Keck School Faculty

Huaiyu Mi, PhD
Huaiyu Mi, PhD
Associate Professor Of Research Preventive Medicine
Preventive Medicine
2001 N Soto Street, #212 Health Sciences Campus Los Angeles

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nat Genet. 2019 Sep 23. . View in PubMed

Systems Biology Graphical Notation: Process Description language Level 1 Version 20. J Integr Bioinform. 2019 Jun 13. . View in PubMed

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse Neuron. 2019 May 22. . View in PubMed

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v14. 0). Nat Protoc. 2019 Mar; 14(3):703-721. . View in PubMed

InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2019 Jan 08; 47(D1):D351-D360. . View in PubMed

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Nucleic Acids Res. 2019 Jan 08; 47(D1):D419-D426. . View in PubMed

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v14. 0). Nat Protoc. 2019 03; 14(3):703-721. . View in PubMed

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Nucleic Acids Res. 2018 Nov 08. . View in PubMed

InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2018 Nov 06. . View in PubMed

InterPro in 2017-beyond protein family and domain annotations Nucleic Acids Res. 2017 Jan 04; 45(D1):D190-D199. . View in PubMed

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Nucleic Acids Res. 2017 Jan 04; 45(D1):D183-D189. . View in PubMed

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Nucleic Acids Res. 2017 01 04; 45(D1):D183-D189. . View in PubMed

InterPro in 2017-beyond protein family and domain annotations Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. . View in PubMed

PANTHER version 10: expanded protein families and functions, and analysis tools Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42. . View in PubMed

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes Database (Oxford). 2016; 2016. . View in PubMed

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2 J Integr Bioinform. 2015 Sep 04; 12(2):264. . View in PubMed

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 12. J Integr Bioinform. 2015 Sep 04; 12(2):265. . View in PubMed

Systems Biology Graphical Notation: Process Description language Level 1 Version 13. J Integr Bioinform. 2015 Sep 04; 12(2):263. . View in PubMed

Regulation of pepc gene expression in Anabaena spPCC 7120 and its effects on cyclic electron flow around photosystem I and tolerances to environmental stresses. J Integr Plant Biol. 2015 May; 57(5):468-76. . View in PubMed

The InterPro protein families database: the classification resource after 15 years Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. . View in PubMed

Recombinant expression and functional analysis of a Chlamydomonas reinhardtii bacterial-type phosphoenolpyruvate carboxylase gene fragment Biotechnol Lett. 2014 Apr; 36(4):821-7. . View in PubMed

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. . View in PubMed

Large-scale gene function analysis with the PANTHER classification system Nat Protoc. 2013 Aug; 8(8):1551-66. . View in PubMed

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees Nucleic Acids Res. 2013 Jan; 41(Database issue):D377-86. . View in PubMed

Software support for SBGN maps: SBGN-ML and LibSBGN Bioinformatics. 2012 Aug 01; 28(15):2016-21. . View in PubMed

InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. . View in PubMed

BioPAX support in CellDesigner Bioinformatics. 2011 Dec 15; 27(24):3437-8. . View in PubMed

PharmGKB summary: dopamine receptor D2 Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. . View in PubMed

Ontologies and standards in bioscience research: for machine or for human Front Physiol. 2011; 2:5. . View in PubMed

The BioPAX community standard for pathway data sharing Nat Biotechnol. 2010 Sep; 28(9):935-42. . View in PubMed

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. . View in PubMed

Dopamine genes and nicotine dependence in treatment-seeking and community smokers Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. . View in PubMed

The Systems Biology Graphical Notation Nat Biotechnol. 2009 Aug; 27(8):735-41. . View in PubMed

A systems biology network model for genetic association studies of nicotine addiction and treatment Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. . View in PubMed

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools Methods Mol Biol. 2009; 563:123-40. . View in PubMed

Ontology annotation: mapping genomic regions to biological function Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. . View in PubMed

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res. 2007 Jan; 35(Database issue):D247-52. . View in PubMed

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W645-50. . View in PubMed

The PANTHER database of protein families, subfamilies, functions and pathways Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8. . View in PubMed

Assessment of genome-wide protein function classification for Drosophila melanogaster Genome Res. 2003 Sep; 13(9):2118-28. . View in PubMed

PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 2003 Sep; 13(9):2129-41. . View in PubMed

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification Nucleic Acids Res. 2003 Jan 01; 31(1):334-41. . View in PubMed

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