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Your search keyword '"Denise Carvalho-Silva"' showing total 20 results
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20 results on '"Denise Carvalho-Silva"'

1. DrugMechDB: A Curated Database of Drug Mechanisms

Author

Adriana Carolina Gonzalez-Cavazos, Anna Tanska, Michael Mayers, Denise Carvalho-Silva, Brindha Sridharan, Patrick A. Rewers, Umasri Sankarlal, Lakshmanan Jagannathan, and Andrew I. Su

Subjects
Science
Abstract

Abstract Computational drug repositioning methods have emerged as an attractive and effective solution to find new candidates for existing therapies, reducing the time and cost of drug development. Repositioning methods based on biomedical knowledge graphs typically offer useful supporting biological evidence. This evidence is based on reasoning chains or subgraphs that connect a drug to a disease prediction. However, there are no databases of drug mechanisms that can be used to train and evaluate such methods. Here, we introduce the Drug Mechanism Database (DrugMechDB), a manually curated database that describes drug mechanisms as paths through a knowledge graph. DrugMechDB integrates a diverse range of authoritative free-text resources to describe 4,583 drug indications with 32,249 relationships, representing 14 major biological scales. DrugMechDB can be employed as a benchmark dataset for assessing computational drug repositioning models or as a valuable resource for training such models.

Published
2023
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2. Help biocurators to maximize the reach of your data

Author

Alexander Holmes, Denise Carvalho-Silva, Zbyslaw Sondka, Madiha Ahmed, Joanna Argasinska, Rachel Lyne, Amaia Sangrador-Vegas, and Sari Ward

Subjects
Biology (General), QH301-705.5
Published
2024

3. The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research [version 1; peer review: 2 approved]

Author

David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutierrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquin Dopazo, Laura I. Furlong, Bo Gao, Leyla Garcia, 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 Leskošek, David Lloyd, Tomas Marques-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, and Christophe Béroud

Subjects
Medicine, Science
Abstract

Copy number variations (CNVs) are major causative contributors both in the genesis of genetic diseases and human neoplasias. While “High-Throughput” sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains to be developed. The aim of this white paper is to provide a guiding framework for the future contributions of ELIXIR’s recently established human CNV Community, with implications beyond human disease diagnostics and population genomics. This white paper is the direct result of a strategy meeting that took place in September 2018 in Hinxton (UK) and involved representatives of 11 ELIXIR Nodes. The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. Here, we provide suggestions on how to align these tasks within the ELIXIR Platforms strategy, and on how to frame the activities of this new ELIXIR Community in the international context.

Published
2020
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4. Ten simple rules for making training materials FAIR.

Author

Leyla Garcia, Bérénice Batut, Melissa L Burke, Mateusz Kuzak, Fotis 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, and Patricia M Palagi

Subjects
Biology (General), QH301-705.5
Abstract

Everything we do today is becoming more and more reliant on the use of computers. The field of biology is no exception; but most biologists receive little or no formal preparation for the increasingly computational aspects of their discipline. In consequence, informal training courses are often needed to plug the gaps; and the demand for such training is growing worldwide. To meet this demand, some training programs are being expanded, and new ones are being developed. Key to both scenarios is the creation of new course materials. Rather than starting from scratch, however, it's sometimes possible to repurpose materials that already exist. Yet finding suitable materials online can be difficult: They're often widely scattered across the internet or hidden in their home institutions, with no systematic way to find them. This is a common problem for all digital objects. The scientific community has attempted to address this issue by developing a set of rules (which have been called the Findable, Accessible, Interoperable and Reusable [FAIR] principles) to make such objects more findable and reusable. Here, we show how to apply these rules to help make training materials easier to find, (re)use, and adapt, for the benefit of all.

Published
2020
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7. Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics.

Author

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 0003, 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, and Ian Dunham

Published
2021
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8. Open Targets Platform: supporting systematic drug-target identification and prioritisation.

Author

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, and Ellen M. McDonagh

Published
2021
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9. Open Targets Platform: new developments and updates two years on.

Author

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, and Ian Dunham

Published
2019
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10. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Author

Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis 0001, Christoph Grabmueller, Navin Kumar, Zicheng Liu 0004, 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, and Andrew D. Yates

Published
2018
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11. Ensembl 2017.

Author

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, and Paul Flicek

Published
2017
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12. Open Targets: a platform for therapeutic target identification and validation.

Author

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, and Ian Dunham

Published
2017
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13. Ensembl Genomes 2016: more genomes, more complexity.

Author

Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis 0001, 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, and Daniel M. Staines

Published
2016
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14. Ensembl 2016.

Author

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, and Paul Flicek

Published
2016
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15. Ensembl 2015.

Author

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, and Paul Flicek

Published
2015
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16. Ensembl 2014.

Author

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 0002, 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, and Stephen M. J. Searle

Published
2014
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17. Ensembl 2013.

Author

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, and Stephen M. J. Searle

Published
2013
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18. Ensembl 2012.

Author

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 0002, 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, and Stephen M. J. Searle

Published
2012
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19. Net-based Training for Work Related Medicine (NetWoRM).

Author

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, and Katja Radon

Published
2009

20. Y Chromosome Diversity in Brazilians: Switching Perspectives from Slow to Fast Evolving Markers.

Author

Denise Carvalho-Silva, Eduardo Tarazona-Santos, Jorge Rocha, Sérgio Pena, and Fabrício Santos

Abstract

We have previously shown that the Y chromosomes of ‘white’ Brazilians have their immediate geographical origin in Europe, with low frequency of sub-Saharan African chromosomes and virtual absence of Amerindian contribution. The typing of slow evolving polymorphisms on the Y chromosome also revealed no differences between Brazilians and Portuguese, the bulk of European immigrants to Brazil, and even among Brazilians from distinct regions of Brazil, the latter being in sharp contrast with mtDNA data. In order to test if the lack of differentiation is a sex-biased and not a marker-biased phenomenon, we decided to study faster evolving Y chromosome markers in samples from Brazil and Portugal previously studied. The population structure revealed by this work confirmed that there were indeed no significant differences between Brazil and Portugal and no population differentiation within the four geographical regions of Brazil, suggesting that this phenomenon is unrelated to the nature of the markers typed. Nevertheless the fast evolving markers did uncover a higher within population diversity in Brazil than Portugal, which could be explained by the input of diverse European Y chromosomes carried by several migration waves to Brazil. Our present data highlight the significance of typing and combining Y markers that evolve according to distinct mutational paces to usefully assess the levels of diversity in a given population, and can be applied in the study of populations derived from distinct geographical origins such as the Brazilians. [ABSTRACT FROM AUTHOR]

Published
2006
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