A5056248422- Cancer Genomics and Diagnostics
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Genomics and Rare Diseases
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Primary Care and Health Outcomes
- Extracellular vesicles in disease
- Health Sciences Research and Education
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
- Health, Environment, Cognitive Aging
- CRISPR and Genetic Engineering
- Acute Myeloid Leukemia Research
- Medical Coding and Health Information
- Health Policy Implementation Science
- Animal Virus Infections Studies
- RNA regulation and disease
- Meta-analysis and systematic reviews
- Bioinformatics and Genomic Networks
- Antimicrobial Peptides and Activities
Roche (United States)
2024
Baylor College of Medicine
2015-2024
Seven Bridges Genomics (United States)
2021-2022
Icahn School of Medicine at Mount Sinai
2012-2013
Child Health and Development Institute
2013
Ashland (United States)
2011
University of Illinois Chicago
2009-2011
Highlights•exceRpt processes and analyzes exRNA profiling data•exceRpt generates quality control metrics, RNA abundance estimates, reports•A user-friendly, browser-based graphical interface is available•exceRpt all RNA-seq datasets in the AtlasSummarySmall sequencing has been widely adopted to study diversity of extracellular RNAs (exRNAs) biofluids; however, analysis samples can be challenging: they are vulnerable contamination artifacts from different isolation techniques, present lower...
In animal gonads, PIWI proteins and their bound 23–30 nt piRNAs guard genome integrity by the sequence specific silencing of transposons. Two branches piRNA biogenesis, namely primary processing ping-pong amplification, have been proposed. Despite an overall conceptual understanding identity and/or function involved players are largely unknown. Here, we demonstrate essential role for female sterility gene shutdown in biology. Shutdown, evolutionarily conserved cochaperone collaborates with...
Abstract Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome interpreting variants to inform healthcare management have lacking. Results Here we present ClinGen Variant Curation Interface (VCI), a global open-source variant...
Abstract Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation 3,753 (69% examined) lincRNAs, with 54% active in one 14 cell/tissue clusters an additional 15% two or three clusters. A larger lincRNA TSSs is marked manner H3K4me1 than H3K4me3....
ABSTRACT Influenza A virus (IAV) is an unremitting that results in significant morbidity and mortality worldwide. Key to the viral life cycle RNA-dependent RNA polymerase (RdRp), a heterotrimeric complex responsible for both transcription replication of segmented genome. Here, we demonstrate utilizes small enhancer regulate enzymatic activity maintain stoichiometric balance We IAV synthesizes RNAs (svRNAs) interact with RdRp order promote genome segment-specific manner. svRNAs localize...
The large diversity and volume of extracellular RNA (exRNA) data that will form the basis exRNA Atlas generated by Extracellular Communication Consortium pose a substantial integration challenge. We here present strategy is being implemented Data Management Resource Repository, which employs metadata, biomedical ontologies Linked technologies, such as Description Framework to integrate diverse set profiles into an enable integrative analysis. focus on following three specific tasks: (a)...
We created the PDX Network (PDXNet) portal (https://portal.pdxnetwork.org/) to centralize access National Cancer Institute-funded PDXNet consortium resources, facilitate collaboration among researchers and make these data easily available for research. The includes sections analysis results, metrics activities, processing protocols training materials data. Currently, contains model information resources from 334 new models across 33 cancer types. Tissue samples of were deposited in NCI's...
To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort extend Gene Ontology (GO) with subcellular structure concepts relevant exRNA domain. By extending GO in this manner, data/metadata will be more easily annotated and queried because it based on a shared set terms relationships research. following consensus-building process, worked several academic societies/consortia, including ERCC, ISEV, ASEMV, identify...
Synthesis and curation of evidence regarding the clinical actionability secondary findings (SFs) from genome-scale sequencing are needed to support decision-making on reporting these findings. To assess SFs in children adolescents, Clinical Genome Resource established Pediatric Actionability Working Group (AWG).The AWG modified framework existing Adult AWG, which included production summary reports for genes associated conditions consensus scores specific outcome-intervention pairs....
MiST is a novel approach to variant calling from deep sequencing data, using the inverted mapping developed for Geoseq. Reads that can map targeted exonic region are identified exact matches tiles region. The reads then aligned targets discover variants. carefully handles paralogous ambiguously genome and clonal arising PCR bias, which two major sources of errors in calling. reduced computational complexity selected regions improves speed, specificity sensitivity detection. Compared with...
Abstract Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome interpreting variants to inform healthcare management have lacking. Results Here we present ClinGen Variant Curation Interface (VCI), a global open-source variant...
Ribosome‐nascent peptide interactions are involved in regulation of expression several bacterial genes. One such example is the induction an antibiotic resistance gene, ermC (erythromycin methyltransferase). Expression controlled by ribosome stalling at a short upstream ORF (uORF) and depends on sequence nascent presence erythromycin. A number other genes that confer to ribosome‐targeting antibiotics inducible, but most cases, underlying mechanisms unknown. comprehensive analysis regions...
Abstract Applying machine learning algorithms to analysis of multi-omics datasets has provided a wealth and interpretations data not easily achievable by conventional methods. The Cancer Genomics Cloud (CGC), powered Seven Bridges, offers many helpful features simplify streamline the performance (ML) tasks on platform. CGC platform contains tools for all steps ML project, from exploration, model generation, production, so that key occur Data Cruncher interactive tool enables users perform...
Abstract The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is an NCI-funded platform that streamlines access to large cancer datasets, bioinformatic tools, and cloud computation for researchers. attributes of the CGC designed democratize data analysis also make it ideal training next generation scientists. During Covid-19 pandemic, has become clear remote/virtual learning great importance workforce development, reducing barriers high quality educational resources critical many...
Abstract The exponential growth and diversity of complex datasets poses severe challenges in terms data access sharing, analysis compute power. Cancer Genomics Cloud (CGC), powered by Seven Bridges, is a NCI-funded resource that provides unified platform for cancer co-localizing three components within the cloud: 1) large from Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC) several others; 2) >400 bioinformatics tools best-practice workflows analyzing...