Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

Dynamic hyper-editing underlies temperature adaptation in Drosophila

(2017) Ilana Buchumenski et al.   PLoS Genetics

Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing

(2017) Rui Zhang et al.   PLoS Genetics

Adaptation of A-to-I RNA editing in Drosophila

(2017) Yuange Duan et al.   PLoS Genetics

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

(2016) Yao Yu et al.   PLoS Genetics

The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster

(2016) Nicolas Svetec et al.   PLoS Genetics

An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

(2016) Ana Catalán et al.   PLoS Genetics

S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning

(2016) Daniel R. Schrider et al.   PLoS Genetics

Dynamic response of RNA editing to temperature in Drosophila

(2015) Leila E Rieder et al.   BMC BIOLOGY

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

(2015) Helen Attrill et al.   NUCLEIC ACIDS RESEARCH

Genetic mapping uncovers cis-regulatory landscape of RNA editing

(2015) Gokul Ramaswami et al.   Nature Communications

Cis Regulatory Effects on A-to-I RNA Editing in Related Drosophila Species

(2015) Anne L. Sapiro et al.   Cell Reports

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel

(2014) Y. B. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimized CRISPR/Cas tools for efficient germline and somatic genome engineering in Drosophila

(2014) F. Port et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila

(2014) Xingjie Ren et al.   Cell Reports

Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

(2014) Alicia R. Martin et al.   PLoS Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

Pool-hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

(2013) Simon Boitard et al.   Molecular Ecology Resources

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing

(2013) Rui Zhang et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

RADAR: a rigorously annotated database of A-to-I RNA editing

(2013) Gokul Ramaswami et al.   NUCLEIC ACIDS RESEARCH

Genome differentiation of Drosophila melanogaster from a microclimate contrast in Evolution Canyon, Israel

(2013) S. Hubner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast

(2013) Jessica Chang et al.   PLoS Genetics

Population and sex differences in Drosophila melanogaster brain gene expression

(2012) Ana Catalán et al.   BMC GENOMICS

Cross species analysis of Prominin reveals a conserved cellular role in invertebrate and vertebrate photoreceptor cells

(2012) Jing Nie et al.   DEVELOPMENTAL BIOLOGY

RNA Editing of the IQ Domain in Cav1.3 Channels Modulates Their Ca2+-Dependent Inactivation

(2012) Hua Huang et al.   NEURON

"Evolution Canyon," a potential microscale monitor of global warming across life

(2012) E. Nevo   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses

(2012) S. Garrett et al.   SCIENCE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

RNAstructure: software for RNA secondary structure prediction and analysis

(2010) Jessica S Reuter et al.   BMC BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Engineered Alterations in RNA Editing Modulate Complex Behavior inDrosophila

(2010) James E. C. Jepson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Protein Phosphatase 4 mediates localization of the Miranda complex during Drosophila neuroblast asymmetric divisions

(2009) R. Sousa-Nunes et al.   GENES & DEVELOPMENT

Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population

(2009) M. Rebeiz et al.   SCIENCE

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE