Optimization of de novo transcriptome assembly from next-generation sequencing data.
暂无分享,去创建一个
[1] X. Huang,et al. A contig assembly program based on sensitive detection of fragment overlaps. , 1992, Genomics.
[2] Thomas L. Madden,et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.
[3] Haixu Tang,et al. Fragment assembly with double-barreled data , 2001, ISMB.
[4] J. Sire. Teeth outside the mouth in teleost fishes: how to benefit from a developmental accident , 2001, Evolution & development.
[5] P. Pevzner,et al. An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[6] Dirk Steinke,et al. Novel Relationships Among Ten Fish Model Species Revealed Based on a Phylogenomic Analysis Using ESTs , 2006, Journal of Molecular Evolution.
[7] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[8] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[9] J. Inoue,et al. The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes. , 2006, Genes & genetic systems.
[10] Alfried P Vogler,et al. Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles). , 2006, Molecular biology and evolution.
[11] Jay Shendure,et al. Multiplex amplification of large sets of human exons , 2007, Nature Methods.
[12] P. Schnable,et al. SNP discovery via 454 transcriptome sequencing , 2007, The Plant journal : for cell and molecular biology.
[13] Evgeny M. Zdobnov,et al. Genome Sequence of Aedes aegypti, a Major Arbovirus Vector , 2007, Science.
[14] Matthew E Hudson,et al. Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality , 2007, Science.
[15] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[16] Mark J. P. Chaisson,et al. Short read fragment assembly of bacterial genomes. , 2008, Genome research.
[17] Hunting hidden transcripts , 2008, Nature Methods.
[18] J. Jackson,et al. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery , 2009, BMC Genomics.
[19] S. Schuster. Next-generation sequencing transforms today's biology , 2008, Nature Methods.
[20] Steven Salzberg,et al. Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads , 2008, PLoS Comput. Biol..
[21] David Hernández,et al. De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. , 2008, Genome research.
[22] M. Gerstein,et al. The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing , 2008, Science.
[23] J. Marden,et al. Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing , 2008, Molecular ecology.
[24] David Q. Matus,et al. Broad phylogenomic sampling improves resolution of the animal tree of life , 2008, Nature.
[25] C. Nusbaum,et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. , 2008, Genome research.
[26]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[27]
Christian Schlötterer,et al.
Gene expression profiling by massively parallel sequencing.
,
2007,
Genome research.
[28]
Patrick J Biggs,et al.
An approach to transcriptome analysis of non-model organisms using short-read sequences.
,
2008,
Genome informatics. International Conference on Genome Informatics.
[29]
Fabien Burki,et al.
Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes
,
2008,
Biology Letters.
[30]
B. Williams,et al.
Mapping and quantifying mammalian transcriptomes by RNA-Seq
,
2008,
Nature Methods.
[31]
Vilmos Ágoston,et al.
Deep sequencing of the zebrafish transcriptome response to mycobacterium infection.
,
2009,
Molecular immunology.
[32]
A. Gnirke,et al.
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
,
2009,
Genome Biology.
[33]
Steven J. M. Jones,et al.
Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access
,
2022
.
[34]
Tissue Compartment Analysis for Biomarker Discovery by Gene Expression Profiling
,
2009,
PloS one.
[35]
Ryan D. Morin,et al.
Next-generation tag sequencing for cancer gene expression profiling.
,
2009,
Genome research.
[36]
Catalin C. Barbacioru,et al.
mRNA-Seq whole-transcriptome analysis of a single cell
,
2009,
Nature Methods.
[37]
Josephine A. Reinhardt,et al.
De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae.
,
2009,
Genome research.
[38]
Next-generation sequencing reveals complex relationships between the epigenome and transcriptome in maize.
,
2009,
Plant signaling & behavior.
[39]
Bradley J. Main,et al.
BMC Genomics BioMed Central Methodology article Allele-specific expression assays using Solexa
,
2009
.
[40]
G. Fraser,et al.
An Ancient Gene Network Is Co-opted for Teeth on Old and New Jaws
,
2009,
PLoS biology.
[41]
Mark Johnston,et al.
Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics.
,
2009,
Molecular biology and evolution.
[42]
M. Gerstein,et al.
RNA-Seq: a revolutionary tool for transcriptomics
,
2009,
Nature Reviews Genetics.
[43]
D. Shoemaker,et al.
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis
,
2009,
BMC Genomics.
[44]
T. Fennell,et al.
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
,
2009,
Genome Biology.
[45]
Michael Q. Zhang,et al.
Updates to the RMAP short-read mapping software
,
2009,
Bioinform..
[46]
J. Montoya-Burgos,et al.
Transcriptome screen for fast evolving genes by Inter-Specific Selective Hybridization (ISSH)
,
2010,
BMC Genomics.
[47]
R. Guigó,et al.
Transcriptome genetics using second generation sequencing in a Caucasian population
,
2010,
Nature.