Paolo Fontana

Paolo Fontana

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Paolo Fontana

Paolo Fontana

Publications by authors named "Paolo Fontana"

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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

A new rare species of Oedipoda Latreille, 1829 (Orthoptera: Acrididae) from South Italy.

Zootaxa 2019 Jun 7;4614(1):zootaxa.4614.1.2. Epub 2019 Jun 7.

Fondazione Edmund Mach di San Michele all'Adige, Via E. Mach 1, 38010 S. Michele all'Adige (Trento), Italy.

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http://dx.doi.org/10.11646/zootaxa.4614.1.2DOI Listing
June 2019

A new voice from Sardinia: Uromenus annae (Targioni-Tozzetti, 1881 (Insecta: Orthoptera: Tettigoniidae: Bradyporinae: Ephippigerini).

Zootaxa 2019 Feb 25;4560(2):zootaxa.4560.2.4. Epub 2019 Feb 25.

Corresponding author, Fondazione Museo Civico di Rovereto, Borgo Santa Caterina, 41-38068 Rovereto TN, Italy..

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http://dx.doi.org/10.11646/zootaxa.4560.2.4DOI Listing
February 2019

"Compatibilization" through Elongational Flow Processing of LDPE/PA6 Blends.

Materials (Basel) 2018 Nov 26;11(12). Epub 2018 Nov 26.

Department of Civil, Environmental, Aerospace, Materials Engineering, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy.

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http://dx.doi.org/10.3390/ma11122375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317011PMC
November 2018

Studies in Mexican Grasshoppers: A new species of Pedies Saussure (Acrididae: Melanoplinae) with comments on the unusual blue coloration on the abdomens of females and live specimen images for three other congenerics.

Zootaxa 2018 Aug 15;4459(3):551-564. Epub 2018 Aug 15.

Department of Entomology, Texas A&M University, Minnie Belle Heep Center, Room 412 Campus MS 2475, College Station, TX 77843-2475, U.S.A..

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http://dx.doi.org/10.11646/zootaxa.4459.3.8DOI Listing
August 2018

Reply to the Letter: "Sensorineural Hearing Loss and Congenital Cytomegalovirus Infection".

Authors:
Paolo Fontana

J Pediatr Genet 2018 Mar 13;7(1):46. Epub 2017 Dec 13.

Department of Molecular Medicine and Medical Biotechnologies, "Federico II" University of Naples, Naples, Italy.

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http://dx.doi.org/10.1055/s-0037-1612597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809168PMC
March 2018

Studies in Mexican Grasshoppers: Three new species of Dactylotini (Acrididae: Melanoplinae) from Mexico and a review of existing conspecifics with comments on their geographical distributions.

Zootaxa 2017 Oct 19;4337(3):301-343. Epub 2017 Oct 19.

Fondazione Edmund Mach - Centro Trasferimento Tecnologico - Protezione delle piante e biodiversità agroforestale, Via della Val, 2- Loc. Costa di Casalino, I-38057 Pergine Valsugana, Italy..

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http://dx.doi.org/10.11646/zootaxa.4337.3.1DOI Listing
October 2017

Alterations in metabolic patterns have a key role in diagnosis and progression of primrose syndrome.

Am J Med Genet A 2017 Jul 30;173(7):1896-1902. Epub 2017 Apr 30.

Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy.

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http://dx.doi.org/10.1002/ajmg.a.38124DOI Listing
July 2017

A novel 5q11.2 microdeletion in a child with mild developmental delay and dysmorphic features.

Am J Med Genet A 2016 09 4;170(9):2445-8. Epub 2016 Jul 4.

Service of Medical Genetics, Cardarelli Hospital, Naples, Italy.

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http://dx.doi.org/10.1002/ajmg.a.37824DOI 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

Eliciting the Functional Taxonomy from protein annotations and taxa.

Sci Rep 2016 08 18;6:31971. Epub 2016 Aug 18.

Department of Molecular Medicine, University of Padova, Padova, 35131, Italy.

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http://dx.doi.org/10.1038/srep31971DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989186PMC
August 2016

Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

Methods 2016 Jan 28;93:15-23. Epub 2015 Aug 28.

Department of Molecular Medicine, University of Padova, Padova, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.08.021DOI Listing
January 2016

Constitutional chromothripsis involving the critical region of 9q21.13 microdeletion syndrome.

Mol Cytogenet 2015 18;8:96. Epub 2015 Dec 18.

Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Naples, Italy.

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http://dx.doi.org/10.1186/s13039-015-0199-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683855PMC
December 2015

Reply: To PMID 24726598.

Ann Thorac Surg 2015 Aug;100(2):770-1

Department of Cardiologic, Thoracic and Vascular Sciences, University of Padua, Padua, Italy.

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http://dx.doi.org/10.1016/j.athoracsur.2015.04.077DOI Listing
August 2015

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

Sci Rep 2015 May 19;5:9743. Epub 2015 May 19.

Fondazione Edmund Mach, Research and Innovation Centre, Computational Biology Department, Via E. Mach 1, 38010 - S. Michele all'Adige (TN), Italy.

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http://www.nature.com/articles/srep09743
Publisher Site
http://dx.doi.org/10.1038/srep09743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4649890PMC
May 2015

keeSeek: searching distant non-existing words in genomes for PCR-based applications.

Bioinformatics 2014 Sep 27;30(18):2662-4. Epub 2014 May 27.

Department of Molecular Medicine, University of Padova, Padova, I-35131, Italy and Department of Computational Biology, Edmund Mach Foundation, S. Michele All'Adige, I-38010 (TN), Italy.

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http://dx.doi.org/10.1093/bioinformatics/btu312DOI Listing
September 2014

Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids.

PLoS One 2013 14;8(10):e77022. Epub 2013 Oct 14.

Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077022PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3796552PMC
June 2014

Studies in Mexican Grasshoppers: Liladownsia fraile, a new genus and species of Dactylotini (Acrididae: Melanoplinae) and an updated molecular phylogeny of Melanoplinae.

Zootaxa 2014 May 1;3793:475-95. Epub 2014 May 1.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816-2368, U.S.A.; Email: unknown.

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http://dx.doi.org/10.11646/zootaxa.3793.4.6DOI Listing
May 2014

Loeys-Dietz syndrome type 4, caused by chromothripsis, involving the TGFB2 gene.

Gene 2014 Mar 15;538(1):69-73. Epub 2014 Jan 15.

Department of Translational Medical Sciences, Division of Pediatrics, Federico II University, Naples, Italy.

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http://dx.doi.org/10.1016/j.gene.2014.01.017DOI Listing
March 2014

Bronchial isomerism in a Kabuki syndrome patient with a novel mutation in MLL2 gene.

BMC Med Genet 2014 Jan 28;15:15. Epub 2014 Jan 28.

Department of Translational Medical Sciences, Section of Pediatrics, Federico II University, Via Sergio Pansini 5, 80131 Naples, Italy.

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http://dx.doi.org/10.1186/1471-2350-15-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925134PMC
January 2014

Studies in Mexican Tettigoniidae: a new genus of Copiphorini and the first description of male Conocephalus (Aphauropus) leptopterus Rehn and Hebard and the female of Insara acutitegmina Fontana, Buzzetti, Mariño-Pérez & García García.

Zootaxa 2013 Nov 21;3737:429-53. Epub 2013 Nov 21.

Department of Biology, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816-2368, U.S.A.; Email: unknown.

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http://biotaxa.org/Zootaxa/article/view/zootaxa.3737.4.6
Publisher Site
http://dx.doi.org/10.11646/zootaxa.3737.4.6DOI Listing
November 2013

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.

Bioinformatics 2013 Jul 5;29(14):1825-6. Epub 2013 Jun 5.

Translational Genomics Unit, Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via La Masa 19, 20159 Milano, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3702260PMC
July 2013

A large-scale evaluation of computational protein function prediction.

Authors:
Predrag Radivojac Wyatt T Clark Tal Ronnen Oron Alexandra M Schnoes Tobias Wittkop Artem Sokolov Kiley Graim Christopher Funk Karin Verspoor Asa Ben-Hur Gaurav Pandey Jeffrey M Yunes Ameet S Talwalkar Susanna Repo Michael L Souza Damiano Piovesan Rita Casadio Zheng Wang Jianlin Cheng Hai Fang Julian Gough Patrik Koskinen Petri Törönen Jussi Nokso-Koivisto Liisa Holm Domenico Cozzetto Daniel W A Buchan Kevin Bryson David T Jones Bhakti Limaye Harshal Inamdar Avik Datta Sunitha K Manjari Rajendra Joshi Meghana Chitale Daisuke Kihara Andreas M Lisewski Serkan Erdin Eric Venner Olivier Lichtarge Robert Rentzsch Haixuan Yang Alfonso E Romero Prajwal Bhat Alberto Paccanaro Tobias Hamp Rebecca Kaßner Stefan Seemayer Esmeralda Vicedo Christian Schaefer Dominik Achten Florian Auer Ariane Boehm Tatjana Braun Maximilian Hecht Mark Heron Peter Hönigschmid Thomas A Hopf Stefanie Kaufmann Michael Kiening Denis Krompass Cedric Landerer Yannick Mahlich Manfred Roos Jari Björne Tapio Salakoski Andrew Wong Hagit Shatkay Fanny Gatzmann Ingolf Sommer Mark N Wass Michael J E Sternberg Nives Škunca Fran Supek Matko Bošnjak Panče Panov Sašo Džeroski Tomislav Šmuc Yiannis A I Kourmpetis Aalt D J van Dijk Cajo J F ter Braak Yuanpeng Zhou Qingtian Gong Xinran Dong Weidong Tian Marco Falda Paolo Fontana Enrico Lavezzo Barbara Di Camillo Stefano Toppo Liang Lan Nemanja Djuric Yuhong Guo Slobodan Vucetic Amos Bairoch Michal Linial Patricia C Babbitt Steven E Brenner Christine Orengo Burkhard Rost Sean D Mooney Iddo Friedberg

Nat Methods 2013 Mar 27;10(3):221-7. Epub 2013 Jan 27.

School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA.

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http://dx.doi.org/10.1038/nmeth.2340DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3584181PMC
March 2013

Pathway-based analysis of microarray and RNAseq data using Pathway Processor 2.0.

Curr Protoc Bioinformatics 2013 Mar;Chapter 7:Unit 7.6

Translational Genomics Unit, Department of Oncology, Mario Negri Research Institute, Milan, Italy.

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http://dx.doi.org/10.1002/0471250953.bi0706s41DOI Listing
March 2013

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data.

Brief Bioinform 2012 May 21;13(3):269-80. Epub 2011 Oct 21.

Information Engineering Department of the University of Padova, Padova, Italy.

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http://dx.doi.org/10.1093/bib/bbr063DOI Listing
May 2012

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

BMC Bioinformatics 2012 Mar 28;13 Suppl 4:S14. Epub 2012 Mar 28.

Department of Molecular Medicine, University of Padova, via U. Bassi 58/B, 35121, Padova, Italy.

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http://dx.doi.org/10.1186/1471-2105-13-S4-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3314586PMC
March 2012

The genome of the domesticated apple (Malus × domestica Borkh.).

Nat Genet 2010 Oct 29;42(10):833-9. Epub 2010 Aug 29.

Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, Trento, Italy.

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http://dx.doi.org/10.1038/ng.654DOI Listing
October 2010

A multi-scale study of Orthoptera species richness and human population size controlling for sampling effort.

Naturwissenschaften 2010 Mar 23;97(3):265-71. Epub 2009 Dec 23.

School of Conservation Sciences, Bournemouth University, Talbot Campus, Poole, BH12 5BB, Bournemouth, UK.

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http://link.springer.com/10.1007/s00114-009-0636-4
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http://dx.doi.org/10.1007/s00114-009-0636-4DOI Listing
March 2010

Ripening and genotype control stilbene accumulation in healthy grapes.

J Agric Food Chem 2008 Dec;56(24):11773-85

IASMA Research Center, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.

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http://dx.doi.org/10.1021/jf8017707DOI Listing
December 2008

Real surgical morbidity and mortality after extrapleural pneumonectomy.

Chir Ital 2007 Jul-Aug;59(4):453-60

Thoracic Surgery Unit, Umberto I General Hospital, Venezia-Mestre.

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December 2007

Intraoperative identification and effective "blood patch" prevention of persistent air leak in lung resections.

Chir Ital 2006 Jul-Aug;58(4):413-21

Thoracic Surgery Unit, Umberto I General Hospital, Venezia-Mestre, Italy.

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November 2006

Surgical outcome of lung cancer patients with carcinomatous pleuritis.

Chir Ital 2005 Nov-Dec;57(6):703-8

UOC Chirurgia Toracica, Ospedale Umberto I, Venezia-Mestre.

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February 2006

The SSEA server for protein secondary structure alignment.

Bioinformatics 2005 Feb 3;21(3):393-5. Epub 2004 Sep 3.

Istituto Agrario di San Michele all'Adige, via E. Mach 1, 38010 S. Michele all'Adige (TN), Italy.

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http://bioinformatics.oxfordjournals.org/content/21/3/393.fu
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bti013DOI Listing
February 2005

[Thoracic outlet syndrome: clinical staging].

Chir Ital 2004 Jan-Feb;56(1):55-62

U.O. di Chirurgia Toracica, Ospedale Civile Umberto I, Mestre, Venezia.

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September 2004

[Pleuro-pneumonectomy, RT and CT for pleural mesothelioma. Prospective study].

Chir Ital 2003 Jan-Feb;55(1):13-20

Unità di Chirurgia Toracica Ospedale Umberto I-Venezia-Mestre.

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December 2003

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

Bioinformatics 2003 Mar;19(5):661-2

CRIBI, Università di Padova, via Ugo Bassi 58/B, Padova, 35131 Italy.

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http://dx.doi.org/10.1093/bioinformatics/btg045DOI Listing
March 2003