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Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE

Background Our understanding of the transcriptional potential of the genome and its functional consequences has undergone a significant change in the last decade. This has been largely contributed by the improvements in technology which could annotate and in many cases functionally characterize a number of novel gene loci in the human genome. Keeping pace with advancements in this ...

Computational Analysis and Predictive Cheminformatics Modeling of Small Molecule Inhibitors of Epigenetic Modifiers

Background The dynamic and differential regulation and expression of genes is majorly governed by the complex interactions of a subset of biomolecules in the cell operating at multiple levels starting from genome organisation to protein post-translational regulation. The regulatory layer contributed by the epigenetic layer has been one of the favourite areas of interest recently. ...

Computational approaches towards understanding human long non-coding RNA biology

Long non-coding RNAs (lncRNAs) form the largest class of non-protein coding genes in the human genome. While a small subset of well-characterized lncRNAs has demonstrated their significant role in diverse biological functions like chromatin modifications, post-transcriptional regulation, imprinting etc., the functional significance of a vast majority of them still remains an ...

zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs

Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw ...

Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana

Salma Jamal 1 Vinod Scaria 0 0 GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology , Mall Road, Delhi 110007 , India 1 CSIR Open Source Drug

Pharmacogenomics for Precision Medicine in the Era of Collaborative Co-creation and Crowdsourcing

The whole gamut of new technologies in the past decade has revolutionized DNA sequencing, making it cheaper, efficient, and scalable. The consequent big-data in genomics have posed new challenges and opportunities. The transformation of internet as a fabric that intertwines multiple technological and social layers and the rise of platforms that can organize and integrate massively ...

Aptamer-Assisted Detection of the Altered Expression of Estrogen Receptor Alpha in Human Breast Cancer

An increase in the expression of estrogen receptors (ER) and the expanded population of ER-positive cells are two common phenotypes of breast cancer. Detection of the aberrantly expressed ERα in breast cancer is carried out using ERα-antibodies and radiolabelled ligands to make decisions about cancer treatment and targeted therapy. Capitalizing on the beneficial advantages of ...

Chamber Specific Gene Expression Landscape of the Zebrafish Heart

The organization of structure and function of cardiac chambers in vertebrates is defined by chamber-specific distinct gene expression. This peculiarity and uniqueness of the genetic signatures demonstrates functional resolution attributed to the different chambers of the heart. Altered expression of the cardiac chamber genes can lead to individual chamber related dysfunctions and ...

Comparative analysis of human mitochondrial methylome show distinct patterns of epigenetic regulation in mitochondria

Scaria 0 0 GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology , Mall Road, Delhi , India 1 Genomics and Molecular Medicine, CSIR Institute of

tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis

Mycobacterium tuberculosis, along with closely related species, commonly known as M. tuberculosis complex (MTBC), causes tuberculosis in humans and other organisms. Tuberculosis is a disease with high morbidity and mortality, especially in the third world. The genetic variability between clinical isolates of MTBC has been poorly understood, although recent years have seen the ...

Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach

Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes ...

Predictive modeling of anti-malarial molecules inhibiting apicoplast formation

Background Malaria is a major healthcare problem worldwide resulting in an estimated 0.65 million deaths every year. It is caused by the members of the parasite genus Plasmodium. The current therapeutic options for malaria are limited to a few classes of molecules, and are fast shrinking due to the emergence of widespread resistance to drugs in the pathogen. The recent availability ...

Human 45,X Fibroblast Transcriptome Reveals Distinct Differentially Expressed Genes Including Long Noncoding RNAs Potentially Associated with the Pathophysiology of Turner Syndrome

Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected ...

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

Background The availability of sequencing technology has enabled understanding of transcriptomes through genome-wide approaches including RNA-sequencing. Contrary to the previous assumption that large tracts of the eukaryotic genomes are not transcriptionally active, recent evidence from transcriptome sequencing approaches have revealed pervasive transcription in many genomes of ...

MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variations

Human mitochondrial DNA (mtDNA) encodes a set of 37 genes which are essential structural and functional components of the electron transport chain. Variations in these genes have been implicated in a broad spectrum of diseases and are extensively reported in literature and various databases. In this study, we describe MitoLSDB, an integrated platform to catalogue disease ...

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

A major fraction of the transcriptome of higher organisms comprised an extensive repertoire of long non-coding RNA (lncRNA) which express in a cell type and development stage-specific manner. While lncRNAs are a proven component of epigenetic gene expression modulation, epigenetic regulation of lncRNA itself remains poorly understood. Here we have analysed pan-genomic DNA ...

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical ...

HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis

Tuberculosis (TB) is an infectious disease caused by fastidious pathogen Mycobacterium tuberculosis. TB has emerged as one of the major causes of mortality in the developing world. Role of host genetic factors that modulate disease susceptibility have not been studied widely. Recent studies have reported few genetic loci that provide impetus to this area of research. The ...