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Huaiyu Mi, PhD

Associate Professor of Research Population and Public Health Sciences

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Phone +1 323 442 7994
Email huaiyumi@usc.edu
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Publications

  • InterPro in 2022 Nucleic Acids Res. 2023 01 06; 51(D1):D418-D427. . View in PubMed
  • The Gene Ontology knowledgebase in 2023 Genetics. 2023 05 04; 224(1). . View in PubMed
  • PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships NPJ Syst Biol Appl. 2023 04 03; 9(1):9. . View in PubMed
  • PANTHER: Making genome-scale phylogenetics accessible to all Protein Sci. 2022 01; 31(1):8-22. . View in PubMed
  • Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation Nucleic Acids Res. 2022 07 05; 50(W1):W57-W65. . View in PubMed
  • Reactome and the Gene Ontology: digital convergence of data resources Bioinformatics. 2021 Oct 11; 37(19):3343-3348. . View in PubMed
  • Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees PLoS Comput Biol. 2021 02; 17(2):e1007948. . View in PubMed
  • The Gene Ontology resource: enriching a GOld mine Nucleic Acids Res. 2021 01 08; 49(D1):D325-D334. . View in PubMed
  • PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API Nucleic Acids Res. 2021 01 08; 49(D1):D394-D403. . View in PubMed
  • The InterPro protein families and domains database: 20 years on Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354. . View in PubMed
  • PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference Plant Direct. 2020 Dec; 4(12):e00293. . View in PubMed
  • PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence PLoS One. 2020; 15(12):e0243791. . View in PubMed
  • Systems Biology Graphical Notation: Process Description language Level 1 Version 20. J Integr Bioinform. 2019 Jun 13; 16(2). . View in PubMed
  • Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nat Genet. 2019 10; 51(10):1429-1433. . 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
  • SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the SynapseNeuron. 2019 07 17; 103(2):217-234. e4. . View in PubMed
  • InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2019 01 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 01 08; 47(D1):D419-D426. . View in PubMed
  • Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Stand Genomic Sci. 2018; 13:17. . 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
  • The InterPro protein families database: the classification resource after 15 years Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. . 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
  • Gene Ontology annotations and resources Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. . View in PubMed
  • Software support for SBGN maps: SBGN-ML and LibSBGN Bioinformatics. 2012 Aug 01; 28(15):2016-21. . View in PubMed
  • A mutation of OSOTP 51 leads to impairment of photosystem I complex assembly and serious photo-damage in rice J Integr Plant Biol. 2012 Feb; 54(2):87-98. . 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
  • [Construction of the dioxin bioassay method based on the clonal expressed aryl hydrocarbon receptor system] Zhonghua Yu Fang Yi Xue Za Zhi. 2009 Aug; 43(8):705-9. . 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
  • Effects of zebra leaf 1–a new variegation mutation–on chloroplast development in rice Fen Zi Xi Bao Sheng Wu Xue Bao. 2008 Oct; 41(5):417-22. . 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
  • PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 2003 Sep; 13(9):2129-41. . View in PubMed
  • Assessment of genome-wide protein function classification for Drosophila melanogaster Genome Res. 2003 Sep; 13(9):2118-28. . View in PubMed
  • [Separation of hydrophobic NAD(P)H dehydrogenase subcomplexes from cyanobacterium Synechocystis PCC6803] Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003 Aug; 35(8):723-7. . 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
  • Distribution of rSlo Ca2+-activated K+ channels in rat astrocyte perivascular endfeet Brain Res. 2002 Nov 29; 956(2):183-93. . View in PubMed
  • Induction of astrocyte differentiation by endothelial cells J Neurosci. 2001 Mar 01; 21(5):1538-47. . View in PubMed
  • The sequence of the human genome Science. 2001 02 16; 291(5507):1304-51. . View in PubMed
  • Identification and localization of Ca(2+)-activated K+ channels in rat sciatic nerve Glia. 1999 Apr; 26(2):166-75. . View in PubMed
  • Purification and characterization of astrocyte precursor cells in the developing rat optic nerve J Neurosci. 1999 Feb 01; 19(3):1049-61. . View in PubMed
  • The Involvement of Plastoquinone in the Pyocyanine-mediated Cyclic Electron Transport around Photosystem I Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 1997; 29(6):579-584. . View in PubMed
  • Inwardly rectifying K+ channels that may participate in K+ buffering are localized in microvilli of Schwann cells J Neurosci. 1996 Apr 15; 16(8):2421-9. . View in PubMed
  • Differential distribution of closely related potassium channels in rat Schwann cells J Neurosci. 1995 May; 15(5 Pt 2):3761-74. . View in PubMed

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