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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
CTSI Profile

Publications

  • Pathway polygenic risk scores (pPRS) for the analysis of gene-environment interaction. PLoS Genet. 2025 Aug; 21(8):e1011543.. View in PubMed
  • Red meat intake interacts with a TGF-β-pathway-based polygenic risk score to impact colorectal cancer risk: Application of a novel approach for polygenic risk score construction. medRxiv. 2025 Jun 16.. View in PubMed
  • A compendium of human gene functions derived from evolutionary modelling. Nature. 2025 Apr; 640(8057):146-154.. View in PubMed
  • InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025 Jan 06; 53(D1):D444-D456.. View in PubMed
  • Pathway Polygenic Risk Scores (pPRS) for the Analysis of Gene-environment Interaction. bioRxiv. 2024 Dec 19.. 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
  • InterPro in 2022. Nucleic Acids Res. 2023 01 06; 51(D1):D418-D427.. 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
  • PANTHER: Making genome-scale phylogenetics accessible to all. Protein Sci. 2022 01; 31(1):8-22.. 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 InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354.. 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 Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 2021 01 08; 49(D1):D325-D334.. 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
  • 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
  • SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. Neuron. 2019 07 17; 103(2):217-234.e4.. View in PubMed
  • Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J Integr Bioinform. 2019 Jun 13; 16(2).. View in PubMed
  • Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0). Nat Protoc. 2019 03; 14(3):703-721.. 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
  • InterPro in 2017-beyond protein family and domain annotations. Nucleic Acids Res. 2017 01 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 01 04; 45(D1):D183-D189.. 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: Process Description language Level 1 Version 1.3. J Integr Bioinform. 2015 Sep 04; 12(2):263.. View in PubMed
  • Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2. J Integr Bioinform. 2015 Sep 04; 12(2):265.. 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
  • The Systems Biology Graphical Notation. Nat Biotechnol. 2009 Aug; 27(8):735-41.. 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
  • 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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