Huaiyu Mi

28 papers Journal 27Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
InterPro in 2022.
Nucleic Acids Res.
Typhaine Paysan-Lafosse, Matthias Blum, Sara Chuguransky, Tiago Grego, Beatriz Lázaro Pinto, Gustavo A. Salazar, Maxwell L. Bileschi, Peer Bork, Alan J. Bridge, Lucy J. Colwell, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman
2022 J jnl
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation.
Nucleic Acids Res.
Zhu Liu, Tremayne Mushayahama, Bryan Queme, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Paul D. Thomas, Huaiyu Mi
2021 J jnl
Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.
PLoS Comput. Biol.
George G. Vega Yon, Duncan C. Thomas, John Morrison, Huaiyu Mi, Paul D. Thomas, Paul Marjoram
2021 J jnl
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.
Nucleic Acids Res.
Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayahama, Paul D. Thomas
2021 J jnl
Reactome and the Gene Ontology: digital convergence of data resources.
Bioinform.
Benjamin M. Good, Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff, Laurent-Philippe Albou, Paul D. Thomas, Christopher J. Mungall, Judith A. Blake, Peter D'Eustachio
2021 J jnl
The InterPro protein families and domains database: 20 years on.
Nucleic Acids Res.
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasamy, Alex L. Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna J. Richardson, Gustavo A. Salazar, Lowri Williams, Peer Bork, Alan J. Bridge, Julian Gough, Daniel H. Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Christine A. Orengo, Arun Prasad Pandurangan, Catherine Rivoire, Christian J. A. Sigrist, Ian Sillitoe, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Alex Bateman, Robert D. Finn
2019 J jnl
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Res.
Alex L. Mitchell, Teresa K. Attwood, Patricia C. Babbitt, Matthias Blum, Peer Bork, Alan J. Bridge, Shoshana D. Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurelien Luciani, Fábio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Arun Prasad Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C. Potter, Matloob Qureshi, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Gustavo A. Salazar, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Siew-Yit Yong, Robert D. Finn
2019 J jnl
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.
Nucleic Acids Res.
Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D. Thomas
2019 J jnl
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.
J. Integr. Bioinform.
Adrien Rougny, Vasundra Touré, Stuart L. Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly A. Sorokin, Falk Schreiber, Augustin Luna
2017 J jnl
InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res.
Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L. Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A. Natale, Marco Necci, Gift Nuka, Christine A. Orengo, Young Mi Park, Sebastien Pesseat, Damiano Piovesan, Simon C. Potter, Neil D. Rawlings, Nicole Redaschi, Lorna J. Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian J. A. Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger G. Sutton, Narmada Thanki, Paul D. Thomas, Silvio C. E. Tosatto, Cathy H. Wu, Ioannis Xenarios, Lai-Su L. Yeh, Siew-Yit Yong, Alex L. Mitchell
2017 J jnl
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.
Nucleic Acids Res.
Huaiyu Mi, Xiaosong Huang, Anushya Muruganujan, Haiming Tang, Caitlin Mills, Diane Kang, Paul D. Thomas
2016 J jnl
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.
Database J. Biol. Databases Curation
Marc Feuermann, Pascale Gaudet, Huaiyu Mi, Suzanna E. Lewis, Paul D. Thomas
2016 J jnl
PANTHER version 10: expanded protein families and functions, and analysis tools.
Nucleic Acids Res.
Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas
2015 J jnl
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 .
J. Integr. Bioinform.
Huaiyu Mi, Falk Schreiber, Stuart L. Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly A. Sorokin, Alice Villéger
2015 J jnl
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.
J. Integr. Bioinform.
Anatoly A. Sorokin, Nicolas Le Novère, Augustin Luna, Tobias Czauderna, Emek Demir, Robin Haw, Huaiyu Mi, Stuart L. Moodie, Falk Schreiber, Alice Villéger
2015 J jnl
Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.
J. Integr. Bioinform.
Stuart L. Moodie, Nicolas Le Novère, Emek Demir, Huaiyu Mi, Alice Villéger
2015 J jnl
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res.
Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn
2014 J jnl
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.
Nucleic Acids Res.
James C. Hu, Gavin Sherlock, Deborah A. Siegele, Suzanne A. Aleksander, Catherine A. Ball, Janos Demeter, Sushanth Gouni, Timothy A. Holland, Peter D. Karp, John E. Lewis, Nathan M. Liles, Brenley K. McIntosh, Huaiyu Mi, Anushya Muruganujan, Farrell Wymore, Paul D. Thomas
2013 J jnl
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.
Nucleic Acids Res.
Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas
2012 J jnl
InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res.
Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong
2012 J jnl
Software support for SBGN maps: SBGN-ML and LibSBGN.
Bioinform.
Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber
2011 — conf
Applications of Pathway Logic Modeling to Target Identification.
Formal Modeling: Actors, Open Systems, Biological Systems
Anupama Panikkar, Merrill Knapp, Huaiyu Mi, Dave Anderson, Krishna Kodukula, Amit K. Galande, Carolyn L. Talcott
2011 J jnl
BioPAX support in CellDesigner.
Bioinform.
Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas
2010 J jnl
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.
Nucleic Acids Res.
Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas
2007 J jnl
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
Nucleic Acids Res.
Huaiyu Mi, Nan Guo, Anish Kejariwal, Paul D. Thomas
2006 J jnl
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucleic Acids Res.
Paul D. Thomas, Anish Kejariwal, Nan Guo, Huaiyu Mi, Michael J. Campbell, Anushya Muruganujan, Betty Lazareva-Ulitsky
2005 J jnl
The PANTHER database of protein families, subfamilies, functions and pathways.
Nucleic Acids Res.
Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody A. Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano, Paul D. Thomas
2003 J jnl
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.
Nucleic Acids Res.
Paul D. Thomas, Anish Kejariwal, Michael J. Campbell, Huaiyu Mi, Karen Diemer, Nan Guo, Istvan Ladunga, Betty Lazareva-Ulitsky, Anushya Muruganujan, Steven Rabkin, Jody A. Vandergriff, Olivier Doremieux