V
Vahid Jalili
Researcher at Oregon Health & Science University
Publications - 14
Citations - 3181
Vahid Jalili is an academic researcher from Oregon Health & Science University. The author has contributed to research in topics: Cloud computing & Password. The author has an hindex of 8, co-authored 12 publications receiving 1747 citations. Previous affiliations of Vahid Jalili include Istituto Italiano di Tecnologia & Polytechnic University of Milan.
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Journal ArticleDOI
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Enis Afgan,Dannon Baker,Bérénice Batut,Marius van den Beek,Dave Bouvier,Martin Čech,John Chilton,Dave Clements,Nate Coraor,Björn Grüning,Aysam Guerler,Jennifer Hillman-Jackson,Saskia Hiltemann,Vahid Jalili,Helena Rasche,Nicola Soranzo,Jeremy Goecks,James Taylor,Anton Nekrutenko,Daniel Blankenberg +19 more
TL;DR: Improvements to Galaxy's core framework, user interface, tools, and training materials enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed.
Journal ArticleDOI
How Machine Learning Will Transform Biomedicine
TL;DR: A vision for how machine learning can transform three broad areas of biomedicine: clinical diagnostics, precision treatments, and health monitoring, where the goal is to maintain health through a range of diseases and the normal aging process is outlined.
Journal ArticleDOI
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Enis Afgan,Anton Nekrutenko,Björn Grüning,Daniel Blankenberg,Jeremy Goecks,Michael C. Schatz,Alexander E. Ostrovsky,Alexandru Mahmoud,Andrew Lonie,Anna Syme,Anne Fouilloux,Anthony Bretaudeau,Anup Kumar,Arthur C. Eschenlauer,Assunta D. Desanto,Aysam Guerler,Beatriz Serrano-Solano,Bérénice Batut,Bradley W. Langhorst,Bridget Carr,Bryan Raubenolt,Cameron J. Hyde,Catherine J. Bromhead,Christopher B. Barnett,Coline Royaux,Cristóbal L. García Gallardo,Daniel Fornika,Dannon Baker,Dave Bouvier,Dave Clements,David A. de Lima Morais,David Lopez Tabernero,Delphine Larivière,E. Nasr,Federico Zambelli,Florian Heyl,Fotis Psomopoulos,Frederik Coppens,Gareth Price,Gianmauro Cuccuru,Gildas Le Corguillé,Gregory Von Kuster,Gulsum Gudukbay,Helena Rasche,Hans-Rudolf Hotz,Ignacio Eguinoa,Igor V. Makunin,Isuru Ranawaka,James Taylor,Jayadev Joshi,Jennifer Hillman-Jackson,John Chilton,Kaivan Kamali,Keith Suderman,Krzysztof Poterlowicz,Yvan Le Bras,Lucille Lopez-Delisle,Luke Sargent,Madeline E. Bassetti,M. A. Tangaro,Marius Van Den Beek,Martin Čech,Matthias Bernt,Matthias Fahrner,Mehmet Tekman,Melanie Föll,Michael R. Crusoe,Miguel Angel Roncoroni,N. K. Kucher,Nathaniel Coraor,Nicholas Stoler,Nick Rhodes,Nicola Soranzo,Niko Pinter,Nuwan Goonasekera,Pablo Moreno,Pavankumar Videm,Petera Melanie,Pietro Mandreoli,Pratik D. Jagtap,Qiang Gu,Ralf J. M. Weber,Ross Lazarus,Ruben H.P. Vorderman,Saskia Hiltemann,Sergey Golitsynskiy,Shilpa Garg,Simon Bray,Simon Gladman,Simone Leo,Subina Mehta,Timothy J. Griffin,Vahid Jalili,Yves Vandenbrouck,Vi-Kwei Wen,Vijaykrishna Nagampalli,W. Bacon,W. L. De Koning,Wolf-Martin Maier,P. J. Briggs +99 more
TL;DR: Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine learning tools.
Journal ArticleDOI
GenoMetric Query Language: a novel approach to large-scale genomic data management
Marco Masseroli,Pietro Pinoli,Francesco Venco,Abdulrahman Kaitoua,Vahid Jalili,Fernando Palluzzi,Heiko Muller,Stefano Ceri +7 more
TL;DR: A high-level, declarative GenoMetric Query Language (GMQL) and a toolkit for its use that provides both abstractions of genomic region data and associated experimental, biological and clinical metadata and interoperability between many data formats is proposed.
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Using combined evidence from replicates to evaluate ChIP-seq peaks.
TL;DR: A general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence is designed.