Publications - Published papers

Please find below publications of our group. Currently, we list 53 papers. Some of the publications are in collaboration with the group of Peter Stadler and are also listed in the publication list for his group. Access to published papers (access) is restricted to our local network and chosen collaborators.
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©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

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Publications of the Computational EvoDevo group 2011

In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC)

Tambunan, U.S.F., N Bramantya and A.A. Parikesit
BMC Bioinformatics.12(Suppl 13):S23
PREPRINT 11-040:
[ Publishers's page ]

Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions

Arli A. Parikesit, Peter F. Stadler, Sonja Prohaska
Genes 2, no. 4: 912-924 (2011)
PREPRINT 11-024: [ Abstract ]   paperID

Evolution of Domain Co-occurrences: Some Striking Results

Arli A. Parikesit, Peter F. Stadler, and Sonja J. Prohaska
GCB2011 Extended Abstract, Poster Track PT-141
PREPRINT 11-019: [ Abstract ]  [ PDF ]

Mutualism or parasitism? Using a phylogenetic approach to characterize the oxpecker-ungulate relationship

Nunn, C. L., Ezenwa, V. O., Arnold, C. & Koenig, W.
Evolution 65(5):1297-304
PREPRINT 11-017: [ Abstract ]  [ PDF ]   paperID

Primate extinction risk and historical patterns of speciation and extinction in relation to body mass

Matthews, L. J., Arnold, C., Machanda, Z., Nunn, C. L.
Proc. R. Soc. B. 278(1709): 1256-1263
PREPRINT 11-016: [ Abstract ]  [ PDF ]   paperID

The sulfate rich and extreme saline sediment of the ephemeral Tirez lagoon: a biotope for acetoclastic sulfate reducing bacteria and hydrogenotrophic methanogenic archaea

L. Montoya, I. Lozada-Chávez, R. Amils, N. Rodríguez, I. Marín
Int J Microb. 2011. doi:10.1155/2011/753758
PREPRINT 11-015: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Hypothesis for the modern RNA world: a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity

Irma Lozada-Chávez, Peter F. Stadler, Sonja J. Prohaska
Orig Life Evol Biosph. 41: 587-607 (2011)
PREPRINT 11-014: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Protein-Coding Structured RNAs
A Computational Survey of Conserved RNA Secondary Structures Overlapping Coding Regions in Drosophilids

Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska and Peter F. Stadler
PREPRINT 11-012: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID

Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis

Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F Stadler, Sonja J. Prohaska
BMC Bioinformatics 2011, 12:124
PREPRINT 11-010: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]   paperID

A Pipeline for Computational Historical Linguistics

Lydia Steiner, Peter F. Stadler, Michael Cysouw
Language Dynamics and Change
PREPRINT 10-038: [ Abstract ]  [ PDF ]  [ Supplement ]   paperID