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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.
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.
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.
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 Edward Roshan Miranda and Mariko Katoh-Kurasawa and Danny Fuller and Gregor Rot and Lan Zagar and Tomaz Curk and Richard Sucgang and Rui Chen and Blaz Zupan and William F Loomis and Adam Kuspa and Gad Shaulsky (2010) Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biology, 11 . R35.
Marko Toplak and Tomaz Curk and Janez Demsar and Blaz Zupan (2010) Does replication groups scoring reduce false positive rate in SNP interaction discovery?. BMC Genomics, 11 . p. 58.
Miha Stajdohar and Minca Mramor and Blaz Zupan and Janez Demsar (2010) FragViz: visualization of fragmented networks. BMC Bioinformatics, 11 (457).
Mojca Mattiazzi and Tomaz Curk and Igor Krizaj and Blaz Zupan and Uros Petrovic (2010) Inference of the Molecular Mechanism of Action from Genetic Interaction and Gene Expression Data. OMICS A journal of Integrative Biology, 14 (4). pp. 357-367.
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.
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 (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Structural & Molecular Biology, 17 . pp. 909-915.
Gregor Rot and Anup Parikh and Tomaz Curk and Adam Kuspa and Gad Shaulsky and Blaz Zupan (2009) dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. BMC Bioinformatics, 10 . p. 265.
Ricardo Franco-Duarte and Lan Umek and Blaz Zupan and Dorit Schuller (2009) Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection. Yeast, 26 (12). pp. 675-692.
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.
Tomaz Curk and Uros Petrovic and Gad Shaulsky and Blaz Zupan (2009) Rule-based clustering for gene promoter structure discovery. Methods of Information in Medicine, 48 (3). pp. 229-235.
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.
Blaz Zupan and Janez Demsar (2008) Open-source tools for data mining. Clinics in Laboratory Medicine, 28 (1). pp. 37-54.
Riccado Bellazzi and Blaz Zupan (2008) Predictive data mining in clinical medicine: Current issues and guidelines. Internation Journal of Medical Informatics, 77 (2). pp. 81-97.
Riccado Bellazzi and Blaz Zupan (2007) Towards knowledge-based gene expression data mining. Journal of Biomedical Informatics, 40 (6). pp. 787-802.
Minca Mramor and Gregor Leban and Janez Demsar and Blaz Zupan (2007) Visualization-based cancer microarray data classification analysis. Bioinformatics, 23 (16). pp. 2147-2154.
Gregor Leban and Blaz Zupan and Gaj Vidmar and Ivan Bratko (2006) VizRank: Data Visualization Guided by Machine Learning. Data Mining and Knowledge Discovery, 13 (2). pp. 119-136.
Peter Juvan and Janez Demsar and Gad Shaulsky and Blaz Zupan (2005) GenePath: from mutations to genetic networks and back. Nucleic Acids Res, 33 (Web Se). W749-W752.
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.
Nancy Van Driessche and Janez Demsar and Ezgi O Booth and Paul Hill and Peter Juvan and Blaz Zupan and Adam Kuspa and Gad Shaulsky (2005) Epistasis analysis with global transcriptional phenotypes. Nature Genetics, 37 (5). pp. 471-477.
Aleks Jakulin and Martin Možina and Janez Demšar and Ivan Bratko and Blaz Zupan (2005) Nomograms for Visualizing Support Vector Machines. In: SIGKDD'05 Chicago, August 2005, Illinois, USA.
Gregor Leban and Minca Mramor and Ivan Bratko and Blaz Zupan (2005) Simple and Effective Visual Models for Gene Expression Cancer Diagnostics. In: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 21-24, 2005, Chicago, IL, USA.
Martin Možina and Janez Demšar and Michael W Kattan and Blaz Zupan (2004) Nomograms for Visualization of Naive Bayesian Classifier. In: European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), September 20-24, 2004, Pisa.
Gregor Leban and Ivan Bratko and Uroš Petrovič and Tomaž Curk and Blaz Zupan (2004) VizRank: Finding Informative Data Projections in Functional Genomics by Machine Learning. Bioinformatics, 21 (3). pp. 413-414.
Aleks Jakulin and Ivan Bratko and Dragica Smrke and Janez Demšar and Blaz Zupan (2003) Attribute Interactions in Medical Data Analysis. In: 9th Conference on Artificial Intelligence in Medicine in Europe (AIME 2003), October 18-22, 2003, Protaras, Cyprus.
Peter Juvan and Blaz Zupan and Gad Shaulsky (2003) Automated construction of genetic networks from mutant data. In: 5th Meeting of the Slovenian Biochemical Society, September 24-28, 2003, Ljubljana, Slovenia.
Blaz Zupan and Janez Demšar and Ivan Bratko and Peter Juvan and John Halter and Adam Kuspa and Gad Shaulsky (2003) GenePath: a System for Automated Construction of Genetic Networks from Mutant Data. Bioinformatics, 19 (3). p. 383.
Peter Juvan and Blaz Zupan and Janez Demšar and Ivan Bratko and John A. Halter and Adam Kuspa and Gad Shaulsky (2001) Web-enabled knowledge-based analysis of genetic data. In: Second International Symposium on Medical Data Analysis, October 8-9, 2001, Madrid, Spain.
Blaz Zupan and Janez Demsar and Michael W Kattan and J Robert Beck and Ivan Bratko (2000) Machine learning for survival analysis: a case study on recurrence of prostate cancer. Artificial Intelligence in Medicine, 20 (1). pp. 59-75.
Marinka Zitnik and Blaz Zupan Matrix factorization-based data fusion for drug-induced liver injury prediction. In: CAMDA, July 2013, Berlin.
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.