Genomicus statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

Genomicus specifications

Information


Unique identifier OMICS_29848
Name Genomicus
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 92.01
Maintained Yes

Documentation


Maintainers


  • person_outline Alexandra Louis
  • person_outline Hugues Roest Crollius

Publications for Genomicus

Genomicus citations

 (55)
call_split

Teleost Fish Specific Preferential Retention of Pigmentation Gene Containing Families After Whole Genome Duplications in Vertebrates

2018
PMCID: 5940169
PMID: 29599177
DOI: 10.1534/g3.118.200201
call_split See protocol

[…] ation event was likely to be due to Ts3R and not to a small-scale duplication (SSD), and to identify large paralogons supporting Ts3R evidence, we conducted for each gene a synteny analysis using the Genomicus web browser (v86; http://genomicus.biologie.ens.fr/genomicus-86.01/cgi-bin/search.pl) ().Finally, as genes can be described in different organisms with different names, we used the unified n […]

library_books

Adaptive genomic evolution of opsins reveals that early mammals flourished in nocturnal environments

2018
BMC Genomics
PMCID: 5800076
PMID: 29402215
DOI: 10.1186/s12864-017-4417-8

[…] tblastn searches with protein sequences of the Homo sapiens and Gallus gallus opsins were performed in the NCBI and Ensembl databases [, ]. Synteny analyses were performed using both the Ensembl and Genomicus 64.1 databases [, ]. Previously published sequences were collected representing the main phylogenetic groups of mammals for each of the studied opsins (Additional file : Table S5). A protein […]

library_books

The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis

2018
Life
PMCID: 5871936
PMID: 29385718
DOI: 10.3390/life8010004

[…] all interaction partners collected above and to investigate the loss of CTCF interactors in the nematode phylum. The structure, size, and gene content of syntenic regions were investigated using the GENOMICUS [,] database, which also offers a framework to examine reconstructed ancestral ortholog clusters and a flexible visualization interface. The Ensemble database (http://www.ensembl.org) was us […]

library_books

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

2017
PLoS Biol
PMCID: 5747502
PMID: 29253856
DOI: 10.1371/journal.pbio.2004086

[…] o matches to a given gene were identified and no ortholog had been annotated in Ensembl, we attempted to confirm that deletion had occurred by viewing the corresponding genomic region in the UCSC and Genomicus genome browsers [,] and by comparing alignments of the orthologous genomic regions derived from species with and without the deleted gene. Deletions could not always be confirmed mainly due […]

library_books

Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine Dissociation Inhibitor Families

2017
Sci Rep
PMCID: 5722932
PMID: 29222525
DOI: 10.1038/s41598-017-16947-5

[…] ented into the RAxML package. Pfam domains were annotated with hmmscan from the HMMER package. The positions of genes orthologous to the human PDIs and RhoGDIs were obtained, when available, from the Genomicus database,. For species that are not featured in this database, we inferred the position directly from the genome assembly. The following data sources were used: Lepisosteus oculatus - https: […]

library_books

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome scale datasets

2017
Nucleic Acids Res
PMCID: 5753386
PMID: 29149270
DOI: 10.1093/nar/gkx1108

[…] owser.Tunicate genomes rapidly diverge at the local sequence level, as well as in their organization. To further explore the conservation of genome organization within deuterostomes, we implemented a Genomicus synteny browser (), based on the refined orthology relationships described above. This tool provides powerful visualization interfaces, such as karyotype View to explore genome organization […]

Citations

Looking to check out a full list of citations?

Genomicus institution(s)
Ecole Normale Superieure, Institut de Biologie de l’ENS, IBENS, Paris, France; Inserm, U1024, Paris, France; CNRS, UMR 8197, Paris, France
Genomicus funding source(s)
Supported by the French Government and implemented by ANR [ANR-10- BINF-01-03, ANR-10-LABX-54 MEMOLIFE, ANR-10- IDEX-0001-02 PSL* Research University]; RENABI-IFB programme [ANR-11-INSB-0013].

Genomicus reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Genomicus