Proteome-wide Systems Genetics to Identify Functional Regulators of Complex Traits

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients

(2020) Dorte B. Bekker-Jensen et al.   MOLECULAR & CELLULAR PROTEOMICS

Reading amino acids in a nanopore

(2020) Stefan Howorka et al.   NATURE BIOTECHNOLOGY

Mouse Systems Genetics as a Prelude to Precision Medicine

(2020) Hao Li et al.   TRENDS IN GENETICS

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

(2020) Yangyang Bian et al.   Nature Communications

Exploiting horizontal pleiotropy to search for causal pathways within a Mendelian randomization framework

(2020) Yoonsu Cho et al.   Nature Communications

eQTLMAPT: Fast and Accurate eQTL Mediation Analysis With Efficient Permutation Testing Approaches

(2020) Tao Wang et al.   Frontiers in Genetics

Label free shotgun proteomics for the identification of protein biomarkers for beef tenderness in muscle and plasma of heifers

(2020) Sabrina Boudon et al.   Journal of Proteomics

Genome-wide selection and genetic improvement during modern maize breeding

(2020) Baobao Wang et al.   NATURE GENETICS

Quantifying genetic effects on disease mediated by assayed gene expression levels

(2020) Douglas W. Yao et al.   NATURE GENETICS

Mendelian randomization accounting for correlated and uncorrelated pleiotropic effects using genome-wide summary statistics

(2020) Jean Morrison et al.   NATURE GENETICS

Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

(2020) Laura M. Raffield et al.   PROTEOMICS

Genetic drug target validation using Mendelian randomisation

(2020) Amand F. Schmidt et al.   Nature Communications

A fully joint Bayesian quantitative trait locus mapping of human protein abundance in plasma

(2020) Hélène Ruffieux et al.   PLoS Computational Biology

Population-scale proteome variation in human induced pluripotent stem cells

(2020) Bogdan Andrei Mirauta et al.   eLife

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases

(2020) Jie Zheng et al.   NATURE GENETICS

In Aptamers They Trust

(2019) Abhishek Joshi et al.   CIRCULATION

Comparison of F-tests for Univariate and Multivariate Mixed-Effect Models in Genome-Wide Association Mapping

(2019) Akio Onogi   Frontiers in Genetics

Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores

(2019) Wei Si et al.   Small

An integrative systems genetic analysis of mammalian lipid metabolism

(2019) Benjamin L. Parker et al.   NATURE

Identification of drought responsive proteins and related pQTLs in barley

(2019) Paweł Rodziewicz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genomic Medicine–Progress, Pitfalls, and Promise

(2019) Jay Shendure et al.   CELL

Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry

(2019) Devin K. Schweppe et al.   ANALYTICAL CHEMISTRY

Analysis of 1508 plasma samples by capillary flow data-independent acquisition profiles proteomics of weight loss and maintenance

(2019) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification

(2019) Shilo Ohayon et al.   PLoS Computational Biology

Novel Drug Targets for Ischemic Stroke Identified Through Mendelian Randomization Analysis of the Blood Proteome

(2019) Michael Chong et al.   CIRCULATION

Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits

(2019) Eleonora Porcu et al.   Nature Communications

Genome and epigenome wide studies of neurological protein biomarkers in the Lothian Birth Cohort 1936

(2019) Robert F. Hillary et al.   Nature Communications

Resolving Chemical Modifications to a Single Amino Acid within a Peptide Using a Biological Nanopore

(2019) Laura Restrepo-Pérez et al.   ACS Nano

Discovery of shared genomic loci using the conditional false discovery rate approach

(2019) Olav B. Smeland et al.   HUMAN GENETICS

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

Translational genomics and precision medicine: Moving from the lab to the clinic

(2019) Eleftheria Zeggini et al.   SCIENCE

Single-Molecule Protein Detection in a Biofluid Using a Quantitative Nanopore Sensor

(2019) Avinash Kumar Thakur et al.   ACS Sensors

Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography

(2019) Johannes Stadlmann et al.   ANALYTICAL CHEMISTRY

Label-Free Detection of Post-translational Modifications with a Nanopore

(2019) Laura Restrepo-Pérez et al.   NANO LETTERS

The human secretome

(2019) Mathias Uhlén et al.   Science Signaling

Multi-platform Affinity Proteomics Identify Proteins Linked to Metastasis and Immune Suppression in Ovarian Cancer Plasma

(2019) Johannes Graumann et al.   Frontiers in Oncology

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore

(2019) Hadjer Ouldali et al.   NATURE BIOTECHNOLOGY

Plasma protein patterns as comprehensive indicators of health

(2019) Stephen A. Williams et al.   NATURE MEDICINE

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer

(2018) Alexander S. Hebert et al.   ANALYTICAL CHEMISTRY

Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion

(2018) Kelly A. Mitok et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

(2018) Florian Meier et al.   NATURE METHODS

Genome-wide association mapping of QTL underlying seed oil and protein contents of a diverse panel of soybean accessions

(2018) Ying-hui Li et al.   PLANT SCIENCE

Identification of single amino acid differences in uniformly charged homopolymeric peptides with aerolysin nanopore

(2018) Fabien Piguet et al.   Nature Communications

A human huntingtin SNP alters post-translational modification and pathogenic proteolysis of the protein causing Huntington disease

(2018) D. D. O. Martin et al.   Scientific Reports

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform

(2018) Claire H. Kim et al.   Scientific Reports

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

(2018) Neil M Davies et al.   BMJ-British Medical Journal

The MR-Base platform supports systematic causal inference across the human phenome

(2018) Gibran Hemani et al.   eLife

Global analysis of A-to-I RNA editing reveals association with common disease variants

(2018) Oscar Franzén et al.   PeerJ

A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics

(2018) Nicolai Bache et al.   MOLECULAR & CELLULAR PROTEOMICS

Genomic atlas of the human plasma proteome

(2018) Benjamin B. Sun et al.   NATURE

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome

(2018) Daria V. Zhernakova et al.   NATURE GENETICS

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

(2018) Amit V. Khera et al.   NATURE GENETICS

Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer

(2018) Jing Gong et al.   NUCLEIC ACIDS RESEARCH

Proteomics of bulked rachides combined with documented QTLs uncovers genotype non-specific players of the Fusarium head blight responses in wheat

(2018) Jiajun Liu et al.   PHYTOPATHOLOGY

A comparative analysis of label-free liquid chromatography-mass spectrometry liver proteomic profiles highlights metabolic differences between pig breeds

(2018) Samuele Bovo et al.   PLoS One

Co-regulatory networks of human serum proteins link genetics to disease

(2018) Valur Emilsson et al.   SCIENCE

Genome‐wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease

(2018) Chen Yao et al.   Nature Communications

R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multi-parent Populations

(2018) Karl W. Broman et al.   GENETICS

Characterization of proteome variation during modern maize breeding

(2018) Lu-Guang Jiang et al.   MOLECULAR & CELLULAR PROTEOMICS

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

(2018) Florian Meier et al.   MOLECULAR & CELLULAR PROTEOMICS

The UK Biobank resource with deep phenotyping and genomic data

(2018) Clare Bycroft et al.   NATURE

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

High-resolution genetic mapping of putative causal interactions between regions of open chromatin

(2018) Natsuhiko Kumasaka et al.   NATURE GENETICS

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

(2017) Christian D. Kelstrup et al.   JOURNAL OF PROTEOME RESEARCH

Cytokine signatures in chronic fatigue syndrome patients: a Case Control Study and the effect of anakinra treatment

(2017) Megan E. Roerink et al.   Journal of Translational Medicine

Pervasive coexpression of spatially proximal genes is buffered at the protein level

(2017) Georg Kustatscher et al.   Molecular Systems Biology

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Population- and individual-specific regulatory variation in Sardinia

(2017) Mauro Pala et al.   NATURE GENETICS

Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues

(2017) Andrew Anand Brown et al.   NATURE GENETICS

Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium

(2017) Terrence F Meehan et al.   NATURE GENETICS

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Protein quantitative trait locus study in obesity during weight-loss identifies a leptin regulator

(2017) Jérôme Carayol et al.   Nature Communications

A complete tool set for molecular QTL discovery and analysis

(2017) Olivier Delaneau et al.   Nature Communications

Connecting genetic risk to disease end points through the human blood plasma proteome

(2017) Karsten Suhre et al.   Nature Communications

Genome-wide proteomic profiling reveals the role of dominance protein expression in heterosis in immature maize ears

(2017) Xiaojiao Hu et al.   Scientific Reports

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases

(2017) Muhammad Ahsan et al.   PLoS Genetics

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease

(2017) Lasse Folkersen et al.   PLoS Genetics

Serum protein pattern associated with organ damage and lupus nephritis in systemic lupus erythematosus revealed by PEA immunoassay

(2017) Anna Petrackova et al.   Clinical Proteomics

A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events

(2017) Colm J. Ryan et al.   Cell Systems

NIA Interventions Testing Program: Investigating Putative Aging Intervention Agents in a Genetically Heterogeneous Mouse Model

(2017) Nancy L. Nadon et al.   EBioMedicine

Genetic Architecture of the Cardiovascular Risk Proteome

(2017) Mark D. Benson et al.   CIRCULATION

Assessment of Variability in the SOMAscan Assay

(2017) Julián Candia et al.   Scientific Reports

Colocalization of GWAS and eQTL Signals Detects Target Genes

(2016) Farhad Hormozdiari et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors

(2016) Xiaoquan Wen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Can Humanized Mice Predict Drug “Behavior” in Humans?

(2016) Dan Xu et al.   Annual Review of Pharmacology and Toxicology

Integration of multi-omics data for prediction of phenotypic traits using random forest

(2016) Animesh Acharjee et al.   BMC BIOINFORMATICS

Associations Between Common and Rare Exonic Genetic Variants and Serum Levels of Twenty Cardiovascular-Related Proteins: The Tromsø Study

(2016) Terry Solomon et al.   Circulation-Cardiovascular Genetics

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

(2016) Philipp E Geyer et al.   Molecular Systems Biology

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Systems proteomics of liver mitochondria function

(2016) E. G. Williams et al.   SCIENCE

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster

(2016) Hirokazu Okada et al.   Nature Communications

Open access resources for genome-wide association mapping in rice

(2016) Susan R. McCouch et al.   Nature Communications

Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD

(2016) Wei Sun et al.   PLoS Genetics

Associations Between Common and Rare Exonic Genetic Variants and Serum Levels of Twenty Cardiovascular-Related Proteins: The Tromsø Study

(2016) Terry Solomon et al.   Circulation-Cardiovascular Genetics

Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways

(2016) Kapil Dev Singh et al.   PLoS One

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean

(2015) Ying-hui Li et al.   BMC GENOMICS

The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis

(2015) Evan G. Williams et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

Genetic Diversity and QTL Mapping of Thermostability of Limit Dextrinase in Barley

(2015) Xiaolei Wang et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Quantitative variability of 342 plasma proteins in a human twin population

(2015) Y. Liu et al.   Molecular Systems Biology

The support of human genetic evidence for approved drug indications

(2015) Matthew R Nelson et al.   NATURE GENETICS

Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

(2015) Sandip M Kale et al.   Scientific Reports

Identification and Validation of Genetic Variants that Influence Transcription Factor and Cell Signaling Protein Levels

(2014) Ronald J. Hause et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

(2014) Yibo Wu et al.   CELL

Heritability and genetic basis of protein level variation in an outbred population

(2014) Leopold Parts et al.   GENOME RESEARCH

Genetics of single-cell protein abundance variation in large yeast populations

(2014) Frank W. Albert et al.   NATURE

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs

(2014) Stefan Enroth et al.   Nature Communications

Protein Quantitative Trait Loci Identify Novel Candidates Modulating Cellular Response to Chemotherapy

(2014) Amy L. Stark et al.   PLoS Genetics

2-Aminoadipic acid is a biomarker for diabetes risk

(2013) Thomas J. Wang et al.   JOURNAL OF CLINICAL INVESTIGATION

Proteomic and Comparative Genomic Analysis of Two Brassica napus Lines Differing in Oil Content

(2013) Lu Gan et al.   JOURNAL OF PROTEOME RESEARCH

The One Hour Yeast Proteome

(2013) Alexander S. Hebert et al.   MOLECULAR & CELLULAR PROTEOMICS

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

NCBI’s Database of Genotypes and Phenotypes: dbGaP

(2013) Kimberly A. Tryka et al.   NUCLEIC ACIDS RESEARCH

Identification of genetic variants influencing the human plasma proteome

(2013) A. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Identification of cis-regulatory variation influencing protein abundance levels in human plasma

(2012) Anbarasu Lourdusamy et al.   HUMAN MOLECULAR GENETICS

The diversity outbred mouse population

(2012) Gary A. Churchill et al.   MAMMALIAN GENOME

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

Identification of proteins associated with malting quality in a subset of wild barley introgression lines

(2012) Timothy J. March et al.   PROTEOMICS

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood

(2011) Martin Lundberg et al.   NUCLEIC ACIDS RESEARCH

Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery

(2011) Larry Gold et al.   PLoS One

A PQL (protein quantity loci) analysis of mature pea seed proteins identifies loci determining seed protein composition

(2011) Michael Bourgeois et al.   PROTEOMICS

Genetic Variation Shapes Protein Networks Mainly through Non-transcriptional Mechanisms

(2011) Eric J. Foss et al.   PLOS BIOLOGY

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

A high-resolution association mapping panel for the dissection of complex traits in mice

(2010) B. J. Bennett et al.   GENOME RESEARCH

Identification of Quantitative Trait Loci Underlying Proteome Variation in Human Lymphoblastoid Cells

(2010) Nikhil Garge et al.   MOLECULAR & CELLULAR PROTEOMICS

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

Advanced technologies for genomic analysis in farm animals and its application for QTL mapping

(2008) Xiaoxiang Hu et al.   GENETICA

Applying Gene Expression, Proteomics and Single-Nucleotide Polymorphism Analysis for Complex Trait Gene Identification

(2008) I. M. Stylianou et al.   GENETICS

Differences in DBA/1J and DBA/2J reveal lipid QTL genes

(2008) Ioannis M. Stylianou et al.   JOURNAL OF LIPID RESEARCH

A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

(2008) David Melzer et al.   PLoS Genetics