Reference-assisted chromosome assembly.

PubWeight™: 1.26‹?› | Rank: Top 10%

🔗 View Article (PMC 3562798)

Published in Proc Natl Acad Sci U S A on January 10, 2013

Authors

Jaebum Kim1, Denis M Larkin, Qingle Cai, Asan, Yongfen Zhang, Ri-Li Ge, Loretta Auvil, Boris Capitanu, Guojie Zhang, Harris A Lewin, Jian Ma

Author Affiliations

1: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Articles citing this

Comparative genomics reveals insights into avian genome evolution and adaptation. Science (2014) 3.01

Inferring the global structure of chromosomes from structural variations. BMC Genomics (2015) 1.37

A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12

Ragout-a reference-assisted assembly tool for bacterial genomes. Bioinformatics (2014) 1.11

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol (2015) 0.91

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. Bioinformatics (2014) 0.91

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics (2014) 0.88

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution. BMC Genomics (2014) 0.86

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev (2016) 0.82

Misassembly detection using paired-end sequence reads and optical mapping data. Bioinformatics (2015) 0.80

Comparative genome mapping between Chinook salmon (Oncorhynchus tshawytscha) and rainbow trout (O. mykiss) based on homologous microsatellite loci. G3 (Bethesda) (2013) 0.80

Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data (2016) 0.80

Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics (2016) 0.80

POPBAM: Tools for Evolutionary Analysis of Short Read Sequence Alignments. Evol Bioinform Online (2013) 0.80

SHEAR: sample heterogeneity estimation and assembly by reference. BMC Genomics (2014) 0.78

High-throughput generation of an activation-tagged mutant library for functional genomic analyses in tobacco. Planta (2014) 0.76

Ancestral gene synteny reconstruction improves extant species scaffolding. BMC Genomics (2015) 0.76

Reconstruction and evolutionary history of eutherian chromosomes. Proc Natl Acad Sci U S A (2017) 0.76

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes. BMC Genomics (2017) 0.75

Diversity, distribution, and significance of transposable elements in the genome of the only selfing hermaphroditic vertebrate Kryptolebias marmoratus. Sci Rep (2017) 0.75

Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One (2014) 0.75

Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis). BMC Genomics (2015) 0.75

Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences. Gigascience (2016) 0.75

Whole Genome Mapping with Feature Sets from High-Throughput Sequencing Data. PLoS One (2016) 0.75

RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes. Int J Genomics (2015) 0.75

Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res (2016) 0.75

Approaches for in silico finishing of microbial genome sequences. Genet Mol Biol (2017) 0.75

Articles cited by this

Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94

The human genome browser at UCSC. Genome Res (2002) 168.23

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91

ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20

An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci U S A (2001) 31.51

Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41

Scaffolding pre-assembled contigs using SSPACE. Bioinformatics (2010) 23.27

High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97

Ultraconserved elements in the human genome. Science (2004) 17.14

GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res (2012) 11.33

Assembly algorithms for next-generation sequencing data. Genomics (2010) 8.56

The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23

An RNA gene expressed during cortical development evolved rapidly in humans. Nature (2006) 7.23

Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered (2009) 7.18

Efficient de novo assembly of large genomes using compressed data structures. Genome Res (2011) 6.05

A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol (2009) 5.93

Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet (2000) 5.88

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (2005) 5.47

Reconstructing contiguous regions of an ancestral genome. Genome Res (2006) 3.68

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science (1993) 3.54

Breakpoint graphs and ancestral genome reconstructions. Genome Res (2009) 2.78

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. Genome Res (2010) 2.31

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res (2004) 2.17

Creating a buzz about insect genomes. Science (2011) 2.17

The infinite sites model of genome evolution. Proc Natl Acad Sci U S A (2008) 1.89

Every genome sequence needs a good map. Genome Res (2009) 1.85

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res (2009) 1.66

DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol (2008) 1.50

Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet (2009) 1.32

Human cytogenetics: 46 chromosomes, 46 years and counting. Nat Rev Genet (2002) 1.07

Articles by these authors

The diploid genome sequence of an Asian individual. Nature (2008) 46.29

Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21

The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76

Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27

The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23

The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23

The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07

Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58

Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science (2005) 5.47

The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84

Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol (2011) 4.13

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11

Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45

Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature (2011) 3.19

Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res (2004) 2.91

Whole-genome sequence of Schistosoma haematobium. Nat Genet (2012) 2.91

Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science (2010) 2.78

On the origin of new genes in Drosophila. Genome Res (2008) 2.69

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68

A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci U S A (2005) 2.62

Nuclear reprogramming of cloned embryos and its implications for therapeutic cloning. Nat Genet (2007) 2.62

Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chromosome 6 affecting milk yield and composition in Holstein cattle. Genome Res (2005) 2.51

Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol (2012) 2.50

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37

The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34

Ascaris suum draft genome. Nature (2011) 2.16

High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell (2006) 2.08

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci (2012) 2.07

Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol (2010) 2.03

Consensus statement on chronic and subacute high altitude diseases. High Alt Med Biol (2005) 1.96

The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution. BMC Genomics (2008) 1.93

A cattle-human comparative map built with cattle BAC-ends and human genome sequence. Genome Res (2003) 1.92

Focal atrial tachycardia originating from the non-coronary aortic sinus: electrophysiological characteristics and catheter ablation. J Am Coll Cardiol (2006) 1.88

Every genome sequence needs a good map. Genome Res (2009) 1.85

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species. Genome Res (2010) 1.81

Preferential electrical coupling regulates neocortical lineage-dependent microcircuit assembly. Nature (2012) 1.75

The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res (2011) 1.70

Genomic diversity and evolution of the head crest in the rock pigeon. Science (2013) 1.68

Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res (2009) 1.66

A susceptibility locus at chromosome 3p21 linked to familial nasopharyngeal carcinoma. Cancer Res (2004) 1.65

Reconstruction of metabolic pathways for the cattle genome. BMC Syst Biol (2009) 1.63

Comparative epigenomic annotation of regulatory DNA. Cell (2012) 1.62

Avian genomes. A flock of genomes. Introduction. Science (2014) 1.60

microRNA-141 is involved in a nasopharyngeal carcinoma-related genes network. Carcinogenesis (2010) 1.59

A physical map of the bovine genome. Genome Biol (2007) 1.56

The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol (2013) 1.52

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci U S A (2013) 1.49

A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates. Genome Res (2004) 1.48

Nutrition-induced ketosis alters metabolic and signaling gene networks in liver of periparturient dairy cows. Physiol Genomics (2007) 1.47

Piggy-BACing the human genome II. A high-resolution, physically anchored, comparative map of the porcine autosomes. Genomics (2005) 1.46

Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46

The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes Dev (2012) 1.43

Genetic basis of Y-linked hearing impairment. Am J Hum Genet (2013) 1.42

FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics (2011) 1.41

The future of livestock breeding: genomic selection for efficiency, reduced emissions intensity, and adaptation. Trends Genet (2012) 1.41

miR-216b suppresses tumor growth and invasion by targeting KRAS in nasopharyngeal carcinoma. J Cell Sci (2011) 1.41

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. BMC Genomics (2012) 1.40

Draft genome sequence of the mulberry tree Morus notabilis. Nat Commun (2013) 1.38

A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS Genet (2010) 1.35

Effect of SPLUNC1 protein on the Pseudomonas aeruginosa and Epstein-Barr virus. Mol Cell Biochem (2007) 1.31

Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun (2013) 1.31

Cloning and characterization of FAM13A1--a gene near a milk protein QTL on BTA6: evidence for population-wide linkage disequilibrium in Israeli Holsteins. Genomics (2004) 1.29

ESTIMA, a tool for EST management in a multi-project environment. BMC Bioinformatics (2004) 1.28

BRD7, a novel bromodomain gene, inhibits G1-S progression by transcriptionally regulating some important molecules involved in ras/MEK/ERK and Rb/E2F pathways. J Cell Physiol (2004) 1.27

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics (2014) 1.27

Global gene expression profiles reveal significant nuclear reprogramming by the blastocyst stage after cloning. Proc Natl Acad Sci U S A (2005) 1.27

Store-operated Ca2+ entry through ORAI1 is critical for T cell-mediated autoimmunity and allograft rejection. J Immunol (2010) 1.27

Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc (2013) 1.24

Cactus graphs for genome comparisons. J Comput Biol (2011) 1.24

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun (2013) 1.22

Draft genome sequence of the Tibetan antelope. Nat Commun (2013) 1.22