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  • Doctoral thesis
  • Manuscript submitted/in preparation
  • Published in peer-reviewed journals
    • 2024
    • 2023
    • 2022
    • 2021
    • 2019
    • 2018
    • 2014
    • 2013
    • 2011
    • BioRxiv/MedRxiv publication
  • Conference Abstract/Papers
  • Patents

Publications

Doctoral thesis

Thesis title: In-silico studies of microRNAs regulation in higher eukaryotes from the perspective of molecular evolution.
Topics of Reasearch: Bioinformatics, Molecular Evolution, MicroRNAs, Human Diseases, Epigenetics.
Supervisor: Prof. T.C. Ghosh
Work place: Bose Institute (J.C. Bose Institute), Kolkata, India
University: Maulana Abul Kalam Azad University of Technology (formerly known as West Bengal University of Technology), West Bengal, India.

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Manuscript submitted/in preparation

  1. Volpe, M., Miralto, M., & Das, J. methylRv2: An EPICv2 user interface solution to DNA methylation array data analysis. 2024 (in preparation)

  2. Volpe, M., Miralto, M., & Das, J TranscriptR: GUI for transcriptome data analysis. 2024 (in preparation)

Published in peer-reviewed journals

2024

Shahin H, Belcastro L, Das J, Perdiki Grigoriadi M, Saager RB, Steinvall I, Sjöberg F, Olofsson P, Elmasry M and El-Serafi AT MicroRNA‐155 mediates multiple gene regulations pertinent to the role of human adipose‐derived mesenchymal stem cells in skin regeneration. Front. Bioeng. Biotechnol. 12:1328504.

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2023

Volpe, M., & Das, J. methylR: a graphical interface for comprehensive DNA methylation array data analysis. Bioinformatics, Volume 39, Issue 4, April 2023, btad184.

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Braian, C., Karlsson, L., Das, J., & Lerm, M. Selected β-Glucans Act as Immune-Training Agents by Improving Anti-Mycobacterial Activity in Human Macrophages: A Pilot Study. J Innate Immun (2023) 15 (1): 751–764.
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Lundquist, H., Andersson, H., Chew, M. S., Das, J., Turkina, M. V., & Welin, A. The Olfactomedin-4-Defined Human Neutrophil Subsets Differ in Proteomic Profile in Healthy Individuals and Patients with Septic Shock. J Innate Immun (2023) 15 (1): 351–364.
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Lundquist, H., Andersson, H., Chew, M. S., Das, J., Turkina, M. V., & Welin, A. miRNome and Proteome Profiling of Human Keratinocytes and Adipose Derived Stem Cells Proposed miRNA-Mediated Regulations of Epidermal Growth Factor and Interleukin 1-Alpha. Int. J. Mol. Sci. 2023, 24(5), 4956.
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Verma, D., Kasic, N.‐K., Jeppsson, F., Eding, C. B., Lysiak, M., Fekri, S. Z., Das, J., & Enerback, C. Differential DNA Methylation of MicroRNA-Encoding Genes in Psoriatic Epidermis Highlights the Wnt Pathway. Journal of Investigative Dermatology, 143(5), S140.
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2022

Das J, Idh N, Sikkeland LI, Paues J, Lerm M. DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types. Epigenetics. 2022 Aug 3;17(8):882-93.
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Huoman J, Sayyab S, Apostolou E, Karlsson L, Porcile L, Rizwan M, Sharma S, Das J, Rosén A, Lerm M. Epigenetic rewiring of pathways related to odour perception in immune cells exposed to SARS-CoV-2 in vivo and in vitro. Epigenetics. 2022 Jun 26:1-7.
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Łysiak M, Das J, Malmström A, Söderkvist P. Methylation associated with long- or short-term survival in glioblastoma patients from the Nordic phase 3 trial. Front Genet. 2022 Aug 25;13:934519.
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2021

Karlsson L, Das J, Nilsson M, Tyrén A, Pehrson I, Idh N, Sayyab S, Paues J, Ugarte-Gil C, Méndez-Aranda M, Lerm M. A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection. Scientific Reports. 2021 Sep 30;11(1):1-3.
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Kalsum S, Andersson B, Das J, Schön T, Lerm M. A high-throughput screening assay based on automated microscopy for monitoring antibiotic susceptibility of Mycobacterium tuberculosis phenotypes. BMC Microbiology. 2021 Dec;21(1):1-4.
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Zhu GH, Azharuddin M, Islam R, Rahmoune H, Deb S, Kanji U, Das J, Osterrieth J, Aulakh P, Ibrahim-Hashi H, Manchanda R, Nilsson PH, Mollnes TE, Bhattacharyya M, Islam MM, Hinkula J, Slater NKH, Patra HK. Innate Immune Invisible Ultrasmall Gold Nanoparticles—Framework for Synthesis and Evaluation. ACS Applied Materials & Interfaces. 2021 May 12;13(20):23410-22.
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Singhania A, Dubelko P, Kuan R, Chronister WD, Muskat K, Das J, Phillips EJ, Mallal SA, Seumois G, Vijayanand P, Sette A, Lerm M, Peters B, Lindestam Arlehamn C. CD4+ CCR6+ T cells dominate the BCG-induced transcriptional signature. EBioMedicine. 2021 Dec 1;74:103746.
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2019

Das J, Verma D, Gustafsson M, Lerm M. Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects. Epigenetics. 2019 Jun 3;14(6):589-601.
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2018

Sen K, Bhattacharyya D, Sarkar A, Das J, Maji N, Basu M, Ghosh Z, Ghosh TC. Exploring the major cross-talking edges of competitive endogenous RNA networks in human Chronic and Acute Myeloid Leukemia. Biochimica et Biophysica Acta (BBA)-General Subjects. 2018 Sep 1;1862(9):1883-92.
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2014

Das, J., Podder, S., & Ghosh, T. C. (2014). Insights into the miRNA regulations in human disease genes. BMC genomics, 15(1), 1-7.
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2013

Das, J., Chakraborty, S., Podder, S., Ghosh, T.C., 2013. Complex-forming proteins escape the robust regulations of miRNA in human. FEBS letters 587, 2284–2287.
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2011

Gupta, S., Kumari, K., Das, J., Lata, C., Puranik, S., & Prasad, M. (2011). Development and utilization of novel intron length polymorphic markers in foxtail millet (Setaria italica (L.) P. Beauv.). Genome, 54(7), 586-602.
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BioRxiv/MedRxiv publication

Das J, Idh N, Pehrson I, Paues J, Lerm M. A DNA methylome biosignature in alveolar macrophages from TB-exposed individuals predicts exposure to mycobacteria. medrxiv. 2021 Jan 1.
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Pehrson I, Das J, Idh N, Karlsson L, Rylander H, af Segerstad HH, Reuterswärd E, Marttala E, Paues J, Méndez-Aranda M, Ugarte-Gil C. DNA methylomes derived from alveolar macrophages display distinct patterns in latent tuberculosis-implication for interferon gamma release assay status determination. MedRxiv. 2021 Jan 1.
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Huoman J, Sayyab S, Apostolou E, Karlsson L, Porcile L, Rizwan M, Sharma S, Das J, Rosen A, Lerm M. Mild SARS-CoV-2 infection modifies DNA methylation of peripheral blood mononuclear cells from COVID-19 convalescents. medRxiv. 2021 Jan 1.
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Pehrson I, Braian C, Karlsson L, Idh N, Danielsson EK, Andersson B, Paues J, Das J, Lerm M. DNA methylation profiling of immune cells from tuberculosis-exposed individuals overlaps with BCG-induced epigenetic changes and correlates with the emergence of anti-mycobacterial’corralling cells’. medRxiv. 2021 Jan 1.
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Lundquist H, Andersson H, Chew MS, Das J, Turkina MV, Welin A. The Olfm4-defined human neutrophil subsets differ in proteomic profile in septic shock. bioRxiv. 2022 Jan 1.
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Conference Abstract/Papers

  1. Shahin, H., Abdallah, S., Das, J., Steinvall, I., Sjöberg, F., Elmasry, M., & El‐Serafi, A. T. (2023). Mirnome and pro‐ teome profiling of human keratinocytes and adipose‐derived stem cells proposed mirna‐mediated regulations pertaining to stem cell differentiation and wound healing. Journal of Plastic, Reconstructive & Aesthetic Surgery, 87, S18–S19. https://doi.org/10.1016/j.bjps.2023.10.040. Abstracts from the 11th EURAPS Research Council Meeting in Stockholm, May 2023.

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  2. D Verma, N Kasic, F Jeppsson, C Eding, M Lysiak, S Fekri, J Das and C Enerbäck. (2023). Altered methylation of microRNA in the psoriatic epidermis highlights the Wnt pathway. Journal of Investigative Dermatology, 143(5), S140.https://doi.org/10.1016/j.jid.2023.03.825. Abstracts from 1st International Societies for Investigative Dermatology Meeting, 10 May 2023–13 May 2023, Tokyo, Japan.

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  3. D Verma, N Kasic, F Jeppsson, C Eding, M Lysiak, S Fekri, J Das and C Enerbäck. (2022). Differential DNA Methylation of microRNA-encoding Genes in Psoriatic Epidermis Highlights the Wnt Pathway. Journal of Investigative Dermatology, 142(12), S229.https://doi.org/10.1016/j.jid.2022.09.297. Abstracts from ESDR 2022 Meeting Abstract Supplement 28 September 2022 - 01 October 2022.

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  4. Lysiak, M., Das, J., Soderkvist, P., & Malmstrom, A. (2022). Methylome analysis of short versus long‐term GBM survivors from the nordic randomised, phase 3 trial. Brain Tumor Res Treat, 10(Suppl). https://doi.org/10.14791/btrt.2022.10.F-1329. E-poster for World Federation of Neuro-oncology Societies (WFNOS 2022) March 24-27, 2022.

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Patents

  1. Lerm, M., & Das, J. (2022). Biomarker for detection of mycobacterial exposure and infection. WO Patent WO2022169394A1.

  2. Lerm, M., Das, J., & Sayyab, S. (2022). Method for determining sars‐cov‐2 exposure with or without remaining symptoms. WO Patent WO2022119495A1.

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