Molecular Sequence Annotation

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  Subject Areas on Research

  • A cis-regulatory map of the Drosophila genome. 
  • A course-based research experience: how benefits change with increased investment in instructional time. 
  • A draft genome sequence of the elusive giant squid, Architeuthis dux. 
  • A high-resolution map of human evolutionary constraint using 29 mammals. 
  • An encyclopedia of mouse DNA elements (Mouse ENCODE). 
  • An integrated encyclopedia of DNA elements in the human genome. 
  • Application of an optimized annotation pipeline to the Cryptococcus deuterogattii genome reveals dynamic primary metabolic gene clusters and genomic impact of RNAi loss. 
  • Architecture of the human regulatory network derived from ENCODE data. 
  • Associations between genetic variants in mRNA splicing-related genes and risk of lung cancer: a pathway-based analysis from published GWASs. 
  • Chromosomal-Level Genome Assembly of the Sea Urchin Lytechinus variegatus Substantially Improves Functional Genomic Analyses. 
  • Comparative analysis of metazoan chromatin organization. 
  • Comparative genomics reveals insights into avian genome evolution and adaptation. 
  • Comparative genomics reveals molecular features unique to the songbird lineage. 
  • Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. 
  • Connecting genetic risk to disease end points through the human blood plasma proteome. 
  • Coordination of platinum therapeutic agents to met-rich motifs of human copper transport protein1. 
  • Differential DNA methylation patterns in human Schlemm's canal endothelial cells with glaucoma. 
  • Differentially Expressed miRNAs in Hepatocellular Carcinoma Target Genes in the Genetic Information Processing and Metabolism Pathways. 
  • Directional Exosome Proteomes Reflect Polarity-Specific Functions in Retinal Pigmented Epithelium Monolayers. 
  • Diversity of variant alleles encoding Kidd, Duffy, and Kell antigens in individuals with sickle cell disease using whole genome sequencing data from the NHLBI TOPMed Program. 
  • Draft genome of the fungicidal biological control agent Burkholderia anthina strain XXVI. 
  • Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution. 
  • Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. 
  • Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. 
  • Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS. 
  • Functional Annotation Signatures of Disease Susceptibility Loci Improve SNP Association Analysis 
  • Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. 
  • GWAS analysis of handgrip and lower body strength in older adults in the CHARGE consortium. 
  • Gene Ontology annotations and resources. 
  • Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii. 
  • Genome-wide analysis of miRNA signature in the APPswe/PS1ΔE9 mouse model of alzheimer's disease. 
  • Global analysis of protein folding thermodynamics for disease state characterization. 
  • Identification of functional elements and regulatory circuits by Drosophila modENCODE. 
  • Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method. 
  • Integrative annotation of variants from 1092 humans: application to cancer genomics. 
  • Investigating the genetic architecture of noncognitive skills using GWAS-by-subtraction. 
  • Know Me! Unraveling the Riddle of Calcific Aortic Valve Disease by Bioinformatics. 
  • Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells. 
  • Loss of Drosophila melanogaster p21-activated kinase 3 suppresses defects in synapse structure and function caused by spastin mutations. 
  • MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. 
  • Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. 
  • Mapping and characterization of structural variation in 17,795 human genomes. 
  • Methylomics of gene expression in human monocytes. 
  • Molecular and genetic evidence for a tetrapolar mating system in the basidiomycetous yeast Kwoniella mangrovensis and two novel sibling species. 
  • Multi-trait genome-wide association study identifies new loci associated with optic disc parameters. 
  • POWRS: position-sensitive motif discovery. 
  • Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events. 
  • Patterns of gut bacterial colonization in three primate species. 
  • Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class. 
  • Predicting gene structure changes resulting from genetic variants via exon definition features. 
  • Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. 
  • Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl. 
  • RNA-seq: impact of RNA degradation on transcript quantification. 
  • Re-annotation of the woodland strawberry (Fragaria vesca) genome. 
  • SNiPA: an interactive, genetic variant-centered annotation browser. 
  • Scanning Quadrupole Data-Independent Acquisition, Part B: Application to the Analysis of the Calcineurin-Interacting Proteins during Treatment of Aspergillus fumigatus with Azole and Echinocandin Antifungal Drugs. 
  • Six reference-quality genomes reveal evolution of bat adaptations. 
  • Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. 
  • Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. 
  • The Disease and Gene Annotations (DGA): an annotation resource for human disease. 
  • The Gene Ontology: enhancements for 2011. 
  • The accessible chromatin landscape of the human genome. 
  • The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
  • Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. 
  • Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. 
  • Using context to improve protein domain identification. 
  • VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era. 
  • Visual presentation as a welcome alternative to textual presentation of gene annotation information. 
  • dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa. 
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  Keywords of People

  • Reddy, Timothy E, Associate Professor of Biostatistics & Bioinformatics, Molecular Genetics and Microbiology