Mst Shamima Khatun, Ph.D.

Instructor

School of Medicine
Department
Medicine
Center for Translational Research in Infection & Inflammation
Mst Shamima Khatun

Biography

Shamima is a faculty member at the Center for Translational Research in Infection & Inflammation (CTRII) at Tulane University School of Medicine. With a strong background in both Statistics and Computer Science, she conducts bioinformatics research across various domains, including bulk RNA-seq, single-cell RNA-seq, single-cell ATAC-seq, spatial transcriptomics, and big data analysis.

Her recent research focuses on analyzing scRNA-seq data from SARS-CoV-2 K18-ACE2 mice to uncover cellular and molecular mechanisms underlying infection-associated cell dysfunction. Her findings suggest that transcriptional changes result from the presence of viral RNA in endothelial cells, which is directly linked to endothelial dysfunction. These mechanistic insights contribute to the development of targeted therapeutics for managing infectious diseases.

Shamima earned her Ph.D. from the Kyushu Institute of Technology, Japan, where she led multiple computational biology projects, including protein and immunopeptide prediction (anti-inflammatory, pro-inflammatory, linear B-cell, and anti-tuberculosis peptides) and DNA analysis using Artificial Intelligence and Machine Learning approaches. She has published over 35 peer-reviewed journal papers, developed eight bioinformatics tools, and accumulated more than 1080 citations, with an h-index of 18. Her tools have accelerated the discovery of novel peptides and drug therapies, enhancing precision and efficiency in biomedical research.

 

Publications

 

  1. Khatun MS, Qin X, Pociask DA, Kolls JK*. SARS-CoV2 Endotheliopathy: Insights from Single Cell RNAseq. American Journal of Respiratory and Critical Care Medicine. 2022 Nov 1;206(9):1178-1179. doi: 10.1164/rccm.202206-1105LE. PMID: 35839476; PMCID: PMC9704844. 
  2.  Khatun MS, Remcho TP, Qin X, Kolls JK*. Cell-intrinsic and -extrinsic effects of SARS-CoV-2 RNA on pathogenesis: single-cell meta-analysis. mSphere.  2023 Oct 24;8(5):e0037523. doi: 10.1128/msphere.00375-23. Epub 2023 Sep 22. PMID: 37737611; PMCID: PMC10597400. 
  3. Wang C#, Khatun MS#, Zhang Z, Allen MJ, Chen Z, Ellsworth CR, Currey JM, Dai G, Tian D, Bach K, Yin XM, Traina-Dorge V, Rappaport J, Maness NJ, Blair RV, Kolls JK, Pociask DA, Qin X*. COVID-19 and influenza infections mediate distinct pulmonary cellular and transcriptomic changes. Communications Biology. 2023 Dec 13;6(1):1265. doi: 10.1038/s42003-023-05626-z. PMID: 38092883; PMCID: PMC10719262. 
  4. Wang C, Khatun MS, Ellsworth CR, Chen Z, Islamuddin M, Nisperuza Vidal AK, Afaque Alam M, Liu S, Mccombs JE, Maness NJ, Blair RV, Kolls JK, Qin X*. Deficiency of Tlr7 and Irf7 in mice increases the severity of COVID-19 through the reduced interferon production. Communications Biology. 2024 Sep 17;7(1):1162. doi: 10.1038/s42003-024-06872-5. PMID: 39289468; PMCID: PMC11408513. 
  5. Currey J, Ellsworth C, Khatun MS, Wang C, Chen Z, Liu S, Midkiff C, Xiao M, Ren M, Liu F, Elgazzaz M, Fox S, Maness NJ, Rappaport J, Lazartigues E, Blair R, Kolls JK, Mauvais-Jarvis F, Qin X*. Upregulation of inflammatory genes and pathways links obesity to severe COVID-19. BBA-Molecular Basis of Disease. 2024 Oct;1870(7):167322. doi: 10.1016/j.bbadis.2024.167322. Epub 2024 Jun 26. PMID: 38942338; PMCID: PMC11330358. 

For more publications, visit Google Scholar: https://scholar.google.com/citations?user=53CnxM0AAAAJ&hl=en