Molecular mechanisms of mutualistic and antagonistic interactions in a plant–pollinator association

Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism

(2021) Gang Wang et al.   Nature Communications

The Role of Evolution in Shaping Ecological Networks

(2020) Simon T. Segar et al.   TRENDS IN ECOLOGY & EVOLUTION

Chemical signal is in the blend: bases of plant-pollinator encounter in a highly specialized interaction

(2020) Magali Proffit et al.   Scientific Reports

Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution

(2020) Xingtan Zhang et al.   CELL

A need to consider the evolutionary genetics of host–symbiont mutualisms

(2020) Kayla S. Stoy et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

A galling insect activates plant reproductive programs during gall development

(2019) Jack C. Schultz et al.   Scientific Reports

Loss of top-down biotic interactions changes the relative benefits for obligate mutualists

(2019) Rong Wang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Multiple parapatric pollinators have radiated across a continental fig tree displaying clinal genetic variation

(2019) Hui Yu et al.   MOLECULAR ECOLOGY

Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps

(2019) Jordan D. Satler et al.   EVOLUTION

Two transcription factors TaPpm1 and TaPpb1 co-regulate anthocyanin biosynthesis in purple pericarps of wheat

(2018) Wenhui Jiang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Origin and maintenance of chemical diversity in a species-rich tropical tree lineage

(2018) Diego Salazar et al.   Nature Ecology & Evolution

Binding affinity characterization of an antennae-enriched chemosensory protein from the white-backed planthopper, Sogatella furcifera (Horváth), with host plant volatiles

(2018) Guang-Lei Chen et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Chemical cues and genetic divergence in insects on plants: conceptual cross pollination between mutualistic and antagonistic systems

(2018) Simon T Segar et al.   Current Opinion in Insect Science

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

Breaking the cipher: ant eavesdropping on the variational trail pheromone of its termite prey

(2017) Xiao-Lan Wen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.)

(2017) Kazuki Mori et al.   Scientific Reports

The sex pheromone of a globally invasive honey bee predator, the Asian eusocial hornet, Vespa velutina

(2017) Ping Wen et al.   Scientific Reports

Assembly scaffolding with PE-contaminated mate-pair libraries

(2016) Kristoffer Sahlin et al.   BIOINFORMATICS

Leaf-mining by Phyllonorycter blancardella reprograms the host-leaf transcriptome to modulate phytohormones associated with nutrient mobilization and plant defense

(2016) Hui Zhang et al.   JOURNAL OF INSECT PHYSIOLOGY

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

(2016) Jeanine L. Olsen et al.   NATURE

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Pollinator sharing and gene flow among closely related sympatric dioecious fig taxa

(2016) Gang Wang et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolving Theory of Evolutionary Radiations

(2016) M. Simões et al.   TRENDS IN ECOLOGY & EVOLUTION

Draft genome of the living fossil Ginkgo biloba

(2016) Rui Guan et al.   GigaScience

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Diversity of fig glands is associated with nursery mutualism in fig trees

(2015) Camila D. Souza et al.   AMERICAN JOURNAL OF BOTANY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

(2015) Roland Bruderer et al.   MOLECULAR & CELLULAR PROTEOMICS

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Arabidopsis thalianaHomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation

(2015) Matías Capella et al.   NEW PHYTOLOGIST

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction

(2015) Ellen O. Martinson et al.   PLoS One

The butterfly plant arms-race escalated by gene and genome duplications

(2015) Patrick P. Edger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De novo transcriptome sequencing in Ficus hirta Vahl. (Moraceae) to investigate gene regulation involved in the biosynthesis of pollinator attracting volatiles

(2015) Hui Yu et al.   Tree Genetics & Genomes

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments

(2014) Meena Choi et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Genetics of ecological divergence during speciation

(2014) Matthew E. Arnegard et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

IQuant: An automated pipeline for quantitative proteomics based upon isobaric tags

(2014) Bo Wen et al.   PROTEOMICS

Fatty aldehyde and fatty alcohol metabolism: Review and importance for epidermal structure and function

(2013) William B. Rizzo   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome

(2013) Jin-Hua Xiao et al.   GENOME BIOLOGY

Plant Defense Against Herbivores: Chemical Aspects

(2012) Axel Mithöfer et al.   Annual Review of Plant Biology

Evidence for intersexual chemical mimicry in a dioecious plant

(2012) Catherine C. L. Soler et al.   ECOLOGY LETTERS

Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol

(2012) Xiaoxu Tian et al.   Journal of Proteomics

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Fig trees at the northern limit of their range: the distributions of cryptic pollinators indicate multiple glacial refugia

(2012) YAN CHEN et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

An Extreme Case of Plant–Insect Codiversification: Figs and Fig-Pollinating Wasps

(2012) Astrid Cruaud et al.   SYSTEMATIC BIOLOGY

Functional characterization and immunolocalization of odorant binding protein 1 in the lucerne plant bug, Adelphocoris lineolatus (GOEZE)

(2011) Shao-Hua Gu et al.   ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Speciation in fig wasps

(2010) JAMES M. COOK et al.   ECOLOGICAL ENTOMOLOGY

Mutualisms in a changing world: an evolutionary perspective

(2010) E. Toby Kiers et al.   ECOLOGY LETTERS

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

Global pollinator declines: trends, impacts and drivers

(2010) Simon G. Potts et al.   TRENDS IN ECOLOGY & EVOLUTION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Private channel: a single unusual compound assures specific pollinator attraction inFicus semicordata

(2009) Chun Chen et al.   FUNCTIONAL ECOLOGY

Accurate and Sensitive Peptide Identification with Mascot Percolator

(2009) Markus Brosch et al.   JOURNAL OF PROTEOME RESEARCH

Macroevolutionary chemical escalation in an ancient plant-herbivore arms race

(2009) J. X. Becerra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary Ecology of Figs and Their Associates: Recent Progress and Outstanding Puzzles

(2008) Edward Allen Herre et al.   Annual Review of Ecology Evolution and Systematics

SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap

(2008) A. D. Johnson et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

(2008) H. Tang et al.   GENOME RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Biosynthesis of plant-derived flavor compounds

(2008) Wilfried Schwab et al.   PLANT JOURNAL

Reverse and Conventional Chemical Ecology Approaches for the Development of Oviposition Attractants for Culex Mosquitoes

(2008) Walter S. Leal et al.   PLoS One