Inferring protein interactions from phylogenetic distance matrices. - Jason Gertz; Georgiy Elfond; Anna Shustrova; Matt Weisinger; Matteo Pellegrini; Shawn Cokus; Bruce Rothschild (Bioinform., 2003)

Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae. - Shawn Cokus; Sherri Rose; David R. Haynor; Niels Grønbech-Jensen; Matteo Pellegrini (BMC Bioinform., 2006)

An improved method for identifying functionally linked proteins using phylogenetic profiles. - Shawn Cokus; Sayaka Mizutani; Matteo Pellegrini (BMC Bioinform., 2007)

Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis. - Robert Riley 002; Matteo Pellegrini; David Eisenberg 001 (PLoS Comput. Biol., 2008)

Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. - Einat Sprinzak; Shawn Cokus; Todd O. Yeates; David Eisenberg 001; Matteo Pellegrini (BMC Syst. Biol., 2009)

A Primer on Regression Methods for Decoding cis-Regulatory Logic. - Debopriya Das; Matteo Pellegrini; Joe W. Gray (PLoS Comput. Biol., 2009)

BS Seeker: precise mapping for bisulfite sequencing. - Pao-Yang Chen; Shawn Cokus; Matteo Pellegrini (BMC Bioinform., 2010)

Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. - David López; David Casero; Shawn Cokus; Sabeeha S. Merchant; Matteo Pellegrini (BMC Bioinform., 2011)

Regulation of the yeast metabolic cycle by transcription factors with periodic activities. - Aliz R. Rao; Matteo Pellegrini (BMC Syst. Biol., 2011)

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. - Jianchao Yao; Kelvin Xi Zhang; Melissa Kramer; Matteo Pellegrini; W. Richard McCombie (Bioinform., 2014)

Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. - Eran Elhaik; Matteo Pellegrini; Tatiana V. Tatarinova (BMC Bioinform., 2014)

A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. - Sagi Snir; Bridgett M. Vonholdt; Matteo Pellegrini (PLoS Comput. Biol., 2016)

LatInfLexi: an Inflected Lexicon of Latin Verbs. - Matteo Pellegrini; Marco Passarotti (CLiC-it, 2018)

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. - Weilong Guo; Ping Zhu 002; Matteo Pellegrini; Michael Q. Zhang; Xiangfeng Wang; Zhongfu Ni (Bioinform., 2018)

Identification of Bridging Centrality in Complex Networks. - Wei Liu 154; Matteo Pellegrini; Aiping Wu (IEEE Access, 2019)

(Stem and Word) Predictability in Italian Verb Paradigms: An Entropy-Based Study Exploiting the New Resource LeFFI. - Matteo Pellegrini; Alessandra Teresa Cignarella (CLiC-it, 2020)

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. - Livia Perfetto; Chiara Pastrello; Noemi del-Toro; Margaret J. Duesbury; Marta Iannuccelli; Max Kotlyar; Luana Licata; Birgit Meldal; Kalpana Panneerselvam; Simona Panni; N. Rahimzadeh; Sylvie Ricard-Blum; et al. (Database J. Biol. Databases Curation, 2020)

The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. - Colin Farrell; Sagi Snir; Matteo Pellegrini (Bioinform., 2020)

ACTINN: automated identification of cell types in single cell RNA sequencing. - Feiyang Ma; Matteo Pellegrini (Bioinform., 2020)

Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. - Brian B. Nadel; Meritxell Oliva; Benjamin L. Shou; Keith Mitchell; Feiyang Ma; Dennis J. Montoya; Alice Mouton; Sarah Kim-Hellmuth; Barbara E. Stranger; Matteo Pellegrini; Serghei Mangul (Briefings Bioinform., 2021)

Computational Morphology with OntoLex-Morph. - Christian Chiarcos; Katerina Gkirtzou; Anas Fahad Khan; Penny Labropoulou; Marco Passarotti; Matteo Pellegrini (LDL@LREC, 2022)

The Index Thomisticus Treebank as Linked Data in the LiLa Knowledge Base. - Francesco Mambrini; Marco Passarotti; Giovanni Moretti; Matteo Pellegrini (LREC, 2022)

Editorial: Computational Methods for Analysis of DNA Methylation Data. - Pietro Di Lena; Christine Nardini; Matteo Pellegrini (Frontiers Bioinform., 2022)

The IntAct database: efficient access to fine-grained molecular interaction data. - Noemi del-Toro; Anjali Shrivastava; Eliot Ragueneau; Birgit Meldal; Colin W. Combe; Elisabet Barrera; Livia Perfetto; Karyn How; Prashansa Ratan; Gautam Shirodkar; Odilia Lu; Bálint Mészáros; et al. (Nucleic Acids Res., 2022)

Enhancing Derivational Information on Latin Lemmas in the LiLa Knowledge Base. A Structural and Diachronic Extension. - Matteo Pellegrini; Marco Passarotti; Eleonora Litta; Francesco Mambrini; Giovanni Moretti; Claudia Corbetta; Martina Verdelli (Prague Bull. Math. Linguistics, 2022)

Beyond Obscuration and Visibility: Thoughts on the Different Strategies of Gender-Fair Language in Italian. - Martina Rosola; Simona Frenda; Alessandra Teresa Cignarella; Matteo Pellegrini; Andrea Marra; Mara Floris (CLiC-it, 2023)

Embed-Search-Align: DNA Sequence Alignment using Transformer Models. - Pavan Holur; Kenneth C. Enevoldsen; Lajoyce Mboning; Thalia Georgiou; Louis-S. Bouchard; Matteo Pellegrini; Vwani Roychowdhury (CoRR, 2023)

Identifying epigenetic aging moderators using the epigenetic pacemaker. - Colin Farrell; Chanyue Hu; Kalsuda Lapborisuth; Kyle Pu; Sagi Snir; Matteo Pellegrini (Frontiers Bioinform., 2023)

Representing Compounding with OntoLex. An Evaluation of Vocabularies for Word Formation Resources. - Elena Benzoni; Matteo Pellegrini; Francesco Dedè; Marco Passarotti (LREC/COLING, 2024)

Editorial: Computational methods for analysis of DNA methylation data, volume II. - Pietro Di Lena; Christine Nardini; Matteo Pellegrini (Frontiers Bioinform., 2024)

BayesAge: A maximum likelihood algorithm to predict epigenetic age. - Lajoyce Mboning; Liudmilla Rubbi; Michael Thompson; Louis-S. Bouchard; Matteo Pellegrini (Frontiers Bioinform., 2024)