Matteo Re

Matteo Re

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Matteo Re

Matteo Re

Publications by authors named "Matteo Re"

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19Publications

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Return to sports and re-rupture rate following anterior cruciate ligament reconstruction in amateur sportsman: long-term outcomes.

J Sports Med Phys Fitness 2019 Nov 18;59(11):1902-1907. Epub 2019 Jun 18.

IRCCS Istituto Ortopedico Galeazzi, Milan, Italy.

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http://dx.doi.org/10.23736/S0022-4707.19.09678-6DOI Listing
November 2019

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

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

Minimally Invasive Plate Osteosynthesis for Proximal Humerus Fractures: A Retrospective Study Describing Principles and Advantages of the Technique.

Adv Orthop 2018 3;2018:5904028. Epub 2018 Jun 3.

Department of Orthopedics and Traumatology, University of East Piedmont, Hospital "Maggiore della Carità", Via Mazzini 18, Novara, Italy.

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http://dx.doi.org/10.1155/2018/5904028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6008804PMC
June 2018

Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants.

Sci Rep 2017 06 7;7(1):2959. Epub 2017 Jun 7.

Anacletolab, Dipartimento di Informatica, Università degli Studi di Milano, Via Comelico 39, 20135, Milan, Italy.

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http://dx.doi.org/10.1038/s41598-017-03011-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462751PMC
June 2017

RANKS: a flexible tool for node label ranking and classification in biological networks.

Bioinformatics 2016 09 2;32(18):2872-4. Epub 2016 Jun 2.

AnacletoLab, Department of Computer Science, University of Milan, 20135 Milan, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btw235DOI Listing
September 2016

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Authors:
Yuxiang Jiang Tal Ronnen Oron Wyatt T Clark Asma R Bankapur Daniel D'Andrea Rosalba Lepore Christopher S Funk Indika Kahanda Karin M Verspoor Asa Ben-Hur Da Chen Emily Koo Duncan Penfold-Brown Dennis Shasha Noah Youngs Richard Bonneau Alexandra Lin Sayed M E Sahraeian Pier Luigi Martelli Giuseppe Profiti Rita Casadio Renzhi Cao Zhaolong Zhong Jianlin Cheng Adrian Altenhoff Nives Skunca Christophe Dessimoz Tunca Dogan Kai Hakala Suwisa Kaewphan Farrokh Mehryary Tapio Salakoski Filip Ginter Hai Fang Ben Smithers Matt Oates Julian Gough Petri Törönen Patrik Koskinen Liisa Holm Ching-Tai Chen Wen-Lian Hsu Kevin Bryson Domenico Cozzetto Federico Minneci David T Jones Samuel Chapman Dukka Bkc Ishita K Khan Daisuke Kihara Dan Ofer Nadav Rappoport Amos Stern Elena Cibrian-Uhalte Paul Denny Rebecca E Foulger Reija Hieta Duncan Legge Ruth C Lovering Michele Magrane Anna N Melidoni Prudence Mutowo-Meullenet Klemens Pichler Aleksandra Shypitsyna Biao Li Pooya Zakeri Sarah ElShal Léon-Charles Tranchevent Sayoni Das Natalie L Dawson David Lee Jonathan G Lees Ian Sillitoe Prajwal Bhat Tamás Nepusz Alfonso E Romero Rajkumar Sasidharan Haixuan Yang Alberto Paccanaro Jesse Gillis Adriana E Sedeño-Cortés Paul Pavlidis Shou Feng Juan M Cejuela Tatyana Goldberg Tobias Hamp Lothar Richter Asaf Salamov Toni Gabaldon Marina Marcet-Houben Fran Supek Qingtian Gong Wei Ning Yuanpeng Zhou Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Stefano Toppo Carlo Ferrari Manuel Giollo Damiano Piovesan Silvio C E Tosatto Angela Del Pozo José M Fernández Paolo Maietta Alfonso Valencia Michael L Tress Alfredo Benso Stefano Di Carlo Gianfranco Politano Alessandro Savino Hafeez Ur Rehman Matteo Re Marco Mesiti Giorgio Valentini Joachim W Bargsten Aalt D J van Dijk Branislava Gemovic Sanja Glisic Vladmir Perovic Veljko Veljkovic Nevena Veljkovic Danillo C Almeida-E-Silva Ricardo Z N Vencio Malvika Sharan Jörg Vogel Lakesh Kansakar Shanshan Zhang Slobodan Vucetic Zheng Wang Michael J E Sternberg Mark N Wass Rachael P Huntley Maria J Martin Claire O'Donovan Peter N Robinson Yves Moreau Anna Tramontano Patricia C Babbitt Steven E Brenner Michal Linial Christine A Orengo Burkhard Rost Casey S Greene Sean D Mooney Iddo Friedberg Predrag Radivojac

Genome Biol 2016 09 7;17(1):184. Epub 2016 Sep 7.

Department of Computer Science and Informatics, Indiana University, Bloomington, IN, USA.

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http://dx.doi.org/10.1186/s13059-016-1037-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015320PMC
September 2016

Network-based drug ranking and repositioning with respect to DrugBank therapeutic categories.

IEEE/ACM Trans Comput Biol Bioinform 2013 Nov-Dec;10(6):1359-71

Universita degli Studi di Milano, Milano.

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http://dx.doi.org/10.1109/TCBB.2013.62DOI Listing
September 2014

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods.

Artif Intell Med 2014 Jun 20;61(2):63-78. Epub 2014 Mar 20.

AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano, Italy.

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http://dx.doi.org/10.1016/j.artmed.2014.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070077PMC
June 2014

Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction.

Gigascience 2014 23;3. Epub 2014 Apr 23.

AnacletoLab - Department of Computer Science, University of Milano, Via Comelico 39/41, 20135 Milano, Italy.

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http://dx.doi.org/10.1186/2047-217X-3-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006453PMC
May 2014

A fast ranking algorithm for predicting gene functions in biomolecular networks.

IEEE/ACM Trans Comput Biol Bioinform 2012 Nov-Dec;9(6):1812-8

Dipartimento di Informatica, Università degli Studi di Milano, Via Comelico 39/41, I-20135 Milano, Italia.

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http://dx.doi.org/10.1109/TCBB.2012.114DOI Listing
July 2013

A neural network algorithm for semi-supervised node label learning from unbalanced data.

Neural Netw 2013 Jul 6;43:84-98. Epub 2013 Feb 6.

Dipartimento di Informatica, Università degli Studi di Milano, Via Comelico 39, 20135 Milano, Italy.

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http://dx.doi.org/10.1016/j.neunet.2013.01.021DOI Listing
July 2013

Cancer module genes ranking using kernelized score functions.

BMC Bioinformatics 2012 7;13 Suppl 14:S3. Epub 2012 Sep 7.

Dipartimento di Informatica, Università degli Studi di Milano, via Comelico 39/41, 20135 Milano MI, Italia.

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http://dx.doi.org/10.1186/1471-2105-13-S14-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439680PMC
May 2013

Noise tolerance of multiple classifier systems in data integration-based gene function prediction.

J Integr Bioinform 2010 Mar 25;7(3). Epub 2010 Mar 25.

Dipartimento di Scienze dell'Informazione, Università degli Studi di Milano, Milano, Italy.

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http://dx.doi.org/10.2390/biecoll-jib-2010-139DOI Listing
March 2010

Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics.

BMC Bioinformatics 2009 Sep 8;10:282. Epub 2009 Sep 8.

Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italia.

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http://dx.doi.org/10.1186/1471-2105-10-282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2758873PMC
September 2009

Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns.

Artif Intell Med 2009 Feb-Mar;45(2-3):117-23. Epub 2008 Sep 21.

Department of Biomolecular Science and Biotechnology, University of Milan, via Celoria 26, 20133 Milan, Italy.

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http://dx.doi.org/10.1016/j.artmed.2008.07.015DOI Listing
May 2009

A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22.

Gene 2006 Jan 15;365:35-40. Epub 2005 Dec 15.

Dipartimento di Scienze Biomolecolari e Biotecnologie, via Celoria 26, 20133 Milano, Italy.

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http://dx.doi.org/10.1016/j.gene.2005.09.041DOI Listing
January 2006