Training Neural Networks with Balanced Mini-batch to Improve the Prediction of Pathogenic Genomic Variants in Mendelian Diseases by Luca Cappelletti, Jessica Gliozzo, Alessandro Petrini, Giorgio Valentini

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The promises of large language models for protein design and modeling by Giorgio Valentini, Giorgio Valentini, Dario Malchiodi, Jessica Gliozzo, Jessica Gliozzo, Marco Mesiti, Mauricio Soto-Gomez, Alberto Cabri, Justin Reese, Elena Casiraghi, Elena Casiraghi, Elena Casiraghi, Peter N. Robinson

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Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques by Luca Cappelletti, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Max Schubach, Martin Kircher, Giorgio Valentini

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Complex Data Imputation by Auto-Encoders and Convolutional Neural Networks—A Case Study on Genome Gap-Filling by Luca Cappelletti, Tommaso Fontana, Guido Walter Di Donato, Lorenzo Di Tucci, Elena Casiraghi, Giorgio Valentini

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Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools. by Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini, Marco Mesiti

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UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction by Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Marco Notaro, Alessandro Petrini, Elena Casiraghi, Giuliano Grossi, Jessica Gliozzo, Giorgio Valentini, Marco Mesiti

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‘Conjugate’ coseismic surface faulting related with the 29 December 2020, Mw 6.4, Petrinja earthquake (Sisak-Moslavina, Croatia) by Emanuele Tondi, Anna Maria Blumetti, Mišo Čičak, Pio Di Manna, Paolo Galli, Chiara Invernizzi, Stefano Mazzoli, Luigi Piccardi, Giorgio Valentini, Eutizio Vittori, Tiziano Volatili

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Abdominal Computed Tomography Imaging Findings in Hospitalized COVID-19 Patients: A Year-Long Experience and Associations Revealed by Explainable Artificial Intelligence by Alice Scarabelli, Massimo Zilocchi, Elena Casiraghi, Pierangelo Fasani, Guido Giovanni Plensich, Andrea Alessandro Esposito, Elvira Stellato, Alessandro Petrini, Justin Reese, Peter Robinson, Giorgio Valentini, Gianpaolo Carrafiello

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Explainable Machine Learning for Early Assessment of COVID-19 Risk Prediction in Emergency Departments by Elena Casiraghi, Dario Malchiodi, Gabriella Trucco, Marco Frasca, Luca Cappelletti, Tommaso Fontana, Alessandro Andrea Esposito, Emanuele Avola, Alessandro Jachetti, Justin Reese, Alessandro Rizzi, Peter N. Robinson, Giorgio Valentini

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Combining Clinical and Genetic Data to Predict Response to Fingolimod Treatment in Relapsing Remitting Multiple Sclerosis Patients: A Precision Medicine Approach by Laura Ferrè, Ferdinando Clarelli, Beatrice Pignolet, Elisabetta Mascia, Marco Frasca, Silvia Santoro, Melissa Sorosina, Florence Bucciarelli, Lucia Moiola, Vittorio Martinelli, Giancarlo Comi, Roland Liblau, Massimo Filippi, Giorgio Valentini, Federica Esposito

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Regeneration-associated WNT Signaling Is Activated in Long-term Reconstituting AC133bright Acute Myeloid Leukemia Cells by Alessandro Beghini, Francesca Corlazzoli, Luca Del Giacco, Matteo Re, Francesca Lazzaroni, Matteo Brioschi, Giorgio Valentini, Fulvia Ferrazzi, Anna Ghilardi, Marco Righi, Mauro Turrini, Marco Mignardi, Clara Cesana, Vincenzo Bronte, Mats Nilsson, Enrica Morra, Roberto Cairoli

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Predictive models of long COVIDResearch in context by Blessy Antony, Hannah Blau, Elena Casiraghi, Johanna J. Loomba, Tiffany J. Callahan, Bryan J. Laraway, Kenneth J. Wilkins, Corneliu C. Antonescu, Giorgio Valentini, Andrew E. Williams, Peter N. Robinson, Justin T. Reese, T.M. Murali, Christopher Chute

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NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study by Justin T. Reese, Ben Coleman, Lauren Chan, Hannah Blau, Tiffany J. Callahan, Luca Cappelletti, Tommaso Fontana, Katie R. Bradwell, Nomi L. Harris, Elena Casiraghi, Giorgio Valentini, Guy Karlebach, Rachel Deer, Julie A. McMurry, Melissa A. Haendel, Christopher G. Chute, Emily Pfaff, Richard Moffitt, Heidi Spratt, Jasvinder A. Singh, Christopher J. Mungall, Andrew E. Williams, Peter N. Robinson

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An open source knowledge graph ecosystem for the life sciences by Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner, Lawrence E. Hunter

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Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmesResearch in context by Justin T. Reese, Hannah Blau, Elena Casiraghi, Timothy Bergquist, Johanna J. Loomba, Tiffany J. Callahan, Bryan Laraway, Corneliu Antonescu, Ben Coleman, Michael Gargano, Kenneth J. Wilkins, Luca Cappelletti, Tommaso Fontana, Nariman Ammar, Blessy Antony, T.M. Murali, J. Harry Caufield, Guy Karlebach, Julie A. McMurry, Andrew Williams, Richard Moffitt, Jineta Banerjee, Anthony E. Solomonides, Hannah Davis, Kristin Kostka, Giorgio Valentini, David Sahner, Christopher G. Chute, Charisse Madlock-Brown, Melissa A. Haendel, Peter N. Robinson, Heidi Spratt, Shyam Visweswaran, Joseph Eugene Flack, IV, Yun Jae Yoo, Davera Gabriel, G. Caleb Alexander, Hemalkumar B. Mehta, Feifan Liu, Robert T. Miller, Rachel Wong, Elaine L. Hill, Lorna E. Thorpe, Jasmin Divers

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

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