Merging metabolomics and genomics provides a catalog of genetic factors that influence molecular phenotypes in pigs linking relevant metabolic pathways

Authors: Samuele Bovo, Anisa Ribani, Flaminia Fanelli, Giuliano Galimberti, Pier Luigi Martelli, Paolo Trevisi, Francesca Bertolini, Matteo Bolner, Rita Casadio, Stefania Dall’Olio, Maurizio Gallo, Diana Luise, Gianluca Mazzoni, Giuseppina Schiavo, Valeria Taurisano, Paolo Zambonelli, Paolo Bosi, Uberto Pagotto, Luca Fontanesi

Source: Genetics Selection Evolution, Vol 57, Iss 1, Pp 1-27 (2025)

Subject Terms: Animal culture, SF1-1100, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1297-9686

Access URL: https://doaj.org/article/b16139be54d1443c98fac54104aef49c

AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation

Authors: Matteo Manfredi, Gabriele Vazzana, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

Source: Computational and Structural Biotechnology Journal, Vol 27, Iss , Pp 461-466 (2025)

Subject Terms: Human enzyme structural and functional annotation, Pfam domains, Enzyme Active site, AlphaFold2, ESMFold, Human Reference Proteome, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S200103702500008X; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/681092a4356842a79e11855a5b1b9e9b

Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

Authors: Sarah L. Stenton, Melanie C. O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W. Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O. B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G. Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M. Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-Luria

Source: Human Genomics, Vol 18, Iss 1, Pp 1-25 (2024)

Subject Terms: Rare disease, Genome sequencing, Genome interpretation, Variant prioritization, Best practices, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1479-7364

Access URL: https://doaj.org/article/29fbe7d26d88463789f004c8908aa4a7

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length

Authors: Gabriele Vazzana, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

Source: Molecules, Vol 29, Iss 19, p 4616 (2024)

Subject Terms: Glutathione S-transferases, protein language models, protein classification, functional annotation, embedding-based alignment, Organic chemistry, QD241-441

File Description: electronic resource

Relation: https://www.mdpi.com/1420-3049/29/19/4616; https://doaj.org/toc/1420-3049

Access URL: https://doaj.org/article/9b1c73c939454a22bc18c307a56fc075

CoCoNat: A Deep Learning–Based Tool for the Prediction of Coiled-coil Domains in Protein Sequences

Authors: Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

Source: Bio-Protocol, Vol 14, Iss 4 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://bio-protocol.org/en/bpdetail?id=4935&type=0; https://doaj.org/toc/2331-8325

Access URL: https://doaj.org/article/9eb7e3597a4349b1b75a73272b5a09a6

Mapping human disease-associated enzymes into Reactome allows characterization of disease groups and their interactions

Authors: Castrense Savojardo, Davide Baldazzi, Giulia Babbi, Pier Luigi Martelli, Rita Casadio

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-10 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/e7970a794c644f6c9226d142a86032ef

Resources and tools for rare disease variant interpretation

Authors: Luana Licata, Allegra Via, Paola Turina, Giulia Babbi, Silvia Benevenuta, Claudio Carta, Rita Casadio, Andrea Cicconardi, Angelo Facchiano, Piero Fariselli, Deborah Giordano, Federica Isidori, Anna Marabotti, Pier Luigi Martelli, Stefano Pascarella, Michele Pinelli, Tommaso Pippucci, Roberta Russo, Castrense Savojardo, Bernardina Scafuri, Lucrezia Valeriani, Emidio Capriotti

Source: Frontiers in Molecular Biosciences, Vol 10 (2023)

Subject Terms: rare disease, genetic disorder, single nucleotide variant (SNV), genome interpretation, precision medicine, genotype-phenotype association, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2023.1169109/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/11124e19b5df45e0a5d0ff3484da618c

Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean

Authors: Adam J. Andrews, Gregory N. Puncher, Darío Bernal-Casasola, Antonio Di Natale, Francesco Massari, Vedat Onar, Nezir Yaşar Toker, Alex Hanke, Scott A. Pavey, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Elisabetta Cilli, Arturo Morales-Muñiz, Barbara Mantovani, Fausto Tinti, Alessia Cariani

Source: Scientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/072efb533433476aa34a2eb4166f3c55

Pathogenic variation types in human genes relate to diseases through Pfam and InterPro mapping

Authors: Giulia Babbi, Castrense Savojardo, Davide Baldazzi, Pier Luigi Martelli, Rita Casadio

Source: Frontiers in Molecular Biosciences, Vol 9 (2022)

Subject Terms: disease associated variant, variation physicochemical type, Pfam domain, InterPro domain, mondo anatomical system categories, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2022.966927/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/3be051471eaf4dc7885ca9f7bfe1d0a3

DeepREx-WS: A web server for characterising protein–solvent interaction starting from sequence

Authors: Matteo Manfredi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

Source: Computational and Structural Biotechnology Journal, Vol 19, Iss , Pp 5791-5799 (2021)

Subject Terms: Residue solvent accessibility, Deep Learning, Protein flexibility, Protein disorder, Surface engineering, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037021004384; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/f6a1c988c0cb4d7481cf93a7c7fbc45b

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

Authors: Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari, Rita Casadio

Source: BMC Bioinformatics, Vol 21, Iss S8, Pp 1-13 (2020)

Subject Terms: Submitochondrial localization, Subcellular localization, Mitochondrial protein, Convolutional neural network, Deep learning, Functional annotation, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03617-z; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/7e3ba0a396bf431c9fee9eb32f1e11d3

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Authors: Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Gemovic, Vladimir R. Perovic, Radoslav S. Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R.K. Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C. McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A. Freitas, Magdalena Antczak, Fabio Fabris, Mark N. Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E. Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J. Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W. Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T. Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L. Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B. Roche, Jonas Reeb, David W. Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C.E. Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S. Black, Dane Jo, Erica Suh, Jonathan B. Dayton, Dallas J. Larsen, Ashton R. Omdahl, Liam J. McGuffin, Danielle A. Brackenridge, Patricia C. Babbitt, Jeffrey M. Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E.E. Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E. Brenner, Christine A. Orengo, Constance J. Jeffery, Giovanni Bosco, Deborah A. Hogan, Maria J. Martin, Claire O’Donovan, Sean D. Mooney, Casey S. Greene, Predrag Radivojac, Iddo Friedberg

Source: Genome Biology, Vol 20, Iss 1, Pp 1-23 (2019)

Subject Terms: Protein function prediction, Long-term memory, Biofilm, Critical assessment, Community challenge, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-019-1835-8; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/4c2b017b155b41ceab8d6d078186cafa

PhenPath: a tool for characterizing biological functions underlying different phenotypes

Authors: Giulia Babbi, Pier Luigi Martelli, Rita Casadio

Source: BMC Genomics, Vol 20, Iss S8, Pp 1-11 (2019)

Subject Terms: Phenotype, Diseases, Molecular pathway, Biological process, Enrichment, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-019-5868-x; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/cae670fc10b2491fab4634773aeae8a7

Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes

Authors: Castrense Savojardo, Giulia Babbi, Pier Luigi Martelli, Rita Casadio

Source: Frontiers in Molecular Biosciences, Vol 8 (2021)

Subject Terms: protein variations, protein structure, protein domain, variation type, disease-related variations, disease variant databases, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2021.617016/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/1fb6bbd532dc400483a5893932992746

Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences

Authors: Castrense Savojardo, Matteo Manfredi, Pier Luigi Martelli, Rita Casadio

Source: Frontiers in Molecular Biosciences, Vol 7 (2021)

Subject Terms: solvent accessible surface area, relative solvent accessibility, protein variations, prediction of solvent accessible surface, pathogenic protein variations, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2020.626363/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/ebcb82afa0154b0298885869984d197a

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

Authors: Giulia Babbi, Pier Luigi Martelli, Giuseppe Profiti, Samuele Bovo, Castrense Savojardo, Rita Casadio

Source: BMC Genomics, Vol 18, Iss S5, Pp 25-34 (2017)

Subject Terms: Gene/disease relationship, Protein-protein interaction, Protein functional annotation, Functional enrichment, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-017-3911-3; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/777fad2d498249e7896608c4ca735efe

Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa

Authors: Maphuti Betty Ledwaba, Barbara Akorfa Glover, Itumeleng Matle, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio, Katiuscia Zilli, Anna Janowicz, Francesca Marotta, Giuliano Garofolo, Henriette van Heerden

Source: Microorganisms, Vol 9, Iss 3, p 570 (2021)

Subject Terms: bovine brucellosis, Brucella abortus, whole genome sequence, single nucleotide polymorphisms, comparative analysis, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/9/3/570; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/fbb90a612c70474c85e08124ddb7e2c1

Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9

Authors: Giulia Babbi, Davide Baldazzi, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

Source: Biomedicines, Vol 8, Iss 8, p 250 (2020)

Subject Terms: enzymes, KEGG pathways KEGG metabolic pathways, protein-protein interaction, protein variation, protein stability, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2227-9059/8/8/250; https://doaj.org/toc/2227-9059

Access URL: https://doaj.org/article/ac59a9543cee4612a54f5b03aceaf177

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

Authors: Profiti, Giuseppe, Pier Luigi Martelli, Casadio, Rita

Source: Nucleic Acids Research; 7/3/2017, Vol. 45 Issue W1, pW285-W290, 6p

The Bologna Annotation Resource: a Non Hierarchical Method for the Functional and Structural Annotation of Protein Sequences Relying on a Comparative Large-Scale Genome Analysis.

Authors: Lisa Bartoli, Ludovica Montanucci, Raffaele Fronza, Pier Luigi Martelli, Piero Fariselli, Luciana Carota, Giacinto Donvito, Giorgio P. Maggi, Rita Casadio

Source: Journal of Proteome Research; Sep2009, Vol. 8 Issue 9, p4362-4371, 10p