Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps

Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation

(2015) Alexander Nater et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

A Single Nucleotide Deletion inGibberellin20-oxidase1Causes Alpine Dwarfism in Arabidopsis

(2015) Yonghai Luo et al.   PLANT PHYSIOLOGY

A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species

(2015) Shosei Kubota et al.   PLoS Genetics

Genetic diversity and population structure ofArabidopsis thalianaalong an altitudinal gradient

(2015) Antariksh Tyagi et al.   AoB Plants

Genomic variability as a driver of plant–pathogen coevolution?

(2014) Talia L Karasov et al.   CURRENT OPINION IN PLANT BIOLOGY

The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

(2014) Y Luo et al.   HEREDITY

Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana

(2014) Christian D. Huber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Deciphering the Adjustment between Environment and Life History in Annuals: Lessons from a Geographically-Explicit Approach in Arabidopsis thaliana

(2014) Esperanza Manzano-Piedras et al.   PLoS One

The latest LGM culmination of the Garda Glacier (Italian Alps) and the onset of glacial termination. Age of glacial collapse and vegetation chronosequence

(2014) Cesare Ravazzi et al.   QUATERNARY SCIENCE REVIEWS

A Genetic Atlas of Human Admixture History

(2014) G. Hellenthal et al.   SCIENCE

Partitioning net interactions among plants along altitudinal gradients to study community responses to climate change

(2013) Richard Michalet et al.   FUNCTIONAL ECOLOGY

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

Adaptation to spring heat and drought in northeastern SpanishArabidopsis thaliana

(2013) Marnin D. Wolfe et al.   NEW PHYTOLOGIST

The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity

(2013) Kazuki Saito et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

EHD1 Functions in Endosomal Recycling and Confers Salt Tolerance

(2013) Maya Bar et al.   PLoS One

AraPath: a knowledgebase for pathway analysis in Arabidopsis

(2012) L. Lai et al.   BIOINFORMATICS

Variation of presence/absence genes among Arabidopsis populations

(2012) Shengjun Tan et al.   BMC EVOLUTIONARY BIOLOGY

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

(2012) Pablo Cingolani et al.   FLY

Ancient Admixture in Human History

(2012) N. Patterson et al.   GENETICS

Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

(2012) S Mamidi et al.   HEREDITY

Demographic fate ofArabidopsis thalianacohorts of autumn- and spring-germinated plants along an altitudinal gradient

(2012) F. Xavier Picó   JOURNAL OF ECOLOGY

Detecting Selective Sweeps from Pooled Next-Generation Sequencing Samples

(2012) S. Boitard et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation

(2012) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Reciprocal transplants demonstrate strong adaptive differentiation of the model organism Arabidopsis thaliana in its native range

(2012) Jon Ågren et al.   NEW PHYTOLOGIST

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

(2012) Laurel Cooper et al.   PLANT AND CELL PHYSIOLOGY

Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

(2012) Yuan Zhu et al.   PLoS One

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring

(2012) S. Lamichhaney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

abc: an R package for approximate Bayesian computation (ABC)

(2012) Katalin Csilléry et al.   Methods in Ecology and Evolution

The Date of Interbreeding between Neandertals and Modern Humans

(2012) Sriram Sankararaman et al.   PLoS Genetics

Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster

(2012) Robert Kofler et al.   PLoS Genetics

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data

(2012) Joseph K. Pickrell et al.   PLoS Genetics

Natural variation in UV-B protection amongst Arabidopsis thaliana accessions

(2012) Dilip K. Biswas et al.   Emirates Journal of Food and Agriculture

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Genomic Determinants of Protein Evolution and Polymorphism in Arabidopsis

(2011) Tanja Slotte et al.   Genome Biology and Evolution

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants

(2011) PATRICK G. MEIRMANS et al.   MOLECULAR ECOLOGY

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

(2011) Tina T Hu et al.   NATURE GENETICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Comparison of Nucleotide-Binding Site-Leucine-Rich Repeat-Encoding Genes in Arabidopsis

(2011) Y.-L. Guo et al.   PLANT PHYSIOLOGY

Altitudinal and Climatic Adaptation Is Mediated by Flowering Traits and FRI, FLC, and PHYC Genes in Arabidopsis

(2011) B. Mendez-Vigo et al.   PLANT PHYSIOLOGY

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana

(2010) Liam H Childs et al.   BMC GENOMICS

Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogaster

(2010) B. Kolaczkowski et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Break zones in the distributions of alleles and species in alpine plants

(2010) Conny Thiel-Egenter et al.   JOURNAL OF BIOGEOGRAPHY

Genome Wide Analyses Reveal Little Evidence for Adaptive Evolution in Many Plant Species

(2010) T. I. Gossmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring the colonization of a mountain range-refugia vs. nunatak survival in high alpine ground beetles

(2010) KONRAD LOHSE et al.   MOLECULAR ECOLOGY

msABC: a modification of Hudson’s ms to facilitate multi-locus ABC analysis

(2010) P. PAVLIDIS et al.   Molecular Ecology Resources

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Arabidopsis thaliana populations show clinal variation in a climatic gradient associated with altitude

(2010) Alicia Montesinos-Navarro et al.   NEW PHYTOLOGIST

AGRIS: the Arabidopsis Gene Regulatory Information Server, an update

(2010) A. Yilmaz et al.   NUCLEIC ACIDS RESEARCH

Spatial pattern of floral morphology: possible insight into the effects of pollinators on plant distributions

(2010) Loïc Pellissier et al.   OIKOS

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice

(2010) Torsten Günther et al.   THEORETICAL AND APPLIED GENETICS

Local-Scale Patterns of Genetic Variability, Outcrossing, and Spatial Structure in Natural Stands of Arabidopsis thaliana

(2010) Kirsten Bomblies et al.   PLoS Genetics

A Coastal Cline in Sodium Accumulation in Arabidopsis thaliana Is Driven by Natural Variation of the Sodium Transporter AtHKT1;1

(2010) Ivan Baxter et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants

(2009) Nadir Alvarez et al.   ECOLOGY LETTERS

Reduced early growing season freezing resistance in alpine treeline plants under elevated atmospheric CO2

(2009) MELISSA MARTIN et al.   GLOBAL CHANGE BIOLOGY

Reconstructing Indian population history

(2009) David Reich et al.   NATURE

Freezing resistance varies within the growing season and with elevation in high-Andean species of central Chile

(2009) Angela Sierra-Almeida et al.   NEW PHYTOLOGIST

Overexpressing AtPAP15 Enhances Phosphorus Efficiency in Soybean

(2009) X. Wang et al.   PLANT PHYSIOLOGY

Divergence between Human Populations Estimated from Linkage Disequilibrium

(2008) John A. Sved et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genetic variation across species’ geographical ranges: the central–marginal hypothesis and beyond

(2008) C. G. ECKERT et al.   MOLECULAR ECOLOGY

Genomic Analysis of Differentiation between Soil Types Reveals Candidate Genes for Local Adaptation in Arabidopsis lyrata

(2008) Thomas L. Turner et al.   PLoS One