Himani Tandon

Himani Tandon
Medical Research Council (UKRI) | mrc · MRC Laboratory of Molecular Biology

PhD Computational Biophysics

About

24
Publications
5,548
Reads
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483
Citations
Introduction
I am a post-doctoral fellow with Prof. Julian Gough at the MRC-Laboratory of Molecular Biology, Cambridge, UK. After my Ph.D. from the Molecular Biophysics Unit, Indian Institute of Science, Bangalore in the area of computational biophysics, I decided to explore the field of transcriptomics and acquire new skills. I am currently working on the cell-reprogramming project in Gough's group.
Additional affiliations
August 2014 - present
Indian Institute of Science Bangalore
Position
  • PhD Student
May 2013 - July 2014
Institute of Microbial Technology
Position
  • Fellow
Education
July 2010 - May 2012
Pondicherry University
Field of study
  • Bioinformatics
August 2007 - June 2010
Panjab University
Field of study
  • Biotechnology

Publications

Publications (24)
Article
Front Cover: The cover image is based on the Article The alteration of structural network upon transient association between proteins studied using graph theory by Vasam Manjveekar Prabantu etal., https://doi.org/10.1002/prot.26606 . image
Preprint
Full-text available
Background Idiopathic pulmonary fibrosis (IPF) is a terminal inflammatory lung disease that causes permanent scarring (fibrogenesis). Bleomycin (BLM) is a drug used to induce fibrosis in mouse models, typically C57BL/6. However, meta-analyses show inter-strain heterogeneity in response, e.g. resistance in BALB/c. This study extends transcriptomic a...
Preprint
Full-text available
Phosphorylation, a fundamental cellular mechanism, intricately regulates protein function and signaling pathways. Our study employs extensive computational analyses on a curated dataset of phosphorylated and unphosphorylated protein structures to explore the multifaceted impact of phosphorylation on protein conformation. Our findings reveal that ph...
Article
Full-text available
Proteins such as enzymes perform their function by predominant non‐covalent bond interactions between transiently interacting units. There is an impact on the overall structural topology of the protein, albeit transient nature of such interactions, that enable proteins to deactivate or activate. This aspect of the alteration of the structural topol...
Article
Full-text available
Cohort-wide sequencing studies have revealed that the largest category of variants is those deemed ‘rare’, even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population. Associative methods give some understanding how rare genetic variants influence disease and organism-level phenotypes. But...
Preprint
Full-text available
Cohort-wide sequencing studies have revealed that the largest category of variants is those deemed ‘rare’, even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population 1–3 ). Our understanding of how rare genetic variants influence disease and organism-level phenotypes has achieved limited p...
Cover Page
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Shaken by handshake. The cover image shows the impact of protein-protein association on the dynamics at sites away from the interface. Protein structures are shown as surface on the left. Structures are represented as a network of Ca residues connected by springs (middle and right) so that NMA can be performed. On the right, nodes are classified as...
Article
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and struc...
Article
Full-text available
Mycobacterium tuberculosis genome encodes over 80 toxin–antitoxin (TA) systems. While each toxin interacts with its cognate antitoxin, the abundance of TA systems presents an opportunity for potential non-cognate interactions. TA systems mediate manifold interactions to manage pathogenicity and stress response network of the cell and non-cognate in...
Article
Full-text available
NS3/4A protease of hepatitis C virus (HCV) plays an important role in viral RNA replication. A 1,4-diphenylbutanedicarboxylic acid derivative, namely, phyllanthin, extracted from the leaf of a herbal plant, Phyllanthus amarus, inhibits HCV NS3/4A protease and replication activities. However, the reduced aqueous solubility, high toxicity, and poor o...
Article
Most biological processes involve formation of transient complexes where binding of a ligand allosterically modulates function. The ccd toxin-antitoxin system is involved in plasmid maintenance and bacterial persistence. The CcdA antitoxin accelerates dissociation of CcdB from its complex with DNA gyrase, binds and neutralizes CcdB, but the mechani...
Article
Full-text available
Mycobacterium tuberculosis possesses an unusually large representation of type II toxin-antitoxin (TA) systems, whose functions and targets are mostly unknown. To better understand the basis of their unique expansion and to probe putative functional similarities among these systems, here we computationally and experimentally investigated their sequ...
Cover Page
Full-text available
Clusters of VapC toxins in Mycobacterium tuberculosis reveal paralogous relationships that enable prediction of functional residues of representative members. Shown are the structures of representative VapC toxins in each cluster, where predicted residues (rendered as sticks), when mutated, abrogated toxic activity.
Article
Full-text available
Toxin-antitoxin (TA) systems are ubiquitously existing addiction modules with essential roles in bacterial persistence and virulence. The genome of Mycobacterium tuberculosis encodes approximately 79 TA systems. Through computational and experimental investigations, we report for the first time that Rv0366c-Rv0367c is a non-canonical PezAT-like tox...
Article
Hepatitis C virus (HCV) infection causes chronic liver disease, which often leads to hepatocellular carcinoma. Earlier, we have demonstrated anti-HCV property of the methanolic extract of Phyllanthus amarus, an age-old folk-medicine against viral hepatitis. Here, we report identification of a principal bioactive component 'corilagin', which showed...
Article
Full-text available
Hepatitis C virus (HCV) is a leading cause of chronic viral hepatitis, but an effective vaccine is still not available to prevent infection. Use of neutralizing antibodies could be a potential therapeutic option. In this study, presence of anti-HCV antibodies in HCV-infected patients' was assessed from 50 patients and examined for the presence of n...
Article
Peptide-based antiviral therapeutics have gradually paved their way into mainstream drug discovery research. Experimental determination of peptides' antiviral activity as expressed by their IC50 values involves a lot of effort. Therefore, we have developed "AVP-IC50 Pred", a regression-based algorithm to predict the antiviral activity in terms of I...
Article
Full-text available
CRISPR system is a powerful defense mechanism in bacteria and archaea to provide immunity against viruses. Recently, this process found a new application in intended targeting of the genomes. CRISPR-mediated genome editing is performed by two main components namely single guide RNA and Cas9 protein. Despite the enormous data generated in this area,...
Article
Full-text available
Antiviral peptides (AVPs) have exhibited huge potential in inhibiting viruses by targeting various stages of their life cycle. Therefore, we have developed AVPdb, available online at http://crdd.osdd.net/servers/avpdb, to provide a dedicated resource of experimentally verified AVPs targeting over 60 medically important viruses including Influenza,...

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