Car

Publications

  1. Heterogeneous responses to high-dose testosterone in castration-resistant prostate cancer tumors with mixed Rb-proficient and Rb-deficient cells, 2025, Mol Cancer Ther.
      2. Maryam Labaf, Wanting Han, Songqi Zhang, Mingyu Liu, Nolan D. Patten, Muqing Li, Susan Patalano, Jill A. Macoska, Steven P. Balk, Dong Han, Kourosh Zarringhalam , Changmeng Cai
  2. Babesia divergens egress from host cells is orchestrated by essential and druggable kinases and proteases, Under Review, BioRxiv.
      3. Brendan Elsworth, Caroline D. Keroack, Yasaman Rezvani, Aditya S. Paul, Keare A. Barazorda, Jacob A. Tennessen, Samantha A. Sack, Cristina K. Moreira, Marc-Jan Gubbels, Marvin J. Meyers, Kourosh Zarringhalam, and Manoj T. Duraisingh
  3. The essential genome of Plasmodium knowlesi reveals determinants of antimalarial susceptibility, 2025, Science.
      4. Brendan Elsworth*, Sida Ye*, Sheena Dass*, Jacob A. Tennessen, Qudseen Sultana, Basil T. Thommen, Aditya S. Paul, Usheer Kanjee, Christof Grüring, Marcelo U. Ferreira, Marc-Jan Gubbels, Kourosh Zarringhalam$, Manoj T. Duraisingh$
  4. Drug resistant pancreatic cancer cells exhibit altered biophysical interactions with stromal fibroblasts in imaging studies of 3D co-culture models. 2024, Nature Scientific Reports.
      5. Eric Struth, Maryam Labaf, Vida Karimnia, Yiran Liu, Gwendolyn Cramer, Joanna B. Dahl, Frank J. Slack, Kourosh Zarringhalam, and Jonathan P. Celli
  5. Single cell expression and chromatin access of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential pivotal controller of a ribosome regulon. 2024, Nature Comunications.
      6. Jingjing Lou, Yasaman Rezvani, Argenis Arriojas, Caroline Keroack, David Degras, Manoj Duraisingh, Kourosh Zarringhalam, and MJ Gubbels
  6. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance 2023, PNAS.
      7. Caroline Keroack, Brendan Elsworth, Jacob Tennessen, Paul AS, Hua R, Ramirez-Ramirez L, Sida Ye, Moreira CM, Meyers MJ, Kourosh Zarringhalam and Manoj Duraisingh
  7. Androgen receptor splice variants drive castration-resistant prostate cancer metastasis by activating distinct transcriptional program 2024, J Clin Invest.
      8. Dong Han, Maryam Labaf, Yawei Zhao, Jude Owiredu, Songqi Zhang, Krishna Patel, Kavita Venkataramani, Jocelyn S Steinfeld, Wanting Han, Muqing Li, Mingyu Liu, Zifeng Wang, Anna Besschetnova, Susan Patalano, Michaela J Mulhearn, Jill A Macoska, Xin Yuan, Steven P Balk, Peter S Nelson, Stephen R Plymate, Shuai Gao, Kellee R Siegfried, Ruihua Liu, Mary M Stangis, Gabrielle Foxa, Piotr J Czernik, Bart Williams, Kourosh Zarringhalam, Xiaohong Li, Changmeng Cai.
  8. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data, 2023, NAR Genomics & Bioinformatics.
      9. Argenis Arriojas, Susan Patalano, Jill Macoska, and Kourosh Zarringhalam
  9. Cell cycle-regulated ApiAP2s and parasite development: The Toxoplasma paradigm, 2023, Current Opinion in Microbiology.
      10. Kourosh Zarringhalam Sida Ye, Jingjing Lou, Yasaman Rezvani, and Marc-Jan Gubbels
  10. Beta-Sitosterol Alters Collagen Distribution in Prostate Fibroblasts, 2023, IJDS.
      11. Quentin D’Arcy, Marissa Sarna-McCarthy, Delaney Bowen, Fidias Soto, Kourosh Zarringhalam, and Jill Macoska
  11. A rising tide of parasite transcriptomics propels pathogen biology, 2023, PLoS Biology.
      12. Manoj T Duraisingh, Marc-Jan Gubbels, and Kourosh Zarringhalam
  12. High-resolution small RNAs landscape provides insights into alkane adaptation in the marine alkane-degrader Alcanivorax dieselolei B-5, 2022, IJMS.
      13. Guangshan Wei, Sujie Li, Sida Ye, Zining Wang, Kourosh Zarringhalam,, Jianguo He, Wanpeng Wang, and Zongze Shao
  13. Increased AR expression in castration-resistant prostate cancer rapidly induces AR signaling reprogramming with the collaboration of EZH2, 2022, Frontiers in Oncology.
      14. Maryam Labaf, Muqing Li, Lily Ting, Breelyn Karno, Shuai Gao, Susan Patalano, Jill A. Macoska, Kourosh Zarringhalam , Dong Han, and Changmeng Cai
  14. Comparative single-cell transcriptional atlases of Babesia species reveal conserved and species-specific expression profiles, 2022, PLoS Biology.
      15. Yasaman Rezvani, Caroline D Keroack, Brendan Elsworth, Argenis Arriojas, Marc-Jan Gubbels, Manoj T Duraisingh, and Kourosh Zarringhalam
  15. The extracellular milieu of Toxoplasma lytic cycle drives lab-adaptation and promotes changes in lipid metabolism primarily driven by transcriptional reprogramming, 2021, mSystems.
      16. Vincent A Primo Jr., Yasaman Rezvani, Andrew Farrell, Amir Vajdi Hoojghan, Gabor T Marth, Kourosh Zarringhalam, and Marc-Jan Gubbels
  16. Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer, 2021, Modern Pathology
      17. Saman Farahmand, Aileen I Fernandez, Fahad Shabbir Ahmed, David L Rimm, Jeffrey H Chuang, Emily Reisenbichler,and Kourosh Zarringhalam
  17. Vitamin A deficiency affects gene expression in the Drosophila melanogaster head, 2021, G3 Genes|Genomes|Genetics .
      18. Deepshe Dewett, Maryam Labaf, Khanh Lam-Kamath, Kourosh Zarringhalam, and Jens Rister.
  18. The modular circuitry of apicomplexan cell division plasticity, 2021, Frontiers in Cellular and Infection Microbiology .
      19. Marc-Jan Gubbels, Isabelle Coppens, Kourosh Zarringhalam, Manoj Duraisingh, and Klemens Engelberg.
  19. Susceptibility-associated genetic variation in NEDD9 contributes to prostate cancer initiation and progression, 2021, Cancer Research.
      20. Dong Han, Jude N. Owiredu, Bridget M. Healy, Muqing Li, Maryam Labaf, Jocelyn S. Steinfeld, Susan Patalano, Shuai Gao, Mingyu Liu, Jill A. Macoska, Kourosh Zarringhalam, Kellee R. Siegfried, Xin Yuan, Timothy R. Rebbeck and Changmeng Cai.
  20. Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images, 2020, Nature Communications.
      21. Javad Noorbakhsh, Saman Farahmand, Ali Foroughi pour, Sandeep Namburi, Dennis Caruana, David Rimm, Mohammad Soltanieh-ha, Kourosh Zarringhalam, Jeffrey H Chuang.
  21. ModEx: A text mining system for extracting mode of regulation of Transcription Factor-gene regulatory interaction, 2019, Journal of Biomedical Informatics.
      22. Saman Farahmand, Todd Riley, Kourosh Zarringhalam .
  22. Causal Inference Engine: A platform for directional gene set enrichment analysis and inference of active transcriptional regulators, 2019, Nucleic Acids Research.
      23. Saman Farahmand, Corey O'Connor, Jill A. Macoska, Kourosh Zarringhalam .
  23. Patch-DCA: Improved Protein Interface Prediction by utilizing Structural Information and Clustering DCA scores, 2019, Bioinformatics.
      24. Amir Vajdi, Kourosh Zarringhalam , Nurit Haspel.
  24. A Free Energy Based Approach For Distance Metric Learning, 2019, ACM SIGKDD, Anchorage, AK, USA.
      25. Sho Inaba, Carl T. Fakhry, Rahul V. Kulkarni, Kourosh Zarringhalam
  25. Clustering on Sparse Data in Non-Overlapping Feature Space with Applications to Cancer Subtyping, 2018, IEEE ICDM, Singapore.
      26. Tianyu Kang*, Kourosh Zarringhalam , Marieke Kuijjer, Ping Chen, John Quackenbush, and Wei Ding
  26. Stochastic Modeling of Gene Regulation by Noncoding Small RNAs in the Strong Interaction Limit, 2018, Biophys J.
      27. N. Kumar, K. Zarringhalam , R. Kulkarni
  27. Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes, 2018, Scientific Reports.
      28. K. Zarringhalam , D. Degras, C. Brockel, D. Ziemek
  28. A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data, 2017, BMC Bioinformatics.
      29. T. Kang, W. Ding, L. Zhang, D. Ziemek, K. Zarringhalam
  29. Bioinformatic Approach for Prediction of CsrA/RsmA-Regulating Small RNAs in Bacteria, 2018, Methods, Mol. Biol. Book Chapter
      30. C. Fakhry, K. Zarringhalam , R. Kulkarni
  30. Prediction of Bacterial small RNAs in the RsmA (CsrA) and ToxT pathways: a machine learning approach, 2017, BMC Genomics.
      31. C. Fakhry, P. Kulkarni, P. Chen, R. Kulkarni, K. Zarringhalam
  31. Identification of competing endogenous rnas (cernas) of the tumor suppressor gene pten: A probabilistic approach, 2017, Scientific Reports.
      32. K. Zarringhalam , Y. Tay, P. Kulkarni, A. Bester, P. P. Pandolfi, R. Kulkarni
  32. Frequency modulation of stochastic gene expression bursts by strongly interacting small RNAs, 2016, Phys. Rev. E.
      33. N. Kumar, T. Jia, K. Zarringhalam , R. Kulkarni
  33. Pressure dependency of localization degree in heavy fermion CeIn3: A density functional theory analysis, 2016, Scientifc Reports.
      34. Yazdani-Kachoei M, Jalali-Asadabadi S, Ahmad I K. Zarringhalam
  34. Interpreting transcriptional changes using causal graphs: New methods and their practical utility on public networks, 2016, BMC Bioinformatics.
      35. C. T. Fakhry, P. Choudhary, A. Gutteridge, B. Sidders, P. Chen, D. Ziemek, K. Zarringhalam
  35. Biomedical Relation Extraction Using Stochastic Difference Equations, 2015, IEEE HPEC.
      36. C. T. Fakhry, K. Zarringhalam , P. Chen
  36. Robust Clinical Outcome Prediction based on Bayesian Analysis of Transcriptional Profiles and Prior Causal Networks, 2014, Bioinformatics.
      37. K. Zarringhalam , A. Enayetallah, P. Reddy, D. Ziemek
  37. Molecular causes of transcriptional response: A Bayesian prior knowledge approach, 2013, Bioinformatics.
      38. K. Zarringhalam , A. Enayetallah, A. Gutteridge, B. Sidders, D. Ziemek
  38. Dynamics of the ethanolamine glycerophospholipid remodeling network, 2012, PLoS ONE.
      39. L. Zhang*, N. Diaz–Diaz*, K. Zarringhalam*, M. Hermansson, P. Somerharju, J. Chuang. ( * co-first authors )
  39. Integrating chemical footprinting data into RNA secondary structure prediction, 2012, PLoS ONE.
      40. K. Zarringhalam, M. Meyer, I. Dotu, J. Chuang, and P. Clote.
  40. Statistical analysis of processes controlling choline and ethanolamine glycerophospholipids molecular species composition, 2012, PLoS ONE.
      41. K. Zarringhalam*, L. Zhang*, M. Kiebish, K. Yang, X. Han, R. Gross, and J. Chuang. (* co-first authors)
  41. An open system for automatic home-cage behavioral analysis and its application to male and female mouse models of Huntington’s disease, 2012, Behavioural Brain Research.
      42. K. Zarringhalam, M. Ka, Y. Kook, J. Terranova, Y. Suh, O. King. and M. Um.
  42. Sequential Adaptive Compressed Sampling Via Huffman Codes, 2011, Sampling Theory in Signal and Image Processing .
      43. A. Aldroubi, H. Wang, and K. Zarringhalam.
  43. Nonlinear Least Squares in RN, 2009, Acta Applicandae Mathematicae .
      44. A. Aldroubi and K. Zaringhalam.
  44. Generating an adaptive multiresolution image analysis with compact cupolets, 2007, Journal of Nonlinear Dynamics.
      45. K. Zarringhalam and K.Short.