A5002722506- Sarcoma Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Cancer-related gene regulation
- Gene expression and cancer classification
- Head and Neck Cancer Studies
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Cancer Cells and Metastasis
- Biomedical Ethics and Regulation
- RNA and protein synthesis mechanisms
- Cancer Treatment and Pharmacology
- Mitochondrial Function and Pathology
- Cancer-related molecular mechanisms research
- Photosynthetic Processes and Mechanisms
- Cancer Research and Treatments
- Smart Agriculture and AI
- Single-cell and spatial transcriptomics
- Genetic diversity and population structure
- Insect Resistance and Genetics
- Genomic variations and chromosomal abnormalities
- Metabolism and Genetic Disorders
- DNA Repair Mechanisms
Jawaharlal Nehru University
2020-2024
Institute of Bioinformatics and Applied Biotechnology
2012-2019
Strand Life Sciences (India)
2018
Biotech Park
2012-2017
Indian Institute of Science Bangalore
2009-2011
Tata Institute of Fundamental Research
2006-2009
Louisiana State University
2004
Louisiana State University Agricultural Center
2004
Abstract Background The Azadirachta indica (neem) tree is a source of wide number natural products, including the potent biopesticide azadirachtin. In spite its widespread applications in agriculture and medicine, molecular aspects biosynthesis neem terpenoids remain largely unexplored. current report describes draft genome four transcriptomes A. attempts to contextualise sequence information terms phylogeny, transcript expression terpenoid pathways. first member family Meliaceae be...
Background The incidence of oral tongue squamous cell carcinoma (OTSCC) is increasing among younger birth cohorts. etiology early‐onset OTSCC (diagnosed before the age 50 years) and cancer driver genes remain largely unknown. Methods Sequencing Consortium Oral Tongue Cancer was established through pooling somatic mutation data specimens (n = 227 [107 cases]) from 7 studies Genome Atlas. Somatic mutations at microsatellite loci Catalog Mutations in signatures were identified. identified with...
Abstract Oral tongue squamous cell carcinomas (OTSCC) are a homogenous group of aggressive tumors in the head and neck region that spread early to lymph nodes have higher incidence regional failure. In addition, there is rising oral cancer younger populations. Studies on functional DNA methylation changes linked with altered gene expression critical for understanding mechanisms underlying tumor development metastasis. Such studies also provide important insight into biomarkers viral...
During mitochondrial replication, spontaneous mutations occur and accumulate asymmetrically during the time spent single stranded by heavy strand (DssH). The predominant appear to be deaminations from adenine hypoxanthine (A →H, which leads an A →G substitution) cytosine thymine (C → T). Previous findings indicated that C →T substitutions rapidly then saturate at high DssH, suggesting protection or repair, whereas accumulates linearly with DssH. We describe here implementation of a simple...
Reconstruction of ancestral DNA and amino acid sequences is an important means inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function processes over the course evolution are used to infer adaptation convergence. Maximum likelihood (ML) generally thought provide relatively accurate reconstructed compared parsimony, but both methods lead inference multiple directional nucleotide frequencies primate mitochondrial (mtDNA). To better...
Secondary structure stability of mitochondrial origins light-strand replication (OL) presumably reduces delayed formation initiating forks on the heavy strand. Delayed initiation prolongs single strandedness More mutations accumulate during prolonged time spent stranded. Presumably, and excess affect biochemical processes ultimately morphological outcomes development at whole-organism level. This predicts that developmental increases with OL secondary OL-like structures by five tRNA genes...
Abstract Neem (Azadirachta indica A. Juss.), an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced published draft genome a neem plant, using mainly short read sequencing data. In this report, we present improved assembly generated additional reads from Illumina long Pacific Biosciences SMRT sequencer. assembled error-corrected Platanus, assembler designed to perform well heterozygous genomes. The...
<ns4:p>Oral tongue squamous cell carcinomas (OTSCC) are a homogeneous group of tumors characterized by aggressive behavior, early spread to lymph nodes and higher rate regional failure. Additionally, the incidence OTSCC among younger population (<50yrs) is on rise; many whom lack typical associated risk factors alcohol and/or tobacco exposure. We present data single nucleotide variations (SNVs), indels, regions with loss heterozygosity (LOH), copy number (CNVs) from fifty-paired oral...
Accurate detection of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) is essential to understanding the role HPV disease prognosis and management patients. We used different analytes methods understand true prevalence a cohort patients with OSCC molecular backgrounds, we correlated data patient survival.We integrated from multiple (HPV DNA, RNA, p16), assays (immunohistochemistry, polymerase chain reaction [PCR], quantitative PCR [qPCR], digital PCR), changes...
Researchers interested in studying and constructing transcriptomes, especially for non-model species, face the conundrum of choosing from a number available de novo genome-guided assemblers. None popular assembly tools use today achieve requisite sensitivity, specificity or recovery full-length transcripts on their own. Here, we present comprehensive comparative study performance various Additionally, an approach to combinatorially augment transciptome by using both tools. In our study,...
Electron microscopy analyses of replicating chloroplast molecules earlier predicted bidirectional Cairns replication as the prevalent mechanism, perhaps followed by rounds a rolling circle mechanism. This standard model is being challenged recent proposition homologous recombination-mediated in chloroplasts. We address this issue our current study analyzing nucleotide composition genome regions between known origins, with an aim to reveal any adenine guanine deamination gradients. These...
Abstract Background Synonymous sites are freer to vary because of redundancy in genetic code. Messenger RNA secondary structure restricts this freedom, as revealed by previous findings mitochondrial genes that mutations at third codon position nucleotides helices more selected against than those loops. This motivated us explore the constraints imposed mRNA on evolutionary variability all positions general, chloroplast systems. Results We found and intrinsic stability these sequences share an...
Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect matched normal tissue, order understand their association the disease. We have devised an accurate, sensitive, easy-to-use tool, COPS, COpy using...
Surgery exposes tumor tissue to severe hypoxia and mechanical stress leading rapid gene expression changes in the its microenvironment, which remain poorly characterized. We biopsied adjacent normal tissues from patients with breast (n = 81) head/neck squamous cancers (HNSC; n 10) at beginning (A), during (B), end of surgery (C). Tumor/normal RNA 46/81 cancer was subjected mRNA-Seq using Illumina short-read technology, nine HNSC whole-transcriptome microarray BeadArray. Pathways genes...
Selection of the right reference gene(s) is crucial in analysis and interpretation gene expression data. The aim present study was to discover validate a minimal set internal control genes head neck tumor studies. We analyzed data from multiple sources (in house whole-genome microarrays, previously published quantitative real-time PCR (qPCR) RNA-seq TCGA) come up with list 18 (discovery set) that had lowest variance, high level across tumors, their matched normal samples. discovery were...
During mitochondrial replication, spontaneous mutations occur and accumulate asymmetrically during the time spent single stranded by heavy strand (D ssH ).The predominant appear to be deaminations from adenine hypoxanthine (A → H, which leads an A G substitution) cytosine thymine (C T).Previous findings indicated that C T substitutions rapidly then saturate at high D , suggesting protection or repair, whereas accumulates linearly with .We describe here implementation of a simple hidden...
Abstract Background Human Rad51 (RAD51), analogous to its bacterial homolog, RecA, binds and unwinds double stranded DNA (dsDNA) in the presence of certain nucleotide cofactors. ATP hydrolysis is not required for this process, because even non hydrolysable analogs like AMP-PNP ATPγS, support unwinding. Even ADP, product hydrolysis, feebly supports Results We find that human Rad52 (RAD52) stimulates RAD51 mediated unwinding all Adenine cofactors, (except AMP no conditions intrinsically fail...
Single stranded DNA binding proteins (SSBs) are vital for the survival of organisms. Studies on SSBs from prototype, Escherichia coli (EcoSSB) and, an important human pathogen, Mycobacterium tuberculosis (MtuSSB) had shown that despite significant variations in their quaternary structures, and oligomerization properties two similar. Here, we used X-ray crystal structure data to design a series chimeric (mβ1, mβ1′β2, mβ1–β5, mβ1–β6 mβ4–β5) by transplanting β1, β1′β2, β1–β5, β1–β6 β4–β5...
Tumor suppression by the extracts of Azadirachta indica (neem) works via anti-proliferation, cell cycle arrest, and apoptosis, demonstrated previously using cancer lines live animal models. However, very little is known about molecular targets pathways that neem their associated compounds act through. Here, we address this a genome-wide functional pooled shRNA screen on head neck squamous carcinoma treated with crude leaf extracts, for anti-tumorigenic activity. We analyzed differences in...
ABSTRACT Purpose The prevalence of human papillomavirus (HPV) in oral cavity squamous cell carcinoma (OSCC) varies significantly based on assay sensitivity and patient geography. Accurate detection is essential to understand the role HPV disease prognosis management patients with OSCC. Methods We generated integrated data from multiple analytes (HPV DNA, RNA, p16), assays (immunohistochemistry, PCR, qPCR digital PCR) molecular changes (somatic mutations DNA methylation) 153 OSCC correlate...