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Items: 11

1.

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

Laenen B, Tedder A, Nowak MD, Toräng P, Wunder J, Wötzel S, Steige KA, Kourmpetis Y, Odong T, Drouzas AD, Bink MCAM, Ågren J, Coupland G, Slotte T.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):816-821. doi: 10.1073/pnas.1707492115. Epub 2018 Jan 4.

2.

MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy.

Marquis J, Lefebvre G, Kourmpetis YAI, Kassam M, Ronga F, De Marchi U, Wiederkehr A, Descombes P.

BMC Genomics. 2017 Apr 26;18(1):326. doi: 10.1186/s12864-017-3695-5.

3.

Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes.

Kourmpetis YA, van Dijk ADj, Ter Braak CJ.

Algorithms Mol Biol. 2013 Mar 27;8(1):10. doi: 10.1186/1748-7188-8-10.

4.

A large-scale evaluation of computational protein function prediction.

Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Törönen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

5.

In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins.

Stergiopoulos I, Kourmpetis YA, Slot JC, Bakker FT, De Wit PJ, Rokas A.

Mol Biol Evol. 2012 Nov;29(11):3371-84. doi: 10.1093/molbev/mss143. Epub 2012 May 23.

PMID:
22628532
6.

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.

Bousios A, Kourmpetis YA, Pavlidis P, Minga E, Tsaftaris A, Darzentas N.

Plant J. 2012 Feb;69(3):475-88. doi: 10.1111/j.1365-313X.2011.04806.x. Epub 2011 Nov 8.

7.

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Goodwin SB, M'barek SB, Dhillon B, Wittenberg AH, Crane CF, Hane JK, Foster AJ, Van der Lee TA, Grimwood J, Aerts A, Antoniw J, Bailey A, Bluhm B, Bowler J, Bristow J, van der Burgt A, Canto-Canché B, Churchill AC, Conde-Ferràez L, Cools HJ, Coutinho PM, Csukai M, Dehal P, De Wit P, Donzelli B, van de Geest HC, van Ham RC, Hammond-Kosack KE, Henrissat B, Kilian A, Kobayashi AK, Koopmann E, Kourmpetis Y, Kuzniar A, Lindquist E, Lombard V, Maliepaard C, Martins N, Mehrabi R, Nap JP, Ponomarenko A, Rudd JJ, Salamov A, Schmutz J, Schouten HJ, Shapiro H, Stergiopoulos I, Torriani SF, Tu H, de Vries RP, Waalwijk C, Ware SB, Wiebenga A, Zwiers LH, Oliver RP, Grigoriev IV, Kema GH.

PLoS Genet. 2011 Jun;7(6):e1002070. doi: 10.1371/journal.pgen.1002070. Epub 2011 Jun 9.

8.

Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge.

Menéndez P, Kourmpetis YA, ter Braak CJ, van Eeuwijk FA.

PLoS One. 2010 Dec 20;5(12):e14147. doi: 10.1371/journal.pone.0014147.

9.

Genome-wide computational function prediction of Arabidopsis proteins by integration of multiple data sources.

Kourmpetis YA, van Dijk AD, van Ham RC, ter Braak CJ.

Plant Physiol. 2011 Jan;155(1):271-81. doi: 10.1104/pp.110.162164. Epub 2010 Nov 22.

10.

Bayesian Markov Random Field analysis for protein function prediction based on network data.

Kourmpetis YA, van Dijk AD, Bink MC, van Ham RC, ter Braak CJ.

PLoS One. 2010 Feb 24;5(2):e9293. doi: 10.1371/journal.pone.0009293.

11.

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation.

Kourmpetis YA, van der Burgt A, Bink MC, Ter Braak CJ, van Ham RC.

In Silico Biol. 2007;7(6):575-82.

PMID:
18467770

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