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

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

by Robert Grossman, Kevin White, Allison Heath, Chaitanya Bandlamudi, Jonathan Spring, Matthew Greenway, Megan McNerney, David Hanley, Powell R, Suarez R,

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PMID: 24464852

Life in a World without Microbes

by Jack Gilbert, Neufeld JD

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PMID: 25513890

Integrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypes

by Kevin White, Everett E. Vokes, Keck MK, Zuo Z, Khattri A, Stricker TP, Brown CD, Imanguli M, Rieke D, Endhardt K, Fang P, Brägelmann J, DeBoer R, El-Dinali M,Aktolga S, Lei Z, Tan P, Rozen SG, Salgia R, Weichselbaum RR, Lingen MW, Story MD, Ang KK, Cohen EE, Seiwert TY

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PMID: 25492084

Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and hexachlorocyclohexane (HCH) degradation pathways

by Jack Gilbert, Verma H, Kumar R, Oldach P, Sangwan N, Khurana JP, Lal R.

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PMID: 25418849

Widespread genetic epistasis among cancer genes

by Kevin White, Megan McNerney, Wang X, Fu AQ

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PMID: 25407795

The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome

by Dionysios Antonopoulos, Folker Meyer, Jack Gilbert, Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Desai N, Glass EM, Paczian T, Wilke A, Kemner KM

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PMID: 24628880

Pri peptides are mediators of ecdysone for the temporal control of development

by Kevin White, Rebecca Spokony, Chanut-Delalande H, Hashimoto Y, Pelissier-Monier A, Dib A, Kondo T, Bohère J, Niimi K, Latapie Y, Inagaki S, Dubois L, Valenti P, Polesello C, Kobayashi S, Moussian B, Plaza S, Kageyama Y, Payre F

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PMID: 25344753

Towards understanding cell penetration by stapled peptides

by Raymond Moellering, Qian Chu, Gerard J. Hilinski, Young-Woo Kim, Tom N. Grossmann, Johannes T.-H. Yeh, Gregory L. Verdine

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Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos

by Kevin White, Lijia Ma, Ozdemir A, Stathopoulos A.

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PMID: 25313963

Transcription Factor Networks In Drosophila Melanogaster

by Kevin White, Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S.

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PMID: 25242320

Mixtures of opposing phosphorylations within hexamers precisely time feedback in the cyanobacterial circadian clock

by Michael Rust, Jenny Lin, Chew J, Chockanathan U

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PMID: 25197081

Intersection of population variation and autoimmunity genetics in human T cell activation

by Barbara Stranger, Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, De Jager P, Mathis D, Regev A, Benoist C.

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PMID: 25214635

Intersection of population variation and autoimmunity genetics in human T cell activation

by Barbara Stranger, Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, De Jager P, Mathis D, Regev A, Benoist C.

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PMID: 25214635

Fractional anisotropy asymmetry and the side of seizure origin for partial onset-temporal lobe epilepsy

by Robert Grossman, Li H, Xue Z, Dulay MF Jr, Verma A, Karmonik C, Wong ST.

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PMID: 25037096

Longitudinal analysis of microbial interaction between humans and the indoor environment

by Jack Gilbert, Sean Gibbons, Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK,Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R

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PMID: 25170151

Comparative Analysis of Regulatory Information and Circuits Across Distant Species

by Kevin White, Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

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PMID: 25164757

Commensal Bacteria Protect Against Food Allergen Sensitization

by Dionysios Antonopoulos, Andrew T. Stefkaa, Taylor Feehleya, Prabhanshu Tripathia, Ju Qiub, Kathy McCoyc, Sarkis K. Mazmaniand, Melissa Y. Tjotae, Goo-Young Seoa, Severine Caoa, Betty R. Theriaultf, Liang Zhoub, Eugene B. Change, Yang-Xin Fua, and Cathryn R. Nagler

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Rhythms in Energy Storage Control the Ability of the Cyanobacterial Circadian Clock to Reset

by Michael Rust, Gopal Pattanayak, Connie Phong

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Yorkie promotes transcription by recruiting a histone methyltransferase complex

by Kevin White, Oh H, Slattery M, Ma L, Mann RS, Irvine KD

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PMID: 25017066

Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas

by Kevin White, Everett E. Vokes, Seiwert TY, Zuo Z, Keck MK, Khattri A, Pedamallu CS, Stricker T, Brown C, Pugh TJ, Stojanov P, Cho J,Lawrence MS, Getz G, Brägelmann J, DeBoer R, Weichselbaum RR, Langerman A, Portugal L, Blair E, Stenson K, Lingen MW, Cohen EE, Hammerman PS.

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PMID: 25056374

Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change.

by Kevin White, Martinez C, Rest JS, Kim AR, Ludwig M, Kreitman M, White K, Reinitz J.

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PMID: 24408913

SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.

by Kevin White, Li G, Ci W, Karmakar S, Chen K, Dhar R, Fan Z, Guo Z, Zhang J, Ke Y, Wang L, Zhuang M, Hu S, Li X, Zhou L, Li X, Calabrese MF, Watson ER, Prasad SM, Rinker-Schaeffer C, Eggener SE, Stricker T, Tian Y, Schulman BA, Liu J, White KP.

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PMID: 24656772

Low grade prostate cancer diverges early from high grade and metastatic disease.

by Kevin White, VanderWeele DJ, Brown CD, Taxy JB, Gillard M, Hatcher DM, Tom WR, Stadler WM, White KP.

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PMID: 24890684

The spectrum of somatic mutations in high-risk acute myeloid leukaemia with -7/del(7q).

by Kevin White, McNerney ME, Brown CD, Peterson AL, Banerjee M, Larson RA, Anastasi J, Le Beau MM, White KP.

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PMID: 24931631

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification.

by Kevin White, Arthur RK, Ma L, Slattery M, Spokony RF, Ostapenko A, Nègre N, White KP.

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PMID: 24985914

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.

by Barbara Stranger, Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL.

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PMID: 24786080

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells.

by Barbara Stranger, Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Stranger BE, Brenner MB, Raychaudhuri S.

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PMID: 24968232

Genomics of alternative splicing: evolution, development and pathophysiology.

by Barbara Stranger, Gamazon ER, Stranger BE.

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PMID: 24378600

Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.

by Barbara Stranger, Li Q, Stram A, Chen C, Kar S, Gayther S, Pharoah P, Haiman C, Stranger B, Kraft P, Freedman ML.

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PMID: 24907074

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.

by Andrey Rzhetsky, Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ.

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PMID: 24895436

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.

by Robert Grossman, Rebecca Spokony, Rob Arthur, Matt Slattery, Lijia Ma, Alec Victorsen, Jason Grundstad, Wenxuan Gao, Jennifer Moran, Edward (Jay) Rehm, Kevin White, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Jameel N, Kellis M.

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PMID: 24985916

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

by Jack Gilbert, Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK.

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PMID: 24451203

Human and environmental impacts on river sediment microbial communities.

by Jack Gilbert, Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA.

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PMID: 24841417

Understanding cultivar-specificity and soil determinants of the cannabis microbiome.

by Jack Gilbert, Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M.

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PMID: 24932479

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

by Jack Gilbert, Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M.

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PMID: 24958360

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

by Jack Gilbert, Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Knight R.

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PMID: 24995004

The complete genome sequence for putative H2 - and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

by Dionysios Antonopoulos, Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Kemner KM, Meyer F.

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PMID: 24628880

High-throughput microfluidic single-cell analysis pipeline for studies of signaling dynamics

by Savas Tay, Kellogg RA, Gómez-Sjöberg R, and Leyrat AA

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PMID: 24967621

Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells

by Barbara Stranger, Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Brenner MB, Raychaudhuri S.

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PMID: 24968232

Immunocytochemical localization of epidermal growth factor-receptor in early embryos of the Japanese medaka fish (Oryzias latipes

by Heather Scott, Boomsma RA1, Scott H, Walters K.

PMID: 11352399

Express primer generator tool for high throughput gene cloning and expression.

by Heather Scott, Scott HN1, Laible PD, Hanson DK.

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PMID: 12826060

Sequences of versatile broad-host-range vectors of the RK2 family.

by Heather Scott, Scott HN1, Laible PD, Hanson DK.

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PMID: 12826060

Towards higher-throughput membrane protein production for structural genomics initiatives.

by Heather Scott, Laible PD1, Scott HN, Henry L, Hanson DK.

PMID: 15263855

Loss of the death receptor CD95 (Fas) expression by dendritic cells protects from a chronic viral infection

by Aly Azeem Khan, Vineeth Varanasi, Alexander V. Chervonskya

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Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

by Jack Gilbert, Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE, Banfield JF.

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PMID: 24674078

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota.

by Jack Gilbert, Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B, Melillo D, Mueller MG, Natale L, Zucchetti I, De Santis R, Pinto MR, Litman GW, Gilbert JA.

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PMID: 24695540

Current developments in arbuscular mycorrhizal fungi research and its role in salinity stress alleviation: a biotechnological perspective.

by Jack Gilbert, Kumar A, Dames JF, Gupta A, Sharma S, Gilbert JA, Ahmad P.

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PMID: 24708070

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments.

by Jack Gilbert, Scott NM, Hess M, Bouskill NJ, Mason OU, Jansson JK, Gilbert JA

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PMID: 24723913

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.

by Dionysios Antonopoulos, Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE.

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PMID: 24529162

Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity.

by Dionysios Antonopoulos, Evans CC, Lepard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ.

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PMID: 24670791

Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis.

by Robert Grossman, Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DB, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA.

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PMID: 24373966

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

by Robert Grossman, Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

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PMID: 24456465

Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability.

by Andrey Rzhetsky, Rzhetsky A, Bagley SC, Wang K, Lyttle CS, Cook EH Jr, Altman RB, Gibbons RD.

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PMID: 24625521

Systems analysis of human multigene disorders. Preface.

by Andrey Rzhetsky, Maltsev N, Rzhetsky A, Conrad Gilliam T.

PMID: 24678533

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

by Barbara Stranger, Raj T, Ryan KJ, Replogle JM, Chibnik LB, Rosenkrantz L, Tang A, Rothamel K, Stranger BE, Bennett DA, Evans DA, De Jager PL, Bradshaw EM

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PMID: 24381305

Genetics of rheumatoid arthritis contributes to biology and drug discovery.

by Barbara Stranger, Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, Carroll RJ, Eyler AE, Greenberg JD, Kremer JM, Pappas DA, Jiang L, Yin J, Ye L, Su DF, Yang J, Xie G, Keystone E, Westra HJ, Esko T, Metspalu A, Zhou X, Gupta N, Mirel D, Stahl EA, Diogo D, Cui J, Liao K, Guo MH, Myouzen K, Kawaguchi T, Coenen MJ, van Riel PL, van de Laar MA, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Bridges SL Jr, Zhernakova A, Toes RE, Tak PP, Miceli-Richard C, Bang SY, Lee HS, Martin J, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Rantapää-Dahlqvist S, Arlestig L, Choi HK, Kamatani Y, Galan P, Lathrop M; RACI consortium; GARNET consortium, Eyre S, Bowes J, Barton A, de Vries N, Moreland LW, Criswell LA, Karlson EW, Taniguchi A, Yamada R, Kubo M, Liu JS, Bae SC, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Raychaudhuri S, Stranger BE, De Jager PL, Franke L, Visscher PM, Brown MA, Yamanaka H, Mimori T, Takahashi A, Xu H, Behrens TW, Siminovitch KA, Momohara S, Matsuda F, Yamamoto K, Plenge RM.

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PMID: 24390342

Common genetic variants modulate pathogen-sensing responses in human dendritic cells.

by Barbara Stranger, Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N.

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PMID: 24604203

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

by Robert Grossman, Kevin White, Heath AP, Greenway M, Powell R, Spring J, Suarez R, Hanley D, Bandlamudi C, McNerney ME, White KP, Grossman RL.

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PMID: 24464852

Protein quantitative trait Loci identify novel candidates modulating cellular response to chemotherapy

by Kevin White, Stark AL, Hause RJ Jr, Gorsic LK, Antao NN, Wong SS, Chung SH, Gill DF, Im HK, Myers JL, White KP, Jones RB, Dolan ME

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PMID: 24699359

Defining functional DNA elements in the human genome

by Kevin White, Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

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PMID: 24753594

The founding charter of the Genomic Observatories Network.

by Folker Meyer, Davies N, Field D, Amaral-Zettler L, Clark MS, Deck J, Drummond A, Faith DP, Geller J, Gilbert J, Glöckner FO, Hirsch PR, Leong JA, Meyer C, Obst M, Planes S, Scholin C, Vogler AP, Gates RD, Toonen R, Berteaux-Lecellier V, Barbier M, Barker K, Bertilsson S, Bicak M, Bietz MJ, Bobe J, Bodrossy L, Borja A, Coddington J, Fuhrman J, Gerdts G, Gillespie R, Goodwin K, Hanson PC, Hero JM, Hoekman D, Jansson J, Jeanthon C, Kao R, Klindworth A, Knight R, Kottmann R, Koo MS, Kotoulas G, Lowe AJ, Marteinsson VT, Meyer F, Morrison N, Myrold DD, Pafilis E, Parker S, Parnell JJ, Polymenakou PN, Ratnasingham S, Roderick GK, Rodriguez-Ezpeleta N, Schonrogge K, Simon N, Valette-Silver NJ, Springer YP, Stone GN, Stones-Havas S, Sansone SA, Thibault KM, Wecker P, Wichels A, Wooley JC, Yahara T, Zingone A

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PMID: 24606731

The cyanobacterial clock and metabolism

by Michael Rust, Gopal Pattanayak

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PMID: 24667330

Gene regulatory networks in the immune system

by Aaron Dinner, Aly Azeem Khan, Harinder Singh

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Transcriptional programming of dendritic cells for enhanced MHC class II antigen presentation

by Aly Azeem Khan, Bryan Vander Lugt, Jason A Hackney, Smita Agrawal, Justin Lesch, Meijuan Zhou, Wyne P Lee, Summer Park, Min Xu, Jason DeVoss, Chauncey J Spooner, Cecile Chalouni, Lelia Delamarre, Ira Mellman & Harinder Singh

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Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

by Barbara Stranger, Mark N. Lee,* Chun Ye,* Alexandra-Chloé Villani, Towfi que Raj, Weibo Li, Thomas M. Eisenhaure, Selina H. Imboywa, Portia I. Chipendo, F. Ann Ran, Kamil Slowikowski, Lucas D. Ward, Khadir Raddassi, Cristin McCabe, Michelle H. Lee, Irene Y. Frohlich, David A. Hafl er, Manolis Kellis, Soumya Raychaudhuri, Feng Zhang, Barbara E. Stranger, Christophe O. Benoist, Philip L. De Jager, Aviv Regev, Nir Hacohen

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Interindividual variation in human T regulatory cells

by Barbara Stranger, Alessandra Ferraroa, Anna Morena D’Alisea, Towfique Rajb, Natasha Asinovskia, Roxanne Phillipsd, Ayla Erguna, Joseph M. Replogleb, Angelina Bernierd, Lori Laffeld, Barbara E. Strangerb, Philip L. De Jagerb, Diane Mathisa, and Christophe Benoista

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PMID: 24610777

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

by Folker Meyer, Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Schriml LM.

PMID: 24152717

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Papers Archive

2014 Research Papers Archive