Genomics meets proteomics: identifying the culprits in disease

Integrative eQTL-Based Analyses Reveal the Biology of Breast Cancer Risk Loci

(2013) Qiyuan Li et al.   CELL

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

Identifying Recent Adaptations in Large-Scale Genomic Data

(2013) Sharon R. Grossman et al.   CELL

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Variation and genetic control of protein abundance in humans

(2013) Linfeng Wu et al.   NATURE

SMIM1 underlies the Vel blood group and influences red blood cell traits

(2013) Ana Cvejic et al.   NATURE GENETICS

Neutron-encoded mass signatures for multiplexed proteome quantification

(2013) Alexander S Hebert et al.   NATURE METHODS

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins

(2013) Hamid Mirzaei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Food Choice as a Key Management Strategy for Functional Gastrointestinal Symptoms

(2012) Peter R Gibson et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Chromatin accessibility, p300, and histone acetylation define PML-RAR  and AML1-ETO binding sites in acute myeloid leukemia

(2012) S. Saeed et al.   BLOOD

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

(2012) T. E. Reddy et al.   GENOME RESEARCH

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Proteobacterial ArfA Peptides Are Synthesized from Non-stop Messenger RNAs

(2012) Ryan E. Schaub et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The episodic nature of episodic-like memories

(2012) A. Easton et al.   LEARNING & MEMORY

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

A high-throughput approach for measuring temporal changes in the interactome

(2012) Anders R Kristensen et al.   NATURE METHODS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions

(2012) Marion Scheibe et al.   NUCLEIC ACIDS RESEARCH

Proteomic workflow for analysis of archival formalin-fixed and paraffin-embedded clinical samples to a depth of 10 000 proteins

(2012) Jacek R. Wiśniewski et al.   Proteomics Clinical Applications

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

The NIH Roadmap Epigenomics Program data resource

(2012) Lisa Helbling Chadwick   Epigenomics

ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus

(2012) Stephanie D. Byrum et al.   Cell Reports

Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding

(2012) Falk Butter et al.   PLoS Genetics

Towards cracking the epigenetic code using a combination of high-throughput epigenomics and quantitative mass spectrometry-based proteomics

(2011) Hendrik G. Stunnenberg et al.   BIOESSAYS

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

(2011) J. Munoz et al.   Molecular Systems Biology

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

(2011) Olivier Harismendy et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Principles for the post-GWAS functional characterization of cancer risk loci

(2011) Matthew L Freedman et al.   NATURE GENETICS

A SILAC-Based Screen for Methyl-CpG Binding Proteins Identifies RBP-J as a DNA Methylation and Sequence-Specific Binding Protein

(2011) Stefanie J. J. Bartels et al.   PLoS One

Maps of Open Chromatin Guide the Functional Follow-Up of Genome-Wide Association Signals: Application to Hematological Traits

(2011) Dirk S. Paul et al.   PLoS Genetics

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

A domesticated transposon mediates the effects of a single-nucleotide polymorphism responsible for enhanced muscle growth

(2010) Falk Butter et al.   EMBO REPORTS

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

Extracting gene function from protein–protein interactions using Quantitative BAC InteraCtomics (QUBIC)

(2010) Nina C. Hubner et al.   METHODS

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

Generating and navigating proteome maps using mass spectrometry

(2010) Christian H. Ahrens et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Decoding signalling networks by mass spectrometry-based proteomics

(2010) Chunaram Choudhary et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

New tools and methods for direct programmatic access to the dbSNP relational database

(2010) Scott F. Saccone et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Purification of Proteins Associated with Specific Genomic Loci

(2009) Jérôme Déjardin et al.   CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

(2009) Paul J Boersema et al.   Nature Protocols

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes

(2009) S. Nejentsev et al.   SCIENCE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

(2009) Li Jia et al.   PLoS Genetics

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

High confidence determination of specific protein–protein interactions using quantitative mass spectrometry

(2008) Michiel Vermeulen et al.   CURRENT OPINION IN BIOTECHNOLOGY

A SILAC-based DNA protein interaction screen that identifies candidate binding proteins to functional DNA elements

(2008) G. Mittler et al.   GENOME RESEARCH

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Sizing up human height variation

(2008) Peter M Visscher   NATURE GENETICS

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS