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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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