Madhusudan Gujral
A5048431290- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Autism Spectrum Disorder Research
- Genetics and Neurodevelopmental Disorders
- Distributed and Parallel Computing Systems
- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Congenital heart defects research
- Nutrition, Genetics, and Disease
- Research Data Management Practices
- Ethnobotanical and Medicinal Plants Studies
- Contact Dermatitis and Allergies
- Pharmacological Effects of Medicinal Plants
- Reproductive Health and Contraception
- RNA and protein synthesis mechanisms
- Natural product bioactivities and synthesis
- Zoonotic diseases and public health
- Cytomegalovirus and herpesvirus research
- Monoclonal and Polyclonal Antibodies Research
- Genomics and Chromatin Dynamics
- Dermatology and Skin Diseases
- Ginseng Biological Effects and Applications
- Pharmacological Effects of Natural Compounds
- Historical Studies on Reproduction, Gender, Health, and Societal Changes
University of California, San Diego
2010-2022
San Diego Supercomputer Center
2010-2020
University of Lucknow
1954
Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set eight structural variant classes comprising both balanced unbalanced variants, which constructed using short-read DNA sequencing data statistically phased onto haplotype blocks 26 populations. Analysing this set, identify gene-intersecting exhibiting population stratification naturally occurring homozygous gene knockouts that suggest...
The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies human genetic diversity and disease association. Here, we apply a suite long-read, short-read, strand-specific technologies, optical mapping, variant discovery algorithms to comprehensively analyze three trios define the full spectrum variation in haplotype-resolved manner. We identify 818,054 indel (<50 bp) 27,622 SVs (≥50 per genome. also discover 156 inversions genome 58 intersect...
Inherited variation contributes to autism About one-quarter of genetic variants that are associated with spectrum disorder (ASD) due de novo mutations in protein-coding genes. Brandler et al. wanted determine whether changes noncoding regions the genome autism. They applied whole-genome sequencing ∼2600 families at least one affected child. Children ASD had inherited structural from their father. Regulatory some specific genes were disrupted among multiple families, supporting idea a...
Short tandem repeats (STRs) and variable number (VNTRs) are important sources of natural disease-causing variation, yet they have been problematic to resolve in reference genomes genotype with short-read technology. We created a framework model the evolution instability STRs VNTRs apes. phased assembled 3 ape (chimpanzee, gorilla, orangutan) using long-read 10x Genomics linked-read sequence data for 21,442 human discovered 6 haplotype-resolved assemblies Yoruban, Chinese, Puerto Rican...
While germline copy-number variants (CNVs) contribute to schizophrenia (SCZ) risk, the contribution of somatic CNVs (sCNVs)-present in some but not all cells-remains unknown. We identified sCNVs using blood-derived genotype arrays from 12,834 SCZ cases and 11,648 controls, filtering at loci recurrently mutated clonal blood disorders. Likely early-developmental were more common (0.91%) than controls (0.51%, p = 2.68e-4), with recurrent deletions exons 1-5
ABSTRACT The incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies human genetic diversity and disease association. Here, we apply a suite long-read, short-read, strand-specific technologies, optical mapping, variant discovery algorithms to comprehensively analyze three parent–child trios define the full spectrum variation in haplotype-resolved manner. We identify 818,054 indel (<50 bp) 27,622 SVs (≥50 per genome. also discover 156...
The collection of T cell receptors (TCRs) generated by somatic recombination is large but unknown. We generate TCR repertoire datasets as a resource to facilitate detailed studies the role clonotypes and repertoires in health disease. estimate size individual human recombined expressed TCRs sequence analysis determine extent sharing between repertoires. Our experiments reveal that each blood sample contains 5 million 21 clonotypes. Three individuals share 8% TCRβ- or 11% TCRα-chain Sorting...
Over the last decade, workflows have been established as a mechanism for scientific developers to create simplified views of complex processes. However, there is need comprehensive system architecture link creating with researchers launching in large scale computing environments. We present CAMERA 2.0 Cyber infrastructure platform that provides scaffold where can be uploaded into system, and user interface components viewing results are automatically generated. In 2.0, metagenomics...
Abstract Genomic copy number variants (CNVs) have been strongly implicated in the etiology of schizophrenia (SCZ). However, apart from a small risk variants, elucidation CNV contribution to has difficult due rarity alleles, all occurring less than 1% cases. We sought address this obstacle through collaborative effort which we applied centralized analysis pipeline SCZ cohort 21,094 cases and 20,227 controls. observed global enrichment burden (OR=1.11, P=5.7e −15 ), persisted after excluding...
Abstract The genetic architecture of autism spectrum disorder (ASD) is known to consist contributions from gene-disrupting de novo mutations and common variants modest effect. We hypothesize that the unexplained heritability ASD also includes rare inherited with intermediate effects. investigated genome-wide distribution functional impact structural (SVs) through whole genome analysis ( ≥ 30X coverage) 3,169 subjects 829 families affected by ASD. Genes are intolerant inactivating in exome...
Abstract Genetic studies of Autism Spectrum Disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment structural variation (SV) has been restricted by the coarse resolution current approaches. By applying a custom pipeline for SV discovery, genotyping assembly genome sequencing 235 subjects, 71 cases, 26 sibling controls their parents, we present an atlas 1.2 million SVs (5,213/genome), comprising 11 different classes. We demonstrate...
Community Cyber infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) is an eScience project to enable the microbial ecology community in managing challenges of metagenomics analysis. CAMERA supports extensive metadata based data acquisition access, as well execution experiments through standard customized scientific workflows. Users can use a wide range analysis tools select invoke integrated annotation genomic datasets. also search sort information on selected...