Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Clinical use of current polygenic risk scores may exacerbate health disparities

(2019) Alicia R. Martin et al.   NATURE GENETICS

Human Immunology through the Lens of Evolutionary Genetics

(2019) Lluis Quintana-Murci   CELL

Multiple Deeply Divergent Denisovan Ancestries in Papuans

(2019) Guy S. Jacobs et al.   CELL

MethylMix 2.0: an R package for identifying DNA methylation genes

(2018) Pierre-Louis Cedoz et al.   BIOINFORMATICS

IDO1 in cancer: a Gemini of immune checkpoints

(2018) Lijie Zhai et al.   Cellular & Molecular Immunology

Gene-by-environment interactions in urban populations modulate risk phenotypes

(2018) Marie-Julie Favé et al.   Nature Communications

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

Human-Specific Mutations and Positively Selected Sites in MARCO Confer Functional Changes

(2017) Kyle E Novakowski et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complex Patterns of Admixture across the Indonesian Archipelago

(2017) Georgi Hudjashov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors

(2016) Michael Dannemann et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments

(2016) Rachel M. Gittelman et al.   CURRENT BIOLOGY

MARCO variants are associated with phagocytosis, pulmonary tuberculosis susceptibility and Beijing lineage

(2016) N T T Thuong et al.   GENES AND IMMUNITY

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia

(2016) François Vallée et al.   GENETICS

Interferon-Inducible GTPases in Host Resistance, Inflammation and Disease

(2016) Danielle Pilla-Moffett et al.   JOURNAL OF MOLECULAR BIOLOGY

Offline: Indonesia—unravelling the mystery of a nation

(2016) Richard Horton   LANCET

Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation

(2016) Murray P. Cox et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics is failing on diversity

(2016) Alice B. Popejoy et al.   NATURE

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

(2016) Swapan Mallick et al.   NATURE

Genomic analyses inform on migration events during the peopling of Eurasia

(2016) Luca Pagani et al.   NATURE

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia

(2016) François Vallée et al.   GENETICS

MethylMix: an R package for identifying DNA methylation-driven genes

(2015) O. Gevaert   BIOINFORMATICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The epigenomic landscape of African rainforest hunter-gatherers and farmers

(2015) Maud Fagny et al.   Nature Communications

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Interactive transcriptome analysis of malaria patients and infectingPlasmodium falciparum

(2014) Junya Yamagishi et al.   GENOME RESEARCH

Interactions between Siglec-7/9 receptors and ligands influence NK cell–dependent tumor immunosurveillance

(2014) Camilla Jandus et al.   JOURNAL OF CLINICAL INVESTIGATION

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Gene-set analysis is severely biased when applied to genome-wide methylation data

(2013) Paul Geeleher et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

MARCO Is Required for TLR2- and Nod2-Mediated Responses to Streptococcus pneumoniae and Clearance of Pneumococcal Colonization in the Murine Nasopharynx

(2012) M. G. Dorrington et al.   JOURNAL OF IMMUNOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania

(2011) David Reich et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genetic Variants in MARCO Are Associated with the Susceptibility to Pulmonary Tuberculosis in Chinese Han Population

(2011) Mai-Juan Ma et al.   PLoS One

The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans

(2011) L. Abi-Rached et al.   SCIENCE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Critical role for the chemokine receptor CXCR6 in NK cell–mediated antigen-specific memory of haptens and viruses

(2010) Silke Paust et al.   NATURE IMMUNOLOGY

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates

(2010) M. P. Cox et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Emerging themes in IFN-γ-induced macrophage immunity by the p47 and p65 GTPase families

(2007) Avinash R. Shenoy et al.   IMMUNOBIOLOGY