Department of Mathematics
Professional Interests: Mathematical biology, methods of applied mathematics, including analysis, dynamics and signal processing.
Recent Publications:
| 2023 | [PMID36696650] A rising tide of parasite transcriptomics propels pathogen biology . PLoS Biol. 2023 Jan 25;21(1):e3001997. --- Duraisingh MT, Gubbels MJ, Zarringhalam K. |
| [PMID36909484] Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases . Res Sq [Preprint]. 2023 Feb 28:rs.3.rs-2553721. --- Elsworth B, Keroack C, Rezvani Y, Paul A, Barazorda K, Tennessen J, Sack S, Moreira C, Gubbels MJ, Meyers M, Zarringhalam K, Duraisingh M. | |
| 2022 | [PMID36408179] Increased AR expression in castration-resistant prostate cancer rapidly induces AR signaling reprogramming with the collaboration of EZH2 . Front Oncol. 2022 Nov 3;12:1021845. --- Labaf M, Li M, Ting L, Karno B, Zhang S, Gao S, Patalano S, Macoska JA, Zarringhalam K, Han D, Cai C. |
| [PMID36137068] Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles . PLoS Biol. 2022 Sep 22;20(9):e3001816. --- Rezvani Y, Keroack CD, Elsworth B, Arriojas A, Gubbels MJ, Duraisingh MT, Zarringhalam K. | |
| [PMID34493825] Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer. . Mod Pathol. 2022 Jan;35(1):44-51. --- Farahmand S, Fernandez AI, Ahmed FS, Rimm DL, Chuang JH, Reisenbichler E, Zarringhalam K. | |
| [PMID36555635] High-Resolution Small RNAs Landscape Provides Insights into Alkane Adaptation in the Marine Alkane-Degrader Alcanivorax dieselolei B-5 . Int J Mol Sci. 2022 Dec 15;23(24):15995. --- Wei G, Li S, Ye S, Wang Z, Zarringhalam K, He J, Wang W, Shao Z. | |
| 2021 | [PMID33632899] Susceptibility-Associated Genetic Variation in NEDD9 Contributes to Prostate Cancer Initiation and Progression . Cancer Res. 2021 Jul 15;81(14):3766-3776. --- 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. |
| [PMID34874774] The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming . mSystems. 2021 Dec 21;6(6):e0119621. --- Primo VA Jr, Rezvani Y, Farrell A, Murphy CQ, Lou J, Vajdi A, Marth GT, Zarringhalam K, Gubbels MJ. | |
| [PMID33912479] The Modular Circuitry of Apicomplexan Cell Division Plasticity . Front Cell Infect Microbiol. 2021 Apr 12;11:670049. --- Gubbels MJ, Coppens I, Zarringhalam K, Duraisingh MT, Engelberg K. | |
| [PMID34849795] Vitamin A deficiency affects gene expression in the Drosophila melanogaster head . G3 (Bethesda). 2021 Oct 19;11(11):jkab297. --- Dewett D, Labaf M, Lam-Kamath K, Zarringhalam K, Rister J. | |
| 2020 | [PMID33311458] Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images. . Nat Commun. 2020 Dec 11;11(1):6367.. --- Noorbakhsh J, Farahmand S, Foroughi Pour A, Namburi S, Caruana D, Rimm D, Soltanieh-Ha M, Zarringhalam K, Chuang JH. |
| [PMID31621841] Patch-DCA: improved protein interface prediction by utilizing structural information and clustering DCA scores . Bioinformatics. 2020 Mar 1;36(5):1460-1467. --- Vajdi A, Zarringhalam K, Haspel N. | |
| [PMID31857203] A text mining system for extracting mode of regulation of transcription factor-gene regulatory interaction . J Biomed Inform. 2020 Feb;102:103353. --- Farahmand S, Riley T, Zarringhalam K. | |
| 2019 | [PMID33708457] A Free Energy Based Approach for Distance Metric Learning . KDD. 2019 Jul;2019:5-13. --- Inaba S, Fakhry CT, Kulkarni RV, Zarringhalam K. |
| [PMID31701125] Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators . Nucleic Acids Res. 2019 Dec 16;47(22):11563-11573. --- Farahmand S, O'Connor C, Macoska JA, Zarringhalam K. | |
| 2018 | [PMID29352257] Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes . Sci Rep. 2018 Jan 19;8(1):1237. --- Zarringhalam K, Degras D, Brockel C, Ziemek D. |
| [PMID29484586] Bioinformatic Approach for Prediction of CsrA/RsmA-Regulating Small RNAs in Bacteria . Methods Mol Biol. 2018;1737:47-56. --- Fakhry CT, Zarringhalam K, Kulkarni RV. | |
| [PMID29874604] Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit . Biophys J. 2018 Jun 5;114(11):2530-2539. --- Kumar N, Zarringhalam K, Kulkarni RV. | |
| 2017 | [PMID29258445] A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data . BMC Bioinformatics. 2017 Dec 19;18(1):565. --- Kang T, Ding W, Zhang L, Ziemek D, Zarringhalam K. |
| [PMID28798471] Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: A probabilistic approach . Sci Rep. 2017 Aug 10;7(1):7755. --- Zarringhalam K, Tay Y, Kulkarni P, Bester AC, Pandolfi PP, Kulkarni RV. | |
| [PMID28830349] Prediction of bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach . BMC Genomics. 2017 Aug 22;18(1):645. --- Fakhry CT, Kulkarni P, Chen P, Kulkarni R, Zarringhalam K. | |
| 2016 | [PMID27841647] Frequency modulation of stochastic gene expression bursts by strongly interacting small RNAs . Phys Rev E. 2016 Oct;94(4-1):042419. --- Kumar N, Jia T, Zarringhalam K, Kulkarni RV. |
| [PMID27553428] Pressure dependency of localization degree in heavy fermion CeIn3: A density functional theory analysis . Sci Rep. 2016 Aug 24;6:31734. --- Yazdani-Kachoei M, Jalali-Asadabadi S, Ahmad I, Zarringhalam K. | |
| [PMID27553489] Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks . BMC Bioinformatics. 2016 Aug 24;17(1):318. --- Fakhry CT, Choudhary P, Gutteridge A, Sidders B, Chen P, Ziemek D, Zarringhalam K. | |
| 2014 | [PMID24932007] Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks . Bioinformatics. 2014 Jun 15;30(12):i69-77. --- Zarringhalam K, Enayetallah A, Reddy P, Ziemek D. |
| 2012 | [PMID22266926] 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 Apr 1;229(1):216-25. --- Zarringhalam K, Ka M, Kook YH, Terranova JI, Suh Y, King OD, Um M. |
| [PMID22662143] Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition . PLoS One. 2012;7(5):e37293. --- Zarringhalam K, Zhang L, Kiebish MA, Yang K, Han X, Gross RW, Chuang J. | |
| [PMID23251394] Dynamics of the ethanolamine glycerophospholipid remodeling network . PLoS One. 2012;7(12):e50858. --- Zhang L, Díaz-Díaz N, Zarringhalam K, Hermansson M, Somerharju P, Chuang J. | |
| [PMID23091593] Integrating chemical footprinting data into RNA secondary structure prediction . PLoS One. 2012;7(10):e45160. --- Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P. | |
| 2011 | [MR2858914] Sequential adaptive compressed sampling via Huffman codes . Sampl. Theory Signal Image Process. 10 (2011), no. 3, 231--254. --- Aldroubi, Akram ; Wang, Haichao ; Zarringhalam, Kourosh |
| 2008 | [MR2392554] Generating an adaptive multiresolution image analysis with compact cupolets . Nonlinear Dynam. 52 (2008), no. 1-2, 51--70. --- Zarringhalam, Kourosh ; Short, Kevin M. |
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Department of Mathematics University of Massachusetts Boston Phone: 617-287-6460; Fax: 617-287-6433 Information: math@umb.edu |
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