Profiling Reactive Metabolites via Chemical Trapping and Targeted Mass SpectrometryDoes the brain listen to the gut?(Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulansA robust adaptive denoising framework for real-time artifact removal in scalp EEG measurementsImputing Gene Expression in Uncollected Tissues Within and Beyond GTExSmall Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand BreakControlling the Cyanobacterial Clock by Synthetically Rewiring MetabolismChoosing experiments to accelerate collective discoveryThe transcriptional landscape of age in human peripheral bloodDigital signaling decouples activation probability and population heterogeneityExpression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic VariationComputational Recipes in EnzymologyThe impact of human copy number variation on gene expressionThe microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslandsKey metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasilianaHealth ROI as a measure of misalignment of biomedical needs and resourcesHospital-associated microbiota and implications for nosocomial infectionsCircadian rhythms: A protein fold switch joins the circadian oscillator to clock output in cyanobacteriaDisentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait LociThe ocean sampling day consortiumAthletic equipment microbiota are shaped by interactions with human skinHuman HLA-G+ extravillous trophoblasts: Immune-activating cells that interact with decidual leukocytesAccurate and fast multiple-testing correction in eQTL studiesWhole genome resequencing of experimental populations reveals polygenic basis of egg size variation in Drosophila melanogasterLifestyle evolution in cyanobacterial symbionts of spongesThe role of the commensal microbiota in the regulation of tolerance to dietary allergensUsing corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseasesNfkb1 is a haploinsufficient DNA damage-specific tumor suppressorAutomated co-culture system for spatiotemporal analysis of cell-to-cell communicationPotential contribution of anammox to nitrogen loss from paddy soils in Southern ChinaMetagenomes from two microbial consortia associated with Santa Barbara seep oilOur unique microbial identityForensic analysis of the microbiome of phones and shoesZodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA DataCollagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leakGenetic similarity between cancers and comorbid Mendelian diseases identifies candidate driver genesThe soil microbiome influences grapevine-associated microbiotaTowards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patientsSpatial and temporal variations in indoor environmental conditions, human occupancy, and operational characteristics in a new hospital buildingOur interface with the built environment: immunity and the indoor microbiotaImmVar project: Insights and design considerations for future studies of "healthy" immune variationNoise facilitates transcriptional control under dynamic inputsSatellite remote sensing data can be used to model marine microbial metabolite turnoverRare occurrence of EGFRvIII deletion in head and neck squamous cell carcinomaA novel mechanism of inherited TBG deficiency: mutation in a liver-specific enhancerBionimbus: a cloud for managing, analyzing and sharing large genomics datasetsLife in a World without MicrobesIntegrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypesComparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathwaysWidespread genetic epistasis among cancer genesThe complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenomePri peptides are mediators of ecdysone for the temporal control of developmentTowards understanding cell penetration by stapled peptidesSu(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryosTranscription Factor Networks In Drosophila MelanogasterMixtures of opposing phosphorylations within hexamers precisely time feedback in the cyanobacterial circadian clockIntersection of population variation and autoimmunity genetics in human T cell activationIntersection of population variation and autoimmunity genetics in human T cell activationFractional anisotropy asymmetry and the side of seizure origin for partial onset-temporal lobe epilepsyLongitudinal analysis of microbial interaction between humans and the indoor environmentComparative Analysis of Regulatory Information and Circuits Across Distant SpeciesCommensal Bacteria Protect Against Food Allergen SensitizationRhythms in Energy Storage Control the Ability of the Cyanobacterial Circadian Clock to ResetYorkie promotes transcription by recruiting a histone methyltransferase complexIntegrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomasAncestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.Low grade prostate cancer diverges early from high grade and metastatic disease.The spectrum of somatic mutations in high-risk acute myeloid leukaemia with -7/del(7q).Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification.Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells. Genomics of alternative splicing: evolution, development and pathophysiology.Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.Human and environmental impacts on river sediment microbial communities.Understanding cultivar-specificity and soil determinants of the cannabis microbiome.Metagenomes from two microbial consortia associated with Santa Barbara seep oil.Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.The complete genome sequence for putative H2 - and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamicsRegulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cellsImmunocytochemical localization of epidermal growth factor-receptor in early embryos of the Japanese medaka fish (Oryzias latipesExpress primer generator tool for high throughput gene cloning and expression. Sequences of versatile broad-host-range vectors of the RK2 family.Towards higher-throughput membrane protein production for structural genomics initiatives.Loss of the death receptor CD95 (Fas) expression by dendritic cells protects from a chronic viral infection Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota.Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation: a biotechnological perspective.The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments.Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity.Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis.Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability.Systems analysis of human multigene disorders. Preface.CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility « Research Papers « Institute for Genomics and Systems Biology

by Barbara Stranger, Dimas AS, Nica AC, Montgomery SB, Stranger BE, Raj T, Buil A, Giger T, Lappalainen T, Gutierrez-Arcelus M; MuTHER Consortium, McCarthy MI, Dermitzakis ET.

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Patterns of cis regulatory variation in diverse human populations.

by Barbara Stranger, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.

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Systems and genome-wide approaches unite to provide a route to personalized medicine.

by Barbara Stranger, Stranger BE, Björkegren J, Dolan ME, Ritchie MD.

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Metagenomics - a guide from sampling to data analysis

by Jack Gilbert, Thomas T, Meyer F.

PMID: 22587947

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.

by Barbara Stranger, Brown KH, Dobrinski KP, Lee AS, Gokcumen O, Mills RE, Shi X, Chong WW, Chen JY, Yoo P, David S, Peterson SM, Raj T, Choy KW, Stranger BE, Williamson RE, Zon LI, Freeman JL, Lee C.

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Research

Papers Archive

2012 Research Papers Archive

Draft genome sequence of Agrobacterium albertimagni strain AOL15.

Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome

Draft genome sequence of Achromobacter piechaudii strain HLE.

A conserved eEF2 coding variant in SCA26 leads to loss of translational fidelity and increased susceptibility to proteostatic insult

Orderly wheels of the cyanobacterial clock

Caffeic acid phenethyl ester suppresses the proliferation of human prostate cancer cells through inhibition of p70S6K and Akt signaling networks

Relating human genetic variation to variation in drug responses.

Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel

Orderly wheels of the cyanobacterial clock

Inhibition of oncogenic Wnt signaling through direct targeting of β-catenin

Coordinating GWAS results with gene expression in a systems immunologic paradigm in autoimmunity.

Sex-biased genetic effects on gene regulation in humans

Patterns of cis regulatory variation in diverse human populations.

Systems and genome-wide approaches unite to provide a route to personalized medicine.

Metagenomics - a guide from sampling to data analysis

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis.