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Denise Carvalho-Silva
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Journal Articles
- 2021
- [j16]David Ochoa
, Andrew Hercules
, Miguel Carmona
, Daniel Suveges, Asier Gonzalez-Uriarte, Cinzia Malangone, Alfredo Miranda, Luca Fumis, Denise Carvalho-Silva, Michaela Spitzer, Jarrod Baker, Javier Ferrer, Arwa Bin Raies
, Olesya Razuvayevskaya, Adam Faulconbridge, Eirini Petsalaki, Prudence Mutowo-Meullenet, Sandra Machlitt-Northen, Gareth Peat, Elaine McAuley, Chuang Kee Ong, Edward Mountjoy
, Maya Ghoussaini, Andrea Pierleoni, Eliseo Papa, Miguel Pignatelli, Gautier Koscielny, Mohd Anisul Karim, Jeremy Schwartzentruber
, David G. Hulcoop, Ian Dunham
, Ellen M. McDonagh
:
Open Targets Platform: supporting systematic drug-target identification and prioritisation. Nucleic Acids Res. 49(Database-Issue): D1302-D1310 (2021) - [j15]Maya Ghoussaini, Edward Mountjoy
, Miguel Carmona
, Gareth Peat, Ellen M. Schmidt, Andrew Hercules
, Luca Fumis, Alfredo Miranda, Denise Carvalho-Silva, Annalisa Buniello
, Tony Burdett
, James D. Hayhurst
, Jarrod Baker, Javier Ferrer, Asier Gonzalez-Uriarte, Simon Jupp, Mohd Anisul Karim, Gautier Koscielny, Sandra Machlitt-Northen, Cinzia Malangone, Zoë May Pendlington, Paola Roncaglia, Daniel Suveges, Daniel Wright, Olga Vrousgou, Eliseo Papa, Helen E. Parkinson
, Jacqueline A. L. MacArthur, John A. Todd, Jeffrey C. Barrett, Jeremy Schwartzentruber
, David G. Hulcoop, David Ochoa
, Ellen M. McDonagh
, Ian Dunham
:
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. Nucleic Acids Res. 49(Database-Issue): D1311-D1320 (2021) - 2020
- [j14]Leyla J. García
, Bérénice Batut
, Melissa L. Burke
, Mateusz Kuzak
, Fotis E. Psomopoulos
, Ricardo Arcila
, Teresa K. Attwood
, Niall Beard
, Denise Carvalho-Silva
, Alexandros C. Dimopoulos
, Victoria Dominguez Del Angel
, Michel Dumontier
, Kim T. Gurwitz
, Roland Krause
, Peter McQuilton
, Loredana Le Pera
, Sarah L. Morgan
, Päivi Rauste
, Allegra Via, Pascal Kahlem, Gabriella Rustici
, Celia W. G. van Gelder
, Patricia M. Palagi
:
Ten simple rules for making training materials FAIR. PLoS Comput. Biol. 16(5) (2020) - 2019
- [j13]Denise Carvalho-Silva, Andrea Pierleoni, Miguel Pignatelli, Chuang Kee Ong
, Luca Fumis
, Nikiforos Karamanis
, Miguel Carmona
, Adam Faulconbridge
, Andrew Hercules
, Elaine McAuley, Alfredo Miranda, Gareth Peat
, Michaela Spitzer
, Jeffrey Barrett, David G. Hulcoop
, Eliseo Papa, Gautier Koscielny, Ian Dunham
:
Open Targets Platform: new developments and updates two years on. Nucleic Acids Res. 47(Database-Issue): D1056-D1065 (2019) - 2018
- [j12]Paul Julian Kersey
, James E. Allen
, Alexis Allot, Matthieu Barba
, Sanjay Boddu
, Bruce J. Bolt
, Denise Carvalho-Silva, Mikkel B. Christensen
, Paul Davis
, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel
, Benjamin Moore
, Mark D. McDowall
, Uma Maheswari
, Guy Naamati
, Victoria Newman, Chuang Kee Ong
, Michael Paulini
, Helder Pedro
, Emily Perry
, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor
, Alessandro Vullo
, Gareth Williams, Amonida Zadissa
, Andrew Olson, Joshua C. Stein
, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani
, Simon C. Potter
, Robert D. Finn
, Martin Urban
, Kim E. Hammond-Kosack
, Dan M. Bolser
, Nishadi De Silva
, Kevin L. Howe
, Nicholas Langridge
, Gareth Maslen
, Daniel Michael Staines
, Andrew D. Yates
:
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 46(Database-Issue): D802-D808 (2018) - [j11]Denise Carvalho-Silva
, Leyla J. García
, Sarah L. Morgan
, Cath Brooksbank
, Ian Dunham
:
Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars. PLoS Comput. Biol. 14(11) (2018) - [j10]Aleksandra Tarkowska
, Denise Carvalho-Silva
, Charles E. Cook
, Edd Turner
, Robert D. Finn
, Andrew D. Yates
:
Eleven quick tips to build a usable REST API for life sciences. PLoS Comput. Biol. 14(12) (2018) - 2017
- [j9]Bronwen L. Aken
, Premanand Achuthan
, Wasiu A. Akanni
, M. Ridwan Amode, Friederike Bernsdorff
, Jyothish Bhai
, Konstantinos Billis
, Denise Carvalho-Silva, Carla A. Cummins
, Peter Clapham, Laurent Gil, Carlos García-Girón
, Leo Gordon, Thibaut Hourlier
, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann
, Stephen Keenan
, Matthew R. Laird
, Ilias Lavidas
, Thomas Maurel, William M. McLaren, Benjamin Moore
, Daniel N. Murphy
, Rishi Nag
, Victoria Newman, Michael Nuhn
, Chuang Kee Ong
, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron R. Taylor, Anja Thormann, Alessandro Vullo
, Brandon Walts, Steven P. Wilder
, Amonida Zadissa
, Myrto Kostadima, Fergal J. Martin
, Matthieu Muffato
, Emily Perry
, Magali Ruffier
, Daniel M. Staines
, Stephen J. Trevanion
, Fiona Cunningham
, Andrew D. Yates
, Daniel R. Zerbino
, Paul Flicek
:
Ensembl 2017. Nucleic Acids Res. 45(Database-Issue): D635-D642 (2017) - [j8]Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham
, Luca Fumis
, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis
, Michael Maguire, Eliseo Papa
, Andrea Pierleoni, Miguel Pignatelli
, Theo Platt, Francis Rowland
, Priyanka Wankar, A. Patrícia Bento, Tony Burdett
, Antonio Fabregat
, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González
, Henning Hermjakob
, Anne Hersey, Steven Jupe
, Senay Kafkas, Maria Keays
, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños
, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes
, Claire O'Donovan
, Irene Papatheodorou
, Helen E. Parkinson
, Barbara Palka
, Justin E. Paschall, Robert Petryszak
, Naruemon Pratanwanich
, Sirarat Sarntivijai
, Gary Saunders
, Konstantinos Sidiropoulos
, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang
, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham:
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017) - 2016
- [j7]Paul Julian Kersey
, James E. Allen
, Irina M. Armean
, Sanjay Boddu
, Bruce J. Bolt
, Denise Carvalho-Silva, Mikkel B. Christensen
, Paul Davis
, Lee J. Falin
, Christoph Grabmueller, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge
, Ernesto Lowy-Gallego
, Mark D. McDowall, Uma Maheswari
, Michael Nuhn, Chuang Kee Ong
, Bert Overduin, Michael Paulini, Helder Pedro
, Emily Perry
, Giulietta Spudich, Electra Tapanari
, Brandon Walts, Gareth Williams, Marcela K. Tello-Ruiz, Joshua C. Stein
, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe
, Eugene Kulesha
, Daniel Lawson
, Gareth Maslen
, Daniel M. Staines:
Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 44(Database-Issue): 574-580 (2016) - [j6]Andrew D. Yates, Wasiu A. Akanni
, M. Ridwan Amode, Daniel Barrell
, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan
, Ilias Lavidas, Fergal J. Martin
, Thomas Maurel
, William M. McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa
, Ewan Birney, Jennifer L. Harrow
, Matthieu Muffato
, Emily Perry
, Magali Ruffier, Giulietta Spudich, Stephen J. Trevanion, Fiona Cunningham
, Bronwen L. Aken, Daniel R. Zerbino
, Paul Flicek:
Ensembl 2016. Nucleic Acids Res. 44(Database-Issue): 710-716 (2016) - 2015
- [j5]Fiona Cunningham
, M. Ridwan Amode, Daniel Barrell
, Kathryn Beal, Konstantinos Billis
, Simon Brent, Denise Carvalho-Silva
, Peter Clapham, Guy Coates
, Stephen Fitzgerald, Laurent Gil
, Carlos García-Girón
, Leo Gordon, Thibaut Hourlier
, Sarah E. Hunt
, Sophie H. Janacek
, Nathan Johnson, Thomas Juettemann
, Andreas K. Kähäri
, Stephen Keenan
, Fergal J. Martin
, Thomas Maurel
, William M. McLaren
, Daniel N. Murphy
, Rishi Nag
, Bert Overduin, Anne Parker, Mateus Patricio
, Emily Perry
, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard
, Kieron R. Taylor
, Anja Thormann
, Alessandro Vullo
, Steven P. Wilder
, Amonida Zadissa
, Bronwen L. Aken
, Ewan Birney
, Jennifer L. Harrow
, Rhoda Kinsella, Matthieu Muffato
, Magali Ruffier
, Stephen M. J. Searle, Giulietta Spudich, Stephen J. Trevanion
, Andy Yates
, Daniel R. Zerbino
, Paul Flicek
:
Ensembl 2015. Nucleic Acids Res. 43(Database-Issue): 662-669 (2015) - 2014
- [j4]Paul Flicek
, M. Ridwan Amode, Daniel Barrell
, Kathryn Beal, Konstantinos Billis
, Simon Brent, Denise Carvalho-Silva
, Peter Clapham, Guy Coates
, Stephen Fitzgerald, Laurent Gil
, Carlos García-Girón
, Leo Gordon, Thibaut Hourlier
, Sarah E. Hunt
, Nathan Johnson, Thomas Juettemann
, Andreas Kähäri
, Stephen Keenan
, Eugene Kulesha
, Fergal J. Martin
, Thomas Maurel
, William M. McLaren
, Daniel N. Murphy
, Rishi Nag
, Bert Overduin, Miguel Pignatelli, Bethan Pritchard
, Emily Pritchard
, Harpreet Singh Riat, Magali Ruffier
, Daniel Sheppard
, Kieron R. Taylor
, Anja Thormann
, Stephen J. Trevanion
, Alessandro Vullo
, Steven P. Wilder, Mark Wilson, Amonida Zadissa
, Bronwen L. Aken
, Ewan Birney
, Fiona Cunningham
, Jennifer L. Harrow
, Javier Herrero
, Tim J. P. Hubbard, Rhoda Kinsella, Matthieu Muffato
, Anne Parker, Giulietta Spudich, Andy Yates
, Daniel R. Zerbino, Stephen M. J. Searle:
Ensembl 2014. Nucleic Acids Res. 42(Database-Issue): 749-755 (2014) - 2013
- [j3]Paul Flicek
, Ikhlak Ahmed
, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates
, Susan Fairley
, Stephen Fitzgerald, Laurent Gil
, Carlos García-Girón
, Leo Gordon, Thibaut Hourlier
, Sarah E. Hunt
, Thomas Juettemann
, Andreas Kähäri
, Stephen Keenan
, Monika Komorowska, Eugene Kulesha
, Ian Longden, Thomas Maurel
, William M. McLaren
, Matthieu Muffato
, Rishi Nag
, Bert Overduin, Miguel Pignatelli, Bethan Pritchard
, Emily Pritchard
, Harpreet Singh Riat, Graham R. S. Ritchie
, Magali Ruffier
, Michael Schuster
, Daniel Sheppard
, Daniel Sobral, Kieron R. Taylor
, Anja Thormann
, Stephen J. Trevanion
, Simon White
, Steven P. Wilder
, Bronwen L. Aken
, Ewan Birney
, Fiona Cunningham
, Ian Dunham
, Jennifer L. Harrow, Javier Herrero
, Tim J. P. Hubbard, Nathan Johnson
, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates
, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2013. Nucleic Acids Res. 41(Database-Issue): 48-55 (2013) - 2012
- [j2]Paul Flicek
, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates
, Susan Fairley
, Stephen Fitzgerald, Laurent Gil
, Leo Gordon, Maurice Hendrix, Thibaut Hourlier
, Nathan Johnson
, Andreas Kähäri
, Damian Keefe, Stephen Keenan
, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha
, Pontus Larsson
, Ian Longden, William M. McLaren
, Matthieu Muffato
, Bert Overduin, Miguel Pignatelli, Bethan Pritchard
, Harpreet Singh Riat, Graham R. S. Ritchie
, Magali Ruffier
, Michael Schuster
, Daniel Sobral, Y. Amy Tang
, Kieron R. Taylor
, Stephen J. Trevanion
, Jana Vandrovcova, Simon White
, Mark Wilson, Steven P. Wilder
, Bronwen L. Aken
, Ewan Birney
, Fiona Cunningham
, Ian Dunham
, Richard Durbin
, Xosé M. Fernández-Suárez, Jennifer L. Harrow, Javier Herrero
, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates
, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2012. Nucleic Acids Res. 40(Database-Issue): 84-90 (2012) - 2009
- [j1]Laura Wengenroth, Maria Julia Calvo, Alain Cantineau, Denise Carvalho-Silva, Inga Hege, Veronica Herrera, Monique Isler, Stefanie Kolb, Tiina Lehtonen, Begona Martinez-Jarreta, Eduard Monso, Elena Ana Pauncu, Paul Smits, Arun Dev Vellore, Katja Radon:
Net-based Training for Work Related Medicine (NetWoRM). Bio Algorithms Med Syst. 5(9): 101 (2009)
Informal and Other Publications
- 2020
- [i1]David Salgado
, Irina M. Armean
, Michael Baudis
, Sergi Beltran
, Salvador Capella-Gutiérrez
, Denise Carvalho-Silva
, Victoria Dominguez Del Angel
, Joaquín Dopazo
, Laura I. Furlong
, Bo Gao
, Leyla Jael García Castro
, Dietlind Gerloff, Ivo Gut
, Attila Gyenesei, Nina Habermann, John M. Hancock
, Marc Hanauer, Eivind Hovig
, Lennart F. Johansson, Thomas Keane, Jan Korbel, Katharina B. Lauer
, Steve Laurie, Brane Leskosek, David Lloyd
, Tomàs Marquès-Bonet, Hailiang Mei, Katalin Monostory, Janet Piñero, Krzysztof Poterlowicz
, Ana Rath, Pubudu Samarakoon, Ferran Sanz
, Gary Saunders
, Daoud Sie, Morris A. Swertz
, Kirill Tsukanov
, Alfonso Valencia, Marko Vidak, Cristina Yenyxe González, Bauke Ylstra
, Christophe Béroud:
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. F1000Research 9: 1229 (2020)
Coauthor Index
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