Snake Recombination Landscapes Are Concentrated in Functional Regions despite PRDM9

Recombination rate variation shapes barriers to introgression across butterfly genomes

(2019) Simon H. Martin et al.   PLOS BIOLOGY

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

(2019) Drew R. Schield et al.   GENOME RESEARCH

Divergent fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish

(2019) Alice F Shanfelter et al.   Genome Biology and Evolution

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

(2019) Yuxing Liao et al.   NUCLEIC ACIDS RESEARCH

CTCF cooperates with CtIP to drive homologous recombination repair of double-strand breaks

(2019) Soon Young Hwang et al.   NUCLEIC ACIDS RESEARCH

Multi-species comparisons of snakes identify coordinated signalling networks underlying post-feeding intestinal regeneration

(2019) Blair W. Perry et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

Natural selection interacts with recombination to shape the evolution of hybrid genomes

(2018) Molly Schumer et al.   SCIENCE

Bayesian Divergence-Time Estimation with Genome-Wide Single-Nucleotide Polymorphism Data of Sea Catfishes (Ariidae) Supports Miocene Closure of the Panamanian Isthmus

(2018) Madlen Stange et al.   SYSTEMATIC BIOLOGY

Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs

(2018) Rebecca E. O’Connor et al.   Nature Communications

Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

(2018) Giulia I. M. Pasquesi et al.   Nature Communications

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

(2018) Blair W Perry et al.   Genome Biology and Evolution

Hotspots for Initiation of Meiotic Recombination

(2018) Andrew J. Tock et al.   Frontiers in Genetics

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

(2017) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

CTCF prevents genomic instability by promoting homologous recombination-directed DNA double-strand break repair

(2017) Fengchao Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

(2017) Nicolas Altemose et al.   eLife

Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

(2017) Zachary Baker et al.   eLife

CTCF facilitates DNA double-strand break repair by enhancing homologous recombination repair

(2017) Khalid Hilmi et al.   Science Advances

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

(2016) Yuchi Zheng et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

(2016) Ingo Braasch et al.   NATURE GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

(2016) Wei Yin et al.   Nature Communications

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

(2015) J. Wang et al.   GENETICS

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum ofFicedulaflycatchers

(2015) Reto Burri et al.   GENOME RESEARCH

The Time Scale of Recombination Rate Evolution in Great Apes

(2015) Laurie S. Stevison et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

Global identification of the genetic networks andcis-regulatory elements of the cold response in zebrafish

(2015) Peng Hu et al.   NUCLEIC ACIDS RESEARCH

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Mechanism and Regulation of Meiotic Recombination Initiation

(2014) Isabel Lam et al.   Cold Spring Harbor Perspectives in Biology

Primate evolution of the recombination regulator PRDM9

(2014) Jerrod J. Schwartz et al.   Nature Communications

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets

(2013) Matthias Merkenschlager et al.   CELL

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

Phylogenetic relationships of the enigmatic longtailed rattlesnakes (Crotalus ericsmithi, C. lannomi, and C. stejnegeri)

(2013) Jacobo Reyes-Velasco et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Common and low-frequency variants associated with genome-wide recombination rate

(2013) Augustine Kong et al.   NATURE GENETICS

Meiotic recombination in mammals: localization and regulation

(2013) Frédéric Baudat et al.   NATURE REVIEWS GENETICS

Genomic signatures of selection at linked sites: unifying the disparity among species

(2013) Asher D. Cutter et al.   NATURE REVIEWS GENETICS

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

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

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

(2013) F. J. Vonk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Recombination Is Targeted towards Gene Promoter Regions in Dogs

(2013) Adam Auton et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

(2012) Eugénie Pessia et al.   Genome Biology and Evolution

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic landscape of species divergence in Ficedula flycatchers

(2012) Hans Ellegren et al.   NATURE

Genetic recombination is directed away from functional genomic elements in mice

(2012) Kevin Brick et al.   NATURE

Recombination is associated with the evolution of genome structure and worker behavior in honey bees

(2012) C. F. Kent et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner

(2012) Frank Sleutels et al.   Epigenetics & Chromatin

Recombination Modulates How Selection Affects Linked Sites in Drosophila

(2012) Suzanne E. McGaugh et al.   PLOS BIOLOGY

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The Anolis Lizard Genome: An Amniote Genome without Isochores

(2011) Matthew K. Fujita et al.   Genome Biology and Evolution

Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

(2011) Stephen R. Voss et al.   GENOME RESEARCH

Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome

(2011) E. Axelsson et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice

(2011) M. W. Nachman et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic islands of divergence in hybridizingHeliconiusbutterflies identified by large-scale targeted sequencing

(2011) Nicola J. Nadeau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What are the genomic drivers of the rapid evolution of PRDM9?

(2011) Chris P. Ponting   TRENDS IN GENETICS

The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

(2011) Laure Ségurel et al.   PLOS BIOLOGY

Genome Evolution in Reptilia, the Sister Group of Mammals

(2010) Daniel E. Janes et al.   Annual Review of Genomics and Human Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

PRDM9 variation strongly influences recombination hot-spot activity and meiotic instability in humans

(2010) Ingrid L Berg et al.   NATURE GENETICS

What drives recombination hotspots to repeat DNA in humans?

(2010) G. McVean   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination

(2010) S. Myers et al.   SCIENCE

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

(2010) Alon Keinan 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

(2009) Peter L. Oliver et al.   PLoS Genetics

Histone H3 lysine 4 trimethylation marks meiotic recombination initiation sites

(2008) Valérie Borde et al.   EMBO JOURNAL

Fast and flexible simulation of DNA sequence data

(2008) G. K. Chen et al.   GENOME RESEARCH

The evolution of restricted recombination in sex chromosomes

(2008) Roberta Bergero et al.   TRENDS IN ECOLOGY & EVOLUTION

The Evolution of Epigenetic Regulators CTCF and BORIS/CTCFL in Amniotes

(2008) Timothy A. Hore et al.   PLoS Genetics