Selected publications by Juris Viksna

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.

S.Ose, J.Viksna. On WQO property for different quasi orderings of set of permutations. Proceedings of MEMICS 2012, Lecture Notes in Computer Science, vol.7721, 190-199, 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, vol. 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, vol 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, vol. 25, doi:10.1093/bioinformatics/btp420, 2768-2769, 2009.

N.Kurbatova and J.Viksna. Exploration of evolutionary relations between protein structures. 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. 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. Artificial Intelligence and Heuristic Methods in Bioinformatics, 128-147, 2003.

J.Viksna and D.Gilbert. Pattern matching and pattern discovery algorithms for protein topologies. 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.

K.Cerans and J.Viksna. Deciding reachability for planar  multi-polynomial systems. Proceedings of the 5th Workshop on Verification and Control of Hybrid Systems, Lecture Notes in Computer Science, vol. 1066, 389-400, 1996.
(Full paper in pdf format available here).

J.Viksna. Probabilistic limit identification up to small sets. Proceedings of the 7th International Workshop on Algorithmic Learning Theory ALT'96, Lecture Notes in Computer Science, vol. 1160, 312-324, 1996.
(Full paper in pdf format available here).

J.Viksna. Inductive inference with deterministic and probabilistic strategies: Abstract of Ph.D. thesis. Bulletin of the EATCS, vol. 55, 428-430, 1995.

J.Viksna. Probabilistic inference of limiting functions with bounded number of mind changes. International Journal of Foundations of Computer Science, vol. 7, 187-208, 1996.
(Full paper in pdf format available here).

J.Viksna. Learning with growing quality. Proceedings of the 4th International Workshop on Algorithmic Learning Theory ALT'93, Lecture Notes in Computer Science, vol. 744, 164-172, 1993.

J.Viksna. Probabilistic inference of approximations. Proceedings of the 2nd International Workshop on Nonmonotonic and Inductive Reasoning, Lecture Notes in Computer Science, vol. 659, 323-332, 1991.

R.Freivalds and J.Viksna. Inductive inference up to immune sets. Proceedings of the 2nd International Workshop on Analogical and Inductive Inference AII'89, Lecture Notes in Computer Science, vol. 397, 138-147, 1989.


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