(Q24814380)

4 July 2017

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title

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform (English)

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4 July 2017

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5

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Pontarotti Pierre

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author name string

Philippe Gouret

1

1 reference

4 July 2017

Vérane Vitiello

2

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4 July 2017

Nathalie Balandraud

3

1 reference

4 July 2017

André Gilles

4

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4 July 2017

Etienne G J Danchin

6

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4 July 2017

Pierre Pontarotti

5

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4 July 2017

language of work or name

English

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publication date

5 August 2005

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4 July 2017

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4 July 2017

6

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4 July 2017

198

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https://scigraph.springernature.com/pub.10.1186/1471-2105-6-198

4 July 2017

1

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exact match

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cites work

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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes

7 April 2017

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RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

7 April 2017

1 reference

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Gene ontology: tool for the unification of biology

7 April 2017

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 April 2017

1 reference

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 April 2017

1 reference

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The neighbor-joining method: a new method for reconstructing phylogenetic trees

7 April 2017

1 reference

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The Sequence of the Human Genome

7 April 2017

1 reference

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The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

7 April 2017

1 reference

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TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

7 April 2017

1 reference

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The Pfam protein families database.

7 April 2017

1 reference

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Profile hidden Markov models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Prediction of complete gene structures in human genomic DNA

7 April 2017

1 reference

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Evolutionary trees from DNA sequences: A maximum likelihood approach

7 April 2017

1 reference

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Phylogenomic inference of protein molecular function: advances and challenges

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Evaluation of gene-finding programs on mammalian sequences

7 April 2017

1 reference

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Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Towards the reconstruction of the bilaterian ancestral pre-MHC region.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

PhyloGenie: automated phylome generation and analysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

The major histocompatibility complex origin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

The Ensembl analysis pipeline

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Cloning and sequence analysis of cDNA for the proteasome activator PA28-β subunit of flounder (Paralichthys olivaceus)

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Evolution of the proto-MHC ancestral region: more evidence for the plesiomorphic organisation of human chromosome 9q34 region.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Pharmacophylogenomics: genes, evolution and drug targets

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Phylogenomics: intersection of evolution and genomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Splitting pairs: the diverging fates of duplicated genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Current methods of gene prediction, their strengths and weaknesses

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Evidence of en bloc duplication in vertebrate genomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Gene recognition via spliced sequence alignment.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Predicting functions from protein sequences--where are the bottlenecks?

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Fully automated genome analysis that reflects user needs and preferences. A detailed introduction to the MAGPIE system architecture.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

MAGPIE: automated genome interpretation.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Statistical evidence for a more than 800-million-year-old evolutionarily conserved genomic region in our genome.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Systematic phylogenomic evidence of en bloc duplication of the ancestral 8p11.21-8p21.3-like region.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

A simple algorithm to infer gene duplication and speciation events on a gene tree.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

The closest BLAST hit is often not the nearest neighbor.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Two methods for improving performance of an HMM and their application for gene finding.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1188056

Modeling the percolation of annotation errors in a database of protein sequences

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16083500

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Statistical methods for testing functional divergence after gene duplication

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16083500

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-6-198

1 reference

journals/bmcbi/GouretVBGPD05

4 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1005383646

0 references

OpenCitations bibliographic resource ID

1214790

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

4 July 2017

1 reference