Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
暂无分享,去创建一个
Jose Lugo-Martinez | Matthew W. Hahn | Daniel R. Schrider | Wesley C. Warren | James F. Denton | Abraham E. Tucker | Jose Lugo-Martinez | W. Warren | M. Hahn | James Denton | M. Hahn | Matthew W. Hahn
[1] G. Hong,et al. Nucleic Acids Research , 2015, Nucleic Acids Research.
[2] Colin N. Dewey,et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004, Nature.
[3] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[4] Xiongfei Zhang,et al. Limitations of the rhesus macaque draft genome assembly and annotation , 2012, BMC Genomics.
[5] Sofia M. C. Robb,et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.
[6] Eugene W. Myers,et al. A whole-genome assembly of Drosophila. , 2000, Science.
[7] Loretta Auvil,et al. The yak genome and adaptation to life at high altitude , 2012, Nature Genetics.
[8] R. Durbin,et al. Efficient de novo assembly of large genomes using compressed data structures. , 2012, Genome research.
[9] Steven J. M. Jones,et al. Physical map-assisted whole-genome shotgun sequence assemblies. , 2006, Genome research.
[10] Paul C. Leyland,et al. FlyBase: improvements to the bibliography , 2012, Nucleic Acids Res..
[11] Anders Krogh,et al. farming suggests key adaptations to advanced social life and fungus Acromyrmex echinatior The genome of the leaf-cutting ant Material Supplemental , 2011 .
[12] M. Berriman,et al. REAPR: a universal tool for genome assembly evaluation , 2013, Genome Biology.
[13] Makedonka Mitreva,et al. A vertebrate case study of the quality of assemblies derived from next-generation sequences , 2011, Genome Biology.
[14] Jean L. Chang,et al. Initial sequence of the chimpanzee genome and comparison with the human genome , 2005, Nature.
[15] Laxmi Parida,et al. Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes , 2011, BMC Genomics.
[16] Wonhee Jang,et al. Linking the human cytogenetic map with nucleotide sequence: the CCAP clone set. , 2006, Cancer genetics and cytogenetics.
[17] Yuan Zhang,et al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars , 2013, Nature Genetics.
[18] Inanç Birol,et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species , 2013, GigaScience.
[19] V. Solovyev,et al. Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.
[20] Peter A. Meric,et al. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse , 2009, PLoS biology.
[21] Adam M. Phillippy,et al. Comparative genome assembly , 2004, Briefings Bioinform..
[22] Anton J. Enright,et al. An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.
[23] Albee Y. Ling,et al. The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes , 2012, Science.
[24] Tomas W. Fitzgerald,et al. Origins and functional impact of copy number variation in the human genome , 2010, Nature.
[25] Gautier Koscielny,et al. Ensembl 2012 , 2011, Nucleic Acids Res..
[26] Steven Salzberg,et al. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads , 2008, PLoS Comput. Biol..
[27] Haixu Tang,et al. A machine-learning approach to combined evidence validation of genome assemblies , 2008, Bioinform..
[28] Dan Graur,et al. Finding the missing honey bee genes: lessons learned from a genome upgrade , 2014, BMC Genomics.
[29] Bindu Nanduri,et al. RNA-Seq-based transcriptional map of the bovine respiratory disease pathogen Histophilus somni 2336 , 2011, Genome Biology.
[30] Kristian Stevens,et al. Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. , 2011, Genome research.
[31] Mira V. Han,et al. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. , 2013, Molecular biology and evolution.
[32] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[33] Shigehiro Kuraku,et al. Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes) , 2011, Briefings Bioinform..
[34] S. Salzberg,et al. Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies , 2011, PloS one.
[35] C. Currie,et al. Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation , 2012, BMC Genomics.
[36] I-Min A. Chen,et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata , 2011, Nucleic Acids Res..
[37] Kui Lin,et al. RNA-Seq improves annotation of protein-coding genes in the cucumber genome , 2011, BMC Genomics.
[38] J A Eisen,et al. Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? , 2001, Science.
[39] Colin N. Dewey,et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , 2007, Nature.
[40] Qunfeng Dong,et al. xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features , 2006, Genome Biology.
[41] T. Matise,et al. Nucleotide Sequence Database Policies , 2002, Science.
[42] Jiongtang Li,et al. L_RNA_scaffolder: scaffolding genomes with transcripts , 2013, BMC Genomics.
[43] Volker Brendel,et al. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes , 2006, Genome Biology.
[44] James C. Costello,et al. Limitations of Pseudogenes in Identifying Gene Losses , 2008, RECOMB-CG.
[45] E. Eichler,et al. Limitations of next-generation genome sequence assembly , 2011, Nature Methods.
[46] M. Schatz,et al. Genome assembly forensics: finding the elusive mis-assembly , 2008, Genome Biology.
[47] Keith Bradnam,et al. Assessing the gene space in draft genomes , 2008, Nucleic acids research.
[48] Sudhir Kumar,et al. Comparative Genomics in Eukaryotes , 2005 .
[49] Jane Rogers,et al. Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17 , 2007, Genome Biology.
[50] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[51] George Newport,et al. The diploid genome sequence of Candida albicans. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[52] Ali Mortazavi,et al. Scaffolding a Caenorhabditis nematode genome with RNA-seq. , 2010, Genome research.
[53] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[54] Fernando A. Villanea,et al. Diet and the evolution of human amylase gene copy number variation , 2007, Nature Genetics.
[55] Mihaela M. Martis,et al. A physical, genetic and functional sequence assembly of the barley genome , 2012, Nature.
[56] Todd H. Oakley,et al. The Ecoresponsive Genome of Daphnia pulex , 2011, Science.
[57] B. Graveley. The developmental transcriptome of Drosophila melanogaster , 2010, Nature.
[58] Don G. Gilbert,et al. wFleaBase: the Daphnia genome database , 2005, BMC Bioinformatics.
[59] Jeffery P. Demuth,et al. The Evolution of Mammalian Gene Families , 2006, PloS one.
[60] Jill P Mesirov,et al. Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. , 2005, Genome research.
[61] Jian Wang,et al. The Genome Sequence of the Malaria Mosquito Anopheles gambiae , 2002, Science.
[62] James C. Costello,et al. All Human-specific Gene Losses Are Present in the Genome as Pseudogenes , 2022 .
[63] F. Denoeud,et al. Annotating genomes with massive-scale RNA sequencing , 2008, Genome Biology.
[64] Mira V. Han,et al. Gene Family Evolution across 12 Drosophila Genomes , 2007, PLoS genetics.
[65] International Human Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004 .
[66] E. Pennisi. A Low Number Wins the GeneSweep Pool , 2003, Science.
[67] Felipe Zapata,et al. Toward a statistically explicit understanding of de novo sequence assembly , 2013, Bioinform..
[68] Albert J. Vilella,et al. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses , 2011, Genome Biology.
[69] Matthew W. Hahn,et al. Sequencing, Assembling, and Correcting Draft Genomes Using Recombinant Populations , 2014, G3: Genes, Genomes, Genetics.
[70] I-Min A. Chen,et al. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..
[71] Manolis Kellis,et al. Error and Error Mitigation in Low-Coverage Genome Assemblies , 2011, PloS one.
[72] C. Ponting,et al. Genome assembly quality: assessment and improvement using the neutral indel model. , 2010, Genome research.
[73] Mario Stanke,et al. Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.
[74] S. Karlin,et al. Prediction of complete gene structures in human genomic DNA. , 1997, Journal of molecular biology.
[75] Justin O. Borevitz,et al. Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster , 2008, Science.