38697-Huang, Kun

Kun Huang, PhD

Chair, Department of Biostatistics & Health Data Science

HITS 3000
Indianapolis, IN
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Kun Huang, PhD, leads the Precision Health Initiative Data Science and Informatics group, and is the director of the Bioinformatics and Computational Biology Core for the TREAT-AD program for Alzheimer’s therapy development. Huang also serves as associate director for data science at the IU Simon Comprehensive Cancer Center and leads the data science and informatics service for the National Cancer Institute Pediatric Cancer SPORE grant-funded research program.

Key Publications

  1.       Sun L, Zhang J, Chen W, Chen Y, Zhang X, Yang M, Xiao M, Ma F, Yao Y, Ye M, Zhang Z, Chen K, Chen F, Ren Y, Ni S, Zhang X, Yan Z, Sun Z-R, Zhou H-M, Yang H, Xie S, Haque ME, Huang K*, Yang Y*. Attenuation of epigenetic regulator SMARCA4 and ERK-ETS signaling suppresses aging-related dopaminergic degeneration. Aging Cell, 19(9): e13210, 2020. (* co-corresponding authors)
  2.        Shao W, Wang T, Sun L, Dong T, Han Z, Huang Z, Zhang J, Zhang D, Huang K. Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers. Medical Image Analysis, 65: 101795, 2020. 
  3.       Cheng J, Han Z, Mehra R, Shao W, Cheng M, Feng Q, Ni D*, Huang K*, Cheng L*, Zhang J*. Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11.2 translocation renal cell carcinoma, Nature Communications, 11(1):1778, 2020. (* co-corresponding authors) PubMed PMID: 32286325; PubMed Central PMCID: PMC7156652.
  4.         Wang T, Johnson T, Shao W, Zhang J*, Huang K*. BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes, Genome Biology, 20(1): 165, 2019. PubMed PMID: 31405383; PubMed Central PMCID: PMC6691531.
  5.         Shao W, Han Z, Cheng J, Cheng L, Wang T, Sun L, Lu Z, Zhang J, Zhang D, Huang K. Integrative analysis of pathological images and multi-dimensional genomic data for early-stage cancer prognosis, IEEE Transactions on Medical Imaging, 39(1): 99-110, 2019. PubMed PMID: 31170067.
  6.       Johnson T, Wang T, Huang Z, Yu CY, Wu Y, Han Y, Zhang Y, Huang K*, Zhang J*., LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection, Bioinformatics, 35(22): 4696-4706, 2019. PubMed PMID: 31038669; PubMed Central PMCID: PMC6853662.
  7.       Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K. Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma. EBioMedicine, 2018 Jan;27:167-175. (PMID: 29273356; PMCID: PMC5828651.)
  8.       Shi W, Xianyu A, Han Z*, Tang X, Li Z, Zhong H, Mao T, Huang K*, Shi S-H*. Ontogenetic establishment of order-specific nuclear organization in the mammalian thalamus. Accepted to Nature Neuroscience, 2017. (*co-corresponding authors)
  9.         Cheng J*, Zhang J*, Han Y, Wang X, Ye X, Meng Y, Pawani A, Han Z, Feng Q, Huang K, Integrative analysis of histopathological images and genomic data for predicting clear cell renal cell carcinoma prognosis, Cancer Research, 77(21): e91-e100, 2017. (*co-first authors)
  10.       Sultan KT, Han Z, Zhang X-J, Xianyu A, Li Z, Huang K*, Shi S-H*. Clonally Related GABAergic Interneurons Do Not Randomly Disperse But Frequently Form Local Clusters in the Forebrain. Accepted to Neuron, 2016. (* co-corresponding authors)
  11.        Xu H-T, Han Z, Gao P, He S, Li Z, Shi W, Kodish O, Shao W, Brown KN, Huang K, Shi S-H. Distinct lineage-dependent structural and functional organization of the hippocampus. Accepted to Cell, 2014.
  12.         Yu Y-C, He S, Chen S, Fu Y, Brown KN, Yao X-H, Ma J, Gao KP, Sosinsky GE, Huang K, Shi S-H. Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly, Nature, 486(7401):113-117, 2012.
  13.          Zhang J, Lu K, Xiang Y, Islam M, Kotian S, Kais Z, Lee C, Arora M, Liu H-W, Parvin JD, Huang K. Weighted frequent gene co-expression network mining to identify genes involved in genome stability, PLoS Computational Biology, 8(8): e1002656, 2012.        
  14.        Brown KN, Chen S, Han Z, Lu C-H, Tan X, Ding L, Zhang X-J, Cruz AL, Saur D, Anderson SA, Huang K, Shi S-H. Clonal production and organization of inhibitory interneurons in the neocortex, Science, 334(6055): 480-486, 2011.

Titles & Appointments

  • Chair, Department of Biostatistics & Health Data Science
  • Chair, Department of Biostatistics, School of Public Health
  • Precision Health Initiative Professor of Genomics Data Sciences
  • Professor of Biostatistics & Health Data Science
  • Professor of Medicine
  • Adjunct Professor of Medical & Molecular Genetics
  • Adjunct Professor of Pharmacology & Toxicology
  • Adjunct Professor, School of Computer Science
  • Associate Director for Data Science, IU Simon Comprehensive Cancer Center
  • Investigator, Regenstrief Institute

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