Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

HINGE: long-read assembly achieves optimal repeat resolution

(2017) Govinda M. Kamath et al.   GENOME RESEARCH

Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing

(2016) Volkan Sevim et al.   BIOINFORMATICS

Mind the gap; seven reasons to close fragmented genome assemblies

(2016) Bart P.H.J. Thomma et al.   FUNGAL GENETICS AND BIOLOGY

Accurate Transposable Element Annotation Is Vital When Analyzing New Genome Assemblies

(2016) Roy N. Platt et al.   Genome Biology and Evolution

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

(2016) Joana Damas et al.   GENOME RESEARCH

Determinants of genetic diversity

(2016) Hans Ellegren et al.   NATURE REVIEWS GENETICS

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

(2016) Helena Staňková et al.   PLANT BIOTECHNOLOGY JOURNAL

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

The Ecology and Evolutionary Dynamics of Meiotic Drive

(2016) Anna K. Lindholm et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary signals of selection on cognition from the great tit genome and methylome

(2016) Veronika N. Laine et al.   Nature Communications

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

(2016) Nagarjun Vijay et al.   Nature Communications

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

(2016) Shubha Vij et al.   PLoS Genetics

Completing the human genome: the progress and challenge of satellite DNA assembly

(2015) Karen H. Miga   CHROMOSOME RESEARCH

Rates of karyotypic evolution in Estrildid finches differ between island and continental clades

(2015) Daniel M. Hooper et al.   EVOLUTION

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

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Transcriptomics of colour patterning and coloration shifts in crows

(2015) J. W. Poelstra et al.   MOLECULAR ECOLOGY

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Crossovers are associated with mutation and biased gene conversion at recombination hotspots

(2015) Barbara Arbeithuber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Constitutive heterochromatin formation and transcription in mammals

(2015) Nehmé Saksouk et al.   Epigenetics & Chromatin

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

(2014) Michael N Romanov et al.   BMC GENOMICS

Centromere identity from the DNA point of view

(2014) Miroslav Plohl et al.   CHROMOSOMA

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Centromere reference models for human chromosomes X and Y satellite arrays

(2014) K. H. Miga et al.   GENOME RESEARCH

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast

(2014) Sarah E Zanders et al.   eLife

The Evolutionary Genomics of Birds

(2013) Hans Ellegren   Annual Review of Ecology Evolution and Systematics

Initiation of Meiotic Recombination: How and Where? Conservation and Specificities Among Eukaryotes

(2013) Bernard de Massy   Annual Review of Genetics

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

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

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

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA

(2012) Carolyn M. George et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

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

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

(2010) W.-H. Shang et al.   GENOME RESEARCH

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

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

(2010) F. Baudat et al.   SCIENCE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Nuclear architecture and gene regulation

(2008) Elena Fedorova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Epigenetic regulation of heterochromatic DNA stability

(2008) Jamy C Peng et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Recombination and Speciation: Loci Near Centromeres Are More Differentiated Than Loci Near Telomeres Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

(2008) M. Carneiro et al.   GENETICS

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

(2008) R. J. Kulathinal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY