SCITUNA: single-cell data integration tool using network alignment. - Houdjedj, Aissa; Marouf, Yacine; Myradov, Mekan; Dogan, Süleyman Onur; Erten, Burak Onur; Tastan, Oznur; Erten, Cesim; Kazan, Hilal (BMC Bioinform., 2025)

Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions. - Berber, Ibrahim; Erten, Cesim; Kazan, Hilal (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)

PersonaDrive: a method for the identification and prioritization of personalized cancer drivers. - Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal; Bahmed, Ahmed Amine Taleb (Bioinform., 2022)

Ranking cancer drivers via betweenness-based outlier detection and random walks. - Erten, Cesim; Houdjedj, Aissa; Kazan, Hilal (BMC Bioinform., 2021)

Sparse data embedding and prediction by tropical matrix factorization. - Omanovic, Amra; Kazan, Hilal; Oblak, Polona; Curk, Tomaz (BMC Bioinform., 2021)

MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules. - Ahmed, Rafsan; Baali, Ilyes; Erten, Cesim; Hoxha, Evis; Kazan, Hilal (Bioinform., 2020)

Data embedding and prediction by sparse tropical matrix factorization. - Omanovic, Amra; Kazan, Hilal; Oblak, Polona; Curk, Tomaz (CoRR, 2020)

RBPSponge: genome-wide identification of lncRNAs that sponge RBPs. - HafezQorani, Saber; Houdjedj, Aissa; Arici, Mehmet; Said, Abdesselam; Kazan, Hilal (Bioinform., 2019)

JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. - Colak, Recep; Kim, TaeHyung; Kazan, Hilal; Oh, Yoomi; Cruz, Miguel; Valladares-Salgado, Adan; Peralta, Jesus; Escobedo, Jorge; Parra, Esteban J.; Kim, Philip M.; Goldenberg, Anna (Bioinform., 2016)

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). - Berkowitz, Nathan D.; Silverman, Ian M.; Childress, Daniel M.; Kazan, Hilal; Wang, Li-San; Gregory, Brian D. (BMC Bioinform., 2016)

Target-Independent Prediction of Drug Synergies Using Only Drug Lipophilicity. - Yilancioglu, Kaan; Weinstein, Zohar B.; Meydan, Cem; Akhmetov, Azat; Toprak, Isil; Durmaz, Arda; Iossifov, Ivan; Kazan, Hilal; Roth, Frederick P.; Cokol, Murat (J. Chem. Inf. Model., 2014)

RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins. - Kazan, Hilal; Morris, Quaid (Nucleic Acids Res., 2013)

A compendium of RNA-binding motifs for decoding gene regulation. - Ray, Debashish; Kazan, Hilal; Cook, Kate B.; Weirauch, Matthew T.; Najafabadi, Hamed S.; Li, Xiao; Gueroussov, Serge; Albu, Mihai; Zheng, Hong; Yang, Ally; Na, Hong; Irimia, Manuel; et al. (Nat., 2013)

Inferring the Binding Preferences of RNA-binding Proteins. - Kazan, Hilal (2012)

RBPDB: a database of RNA-binding specificities. - Cook, Kate B.; Kazan, Hilal; Zuberi, Khalid; Morris, Quaid; Hughes, Timothy R. (Nucleic Acids Res., 2011)

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins. - Kazan, Hilal; Ray, Debashish; Chan, Esther T.; Hughes, Timothy R.; Morris, Quaid (PLoS Comput. Biol., 2010)