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MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy.
BMC Genomics. 2017 Apr 26;18(1):326. doi: 10.1186/s12864-017-3695-5.
BMC Genomics. 2017.
PMID: 28441938
Free PMC article.
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.
Radivojac P, et al.
Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.
Nat Methods. 2013.
PMID: 23353650
Free PMC article.
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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.
Stergiopoulos I, et al.
Mol Biol Evol. 2012 Nov;29(11):3371-84. doi: 10.1093/molbev/mss143. Epub 2012 May 23.
Mol Biol Evol. 2012.
PMID: 22628532
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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.
Bousios A, et al.
Plant J. 2012 Feb;69(3):475-88. doi: 10.1111/j.1365-313X.2011.04806.x. Epub 2011 Nov 8.
Plant J. 2012.
PMID: 21967390
Free article.
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Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge.
Menéndez P, Kourmpetis YA, ter Braak CJ, van Eeuwijk FA.
Menéndez P, et al.
PLoS One. 2010 Dec 20;5(12):e14147. doi: 10.1371/journal.pone.0014147.
PLoS One. 2010.
PMID: 21188141
Free PMC article.
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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.
Kourmpetis YA, et al.
Plant Physiol. 2011 Jan;155(1):271-81. doi: 10.1104/pp.110.162164. Epub 2010 Nov 22.
Plant Physiol. 2011.
PMID: 21098674
Free PMC article.
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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.
Kourmpetis YA, et al.
PLoS One. 2010 Feb 24;5(2):e9293. doi: 10.1371/journal.pone.0009293.
PLoS One. 2010.
PMID: 20195360
Free PMC article.
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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.
Kourmpetis YA, et al.
In Silico Biol. 2007;7(6):575-82.
In Silico Biol. 2007.
PMID: 18467770
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