Items where Division is "Faculty of Computer and Information Science > Bioinformatics Laboratory"

Article

Marinka Zitnik and Blaz Zupan (2015) Data Fusion by Matrix Factorization. IEEE Transactions on Pattern Analysis & Machine Intelligence, 37 (1). pp. 41-53.

Anze Staric and Janez Demsar and Blaz Zupan (2015) Concurrent software architectures for exploratory data analysis. WIREs Data Mining Knowl Discov, 5 . pp. 165-180.

Marinka Zitnik and Blaz Zupan (2015) Gene network inference by fusing data from diverse distributions. Bioinformatics, 31 (12). i230-9.

Rafael David Rosengarten and Balaji Santhanam and Danny Fuller and Mariko Katoh-Kurasawa and William F Loomis and Blaz Zupan and Gad Shaulsky (2015) Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum. BMC Genomics, 16 . p. 294.

Marinka Zitnik and Edward A Nam and Christopher Dinh and Adam Kuspa and Gad Shaulsky and Blaz Zupan (2015) Gene prioritization by compressive data fusion and chaining. PLoS Computational Biology, 11 (10). e1004552.

Marko Toplak and Rok Mocnik and Matija Polajnar and Zoran Bosnic and Lars Carlsson and C Hasselgren and Janez Demsar and S Boyer and Blaz Zupan and Jonna Stalring (2014) Assessment of machine learning reliability methods for quantifying the applicability domain of QSAR regression models. J Chem Inf Model, 54 (2). pp. 431-441.

Marinka Zitnik and Blaz Zupan (2014) Matrix factorization-based data fusion for drug-induced liver injury prediction. Systems Biomedicine, 2 . e28527.

Blaz Zupan and Marinka Zitnik (2014) Gene network inference by probabilistic scoring of relationships from a factorized model of interactions. Bioinformatics, 30 (12). i246-i254.

Ricardo Franco-Duarte and Ines Mendes and Lan Umek and Joao Drumonde-Neves and Blaz Zupan and Dorit Schuller (2014) Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae. Yeast, 31 . pp. 265-277.

Marinka Zitnik and Blaz Zupan (2014) Survival regression by data fusion. Systems Biomedicine, 2 (3). pp. 49-55.

Mendes Mendes and Ricardo Franco-Duarte and Lan Umek and Elza Fonseca and Joao Drumonde-Neves and Sylvie Dequin and Blaz Zupan and Dorit Schuller (2013) Computational models for prediction of yeast strain potential for winemaking from phenotypic profiles. PLoS One, 8 (7). e66523.

Edward Roshan Miranda and Olga Zhuchenko and Marko Toplak and Balaji Santhanam and Blaz Zupan and Adam Kuspa and Gad Shaulsky (2013) ABC transporters in Dictyostelium discoideum development. PLoS One, 8 (8). e70040.

Waleed Nasser and Balaji Santhanam and Edward Roshan Miranda and Anup Parikh and Kavina Juneja and Gregor Rot and Christopher Dinh and Rui Chen and Blaz Zupan and Gad Shaulsky and Adam Kuspa (2013) Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Current Biology, 23 (10). pp. 862-872.

Janez Demšar and Tomaž Curk and Aleš Erjavec and Črtomir Gorup and Tomaž Hočevar and Mitar Milutinović and Martin Možina and Matija Polajnar and Marko Toplak and Anže Starič and Miha Štajdohar and Lan Umek and Lan Žagar and Jure Žbontar and Marinka Žitnik and Blaz Zupan (2013) Orange: data mining toolbox in Python. Journal of Machine Learning Research, 14 . pp. 2349-2353.

Marinka Zitnik and Vuk Janjic and Chris Larminie and Blaz Zupan and Natasa Przulj (2013) Discovering disease-disease associations by fusing systems-level molecular data. Scientific Reports, 13 . p. 3202.

Davor Sluga and Tomaz Curk and Blaz Zupan and Lotric Uros (2013) Heterogeneous computing architecture for fast detection of SNP-SNP interactions. BMC Bioinformatics, 15 . p. 216.

Sanja Brdar and Vladimir Crnojevic and Zupan Blaz (2013) Integrative clustering by non-negative matrix factorization can reveal coherent functional groups from gene profile data. IEEE Journal of Biomedical and Health Informatics . (In Press)

Marinka Zitnik and Blaz Zupan (2012) NIMFA: A Python Library for Nonnegative Matrix Factorization. Journal of Machine Learning Research, 13 . pp. 849-853.

Francesca Mulas and Lucia Sacchi and Lan Zagar and Silvia Garagna and Maurizio Zuccotti and Blaz Zupan and Riccado Bellazzi (2012) Knowledge-based bioinformatics for the study of mammalian oocytes. International Journal of Developmental Biology, 56 (10-12). pp. 859-866.

Lan Umek and Blaz Zupan (2011) Subgroup discovery in data sets with multi-dimensional responses. Intelligent Data Analysis, 15 (4). pp. 533-549.

Lan Zagar and Francesca Mulas and Silvia Garagna and Zuccotti Maurizio and Riccado Bellazzi and Blaz Zupan (2011) Stage prediction of embryonic stem cell differentiation from genome-wide expression data. Bioinformatics, 27 (18). pp. 2546-2553.

James R Tollervey and Tomaz Curk and Boris Rogelj and Michael Briese and Matteo Cereda and Melis Kayikci and Julian Konig and Tibor Hortobágyi and Agnes L Nishimura and Vera Zupunski and Rickie Patani and Siddharthan Chandran and Gregor Rot and Blaz Zupan and Christopher E Shaw and Jernej Ule (2011) Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nature Neuroscience, 14 (4). pp. 452-458.

Tomaz Curk and Gregor Rot and Blaz Zupan (2011) SNPsyn: detection and exploration of SNP-SNP interactions. Nucleic Acids Res, 39 (Suppl ). W444-9.

Julian Konig and Kathi Zarnack and Gregor Rot and Tomaz Curk and Melis Kayikci and Blaz Zupan and Daniel J Turner and Nicholas M Luscombe and Jernej Ule (2011) iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution. Journal of Visualized Experiments, 50 . pii: 2638.

Stefania Crippa and Marco Cassano and Graziella Messina and Daniela Galli and Beatriz G. Galvez and Tomaz Curk and Claudia Altomare and Flavio Ronzoni and Jaan Toelen and Rik Gijsbers and Zeger Debyser and Stefan Janssens and Blaz Zupan and Antonio Zaza and Giulio Cossu and Maurilio Sampaolesi (2011) miR669a and miR669q prevent skeletal muscle differentiation in postnatal cardiac progenitors. J Cell Biol, 193 . pp. 1197-1212.

Zheng Wang and Melis Kayikci and Michael Briese and Kathi Zarnack and Nicholas M Luscombe and Gregor Rot and Blaz Zupan and Tomaz Curk and Jernej Ule (2010) iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biology, 8 (10). e1000530.

Dragica Smrke and Mirza Biscevic and Barbara UR Smrke and Blaz Zupan (2010) Biomechanical and clinical alterations of the hip joint following femoral neck fracture and implantation of bipolar hip endoprosthesis. Collegium Antropologicum, 34 (3). pp. 931-935.

Anup Parikh and Eryong Huang and Christopher Dinh and Blaz Zupan and Adam Kuspa and Devika Subramanian and Gad Shaulsky (2010) New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data. BMC Bioinformatics, 11 . p. 163.

Rocio Benabentos and Shigenori Hirose and Richard Sucgang and Tomaz Curk and Mariko Katoh and Elizabeth A Ostrowski and Joan E Strassmann and David C Queller and Blaz Zupan and Gad Shaulsky and Adam Kuspa (2009) Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Current Biology, 19 (7). pp. 567-572.

Petra Fey and Pascale Gaudet and Tomaz Curk and Blaz Zupan and Eric M Just and Siddhartha Basu and Sohel N Merchant and Yulia A Bushmanova and Gad Shaulsky and Warren A Kibbe and Rex L Chisholm (2009) dictyBase-a Dictyostelium bioinformatics resource update. Nucleic Acids Res, 37 (Suppl 1). D515-D519.

Tomaz Curk and Janez Demsar and Qikai Xu and Gregor Leban and Uros Petrovic and Ivan Bratko and Gad Shaulsky and Blaz Zupan (2005) Microarray data mining with visual programming. Bioinformatics, 21 (3). pp. 396-398.

Davor Sluga and Tomaz Curk and Uros Lotric and Blaz Zupan Heterogeneous computing architecture for fast detection of SNP-SNP interactions. BMC Bioinformatics, 15 . p. 216.

Conference or Workshop Item

Marinka Zitnik and Blaz Zupan (2014) Matrix factorization-based data fusion for gene function prediction in baker's yeast and slime mold. In: PSB, Jan 2014, The Big Island of Hawaii.

Marinka Zitnik and Blaz Zupan (2014) Imputation of quantitative genetic interactions in epistatic MAPs by interaction propagation matrix completion. In: RECOMB, Pittsburgh.

Marinka Zitnik and Blaz Zupan Matrix factorization-based data fusion for drug-induced liver injury prediction. In: CAMDA, July 2013, Berlin.