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

Autor: Vazzana G; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy., Savojardo C; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy., Martelli PL; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy., Casadio R; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.

Publikováno v: Molecules (Basel, Switzerland) [Molecules] 2024 Sep 29; Vol. 29 (19). Date of Electronic Publication: 2024 Sep 29.

Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and ESMFold Models of the Human Reference Proteome.

Autor: Manfredi M; Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy., Savojardo C; Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy. Electronic address: castrense.savojardo2@unibo.it., Iardukhin G; Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy., Salomoni D; INFN-CNAF, Bologna, Italy., Costantini A; INFN-CNAF, Bologna, Italy., Martelli PL; Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy. Electronic address: pierluigi.martelli@unibo.it., Casadio R; Biocomputing Group, Dept. of Pharmacy and Biotechnology, University of Bologna, Italy.

Publikováno v: Journal of molecular biology [J Mol Biol] 2024 Sep 01; Vol. 436 (17), pp. 168593. Date of Electronic Publication: 2024 May 06.

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A.

Autor: Jain S; The Institute for Experiential AI, Northeastern University, Boston, MA, USA.; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Trinidad M; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA., Nguyen TB; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia., Jones K; Tuskegee University, Tuskegee, AL, USA., Neto SD; Universidad Nacional de Rosario, Rosario, Argentina., Ge F; State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing, China., Glagovsky A; National University of Tucuman, Tucuman, Argentina., Jones C; Tuskegee University, Tuskegee, AL, USA., Moran G; University of Puerto Rico, San Juan, PR, USA., Wang B; Department of Bioinformatics and System Biology, University of California, San Diego, La Jolla, CA, USA., Rahimi K; Department of Computational Biology, School of Life Sciences, Ochanomizu University, Tokyo, Japan., Çalıcı SZ; Department of Genomics, Faculty of Aquatic Science, Istanbul University, Istanbul, Türkiye., Cedillo LR; University of Texas at El Paso, El Paso, USA., Berardelli S; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.; enGenome srl, Pavia, Italy., Özden B; Program of Molecular Biotechnology and Genetics, Institute of Science, Istanbul University, Istanbul, Türkiye., Chen K; University of California, Berkeley, Berkeley, CA, USA., Katsonis P; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Williams A; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Lichtarge O; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Rana S; TCS Research, India., Pradhan S; TCS Research, India., Srinivasan R; TCS Research, India., Sajeed R; TCS Research, India., Joshi D; TCS Research, India., Faraggi E; Research and Information Systems LLC, Indianapolis, IN, USA.; Physics Department, Indiana University-Purdue University, Indianapolis, IN, USA., Jernigan R; Roy J. Carver Department of Biochemistry, Iowa State University, Ames, IA, USA., Kloczkowski A; Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA., Xu J; University of California, Berkeley, Berkeley, CA, USA., Song Z; Peking University, Beijing, China., Özkan S; Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.; Universitat Autònoma de Barcelona, Barcelona, Spain., Padilla N; Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.; Universitat Autònoma de Barcelona, Barcelona, Spain., de la Cruz X; Vall d'Hebron Institute of Research (VHIR), Barcelona, Spain.; Universitat Autònoma de Barcelona, Barcelona, Spain.; Institucío Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain., Acuna-Hidalgo R; Nostos Genomics GmbH, Berlin, Germany., Grafmüller A; Nostos Genomics GmbH, Berlin, Germany., Jiménez Barrón LT; Nostos Genomics GmbH, Berlin, Germany., Manfredi M; Biocomputing Group, University of Bologna, Bologna, Italy., Savojardo C; Biocomputing Group, University of Bologna, Bologna, Italy., Babbi G; Biocomputing Group, University of Bologna, Bologna, Italy., Martelli PL; Biocomputing Group, University of Bologna, Bologna, Italy., Casadio R; Biocomputing Group, University of Bologna, Bologna, Italy., Sun Y; Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA., Zhu S; Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA., Shen Y; Department of Electrical & Computer Engineering, Texas A&M University, College Station, TX, USA., Pucci F; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium., Rooman M; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium., Cia G; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium., Raimondi D; ESAT-STADIUS, Katholieke Universiteit Leuven, Leuven, Belgium., Hermans P; Computational Biology and Bioinformatics, Université Libre de Bruxelles, Bruxelles, Belgium., Kwee S; University of California, Berkeley, Berkeley, CA, USA., Chen E; University of California, Berkeley, Berkeley, CA, USA., Astore C; San Diego, CA, USA., Kamandula A; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Pejaver V; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Ramola R; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Velyunskiy M; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Zeiberg D; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Mishra R; Department of Bioengineering, University of California, Berkeley, CA, USA.; Department of Bioengineering, University of California, San Francisco, CA, USA., Sterling T; San Anselmo, CA, USA., Goldstein JL; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Lugo-Martinez J; Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA., Kazi S; Houston, TX, USA., Li S; University of California, Berkeley, Berkeley, CA, USA., Long K; University of California, Berkeley, Berkeley, CA, USA., Brenner SE; University of California, Berkeley, Berkeley, CA, USA., Bakolitsa C; University of California, Berkeley, Berkeley, CA, USA., Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Suhr D; MLD Foundation, West Linn, OR, USA., Suhr T; MLD Foundation, West Linn, OR, USA., Clark WT; Greens Fork, IN, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 17. Date of Electronic Publication: 2024 Jun 17.

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

Autor: Stenton SL; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA., O'Leary MC; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Lemire G; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., VanNoy GE; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., DiTroia S; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Ganesh VS; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA., Groopman E; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., O'Heir E; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Mangilog B; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Osei-Owusu I; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Pais LS; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Serrano J; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Singer-Berk M; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Weisburd B; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Wilson MW; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Austin-Tse C; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA., Abdelhakim M; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia., Althagafi A; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.; Computer Science Department, College of Computers and Information Technology, Taif University, Taif, Saudi Arabia., Babbi G; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Bellazzi R; enGenome Srl, Pavia, Italy.; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy., Bovo S; Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy., Carta MG; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy., Casadio R; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Coenen PJ; Invitae, San Francisco, CA, USA.; Codon One, Louvain, EU, Belgium., De Paoli F; enGenome Srl, Pavia, Italy., Floris M; Department of Biomedical Sciences, University of Sassari, Sassari, Italy., Gajapathy M; Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA.; Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.; Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA., Hoehndorf R; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.; Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia., Jacobsen JOB; William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK., Joseph T; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Kamandula A; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Katsonis P; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Kint C; Invitae, San Francisco, CA, USA., Lichtarge O; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Structural and Computational Biology and Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, USA.; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, USA., Limongelli I; enGenome Srl, Pavia, Italy., Lu Y; Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China., Magni P; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy., Mamidi TKK; Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA.; Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.; Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA., Martelli PL; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Mulargia M; Department of Biomedical Sciences, University of Sassari, Sassari, Italy., Nicora G; enGenome Srl, Pavia, Italy.; Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy., Nykamp K; Invitae, San Francisco, CA, USA., Pejaver V; Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA., Peng Y; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Pham THC; University of Medicine and Pharmacy, Hue University, Hue, Vietnam., Podda MS; Department of Biomedical Sciences, University of Sassari, Sassari, Italy.; Institute of Clinical Physiology (IFC), CNR, Via Moruzzi 1, 56124, Pisa, Italy.; University of Siena, Siena, Italy.; CTGLab, Institute of Informatics and Telematics (IIT), CNR, ViaMoruzzi 1, 56124, Pisa, Italy., Rao A; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Rizzo E; enGenome Srl, Pavia, Italy., Saipradeep VG; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Savojardo C; Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy., Schols P; Invitae, San Francisco, CA, USA.; Codon One, Louvain, EU, Belgium., Shen Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA.; Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA.; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA., Sivadasan N; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Smedley D; William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, UK., Soru D; Independent Consultant, Ovodda, Italy., Srinivasan R; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Sun Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA., Sunderam U; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Tan W; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA., Tiwari N; TCS Research, Tata Consultancy Services (TCS) Ltd, Deccan Park, Madhapur, Hyderabad, India., Wang X; Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China., Wang Y; Center for Molecular Medicine, Pediatric Research Institute, Children's Hospital of Fudan University, Shanghai, China., Williams A; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Worthey EA; Center for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, AL, USA.; Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA.; Hugh Kaul Precision Medicine Institute, The University of Alabama at Birmingham, Birmingham, AL, USA., Yin R; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA., You Y; Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA., Zeiberg D; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Zucca S; enGenome Srl, Pavia, Italy., Bakolitsa C; Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA., Brenner SE; Department of Plant and Microbial Biology and Center for Computational Biology, University of California, Berkeley, CA, USA., Fullerton SM; Department of Bioethics and Humanities, University of Washington School of Medicine, Seattle, WA, USA., Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA., Rehm HL; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA., O'Donnell-Luria A; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. odonnell@broadinstitute.org.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. odonnell@broadinstitute.org.; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. odonnell@broadinstitute.org.

Publikováno v: Human genomics [Hum Genomics] 2024 Apr 29; Vol. 18 (1), pp. 44. Date of Electronic Publication: 2024 Apr 29.

DOME: recommendations for supervised machine learning validation in biology

Autor: Walsh, I., Fishman, D., Garcia-Gasulla, D., Titma, T., Pollastri, G., Capriotti, E., Casadio, R., Capella-Gutierrez, S., Cirillo, D., Del Conte, A., Dimopoulos, A. C., Del Angel, V. D., Dopazo, J., Fariselli, P., Fernandez, J. M., Huber, F., Kreshuk, A., Lenaerts, T., Martelli, P. L., Navarro, A., Broin, P. O., Pinero, J., Piovesan, D., Reczko, M., Ronzano, F., Satagopam, V., Savojardo, C., Spiwok, V., Tangaro, M. A., Tartari, G., Salgado, D., Valencia, A., Zambelli, F., Harrow, J., Psomopoulos, F. E., Tosatto, S. C. E.

Publikováno v: UPCommons. Portal del coneixement obert de la UPC
ORCID
arXiv.org e-Print Archive
Archivio istituzionale della ricerca-Alma Mater Studiorum Università di Bologna
Archivio Istituzionale della Ricerca dell'Università degli Studi di Milano
Universitat Politècnica de Catalunya (UPC)
Nature Methods

Supervised machine learning is widely used in biology and deserves more scrutiny. We present a set of community-wide recommendations (DOME) aiming to help establish standards of supervised machine learning validation in biology. Formulated as questio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e3820fb0b766649020b580b623bdf29
https://doi.org/10.1038/s41592-021-01205-4