A5073053169- Epigenetics and DNA Methylation
- Congenital Heart Disease Studies
- Congenital heart defects research
- Cancer Genomics and Diagnostics
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- Histone Deacetylase Inhibitors Research
- Ubiquitin and proteasome pathways
- Pancreatic and Hepatic Oncology Research
- RNA modifications and cancer
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Metabolomics and Mass Spectrometry Studies
- Gestational Diabetes Research and Management
- Prenatal Substance Exposure Effects
- Tracheal and airway disorders
- Chemical Synthesis and Analysis
- Gene expression and cancer classification
- DNA Repair Mechanisms
- Genomics and Phylogenetic Studies
- Heat shock proteins research
- Congenital Diaphragmatic Hernia Studies
- Protein Structure and Dynamics
St. Jude Children's Research Hospital
2023-2025
University of Nebraska Medical Center
2015-2024
Indian Institute of Science Education and Research Kolkata
2024
Indian Institute of Technology Ropar
2022
Nebraska Medical Center
2020
Noble Research Institute
2013-2014
Institute of Microbial Technology
2007-2011
University of Iceland
2011
Antibacterial peptides are one of the effecter molecules innate immune system. Over last few decades several antibacterial have successfully approved as drug by FDA, which has prompted an interest in these peptides. In our recent study we analyzed 999 peptides, were collected from Peptide Database (APD). We also developed methods to predict and classify using Support Vector Machine (SVM).During analysis observed that certain residues preferred over other peptide, particularly at N C...
Abstract Background One of the major challenges in post-genomic era is to provide functional annotations for large number proteins arising from genome sequencing projects. The function many depends on their interaction with small molecules or ligands. ATP one such important ligand that plays critical role as a coenzyme functionality proteins. There need develop method identifying interacting residues binding (ABPs), order understand mechanism protein-ligands interaction. Results We have...
Background Membrane transport proteins (transporters) move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of that differ topology, energy coupling mechanism, substrate specificity as well sequence similarity. Among the functional annotations transporters, information about their transporting is especially important. The experimental identification characterization transporters currently costly...
Pancreatic cancer (PC) is the fourth leading cause of deaths in United States with a five-year patient survival rate only 6%. Early detection and treatment this disease hampered due to lack reliable diagnostic prognostic markers. Recent studies have shown that dynamic changes global DNA methylation gene expression patterns play key roles PC development; hence, provide valuable insights for better understanding initiation progression PC. In current study, we used methylation, expression, copy...
Pancreatic ductal adenocarcinoma (PDAC) is the most common and among deadliest of pancreatic cancers. Its 5-year survival only ∼8%. cancers are a heterogeneous group diseases, which PDAC particularly aggressive. Like many other cancers, also starts as pre-invasive precursor lesion (known intraepithelial neoplasia, PanIN), offers an opportunity for both early detection treatment. Even advanced can benefit from prognostic biomarkers. However, reliable biomarkers diagnosis or those prognosis...
Abstract Background Different isoforms of Cytochrome P450 (CYP) metabolized different types substrates (or drugs molecule) and make them soluble during biotransformation. Therefore, fate any drug molecule depends on how they are treated or by CYP isoform. There is a need to develop models for predicting substrate specificity major P450, in order understand whether given will be not. This paper describes an in-silico method the metabolizing capability (e.g. 3A4, 2D6, 1A2, 2C9 2C19). Results...
The etiology of cerebral palsy (CP) is complex and remains inadequately understood. Early detection CP an important clinical objective as this improves long term outcomes. We performed genome-wide DNA methylation analysis to identify epigenomic predictors in newborns investigate disease pathogenesis. Methylation newborn blood using Illumina HumanMethylation450K array was 23 cases 21 unaffected controls. There were 230 significantly differentially-methylated CpG loci 258 genes. Each locus had...
Ventricular Septal Defect (VSD), the most common congenital heart defect, is characterized by a hole in septum between right and left ventricles. The pathogenesis of VSD unknown clinical cases. There paucity data relevant to epigenetic changes VSD. placenta fetal tissue crucial cardiac development potentially useful surrogate for evaluating tissue. To understand mechanisms that may play role VSD, genome-wide DNA methylation assay on placentas 8 term subjects with isolated no known or...
CHIP/STUB1 ubiquitin ligase is a negative co-chaperone for HSP90/HSC70, and its expression reduced or lost in several cancers, including breast cancer. Using an extensive well-annotated cancer tissue collection, we identified the loss of nuclear but not cytoplasmic CHIP to predict more aggressive tumorigenesis shorter patient survival, with two thirds ErbB2+ triple-negative cancers (TNBC) one third ER+ cancers. Reduced was seen patient-derived xenograft tumors TNBC cell lines. Ectopic lines...
Gene fusions that contribute to oncogenicity can be explored for identifying cancer biomarkers and potential drug targets. To investigate the nature distribution of fusion transcripts in cancer, we examined transcriptome data about 9,000 primary tumors from 33 different cancers TCGA (The Cancer Genome Atlas) along with cell line CCLE (Cancer Cell Line Encyclopedia) using ChimeRScope, a novel detection algorithm. We identified several sense (canonical, 39%) or antisense (non-canonical, 61%)...
Advances in omics and computational Artificial Intelligence (AI) have been said to be key meeting the objectives of precision cardiovascular medicine. The focus medicine includes a better assessment disease risk understanding mechanisms. Our objective was determine whether significant epigenetic changes occur isolated, non-syndromic CoA. Further, we evaluated AI analysis DNA methylation for prediction CoA.Genome-wide newborn blood performed 24 CoA cases 16 controls using Illumina...
Osteosarcoma (OS) is a common bone malignancy in children and adolescents. Although histological subtyping followed by improved OS treatment regimens have helped achieve favorable outcomes, lack of understanding the molecular subtypes remains challenge to characterize its genetic heterogeneity subsequently identify diagnostic prognostic biomarkers for developing effective treatments. In present study, global analysis DNA methylation, mRNA miRNA gene expression patient samples were correlated...
Abstract Background Guanosine triphosphate (GTP)-binding proteins play an important role in regulation of G-protein. Thus prediction GTP interacting residues a protein is one the major challenges field computational biology. In this study, attempt has been made to develop method for predicting with high accuracy (Acc), precision (Prec) and recall (Rc). Result All models developed study have trained tested on non-redundant (40% similarity) dataset using five-fold cross-validation. Firstly, we...
Abstract Myopia, commonly referred to as nearsightedness, is one of the most common causes visual disability throughout world. It affects more people worldwide than any other chronic impairment condition. Although prevalence varies among various ethnic groups, incidence myopia increasing in all populations across globe. Thus, it considered a pressing public health problem. Both genetics and environment play role development myopia. To elucidate epigenetic mechanism(s) underlying...
Abstract Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The initial interaction between Transmembrane Serine Protease 2 (TMPRSS2) primed SARS-CoV-2 spike (S) protein and host cell receptor angiotensin-converting enzyme (ACE-2) a pre-requisite step for this novel coronavirus pathogenesis. Here, we expressed GFP-tagged S-Ectodomain in Tni insect cells. That contained sialic acid-enriched N- O-glycans. Surface resonance plasmon...
Kinases are a group of intracellular signaling molecules that play critical roles in various biological processes. Even though kinases comprise one the most well-known therapeutic targets, many have been understudied and therefore warrant further investigation. DNA methylation is key epigenetic regulators modulate gene expression. In this study, human kinome’s expression patterns were analyzed using level-3 TCGA data for 32 cancers. Unsupervised clustering based on kinome revealed grouping...
DNA cytosine nucleotide methylation (epigenomics and epigenetics) is an important mechanism for controlling gene expression in cardiac development. Combined artificial intelligence whole-genome epigenomic analysis of circulating cell-free maternal blood has the potential detection fetal congenital heart defects.This study aimed to use genome-wide analyses minimally invasive defects.In this prospective study, was performed on using Illumina Infinium MethylationEPIC BeadChip array. Multiple...
Flavin binding proteins (FBP) plays a critical role in several biological functions such as electron transport system (ETS). These flavoproteins contain very tightly bound, sometimes covalently, flavin adenine dinucleotide (FAD) or mono nucleotide (FMN). The interaction between and amino acids of flavoprotein is essential for their functionality. Thus identification FAD interacting residues FBP an important step understanding function mechanism. In this study, we describe models developed...
Background Mannose binding proteins (MBPs) play a vital role in several biological functions such as defense mechanisms. These bind to mannose on the surface of wide range pathogens and help eliminating these from our body. Thus, it is important identify interacting residues (MIRs) order understand mechanism recognition by MBPs. Results This paper describes modules developed for predicting MIRs protein. Support vector machine (SVM) based models have been 120 protein chains, where no two...
Breast cancers exhibit highly heterogeneous molecular profiles. Although gene expression profiles have been used to predict the risks and prognostic outcomes of breast cancers, high variability limits its clinical application. In contrast, genetic mutation would be more advantageous than because mutations can stably detected mutational heterogeneity widely exists in cancer genomes. We analyzed 98 whole exome samples that were sorted into three subtypes, two grades stages. The sum deleterious...