIGR assembler in shotgun sequencing projects

1 reference

https://pubmed.ncbi.nlm.nih.gov/15345045

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/GB-2004-5-9-R61

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Dimensions Publication ID

0 references

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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