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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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