A5067815042- Genomics and Rare Diseases
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Connexins and lens biology
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Antimicrobial Peptides and Activities
- Chromosomal and Genetic Variations
- Cancer-related molecular mechanisms research
- 14-3-3 protein interactions
- Microbial Natural Products and Biosynthesis
- Gene Regulatory Network Analysis
- Lung Cancer Treatments and Mutations
- Sarcoma Diagnosis and Treatment
- Bone Tumor Diagnosis and Treatments
- Viral Infectious Diseases and Gene Expression in Insects
- Cardiovascular Function and Risk Factors
- Health, Environment, Cognitive Aging
- Genetic Associations and Epidemiology
- Gene expression and cancer classification
- RNA regulation and disease
- Environmental DNA in Biodiversity Studies
Seven Bridges Genomics (United States)
2020-2023
Indiana University – Purdue University Indianapolis
2016-2018
Walker (United States)
2017-2018
Middle East Technical University
2012-2015
The precisionFDA Truth Challenge V2 aimed to assess the state of art variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 call sets for one or more sequencing technologies (Illumina, PacBio HiFi, Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants updated Genome a Bottle benchmark genome stratifications. submissions included numerous...
Summary The precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their pipelines submitted 64 callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices benchmarking small variants new GIAB benchmark sets genome...
Accurate identification of de novo variants (DNVs) remains challenging despite advances in sequencing technologies, often requiring ad hoc filters and manual inspection. Here, we explored a purely informatic, consensus-based approach for identifying DNVs proband-parent trios using short-read genome data. We evaluated variant calls generated by three sequence analysis pipelines-GATK HaplotypeCaller, DeepTrio, Velsera GRAF-and examined the assumption that requirement consensus can serve as an...
Lens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations splicing events during mouse lens formation using RNA-seq data from multiple developmental stages, construct molecular portrait of known novel transcripts. We show that extent novelty expressed transcripts decreases significantly in post-natal compared to embryonic stages. Characterization into partially (PNTs) completely (CNTs) (novelty score ≥ 70%) revealed...
Abstract Graph-based genome reference representations have seen significant development, motivated by the inadequacy of current human to represent diverse genetic information from different populations and its inability maintain same level accuracy for non-European ancestries. While there been many efforts develop computationally efficient graph-based toolkits NGS read alignment variant calling, methods curate genomic variants subsequently construct graphs remain an understudied problem that...
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the proteins into cells leads to changes in signaling mechanism either by activating or inhibiting proteins. Given infection modifies response network host, more coherent view underlying biological processes and networks can be obtained using modeling approach based on reverse engineering principles. In this work, we have used published temporal phosphoproteomic dataset...
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants CLIP (crosslinking and immunoprecipitation) protocols are currently available study global protein–RNA interaction landscape single-nucleotide resolution a cell, there very few tools that can facilitate understanding dissecting functional associations RBPs from resulting maps. Here, we present Seten, web-based...
Survival analysis in biomedical sciences is generally performed by correlating the levels of cellular components with patients’ clinical features as a common practice prognostic biomarker discovery. While and primary focus such cancer genomics so far has been to identify potential genes, alternative splicing – posttranscriptional regulatory mechanism that affects functional form protein due inclusion or exclusion individual exons giving rise products, increasingly gained attention prevalence...
ABSTRACT Accurate identification of germline de novo variants (DNVs) remains a challenging problem despite rapid advances in sequencing technologies as well methods for the analysis data they generate, with putative solutions often involving ad hoc filters and visual inspection identified variants. Here, we present purely informatic method DNVs by analyzing short-read genome from proband-parent trios. Our evaluates variant calls generated three sequence pipelines utilizing different...
Abstract It has recently been shown that patients from non-European ancestries are at a higher risk of inappropriate clinical intervention because inaccurate biomarker estimation, arising the reference bias inherent in standard methods for determining tumor genome sequencing data. Here we demonstrate these inaccuracies can be reduced by using pangenome appropriate patient’s population. We constructed novel secondary analysis workflow where serves as scaffold mapping reads, and is also...
ABSTRACT Gene panels represent a widely used strategy for genetic testing in vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection short coding variants, it fails to detect most larger variants. Recent studies have recommended the adoption pangenomes augment large variants from targeted sequencing, potentially providing diagnostic laboratories with possibility streamline work-ups and reduce costs. Here, we analyze large-scale cohort comprising 1,952...
ABSTRACT Graph-based genome reference representations have seen significant development, motivated by the inadequacy of current human to represent diverse genetic information from different populations and its inability maintain same level accuracy for non-European ancestries. While there been many efforts develop computationally efficient graph-based toolkits NGS read alignment variant calling, methods curate genomic variants subsequently construct graphs remains an understudied problem...
In synthetic biology, designing a new genetic construct demands in-detail studies of its candidate components individually and in composition with each other. These costly wet lab experiments require considerable amount time usually result undesired output. this paper, we propose method for the extraction existing or novel devices from available biological parts iGEMs BioParts Registry ordered resulting based on their computed reliabilities. This is very efficient it helps wetlab biologists...
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the proteins into cells leads to changes in signaling mechanism either by activating or inhibiting proteins. Using high-throughput ‘omic’ technologies, components can be quantified at different levels; however, experimental hits are incomplete represent whole system as some driver stay hidden within data. Given infection modifies response network host, more coherent view...
Extraskeletal myxoid chondrosarcoma (EMC) is an ultra-rare cancer that makes up less than 3% of all soft tissue sarcomas. It most often arises in the tissues proximal limbs and has a higher incidence males. Though EMC good prognosis, it indolent course with high rates local recurrence as well metastasis to lungs. characterized 70% cases by EWS1-NR4A3 translocation, leading constitutive expression NR4A3. Structural variants (SVs) EMC, especially large-scale genomic alterations, have not been...