CV

Education

• Ph.D in Biological Sciences, IISER Kolkata, India 2019 - 2024
• M. Sc in Zoology (Specialization in Genetics and Molecular Biology), Vidyasagar University, India, 2016 - 2018
• B. Sc in Zoology (Hons), Bajkul Milani Mahavidyalays (Vidyasagar University), India 2013 - 2016

Research experience

• Research Scholar 2019 - 2024
  • Indian Institute of Science Education and Research Kolkata (IISER Kolkata)
  • Project title: Unraveling the Role of Bromodomain and PHD finger (BRPF) Proteins in Epigenetic Regulation of Hepatocellular Carcinoma
  • Supervisor: Dr. Babu Sudhamalla
• Project Student (Master’s Thesis) 2017 - 2018
  • Vidyasagar University (Midnapore, India)
  • Project title: Neurotoxic Effects of Lead (pb) on Mus musculus and its Recovery by Phyllanthus emblica
  • Supervisor: Prof. Jayanta Kumar Kundu

Skills

• Molecular Biology
  • SDS-PAGE, Agarose Gel Electrophoresis, Westernblot, DNA/RNA/nucleosome/histone isolation, RT-PCR, qPCR, Immunoprecipitation (IP), Plasmid Expression and Isolation, Coimmunoprecipitation (coIP), Chromatin Immunoprecipitation (ChIP)
• Protein Biochemistry
  • Bacterial Expression of Protein, Protein Purification by Affinity Chromatography (Ni-NTA, GST) and Size Exclusion Chromatography (FPLC), Isothermal Titration Calorimetry (ITC), Surface Plasmon Resonance (SPR), Fluorescence Polarization (FP), In-Gel Fluorescence, Photocrosslinking (in vitro), Unnatural Amino Acids Mutagenesis(AzF,BzF)
  • Sub-skill 2.2
  • Sub-skill 2.3
• Cell Culture
  • Adherent Cell Culture of Mammalian Cells, Cells Freezing, Reviving and Passaging, Cell Counting in Hemocytometer, Transfection
• Bioinformatics Tools
  • Virtual Screening Using Autodock Vina, PyMOL, Chimera, Discovery Studio Visualizer, Schrodinger Software 2018, Molecular Dynamics Using Gromacs, ChIP Seq Data Analysis, ATAC Seq Data Analysis, RNA Seq Data Analysis, Single-Cell RNA-Seq Analysis, Proteomics Data Analysis Using Maxquant, Galaxy
• Analytics and Programming
  • Origin, Graphpad Prism, Gnu Plot, Xmgrace, Python Basics and R (For analysis of Molecular Dynamics, ChIP seq, Bulk RNA Seq and Single-Cell RNA-Seq Data Analysis)
• Vector Designing
  • Adobe Illustrator, Blender

Publications

Amyloid β‑Peptide Segment Conjugated Side-Chain Proline-Based Polymersas Potent Inhibitors in Lysozyme Amyloidosis

Nayak K, Ghosh P, Barman S, Sudhamalla B, Theato P, De P. Amyloid β-Peptide Segment Conjugated SideChain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis. Bioconjugate Chemistry. 2024 Feb 12.

Uncovering the non-histone interactome of the BRPF1 bromodomain using site-specific azide-acetyllysine photochemistry

Barman S , Padhan J, Sudhamalla B. Uncovering the Nonhistone Interactome of BRPF1 Bromodomain Using SiteSpecific Azide-Acetyllysine Photochemistry. JBC. 2023 Dec 3; DOI:https://doi.org/10.1016/j.jbc.2023.105551.

Integrated virtual screening and MD simulation approaches toward discovering potential inhibitors for targeting BRPF1 bromodomain in hepatocellular carcinoma

Barman S, Bardhan I, Padhan J, Sudhamalla B.Integrated virtual screening and MD simulation approaches toward discovering potential inhibitors for targeting BRPF1 bromodomain in hepatocellular carcinoma. Journal of Molecular Graphics and Modelling. 2023, 108642, ISSN 1093-3263.

Novel insights into the recognition of acetylated histone H4 tail by the TRIM24 PHD-Bromo module

Bardhan I, Barman S, Roy A, Sudhamalla B. Novel insights into the recognition of acetylated histone H4 tail by the TRIM24 PHD-Bromo module. Biochem J. 2023 May 17; 480 (9): 629-647.

Insulin fibril inhibition using glycopolymeric nanoassemblies

Bera A, Ghosh P, Barman S, Bhattacharya S, Sudhamalla B, Goswami K, De P. Insulin fibril inhibition using glycopolymeric nanoassemblies. Biomater Sci. 2023 Mar 31:1-13.

Uncovering the Domain-Specific Interactome of the TAF1 Tandem Reader Using Site-Specific Azide-Acetyllysine Photochemistry

Yadav Y, Barman S#, Roy A#, Padhan J, Sudhamalla B. Uncovering the Domain-Specific Interactome of the TAF1 Tandem Reader Using Site-Specific Azide-Acetyllysine Photochemistry. Biochemistry. 2023 Jan 17;62(2):270-280

Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation

Barman S, Sahoo SS, Padhan J, Sudhamalla B. Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation. J Biomol Struct Dyn. 2022 Dec 16:1-13.

Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain.

Barman S, Roy A, Padhan J, Sudhamalla B. Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain. Biochemistry. 2022 Sep 6;61(17):1774-1789.

Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain

Barman S, Roy A, Bardhan I, Kandasamy T, Shivani S, Sudhamalla B. Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain. Chem Asian J. 2021 Nov 2;16(21):3404-3412.

Engineering an acetyllysine reader with a photocrosslinking amino acid for interactome profiling

Roy A, Barman S, Padhan J, Sudhamalla B. Engineering an acetyllysine reader with a photocrosslinking amino acid for interactome profiling. Chem Commun (Camb). 2021 Sep 28;57(77):9866-9869

Talks

Uncovering the Non-histone Interactome of the BRPF1 Bromodomain Using Site-Specific Azide-Acetyllysine Photochemistry

March 01, 2023

Poster at Sustainibility Interdisciplinary in Chemical Sciences (SICS 2023) Conference, Indian Institute of Science Education and Research,Department of Chemical Science, Kolkata, India

Uncovering Epigenetic Mechanisms at the Crossroad of Chemistry and Biology

March 01, 2023

Poster Presentation at Poster presentation in DBS day 2020, Indian Institute of Science Education and Research, (Kolkata, India), Kolkata, India

Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain

January 01, 2023

Poster at Poster presentation in Frontiers in Modern Biology (FIMB-2023) 2023, Indian Institute of Science Education and Research, (Kolkata, India), Kolkata, India

Molecular Insights into the Recognition of Acetylated Histone Modifications by the BRPF2 Bromodomain

December 01, 2022

Poster at Poster presentation in An Interdiscplinary Approach to Biological Sciences (IABS 2023) 2023, The Indian Association for the Cultivation of Science, (Kolkata, India), Kolkata, India

Recent Advances In Microscopy Methods and Techniques

March 01, 2022

Workshop at Karyashala (Workshop) on advanced bio-analytical methods and applications-2022, 2022, Indian Institute of Science Education and Research, (Kolkata, India), Kolkata, India

Surface Plasmon Resonance (SPR)

January 01, 2022

Tutorial at Karyashala (Workshop) on advanced bio-analytical methods and applications-2022, 2022, Indian Institute of Science Education and Research, (Kolkata, India), Kolkata, India

Teaching

Teaching Assistant for Cell Biology and Imaging Laboratory (LS3104) Spring 2022

Teaching Assistant for Bioinformatics (LS3205) Autum 2021

Teaching Assistant for Cloning and Protein Expression Laboratory (LS4205) Spring 2021