combAlign: A protein sequence comparison algorithm considering recombinations. - Katja Wegner; Stephan Jansen; Stefan Wuchty; Ralph Gauges; Ursula Kummer (Silico Biol., 2004)

Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. - Chengbang Huang; Faruck Morcos; Simon P. Kanaan; Stefan Wuchty; Danny Z. Chen; Jesús A. Izaguirre (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum. - Yang Huang; Stefan Wuchty; Michael T. Ferdig; Teresa M. Przytycka (Bioinform., 2009)

Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases. - Yoo-Ah Kim; Stefan Wuchty; Teresa M. Przytycka (RECOMB, 2010)

FastMEDUSA: a parallelized tool to infer gene regulatory networks. - Serdar Bozdag; Aiguo Li; Stefan Wuchty; Howard A. Fine (Bioinform., 2010)

Gene pathways and subnetworks distinguish between major glioma subtypes and elucidate potential underlying biology. - Stefan Wuchty; Alice Zhang; Jennifer Walling; Susie Ahn; Aiguo Li; Martha Quezado; Carl Oberholtzer; Jean-Claude Zenklusen; Howard A. Fine (J. Biomed. Informatics, 2010)

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases. - Yoo-Ah Kim; Stefan Wuchty; Teresa M. Przytycka (PLoS Comput. Biol., 2011)

Module Cover - A New Approach to Genotype-Phenotype Studies. - Yoo-Ah Kim; Raheleh Salari; Stefan Wuchty; Teresa M. Przytycka (Pacific Symposium on Biocomputing, 2013)

Important miRs of Pathways in Different Tumor Types. - Stefan Wuchty; Dolores Arjona; Peter O. Bauer (PLoS Comput. Biol., 2013)

Analysis of the Evolution of Research Groups and Topics in the ISMIR Conference. - Mohamed Sordo; Mitsunori Ogihara; Stefan Wuchty (ISMIR, 2015)

The road to linking genomics and proteomics of pathogenic bacteria: from binary protein complexes to interaction pathways. - Sarah L. Keasey; Mohan Natesan; Christine Pugh; Teddy Kamata; Stefan Wuchty; Robert G. Ulrich (BMC Bioinform., 2015)

Essentiality and centrality in protein interaction networks revisited. - Sawsan Khuri; Stefan Wuchty (BMC Bioinform., 2015)

Bacterial protein meta-interactomes predict cross-species interactions and protein function. - J. Harry Caufield; Christopher Wimble; Shary Semarjit; Stefan Wuchty; Peter Uetz (BMC Bioinform., 2017)

A stable hybrid method for feature subset selection using particle swarm optimization with local search. - Hassen Dhrif; Luis G. Sánchez Giraldo; Miroslav Kubat; Stefan Wuchty (GECCO, 2019)

A Stable Combinatorial Particle Swarm Optimization for Scalable Feature Selection in Gene Expression Data. - Hassen Dhrif; Luis G. Sánchez Giraldo; Miroslav Kubat; Stefan Wuchty (CoRR, 2019)

Stable Feature Selection for Gene Expression using Enhanced Binary Particle Swarm Optimization. - Hassen Dhrif; Stefan Wuchty (ICAART (2), 2020)

Gene Subset Selection for Transfer Learning using Bilevel Particle Swarm Optimization. - Hassen Dhrif; Verónica Bolón-Canedo; Stefan Wuchty (ICMLA, 2020)

Multi-scale Convolutional Neural Networks for the Prediction of Human-virus Protein Interactions. - Xiaodi Yang; Ziding Zhang; Stefan Wuchty (ICAART (2), 2021)

HVIDB: a comprehensive database for human-virus protein-protein interactions. - Xiaodi Yang; Xianyi Lian; Chen Fu; Stefan Wuchty; Shiping Yang; Ziding Zhang (Briefings Bioinform., 2021)

Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. - Xiaodi Yang; Shiping Yang; Xianyi Lian; Stefan Wuchty; Ziding Zhang (Bioinform., 2021)

Interdisciplinary Papers Supported by Disciplinary Grants Garner Deep and Broad Scientific Impact. - Minsu Park; Suman Kalyan Maity; Stefan Wuchty; Dashun Wang (CoRR, 2023)

SGPPI: structure-aware prediction of protein-protein interactions in rigorous conditions with graph convolutional network. - Yan Huang; Stefan Wuchty; Yuan Zhou; Ziding Zhang (Briefings Bioinform., 2023)

Improving Audience Ratings Prediction of Japanese TV Dramas Using Knowledge-Based Embeddings. - Jerry Bonnell; Stefan Wuchty; Mitsunori Ogihara (ICMLA, 2024)

Multi-modal features-based human-herpesvirus protein-protein interaction prediction by using LightGBM. - Xiaodi Yang; Stefan Wuchty; Zeyin Liang; Li Ji; Bingjie Wang; Jialin Zhu; Ziding Zhang; Yujun Dong (Briefings Bioinform., 2024)