Graph theory analysis of genomics problems: Community analysis of fragile sites correlations and of pseudogenes alignments. - Angela Re; Ivan Molineris; Michele Caselle (Comput. Math. Appl., 2008)

Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR. - Rosario Michael Piro; Ivan Molineris; Ugo Ala; Paolo Provero; Ferdinando Di Cunto (Bioinform., 2010)

A New Approach for the Identification of Processed Pseudogenes. - Ivan Molineris; Gabriele Sales; Federico Bianchi 007; Ferdinando Di Cunto; Michele Caselle (J. Comput. Biol., 2010)

KungFQ: A Simple and Powerful Approach to Compress fastq Files. - Elena Grassi; Federico Di Gregorio; Ivan Molineris (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities. - Rosario M. Piro; Ivan Molineris; Ferdinando Di Cunto; Roland Eils; Rainer König (Bioinform., 2013)

Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs). - Ivan Molineris; Ugo Ala; Paolo Provero; Ferdinando Di Cunto (BMC Bioinform., 2013)

Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries. - Elena Grassi; Elisa Mariella; Antonio Lembo; Ivan Molineris; Paolo Provero (BMC Bioinform., 2016)

In silico prediction of lncRNA function using tissue specific and evolutionary conserved expression. - Umberto Perron; Paolo Provero; Ivan Molineris (BMC Bioinform., 2017)

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. - Marco Antonio Tangaro; Pietro Mandreoli; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Manila Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; et al. (BMC Bioinform., 2021)

Snakemaker: Seamlessly transforming ad-hoc analyses into sustainable Snakemake workflows with generative AI. - Marco Masera; Alessandro Leone; Johannes Köster; Ivan Molineris (CoRR, 2025)