Matteo Pellegrini

33 papers B 1Journal 27Unranked 5
YearRankTypeTitle / Venue / Authors
2025 J jnl
Embed-Search-Align: DNA sequence alignment using Transformer models.
Bioinform.
Pavan Holur, Kenneth C. Enevoldsen, Shreyas Rajesh, Lajoyce Mboning, Thalia Georgiou, Louis-S. Bouchard, Matteo Pellegrini, Vwani Roychowdhury
2025 J jnl
PrinParLat: a lexicon of principal parts of Latin verbs linked to the LiLa Knowledge Base.
Lang. Resour. Evaluation
Matteo Pellegrini, Marco Passarotti, Francesco Mambrini, Giovanni Moretti
2024 J jnl
BayesAge: A maximum likelihood algorithm to predict epigenetic age.
Frontiers Bioinform.
Lajoyce Mboning, Liudmilla Rubbi, Michael Thompson, Louis-S. Bouchard, Matteo Pellegrini
2024 J jnl
Editorial: Computational methods for analysis of DNA methylation data, volume II.
Frontiers Bioinform.
Pietro di Lena, Christine Nardini, Matteo Pellegrini
2024 — conf
Representing Compounding with OntoLex. An Evaluation of Vocabularies for Word Formation Resources.
LREC/COLING
Elena Benzoni, Matteo Pellegrini, Francesco Dedè, Marco Passarotti
2023 — conf
Beyond Obscuration and Visibility: Thoughts on the Different Strategies of Gender-Fair Language in Italian.
CLiC-it
Martina Rosola, Simona Frenda, Alessandra Teresa Cignarella, Matteo Pellegrini, Andrea Marra, Mara Floris
2023 J jnl
Embed-Search-Align: DNA Sequence Alignment using Transformer Models.
CoRR
Pavan Holur, Kenneth C. Enevoldsen, Lajoyce Mboning, Thalia Georgiou, Louis-S. Bouchard, Matteo Pellegrini, Vwani Roychowdhury
2023 J jnl
Identifying epigenetic aging moderators using the epigenetic pacemaker.
Frontiers Bioinform.
Colin Farrell, Chanyue Hu, Kalsuda Lapborisuth, Kyle Pu, Sagi Snir, Matteo Pellegrini
2022 — conf
Computational Morphology with OntoLex-Morph.
LDL@LREC
Christian Chiarcos, Katerina Gkirtzou, Anas Fahad Khan, Penny Labropoulou, Marco Passarotti, Matteo Pellegrini
2022 J jnl
Editorial: Computational Methods for Analysis of DNA Methylation Data.
Frontiers Bioinform.
Pietro di Lena, Christine Nardini, Matteo Pellegrini
2022 J jnl
Enhancing Derivational Information on Latin Lemmas in the LiLa Knowledge Base. A Structural and Diachronic Extension.
Prague Bull. Math. Linguistics
Matteo Pellegrini, Marco Passarotti, Eleonora Litta, Francesco Mambrini, Giovanni Moretti, Claudia Corbetta, Martina Verdelli
2022 B conf
The Index Thomisticus Treebank as Linked Data in the LiLa Knowledge Base.
LREC
Francesco Mambrini, Marco Passarotti, Giovanni Moretti, Matteo Pellegrini
2022 J jnl
The IntAct database: efficient access to fine-grained molecular interaction data.
Nucleic Acids Res.
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, Xavier Watkins, Sangya Pundir, Luana Licata, Marta Iannuccelli, Matteo Pellegrini, Maria Jesus Martin, Simona Panni, Margaret J. Duesbury, Sylvain D. Vallet, Juri Rappsilber, Sylvie Ricard-Blum, Gianni Cesareni, Lukasz Salwínski, Sandra E. Orchard, Pablo Porras, Kalpana Panneerselvam, Henning Hermjakob
2021 J jnl
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples.
Briefings Bioinform.
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
2020 — conf
(Stem and Word) Predictability in Italian Verb Paradigms: An Entropy-Based Study Exploiting the New Resource LeFFI.
CLiC-it
Matteo Pellegrini, Alessandra Teresa Cignarella
2020 J jnl
ACTINN: automated identification of cell types in single cell RNA sequencing.
Bioinform.
Feiyang Ma, Matteo Pellegrini
2020 J jnl
The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework.
Bioinform.
Colin Farrell, Sagi Snir, Matteo Pellegrini
2020 J jnl
The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions.
Database J. Biol. Databases Curation
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, Lukasz Salwínski, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra E. Orchard, Igor Jurisica, Henning Hermjakob, Pablo Porras
2019 J jnl
Identification of Bridging Centrality in Complex Networks.
IEEE Access
Wei Liu, Matteo Pellegrini, Aiping Wu
2018 J jnl
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.
Bioinform.
Weilong Guo, Ping Zhu, Matteo Pellegrini, Michael Q. Zhang, Xiangfeng Wang, Zhongfu Ni
2018 — conf
LatInfLexi: an Inflected Lexicon of Latin Verbs.
CLiC-it
Matteo Pellegrini, Marco Passarotti
2016 J jnl
A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging.
PLoS Comput. Biol.
Sagi Snir, Bridgett M. Vonholdt, Matteo Pellegrini
2014 J jnl
FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.
Bioinform.
Jianchao Yao, Kelvin Xi Zhang, Melissa Kramer, Matteo Pellegrini, W. Richard McCombie
2014 J jnl
Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa.
BMC Bioinform.
Eran Elhaik, Matteo Pellegrini, Tatiana V. Tatarinova
2011 J jnl
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
BMC Bioinform.
David López, David Casero, Shawn Cokus, Sabeeha S. Merchant, Matteo Pellegrini
2011 J jnl
Regulation of the yeast metabolic cycle by transcription factors with periodic activities.
BMC Syst. Biol.
Aliz R. Rao, Matteo Pellegrini
2010 J jnl
BS Seeker: precise mapping for bisulfite sequencing.
BMC Bioinform.
Pao-Yang Chen, Shawn Cokus, Matteo Pellegrini
2009 J jnl
A Primer on Regression Methods for Decoding
PLoS Comput. Biol.
Debopriya Das, Matteo Pellegrini, Joe W. Gray
2009 J jnl
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.
BMC Syst. Biol.
Einat Sprinzak, Shawn Cokus, Todd O. Yeates, David Eisenberg, Matteo Pellegrini
2008 J jnl
Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of
PLoS Comput. Biol.
Robert Riley, Matteo Pellegrini, David Eisenberg
2007 J jnl
An improved method for identifying functionally linked proteins using phylogenetic profiles.
BMC Bioinform.
Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
2006 J jnl
Modelling the network of cell cycle transcription factors in the yeast
BMC Bioinform.
Shawn Cokus, Sherri Rose, David R. Haynor, Niels Grønbech-Jensen, Matteo Pellegrini
2003 J jnl
Inferring protein interactions from phylogenetic distance matrices.
Bioinform.
Jason Gertz, Georgiy Elfond, Anna Shustrova, Matt Weisinger, Matteo Pellegrini, Shawn Cokus, Bruce Rothschild