Ruth Y. Eberhardt

Publication Activity (10 Years)

Years Active: 2004-2016
Publications (10 Years): 1

Top Topics

Tensor Factorization

Protein Sequences

Protein Families

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Publications

Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44 (Database-Issue) (2016)
Eric P. Nawrocki, Sarah W. Burge, Alex Bateman, Jennifer Daub, Ruth Y. Eberhardt, Sean R. Eddy, Evan W. Floden, Paul P. Gardner, Thomas A. Jones, John G. Tate, Robert D. Finn
Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 43 (Database-Issue) (2015)
Anna Sheydina, Ruth Y. Eberhardt, Daniel J. Rigden, Yuanyuan Chang, Zhanwen Li, Christian M. Zmasek, Herbert L. Axelrod, Adam Godzik
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinform. 15 (2014)
Daniel J. Rigden, Ruth Y. Eberhardt, Harry J. Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinform. 15 (2014)
Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta
Pfam: the protein families database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Christine B. Trame, Yuanyuan Chang, Herbert L. Axelrod, Ruth Y. Eberhardt, Penelope Coggill, Marco Punta, Neil D. Rawlings
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. BMC Bioinform. 15 (2014)
Ruth Y. Eberhardt, Yuanyuan Chang, Alex Bateman, Alexey G. Murzin, Herbert L. Axelrod, William C. Hwang, L. Aravind
Filling out the structural map of the NTF2-like superfamily. BMC Bioinform. 14 (2013)
Sarah W. Burge, Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Lars Barquist, Eric P. Nawrocki, Sean R. Eddy, Paul P. Gardner, Alex Bateman
Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 41 (Database-Issue) (2013)
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013)
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013)
William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik
LUD, a new protein domain associated with lactate utilization. BMC Bioinform. 14 (2013)
Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. BMC Bioinform. 14 (2013)
Emily C. Dimmer, Rachael P. Huntley, Yasmin Alam-Faruque, Tony Sawford, Claire O'Donovan, Maria Jesus Martin, Benoit Bely, Paul Browne, Wei Mun Chan, Ruth Y. Eberhardt, Michael Gardner, Kati Laiho, Duncan Legge, Michele Magrane, Klemens Pichler, Diego Poggioli, Harminder Sehra, Andrea H. Auchincloss, Kristian B. Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Silvia Braconi-Quintaje, Lionel Breuza, Alan Bridge, Elisabeth Coudert, Anne Estreicher, Maria Livia Famiglietti, Serenella Ferro-Rojas, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Janet James, Silvia Jimenez, Florence Jungo, Guillaume Keller, Phillippe Lemercier, Damien Lieberherr, Patrick Masson, Madelaine Moinat, Ivo Pedruzzi, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Andre Stutz, Shyamala Sundaram, Michael Tognolli, Lydie Bougueleret, Ghislaine Argoud-Puy, Isabelle Cusin, Paula Duek-Roggli, Ioannis Xenarios, Rolf Apweiler
The UniProt-GO Annotation database in 2011. Nucleic Acids Res. 40 (Database-Issue) (2012)
Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn
The Pfam protein families database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman
AntiFam: a tool to help identify spurious ORFs in protein annotation. Database J. Biol. Databases Curation 2012 (2012)
Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Y. Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 36 (Database-Issue) (2008)
Tamara Kulikova, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Lawrence Bower, Paul Browne, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, Gemma Hoad, Carola Kanz, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Sheila Plaister, Siamak Sobhany, Peter Stoehr, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
EMBL Nucleotide Sequence Database in 2006. Nucleic Acids Res. 35 (Database-Issue) (2007)
Guy Cochrane, Philippe Aldebert, Nicola Althorpe, Mikael Andersson, Wendy Baker, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, Paul Browne, Alexandra van den Broek, Matias Castro, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, John Gamble, Carola Kanz, Tamara Kulikova, Charles Lee, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Michelle McHale, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Maria Pilar Garcia Pastor, Siamak Sobhany, Peter Stoehr, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
EMBL Nucleotide Sequence Database: developments in 2005. Nucleic Acids Res. 34 (Database-Issue) (2006)
Carola Kanz, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Alastair Baldwin, Kirsty Bates, Paul Browne, Alexandra van den Broek, Matias Castro, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, John Gamble, Federico Garcia Diez, Nicola Harte, Tamara Kulikova, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Siamak Sobhany, Peter Stoehr, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33 (Database-Issue) (2005)
Tamara Kulikova, Philippe Aldebert, Nicola Althorpe, Wendy Baker, Kirsty Bates, Paul Browne, Alexandra van den Broek, Guy Cochrane, Karyn Duggan, Ruth Y. Eberhardt, Nadeem Faruque, Maria Garcia-Pastor, Nicola Harte, Carola Kanz, Rasko Leinonen, Quan Lin, Vincent Lombard, Rodrigo Lopez, Renato Mancuso, Michelle McHale, Francesco Nardone, Ville Silventoinen, Peter Stoehr, Guenter Stoesser, Mary Ann Tuli, Katerina Tzouvara, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler
The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 32 (Database-Issue) (2004)