Photo of Kourosh Zarringhalam,  PhD

Kourosh Zarringhalam, PhD

University Of Massachusetts - Boston

University Of Massachusetts - Boston
Phone: (617) 287-7486


kourosh.zarringhalam@umb.edu

Kourosh Zarringhalam, PhD

University Of Massachusetts - Boston

EDUCATIONAL TITLES

  • Assistant Professor, College of Science and Math, University Of Massachusetts - Boston

DF/HCC PROGRAM AFFILIATION

Research Abstract

I am interested in application of mathematics and computational methods for modeling biological processes. Current projects of interest include, post-transcriptional regulation of tumor suppressor genes via competing endogenous RNAs (ceRNAs), machine learning methods for biomarker discovery, and causal reasoning on biological networks.

Publications

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  • Han D, Owiredu JN, Healy BM, Li M, Labaf M, Steinfeld JS, Patalano S, Gao S, Liu M, Macoska JA, Zarringhalam K, Siegfried KR, Yuan X, Rebbeck TR, Cai C. Susceptibility-associated genetic variation in NEDD9 contributes to prostate cancer initiation and progression. Cancer Res 2021. PubMed
  • Noorbakhsh J, Farahmand S, Foroughi Pour A, Namburi S, Caruana D, Rimm D, Soltanieh-Ha M, Zarringhalam K, Chuang JH. Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images. Nat Commun 2021; 11:6367. PubMed
  • Farahmand S, O'Connor C, Macoska JA, Zarringhalam K. Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Nucleic Acids Res 2019; 47:11563-11573. PubMed
  • Vajdi A, Zarringhalam K, Haspel N. Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores. Bioinformatics 2019. PubMed
  • Inaba S, Fakhry CT, Kulkarni RV, Zarringhalam K. A Free Energy Based Approach for Distance Metric Learning. KDD 2021; 2019:5-13. PubMed
  • Kumar N, Zarringhalam K, Kulkarni RV. Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit. Biophys J 2018; 114:2530-2539. PubMed
  • Zarringhalam K, Degras D, Brockel C, Ziemek D. Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes. Sci Rep 2018; 8:1237. PubMed
  • Kang T, Ding W, Zhang L, Ziemek D, Zarringhalam K. A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data. BMC Bioinformatics 2017; 18:565. PubMed
  • Zarringhalam K, Tay Y, Kulkarni P, Bester AC, Pandolfi PP, Kulkarni RV. Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach. Sci Rep 2017; 7:7755. PubMed
  • Kumar N, Jia T, Zarringhalam K, Kulkarni RV. Frequency modulation of stochastic gene expression bursts by strongly interacting small RNAs. Phys Rev E 2016; 94:042419. PubMed
  • Fakhry CT, Choudhary P, Gutteridge A, Sidders B, Chen P, Ziemek D, Zarringhalam K. Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinformatics 2016; 17:318. PubMed
  • Zarringhalam K, Enayetallah A, Reddy P, Ziemek D. Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. Bioinformatics 2014; 30:i69-77. PubMed
  • Zarringhalam K, Enayetallah A, Gutteridge A, Sidders B, Ziemek D. Molecular causes of transcriptional response: a Bayesian prior knowledge approach. Bioinformatics 2013; 29:3167-73. PubMed
  • Zarringhalam K, Ka M, Kook YH, Terranova JI, Suh Y, King OD, Um M. An open system for automatic home-cage behavioral analysis and its application to male and female mouse models of Huntington's disease. Behav Brain Res 2012; 229:216-25. PubMed
  • Zhang L, Díaz-Díaz N, Zarringhalam K, Hermansson M, Somerharju P, Chuang J. Dynamics of the ethanolamine glycerophospholipid remodeling network. PLoS ONE 2012; 7:e50858. PubMed
  • Zarringhalam K, Zhang L, Kiebish MA, Yang K, Han X, Gross RW, Chuang J. Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition. PLoS ONE 2012; 7:e37293. PubMed
  • Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P. Integrating chemical footprinting data into RNA secondary structure prediction. PLoS ONE 2012; 7:e45160. PubMed
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