Huaiyu Mi

发表

Systems Biology Graphical Notation: Activity Flow language Level 1

Nicolas Le Novère, Falk Schreiber, Huaiyu Mi, 2009 .

Automation of gene function prediction through modeling human curators' decisions in GO phylogenetic annotation project

Huaiyu Mi, Haiming Tang, Paul D Thomas, 2018, 1802.07204.

BioPAX support in CellDesigner

Yukiko Matsuoka, Hiroaki Kitano, Anushya Muruganujan, 2011, Bioinform..

Systems Biology Graphical Notation: Entity Relationship language Level 1

Nicolas Le Novère, Falk Schreiber, Huaiyu Mi, 2010 .

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

Nan Guo, Huaiyu Mi, Paul D. Thomas, 2006, Nucleic Acids Res..

Systems Biology Graphical Notation: Process Description language Level 1

Nicolas Le Novère, Emek Demir, Huaiyu Mi, 2009 .

Applications of Pathway Logic Modeling to Target Identification

Carolyn L. Talcott, Merrill Knapp, Huaiyu Mi, 2011, Formal Modeling: Actors, Open Systems, Biological Systems.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Nicolas Le Novère, Falk Schreiber, Emek Demir, 2015, Journal of integrative bioinformatics.

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

Anushya Muruganujan, Huaiyu Mi, Xiaosong Huang, 2019, Nature Protocols.

Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)

Nicolas Le Novère, Emek Demir, Huaiyu Mi, 2011 .

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2018, Nucleic Acids Res..

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Nicolas Le Novère, Falk Schreiber, Emek Demir, 2015, J. Integr. Bioinform..

Software support for SBGN maps: SBGN-ML and LibSBGN

Yukiko Matsuoka, Hiroaki Kitano, Nicolas Le Novère, 2012, Bioinform..

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

Nicolas Le Novère, Emek Demir, Huaiyu Mi, 2011, J. Integr. Bioinform..

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Falk Schreiber, Emek Demir, Augustin Luna, 2015, Journal of integrative bioinformatics.

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Ugur Dogrusoz, Andreas Dräger, Emek Demir, 2019, J. Integr. Bioinform..

Ontologies and Standards in Bioscience Research: For Machine or for Human

Huaiyu Mi, Paul D. Thomas, P. Thomas, 2010, Front. Physio..

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Chris J. Myers, Carole Goble, Dagmar Waltemath, 2011, Standards in Genomic Sciences.

Systems Biology Graphical Notation: Process Diagram Level 1 Notes on Typographical Conventions

Yukiko Matsuoka, Hiroaki Kitano, Nicolas Le Novère, 2008 .

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2012, Nucleic Acids Res..

PANTHER version 10: expanded protein families and functions, and analysis tools

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2015, Nucleic Acids Res..

BDQC: a general-purpose analytics tool for domain-blind validation of Big Data

Arthur W. Toga, Anushya Muruganujan, Carl Kesselman, 2018, bioRxiv.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Robert D. Finn, 2018, Nucleic Acids Res..

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

Anushya Muruganujan, Suzanna Lewis, Qing Dong, 2009, Nucleic Acids Res..

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Anushya Muruganujan, Peter D. Karp, Deborah A. Siegele, 2013, Nucleic Acids Res..

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Suzanna Lewis, Huaiyu Mi, Paul D. Thomas, 2016, Database J. Biol. Databases Curation.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2016, Nucleic Acids Res..

InterPro in 2011: new developments in the family and domain prediction database

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

Reactome and the Gene Ontology: digital convergence of data resources

Kimberly Van Auken, Judith A. Blake, Benjamin M. Good, 2021, Bioinform..

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2020, Nucleic Acids Res..

The Gene Ontology resource: enriching a GOld mine

Anushya Muruganujan, Cathy H. Wu, Alex Bateman, 2020, Nucleic Acids Res..

Erratum: The BioPAX community standard for pathway data sharing (Nat. Biotechnol. (2010) 28 (935-942)

Kei-Hoi Cheung, Frank Schacherer, Edgar Wingender, 2010 .

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Benjamin M. Good, David Osumi-Sutherland, Seth Carbon, 2019, Nature Genetics.

SBGN Activity Flow Update

Huaiyu Mi, 2011, Nature Precedings.

Ontology annotation: mapping genomic regions to biological function.

Huaiyu Mi, Paul D Thomas, Suzanna Lewis, 2007, Current opinion in chemical biology.

GOTaxon: Representing the evolution of biological functions in the Gene Ontology

Huaiyu Mi, Haiming Tang, Paul D Thomas, 2018, 1802.06004.

The BioPAX community standard for pathway data sharing (Nature Biotechnology (2010) 28, (935-942))

Kei-Hoi Cheung, Gary D. Bader, Frank Schacherer, 2012 .

Assessment of genome-wide protein function classification for Drosophila melanogaster.

Michael Ashburner, Huaiyu Mi, William H. Majoros, 2003, Genome research.