Publications

A.Brazma, K.Cerans, D.Ruklisa, T.Schlitt, J.Viksna. Modeling and analysis of qualitative behaviour of gene regulatory networks. Proceedings of HSB 2014, Lecture Notes in Computer Science, vol. 7699, pp.51-66, 2015.

G.Scelo, Y.Riazalhosseini, L.Greger, L.Letourneau, M.Gonzàlez-Porta, M.Wozniak, M.Bourgey, P.Harnden, L.Egevad, S.Jackson, M.Karimzadeh, M.Arseneault, P.Lepage, A.How-Kit, A.Daunay, V.Renault, H.Blanché, E.Tubacher, J.Sehmoun, J.Viksna, E.Celms, M.Opmanis, A.Zarins, N.Vasudev, M.Seywright, B.Abedi-Ardekani, C.Carreira, P.J.Selby, J.Cartledge, G.Byrnes, J.Zavadil, J.Su, I.Holcatova, A.Brisuda, D.Zaridze, A.Moukeria, L.Foretova, M.Navratilova, D.Mates, V.Jinga, A.Artemov, A.Nedoluzhko, A.Mazur, S.Rastorguev, E.Boulygina, S.Heath, M.Gut, M.Bihoreau, D.Lechner, M.Foglio, I.Gut, K.Skryabin, E.Prokhortchouk, A.Cambon-Thomsen, J.Rung, G.Bourque, P.Brennan, J.Tost, R.Banks, A.Brazma, M.Lathrop. Variation in genomic landscape of clear cell renal cell carcinoma across Europe. Nature Communications, vol. 5, doi:10.1038/ncomms6135, 2014.

A.Brazma, K.Cerans, D.Ruklisa, T.Schlitt, J.Viksna. HSM - a hybrid system based approach for modelling intracellular networks. Gene, vol. 518, doi: 10.1016/j.gene.2012.11.084, 70-77, 2013.

G.Nicholson, M.Rantalainen, J.Li, A.Maher, D.Malmodin, K.Ahmadi, J.Faber, A.Barrett, J.Min, N.Rayner, H.Toft, M.Krestyaninova, J.Viksna,S.Guha Neogi, M.Dumas, U.Sarkans, MolPAGE Consortium, P.Donnelly, T.Illig, J.Adamski, K.Suhre, M.Allen, K.Zondervan, T.Spector, J.Nicholson, J.Lindon, D.Baunsgaard, E.Holmes, M.McCarthy, C.Holmes. A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genetics 9(7) e1002270.doi:10.1371/journal.pgen.1002270, 18p, 2011.

G.Nicholson, M.Rantalainen, A.Maher, J.Li, D.Malmodin, K.Ahmadi, J.Faber, I.Hallgrímsdóttir, A.Barrett, H.Toft, M.Krestyaninova, J.Viksna, S.Guha Neogi, M.E.Dumas, U.Sarkans, The MolPAGE Consortium, B.Silverman, P.Donnelly, J.Nicholson, M.Allen, K.Zondervan, J.Lindon, T.Spector, M.McCarthy, E.Holmes, D.Baunsgaard, C.Holmes. Human metabolic profiles are stably controlled by genetic and environmental variation. Molecular Systems Biology 7:525 doi:10.1038/msb.2011.57, 12p, 2011.

M.Krestyaninova, A.Zarins, J.Viksna, N.Kurbatova, P.Rucevskis, S.Guha Neogi, M.Gostev, T.Perheentupa, J.Knuuttila, A.Barrett, I.Lappalainen, J.Rung, K.Podnieks, U.Sarkans, M.McCarthy, A.Brazma. A System for Information Management in BioMedical Studies – SIMBioMS. Bioinformatics, doi:10.1093/bioinformatics/btp420, 2009.

R.Najmanovich, N.Kurbatova and J. Thornton. Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein binding sites. Bioinformatics, vol. 24, i105-i111, 2008.

N.Kurbatova and J.Viksna. Exploration of evolutionary relations between protein structures. In Proceedings of BIRD 2008, Communications in Computer and Information Science, vol. 13, 154-166, 2008.

N.Kurbatova, L.Mancinska and J.Viksna. Protein structure comparison based on fold evolution. In Proceedings of GCB 2007, Lecture Notes in Informatics, vol. 115, 78-89, 2007.

J.Viksna and D.Gilbert. Assessment of the probabilities for evolutionary structural changes in protein folds. Bioinformatics, vol. 23, 832-841, 2007.

J.Viksna, E.Celms, M.Opmanis, K.Podnieks, P.Rucevskis, A.Zarins, A.Barrett, S.Guha Neogi, M.Krestyaninova, M.McCarthy, A.Brazma and U.Sarkans. PASSIM - an open source software system for managing information in biomedical studies. BMC Bioinformatics, vol. 8:52, 2007.

D.Ruklisa, A.Brazma and J.Viksna. Reconstruction of gene regulatory networks under the Finite State Linear Model. Genome Informatics, vol. 16(2), 225-236, 2005.

J.Viksna, D.Gilbert and G.Torrence. Domain discovery method for topological profile searches in protein structures. Genome Informatics, vol. 15(2), 72-81, 2004.

D.Gilbert, D.Westhead and J.Viksna. Techniques for comparison, pattern matching and pattern discovery: From sequences to protein topology. In Artificial Intelligence and Heuristic Methods in Bioinformatics, 128-147, 2003.

J.Viksna, D.Gilbert and G.Torrance. Protein Structure Comparison Based on Profiles of Topological Motifs: a Feasible Way to Deal with Information from Negative Examples. In Proceedings of GCB 2003, 159-165, 2003.

J.Rung, T.Schlitt, A.Brazma, K.Freivalds and J.Vilo. Building and analysing genome-wide gene disruption networks. Bioinformatics, vol. 18 (Supplement 2), 202-210, 2002.

J.Viksna and D.Gilbert. Pattern matching and pattern discovery algorithms for protein topologies. In Proceedings of WABI 2001, Lecture Notes in Computer Science, vol. 2149, 98-111, 2001.

D.Gilbert, D.Westhead, J.Viksna and J.Thornton. Topology-based protein structure comparison using a pattern discovery technique. Computers & Chemistry, vol. 26(1), 23-30, 2001.