Shilpa Garg
A5060605357- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Dermatologic Treatments and Research
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Acne and Rosacea Treatments and Effects
- Genomic variations and chromosomal abnormalities
- Ovarian cancer diagnosis and treatment
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Cancer and Skin Lesions
- melanin and skin pigmentation
- Sarcoma Diagnosis and Treatment
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Facial Rejuvenation and Surgery Techniques
- Breast Lesions and Carcinomas
- Antifungal resistance and susceptibility
- Cancer Genomics and Diagnostics
- Genital Health and Disease
- Nail Diseases and Treatments
- Skin Protection and Aging
- Single-cell and spatial transcriptomics
- Neonatal skin health care
- Genetic Mapping and Diversity in Plants and Animals
Syngene International (India)
2022-2025
Biocon (India)
2025
Bristol-Myers Squibb (India)
2025
Graphic Era University
2025
Technical University of Denmark
2023-2024
Novo Nordisk Foundation
2023-2024
University of Manchester
2024
University of Copenhagen
2021-2023
Shilpa (India)
2022
Harvard University
2019-2021
Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues use, maintain contribute the project, support from multiple national infrastructure providers that enable freely analysis training services. The Training Network supports free, self-directed, virtual >230 integrated tutorials. Project engagement metrics have continued grow...
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
Abstract Read-based phasing allows to reconstruct the haplotypes of a sample purely from sequencing reads. While is an important step for answering questions about population genetics, compound heterozygosity, and aid in clinical decision making, there has been lack accurate, usable standards-based software. WhatsHap production-ready tool highly accurate read-based phasing. It was designed beginning leverage third-generation technologies, whose long reads can span many variants are therefore...
Haplotype-resolved or phased genome assembly provides a complete picture of genomes and their complex genetic variations. However, current algorithms for either do not generate chromosome-scale phasing require pedigree information, which limits application. We present method named diploid (DipAsm) that uses long, accurate reads long-range conformation data single individuals to within 1 day. Applied four public human genomes, PGP1, HG002, NA12878 HG00733, DipAsm produced haplotype-resolved...
Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still many gaps and errors, does not represent biological genome as is blend multiple individuals 3,4 Recently, telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but derived from hydatidiform mole cell line nearly homozygous 5 To address these limitations, Human Pangenome...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. contains 47 phased, diploid assemblies from cohort of genetically diverse individuals. These cover more than 99% the expected sequence and are accurate at structural base-pair levels. Based on alignments assemblies, we generated that captures known variants haplotypes, reveals novel alleles structurally complex loci, adds 119 million base pairs euchromatic polymorphic 1,529 gene...
Abstract Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared pattern SNVs between unique duplicated regions 3,4 We find that are elevated 60% to estimate at least 23% this increase is due interlocus gene conversion (IGC) with up 4.3 megabase pairs SD sequence...
Abstract The diploid nature of the human genome is neglected in many analyses done today, where a perceived as set unphased variants with respect to reference genome. This lack haplotype-level can be explained by methods that produce dense and accurate chromosome-length haplotypes at reasonable costs. Here we introduce an integrative phasing strategy combines global, but sparse obtained from strand-specific single-cell sequencing (Strand-seq) dense, yet local, haplotype information available...
Abstract Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long and linked now enable us construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5 million base-pair (bp) region where diploid assembly is particularly useful - Major Histocompatibility Complex (MHC). Here, we develop genome benchmark derived from for openly-consented Genome in Bottle sample HG002. assemble single contig each...
A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction have information available. In 2018, scientists across the world united under Earth BioGenome Project (EBP), aiming produce high-quality reference genomes containing ~1.5 million recognized species. As European node EBP, Reference Genome Atlas (ERGA) sought implement new decentralised, equitable and inclusive model for producing genomes. For this, ERGA launched...
<b>Background:</b> Atrophic acne scars are difficult to treat. The demand for less invasive but highly effective treatment is growing. Objective: To assess the efficacy of combination therapy using subcision, microneedling and 15% trichloroacetic acid (TCA) peel in management atrophic scars. <b>Materials Methods:</b> Fifty patients with were graded Goodman Baron Qualitative grading. After dermaroller TCA performed alternatively at 2-weeks interval a total 6 sessions each. Grading scar...
Scar formation is an inevitable consequence of wound healing from either a traumatic or surgical intervention. The aesthetic appearance scar the most important criteria to judge outcome. An understanding anatomy and along with experience, meticulous planning technique can reduce complications improve revision does not erase but helps make it less noticeable more acceptable. Both non-surgical techniques, used alone in combination be for revising scar. In surgeon should decide on when act type...
Abstract Motivation Constructing high-quality haplotype-resolved de novo assemblies of diploid genomes is important for revealing the full extent structural variation and its role in health disease. Current assembly approaches often collapse two sequences into one haploid consensus sequence and, therefore, fail to capture nature organism under study. Thus, building an assembler capable producing accurate complete assemblies, while being resource-efficient with respect sequencing costs, a key...
Abstract New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, comprehensiveness. Translating these routine research clinical practice requires robust benchmark sets. We developed the first set for identification of both false negative positive germline SVs, which complements recent efforts emphasizing increasingly comprehensive characterization SVs. To create this a broadly consented son in Personal...
Abstract To extend the frontier of genome editing and enable repetitive elements mammalian genomes, we made use a set dead-Cas9 base editor (dBE) variants that allow at tens thousands loci per cell by overcoming death associated with DNA double-strand breaks single-strand breaks. We used gRNAs targeting elements—ranging in target copy number from about 32 to 161 000 cell. dBEs enabled survival after large-scale editing, allowing targeted mutations up ∼13 200 ∼12 293T human induced...
Abstract Cancer genomes are highly complex and heterogeneous. The standard short-read sequencing analytical methods unable to provide the complete precise base-level structural variant landscape of cancer genomes. In this work, we apply high-resolution long accurate HiFi long-range Hi-C melanoma COLO829 line. Also, develop an efficient graph-based approach that processes these data types for chromosome-scale haplotype-resolved reconstruction characterise landscape. Our method produces...
Immunotherapy is an evolving therapeutic modality for the treatment of warts. We conducted a study to assess efficacy and safety intralesional Mycobacterium w vaccine warts at sites that were difficult treat.Thirty patients with least one wart present on either plantar surface their feet, palms, volar aspect fingers, or periungual subungual region, treated 0.1 ml killed given intralesionally in single wart, without any prior sensitisation dose. Thereafter, injection was intervals four weeks...