Abductive Inference of Genetic Networks. - Blaz Zupan; Ivan Bratko; Janez Demsar; J. Robert Beck; Adam Kuspa; Gad Shaulsky (AIME, 2001)

Web-Enabled Knowledge-Based Analysis of Genetic Data. - Peter Juvan; Blaz Zupan; Janez Demsar; Ivan Bratko; John A. Halter; Adam Kuspa; Gad Shaulsky (ISMDA, 2001)

GenePath: A Computer Program for Genetic Pathway Discovery from Mutant Data. - Janez Demsar; Blaz Zupan; Ivan Bratko; Adam Kuspa; John A. Halter; Robert J. Beck; Gad Shaulsky (MedInfo, 2001)

GenePath: a system for inference of genetic networks and proposal of genetic experiments. - Blaz Zupan; Ivan Bratko; Janez Demsar; Peter Juvan; Tomaz Curk; Urban Borstnik; J. Robert Beck; John A. Halter; Adam Kuspa; Gad Shaulsky (Artif. Intell. Medicine, 2003)

GenePath: a system for automated construction of genetic networks from mutant data. - Blaz Zupan; Janez Demsar; Ivan Bratko; Peter Juvan; John A. Halter; Adam Kuspa; Gad Shaulsky (Bioinform., 2003)

Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes. - Ezgi O. Booth; Nancy Van Driessche; Olga Zhuchenko; Adam Kuspa; Gad Shaulsky (Bioinform., 2005)

Microarray data mining with visual programming. - Tomaz Curk; Janez Demsar; Qikai Xu; Gregor Leban; Uros Petrovic; Ivan Bratko; Gad Shaulsky; Blaz Zupan (Bioinform., 2005)

GenePath: from mutations to genetic networks and back. - Peter Juvan; Janez Demsar; Gad Shaulsky; Blaz Zupan (Nucleic Acids Res., 2005)

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage. - Jie Song; Qikai Xu; Rolf Olsen; William F. Loomis; Gad Shaulsky; Adam Kuspa; Richard Sucgang (PLoS Comput. Biol., 2005)

Discovery of Genetic Networks Through Abduction and Qualitative Simulation. - Blaz Zupan; Ivan Bratko; Janez Demsar; Peter Juvan; Adam Kuspa; John A. Halter; Gad Shaulsky (Computational Discovery of Scientific Knowledge, 2007)

dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. - Gregor Rot; Anup Parikh; Tomaz Curk; Adam Kuspa; Gad Shaulsky; Blaz Zupan (BMC Bioinform., 2009)

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

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

Gene Prioritization by Compressive Data Fusion and Chaining. - Marinka Zitnik; Edward A. Nam; Christopher Dinh; Adam Kuspa; Gad Shaulsky; Blaz Zupan (PLoS Comput. Biol., 2015)

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. - Miha Stajdohar; Rafael D. Rosengarten; Janez Kokosar; Luka Jeran; Domen Blenkus; Gad Shaulsky; Blaz Zupan (BMC Bioinform., 2017)

scOrange - a tool for hands-on training of concepts from single-cell data analytics. - Martin Strazar; Lan Zagar; Jaka Kokosar; Vesna Tanko; Ales Erjavec; Pavlin G. Policar; Anze Staric; Janez Demsar; Gad Shaulsky; Vilas Menon; Andrew Lemire; Anup Parikh; et al. (Bioinform., 2019)