Publications

DomRates

Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C, The modular nature of protein evolution: domain rearrangement rates across eukaryotic life, BMC Evolutionary Biology, 2020

PUBMED: 32059645 DOI: 10.1186/s12862-020-1591-0

DOGMA - Webserver

Kemena C, Dohmen E, Bornberg-Bauer E, DOGMA: a web server for proteome and transcriptome quality assessment, Nucleic Acids Research, 2019

PUBMED: 31076763 DOI: 10.1093/nar/gkz366

DOGMA

Dohmen E, Kremer LPM, Bornberg-Bauer E, Kemena C, DOGMA: Domain-based transcriptome and proteome quality assessment, Bioinformatics, 32:2577–81, 2016

PUBMED: 27153665 DOI: 10.1093/bioinformatics/btw231

MDAT

Kemena C, Bitard-Feildel T, Bornberg-Bauer E, MDAT - Aligning multiple domain arrangements, BMC Bioinformatics, 16, 2015

PUBMED: 25626688 DOI: 10.1186/s12859-014-0442-7

pOrthoDom

Bitard-Feildel T, Kemena C, Greenwood JM, Bornberg-Bauer E, Domain similarity based orthology detection, BMC Bioinformatics, 2015

PUBMED: 25968113 DOI: 10.1186/s12859-015-0570-8

DOMOSAICS

Moore AD, Held A, Terrapon N, Weiner J, Bornberg-Bauer E, DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins, Bioinformatics, 2014 15;30(2):282-3.

PUBMED: 24222210 DOI: 10.1093/bioinformatics/btt640

RADS

Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E, Rapid similarity search of proteins using alignments of domain arrangements, Bioinformatics, 30, 274-281, 2014

PUBMED: 23828785 DOI: 10.1093/bioinformatics/btt379

CODD

Terrapon N, Gascuel O, Maréchal E, Bréehélin L, Detection of new protein domains using co-occurrence: application to Plasmodium falciparum, Bioinformatics, 25:3077–83, 2009

PUBMED: 19786484 DOI: 10.1093/bioinformatics/btp560

AIDAN

Beaussart F, Weiner J 3rd, Bornberg-Bauer E, Automated Improvement of Domain ANnotations using context analysis of Domain Arrangements (AIDAN), Bioinformatics, 23:1834-1836, 2007

PUBMED: 17483506 DOI: 10.1093/bioinformatics/btm240s

RASPODOM

Weiner J, Thomas G, Bornberg-Bauer E, Rapid Motif-Based Prediction of Circular Permutations in Multi-Domain Proteins, Bioinformatics, 21(7):932-7, 2005

PUBMED: 15788783 DOI: 10.1093/bioinformatics/bti085