相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise
Valentina Peona et al.
MOLECULAR ECOLOGY RESOURCES (2021)
Three-dimensional chromatin in disease: What holds us together and what drives us apart?
Daniel M. Ibrahim et al.
CURRENT OPINION IN CELL BIOLOGY (2020)
Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation
Abbas Roayaei Ardakany et al.
GENOME BIOLOGY (2020)
A willow sex chromosome reveals convergent evolution of complex palindromic repeats
Ran Zhou et al.
GENOME BIOLOGY (2020)
The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
Drew R. Schield et al.
GENOME RESEARCH (2019)
Molecular cytogenetic characterization of repetitive sequences comprising centromeric heterochromatin in three Anseriformes species
Yoshinobu Uno et al.
PLOS ONE (2019)
Principles of genome folding into topologically associating domains
Quentin Szabo et al.
SCIENCE ADVANCES (2019)
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
Luohao Xu et al.
NATURE ECOLOGY & EVOLUTION (2019)
Two major mechanisms of chromosome organization
Leonid A. Mirny et al.
CURRENT OPINION IN CELL BIOLOGY (2019)
Heterochromatin drives compartmentalization of inverted and conventional nuclei
Martin Falk et al.
NATURE (2019)
Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds
Luohao Xu et al.
GENOME BIOLOGY AND EVOLUTION (2019)
Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells
Yanxiao Zhang et al.
NATURE GENETICS (2019)
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Jay Ghurye et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Heterochromatic regions in Japanese quail chromosomes: comprehensive molecular-cytogenetic characterization and 3D mapping in interphase nucleus
Anna Zlotina et al.
CHROMOSOME RESEARCH (2019)
SQuIRE reveals locus-specific regulation of interspersed repeat expression
Wan R. Yang et al.
NUCLEIC ACIDS RESEARCH (2019)
3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes' chromatin
Veniamin Fishman et al.
NUCLEIC ACIDS RESEARCH (2019)
Innate Immune Responses to Avian Influenza Viruses in Ducks and Chickens
Danyel Evseev et al.
VETERINARY SCIENCES (2019)
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Michael Alonge et al.
GENOME BIOLOGY (2019)
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
Robert M. Waterhouse et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)
Rory J. Craig et al.
MOLECULAR ECOLOGY (2018)
Sex chromosomes and speciation in birds and other ZW systems
Darren E. Irwin
MOLECULAR ECOLOGY (2018)
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Fidel Ramirez et al.
NATURE COMMUNICATIONS (2018)
An intercross population study reveals genes associated with body size and plumage color in ducks
Zhengkui Zhou et al.
NATURE COMMUNICATIONS (2018)
De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Shivani Mahajan et al.
PLOS BIOLOGY (2018)
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Michael J. Roach et al.
BMC BIOINFORMATICS (2018)
Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Joana Damas et al.
GENOME BIOLOGY (2018)
Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes
Rebecca E. O'Connor et al.
GENOME BIOLOGY (2018)
Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
Joana Damas et al.
GENOME RESEARCH (2017)
Ensembl 2017
Bronwen L. Aken et al.
NUCLEIC ACIDS RESEARCH (2017)
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
Wesley C. Warren et al.
G3-GENES GENOMES GENETICS (2017)
Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds
Fidel Botero-Castro et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl
Georg A. Busslinger et al.
NATURE (2017)
Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators
Daniel W. Bellott et al.
NATURE GENETICS (2017)
Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
Derek M. Bickhart et al.
NATURE GENETICS (2017)
Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
Nathan Harmston et al.
NATURE COMMUNICATIONS (2017)
De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
Jonas Korlach et al.
GIGASCIENCE (2017)
Chromosomal inversion differences correlate with range overlap in passerine birds
Daniel M. Hooper et al.
NATURE ECOLOGY & EVOLUTION (2017)
runBNG: a software package for BioNano genomic analysis on the command line
Yuxuan Yuan et al.
BIOINFORMATICS (2017)
Genome Organization Drives Chromosome Fragility
Andres Canela et al.
CELL (2017)
Phased diploid genome assembly with single-molecule real-time sequencing
Chen-Shan Chin et al.
NATURE METHODS (2016)
Fitness consequences of polymorphic inversions in the zebra finch genome
Ulrich Knief et al.
GENOME BIOLOGY (2016)
Three-dimensional architecture of tandem repeats in chicken interphase nucleus
Antonina Maslova et al.
CHROMOSOME RESEARCH (2015)
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim et al.
NATURE METHODS (2015)
Assembly and diploid architecture of an individual human genome via single-molecule technologies
Matthew Pendleton et al.
NATURE METHODS (2015)
The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver
Lizhi Lu et al.
GENOME BIOLOGY (2015)
Repbase Update, a database of repetitive elements in eukaryotic genomes
Weidong Bao et al.
MOBILE DNA (2015)
A new time tree reveals Earth history's imprint on the evolution of modern birds
Santiago Claramunt et al.
SCIENCE ADVANCES (2015)
Development of Avian External Genitalia: Interspecific Differences and Sexual Differentiation of the Male and Female Phallus
Ana M. Herrera et al.
SEXUAL DEVELOPMENT (2015)
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
Nicolas Servant et al.
GENOME BIOLOGY (2015)
Comparison of the Chromosome Structures between the Chicken and Three Anserid Species, the Domestic Duck (Anas platyrhynchos), Muscovy Duck (Cairina moschata), and Chinese Goose (Anser cygnoides), and the Delineation of their Karyotype Evolution by Comparative Chromosome Mapping
Fhamida B. Islam et al.
JOURNAL OF POULTRY SCIENCE (2014)
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
Takeshi Kawakami et al.
MOLECULAR ECOLOGY (2014)
Topologically associating domains are stable units of replication-timing regulation
Benjamin D. Pope et al.
NATURE (2014)
Origins and functional evolution of Y chromosomes across mammals
Diego Cortez et al.
NATURE (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
Complex evolutionary trajectories of sex chromosomes across bird taxa
Qi Zhou et al.
SCIENCE (2014)
Whole-genome analyses resolve early branches in the tree of life of modern birds
Erich D. Jarvis et al.
SCIENCE (2014)
Comparative genomics reveals insights into avian genome evolution and adaptation
Guojie Zhang et al.
SCIENCE (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
DNA-Binding Specificities of Human Transcription Factors
Arttu Jolma et al.
CELL (2013)
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species
Yinhua Huang et al.
NATURE GENETICS (2013)
HiTC: exploration of high-throughput 'C' experiments
Nicolas Servant et al.
BIOINFORMATICS (2012)
The long and the short of avian W chromosomes: no evidence for gradual W shortening
Joanna Rutkowska et al.
BIOLOGY LETTERS (2012)
A duck RH panel and its potential for assisting NGS genome assembly
Man Rao et al.
BMC GENOMICS (2012)
Intrachromosomal rearrangements in avian genome evolution: evidence for regions prone to breakpoints
B. M. Skinner et al.
HEREDITY (2012)
Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes
Jennifer F. Hughes et al.
NATURE (2012)
Analyses of pig genomes provide insight into porcine demography and evolution
Martien A. M. Groenen et al.
NATURE (2012)
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon et al.
NATURE (2012)
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
Adam C. English et al.
PLOS ONE (2012)
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
Heng Li
BIOINFORMATICS (2011)
Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G. Grabherr et al.
NATURE BIOTECHNOLOGY (2011)
Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds
Alexander Suh et al.
NATURE COMMUNICATIONS (2011)
A W-linked palindrome and gene conversion in New World sparrows and blackbirds
Jamie K. Davis et al.
CHROMOSOME RESEARCH (2010)
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
Tyrone Ryba et al.
GENOME RESEARCH (2010)
Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution
Martin Volker et al.
GENOME RESEARCH (2010)
Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition
Daniel W. Bellott et al.
NATURE (2010)
How and Why Chromosome Inversions Evolve
Mark Kirkpatrick
PLOS BIOLOGY (2010)
Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes
Laurent Duret et al.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis
Benjamin M. Skinner et al.
BMC GENOMICS (2009)
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation
Claire Lemaitre et al.
BMC GENOMICS (2009)
Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories
Denis M. Larkin et al.
GENOME RESEARCH (2009)
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Erez Lieberman-Aiden et al.
SCIENCE (2009)
Characterization of chromosome structures of Falconinae (Falconidae, Falconiformes, Aves) by chromosome painting and delineation of chromosome rearrangements during their differentiation
Chizuko Nishida et al.
CHROMOSOME RESEARCH (2008)
Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination
I. Nanda et al.
CYTOGENETIC AND GENOME RESEARCH (2008)
Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments
Brian J. Haas et al.
GENOME BIOLOGY (2008)
Description of the mallard duck (Anas platyrhynchos) karyotype
Ewa Wojcik et al.
FOLIA BIOLOGICA-KRAKOW (2007)
Chromosome repatterning in three representative parrots (Psittaciformes) inferred from comparative chromosome painting
I. Nanda et al.
CYTOGENETIC AND GENOME RESEARCH (2007)
The evolution of the avian genome as revealed by comparative molecular cytogenetics
D. K. Griffin et al.
CYTOGENETIC AND GENOME RESEARCH (2007)
Reconstructing contiguous regions of an ancestral genome
Jian Ma et al.
GENOME RESEARCH (2006)
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources
M Stanke et al.
BMC BIOINFORMATICS (2006)
Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps
WJ Murphy et al.
SCIENCE (2005)
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
I Yanai et al.
BIOINFORMATICS (2005)
GeneWise and genomewise
E Birney et al.
GENOME RESEARCH (2004)
Versatile and open software for comparing large genomes
S Kurtz et al.
GENOME BIOLOGY (2004)
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
P Pevzner et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Abundant gene conversion between arms of palindromes in human and ape Y chromosomes
S Rozen et al.
NATURE (2003)
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
H Skaletsky et al.
NATURE (2003)
Origin and evolution of avian microchromosomes
DW Burt
CYTOGENETIC AND GENOME RESEARCH (2002)
Dosage compensation in birds
HA McQueen et al.
CURRENT BIOLOGY (2001)
The degeneration of Y chromosomes
B Charlesworth et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2000)
Characterization and chromosomal distribution of a novel satellite DNA sequence of Japanese quail (Coturnix coturnix japonica)
K Tanaka et al.
JOURNAL OF HEREDITY (2000)