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Anna N. Melidoni
Researcher at European Bioinformatics Institute
Publications - 15
Citations - 2626
Anna N. Melidoni is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Embryonic stem cell & Cellular differentiation. The author has an hindex of 8, co-authored 13 publications receiving 2224 citations. Previous affiliations of Anna N. Melidoni include Queen Mary University of London & University of Ioannina.
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Journal ArticleDOI
The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases.
Sandra Orchard,Mais G. Ammari,Bruno Aranda,Lionel Breuza,Leonardo Briganti,Fiona Broackes-Carter,Nancy H. Campbell,Gayatri Chavali,Carol Chen,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Eugenia Galeota,Ursula Hinz,Marta Iannuccelli,Sruthi Jagannathan,Rafael C. Jimenez,Jyoti Khadake,Astrid Lagreid,Luana Licata,Ruth C. Lovering,Birgit H M Meldal,Anna N. Melidoni,Mila Milagros,Daniele Peluso,Livia Perfetto,Pablo Porras,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Andre Stutz,Michael Tognolli,Kim Van Roey,Gianni Cesareni,Henning Hermjakob +34 more
TL;DR: All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Journal ArticleDOI
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang,Tal Ronnen Oron,Wyatt T. Clark,Asma R. Bankapur,Daniel D'Andrea,Rosalba Lepore,Christopher S. Funk,Indika Kahanda,Karin Verspoor,Asa Ben-Hur,Da Chen Emily Koo,Duncan Penfold-Brown,Dennis Shasha,Noah Youngs,Richard Bonneau,Alexandra Lin,Sayed Mohammad Ebrahim Sahraeian,Pier Luigi Martelli,Giuseppe Profiti,Rita Casadio,Renzhi Cao,Zhaolong Zhong,Jianlin Cheng,Adrian M. Altenhoff,Adrian M. Altenhoff,Nives Škunca,Nives Škunca,Christophe Dessimoz,Christophe Dessimoz,Christophe Dessimoz,Tunca Doğan,Kai Hakala,Suwisa Kaewphan,Farrokh Mehryary,Tapio Salakoski,Filip Ginter,Hai Fang,Ben Smithers,Matt E. 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,Pooya Zakeri,Sarah ElShal,Sarah ElShal,Léon-Charles Tranchevent,Léon-Charles Tranchevent,Sayoni Das,Natalie L. Dawson,David A. Lee,Jonathan G. Lees,Ian Sillitoe,Prajwal Bhat,Tamás Nepusz,Alfonso E. Romero,Rajkumar Sasidharan,Haixuan Yang,Alberto Paccanaro,Jesse Gillis,Adriana E. Sedeno-Cortes,Paul Pavlidis,Shou Feng,Juan Miguel Cejuela,Tatyana Goldberg,Tobias Hamp,Lothar Richter,Asaf Salamov,Toni Gabaldón,Toni Gabaldón,Marina Marcet-Houben,Fran Supek,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. Vêncio,Malvika Sharan,Jörg Vogel,Lakesh Kansakar,Shanshan Zhang,Slobodan Vucetic,Zheng Wang,Michael J.E. Sternberg,Mark N. Wass,Rachael P. Huntley,Maria Jesus 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,Iddo Friedberg,Predrag Radivojac +156 more
TL;DR: The second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function, was conducted by as mentioned in this paper. But the results of the CAFA2 assessment are limited.
Additional file 1 of An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang,Tal Ronnen Oron,Wyatt T. Clark,Asma R. Bankapur,Daniel D'Andrea,Rosalba Lepore,Christopher S. Funk,Indika Kahanda,Karin 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 M. Altenhoff,Nives Škunca,Christophe Dessimoz,Tunca Doğan,Kai Hakala,Suwisa Kaewphan,Farrokh Mehryary,Tapio Salakoski,Filip Ginter,Hai Fang,Ben Smithers,Matt E. 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 A. 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 Miguel Cejuela,Tatyana Goldberg,Tobias Hamp,Lothar Richter,Asaf Salamov,Toni Gabaldón,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. Vêncio,Malvika Sharan,Jörg Vogel,Lakesh Kansakar,Shanshan Zhang,Slobodan Vucetic,Zheng Wang,Michael J.E. Sternberg,Mark N. Wass,Rachael P. Huntley,Maria Jesus 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 +146 more
TL;DR: The second critical assessment of functional annotation (CAFA) conducted, a timed challenge to assess computational methods that automatically assign protein function, revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies.
Journal ArticleDOI
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Yuxiang Jiang,Tal Ronnen Oron,Wyatt T. Clark,Asma R. Bankapur,Daniel D'Andrea,Rosalba Lepore,Christopher S. Funk,Indika Kahanda,Karin Verspoor,Asa Ben-Hur,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 M. Altenhoff,Nives Škunca,Christophe Dessimoz,Tunca Doğan,Kai Hakala,Suwisa Kaewphan,Farrokh Mehryary,Tapio Salakoski,Filip Ginter,Hai Fang,Ben Smithers,Matt E. 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,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 A. Lee,Jonathan G. Lees,Ian Sillitoe,Prajwal Bhat,Tamás Nepusz,Alfonso E. Romero,Rajkumar Sasidharan,Haixuan Yang,Alberto Paccanaro,Jesse Gillis,Adriana E. Sedeno-Cortes,Paul Pavlidis,Shou Feng,Juan Miguel Cejuela,Tatyana Goldberg,Tobias Hamp,Lothar Richter,Asaf Salamov,Toni Gabaldón,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. Vêncio,Malvika Sharan,Jörg Vogel,Lakesh Kansakar,Shanshan Zhang,Slobodan Vucetic,Zheng Wang,Michael J.E. Sternberg,Mark N. Wass,Rachael P. Huntley,Maria Jesus 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 +145 more
TL;DR: The second Critical Assessment of Functional Annotation (CAFA) challenge as mentioned in this paper was the first attempt to assess computational methods that automatically assign protein function. And the results of CAFA2 showed that computational function prediction is improving.
Journal ArticleDOI
The complex portal - an encyclopaedia of macromolecular complexes
Birgit H M Meldal,Oscar Forner-Martinez,Maria C. Costanzo,Jose M. Dana,Janos Demeter,Marine Dumousseau,Selina S. Dwight,Anna Gaulton,Luana Licata,Anna N. Melidoni,Sylvie Ricard-Blum,Bernd Roechert,Marek S. Skyzypek,Manu D. Tiwari,Sameer Velankar,Edith D. Wong,Henning Hermjakob,Sandra Orchard +17 more
TL;DR: The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download.