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Pairwise comparisons across species are problematic when analyzing functional genomic data.

Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A.

Proc Natl Acad Sci U S A. 2018 Jan 16;115(3):E409-E417. doi: 10.1073/pnas.1707515115. Epub 2018 Jan 4.


PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages.

Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN.

PeerJ. 2017 Aug 28;5:e3712. doi: 10.7717/peerj.3712. eCollection 2017.


From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.

Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC.

mSystems. 2016 Dec 27;1(6). pii: e00101-16. doi: 10.1128/mSystems.00101-16. eCollection 2016 Nov-Dec.


Comparative genomics reveals genes significantly associated with woody hosts in the plant pathogen Pseudomonas syringae.

Nowell RW, Laue BE, Sharp PM, Green S.

Mol Plant Pathol. 2016 Dec;17(9):1409-1424. doi: 10.1111/mpp.12423. Epub 2016 Jul 15.


Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs.

Huo T, Liu W, Guo Y, Yang C, Lin J, Rao Z.

BMC Bioinformatics. 2015 Mar 26;16:100. doi: 10.1186/s12859-015-0535-y.


Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling.

Dey G, Jaimovich A, Collins SR, Seki A, Meyer T.

Cell Rep. 2015 Feb 11. pii: S2211-1247(15)00050-9. doi: 10.1016/j.celrep.2015.01.025. [Epub ahead of print]


Practical aspects of protein co-evolution.

Ochoa D, Pazos F.

Front Cell Dev Biol. 2014 Apr 22;2:14. doi: 10.3389/fcell.2014.00014. eCollection 2014. Review.


Expansion of biological pathways based on evolutionary inference.

Li Y, Calvo SE, Gutman R, Liu JS, Mootha VK.

Cell. 2014 Jul 3;158(1):213-25. doi: 10.1016/j.cell.2014.05.034.


EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles.

Dittmar WJ, McIver L, Michalak P, Garner HR, Valdez G.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W72-5. doi: 10.1093/nar/gku442. Epub 2014 May 21.


Computational prediction of the human-microbial oral interactome.

Coelho ED, Arrais JP, Matos S, Pereira C, Rosa N, Correia MJ, Barros M, Oliveira JL.

BMC Syst Biol. 2014 Feb 27;8:24. doi: 10.1186/1752-0509-8-24.


Advancing data reuse in phyloinformatics using an ontology-driven Semantic Web approach.

Panahiazar M, Sheth AP, Ranabahu A, Vos RA, Leebens-Mack J.

BMC Med Genomics. 2013;6 Suppl 3:S5. doi: 10.1186/1755-8794-6-S3-S5. Epub 2013 Nov 11.


Molecular evolution of Zika virus during its emergence in the 20(th) century.

Faye O, Freire CC, Iamarino A, Faye O, de Oliveira JV, Diallo M, Zanotto PM, Sall AA.

PLoS Negl Trop Dis. 2014 Jan 9;8(1):e2636. doi: 10.1371/journal.pntd.0002636. eCollection 2014.


Reconciliation-based detection of co-evolving gene families.

Chan YB, Ranwez V, Scornavacca C.

BMC Bioinformatics. 2013 Nov 20;14:332. doi: 10.1186/1471-2105-14-332.


FunCoup 3.0: database of genome-wide functional coupling networks.

Schmitt T, Ogris C, Sonnhammer EL.

Nucleic Acids Res. 2014 Jan;42(Database issue):D380-8. doi: 10.1093/nar/gkt984. Epub 2013 Oct 31.


Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.

Press MO, Li H, Creanza N, Kramer G, Queitsch C, Sourjik V, Borenstein E.

PLoS Genet. 2013;9(7):e1003631. doi: 10.1371/journal.pgen.1003631. Epub 2013 Jul 11.


DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.

Xia X.

Mol Biol Evol. 2013 Jul;30(7):1720-8. doi: 10.1093/molbev/mst064. Epub 2013 Apr 5.


Peptidoglycan: a post-genomic analysis.

Cayrou C, Henrissat B, Gouret P, Pontarotti P, Drancourt M.

BMC Microbiol. 2012 Dec 18;12:294. doi: 10.1186/1471-2180-12-294. Erratum in: BMC Microbiol. 2014;14:123.


Protein fragments: functional and structural roles of their coevolution networks.

Dib L, Carbone A.

PLoS One. 2012;7(11):e48124. doi: 10.1371/journal.pone.0048124. Epub 2012 Nov 5.


Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA.

Cheng N, Mao Y, Shi Y, Tao S.

PLoS One. 2012;7(9):e44376. doi: 10.1371/journal.pone.0044376. Epub 2012 Sep 4.


The evolution of intron size in amniotes: a role for powered flight?

Zhang Q, Edwards SV.

Genome Biol Evol. 2012;4(10):1033-43. doi: 10.1093/gbe/evs070.

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