The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
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[1] Wei Shi,et al. Global changes in the mammary epigenome are induced by hormonal cues and coordinated by Ezh2. , 2013, Cell reports.
[2] Roderic Guigó,et al. The GEM mapper: fast, accurate and versatile alignment by filtration , 2012, Nature Methods.
[3] Knut Reinert,et al. RazerS 3: Faster, fully sensitive read mapping , 2012, Bioinform..
[4] Neil Moore,et al. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses , 2012, Nature Genetics.
[5] Dario Strbenac,et al. Copy-number-aware differential analysis of quantitative DNA sequencing data , 2012, Genome research.
[6] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[7] Leping Li,et al. ART: a next-generation sequencing read simulator , 2012, Bioinform..
[8] Davis J. McCarthy,et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.
[9] Zhenxin Zhang,et al. A 14 bp indel variation in the NCX1 gene modulates the age at onset in late-onset Alzheimer’s disease , 2012, Journal of Neural Transmission.
[10] Knut Reinert,et al. STELLAR: fast and exact local alignments , 2011, BMC Bioinformatics.
[11] Martha R. Stampfer,et al. Epigenetic regulation of normal human mammary cell type-specific miRNAs. , 2011, Genome research.
[12] Lucian Ilie,et al. SHRiMP2: Sensitive yet Practical Short Read Mapping , 2011, Bioinform..
[13] M. DePristo,et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data , 2011, Nature Genetics.
[14] Ping Zhang,et al. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb , 2011, Nucleic acids research.
[15] Wei-keng Liao,et al. Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing , 2011, Bioinform..
[16] Knut Reinert,et al. A novel and well-defined benchmarking method for second generation read mapping , 2011, BMC Bioinformatics.
[17] Wei Shi,et al. Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips , 2010, Nucleic acids research.
[18] Manuel Holtgrewe,et al. Mason – A Read Simulator for Second Generation Sequencing Data , 2010 .
[19] D. Altshuler,et al. A map of human genome variation from population-scale sequencing , 2010, Nature.
[20] Heng Li,et al. A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..
[21] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[22] Dominique Lavenier,et al. GASSST: global alignment short sequence search tool , 2010, Bioinform..
[23] B. Langmead,et al. Cloud-scale RNA-sequencing differential expression analysis with Myrna , 2010, Genome Biology.
[24] Thomas J. Hardcastle,et al. baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data , 2010, BMC Bioinformatics.
[25] Faraz Hach,et al. mrsFAST: a cache-oblivious algorithm for short-read mapping , 2010, Nature Methods.
[26] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[27] W. Huber,et al. which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .
[28] Serban Nacu,et al. Fast and SNP-tolerant detection of complex variants and splicing in short reads , 2010, Bioinform..
[29] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[30] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[31] S. Nelson,et al. BFAST: An Alignment Tool for Large Scale Genome Resequencing , 2009, PloS one.
[32] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[33] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[34] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[35] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[36]
R. Durbin,et al.
Mapping Quality Scores Mapping Short Dna Sequencing Reads and Calling Variants Using P ,
2022
.
[37]
Bin Ma,et al.
ZOOM! Zillions of oligos mapped
,
2008,
Bioinform..
[38]
R. Irizarry,et al.
Consolidated strategy for the analysis of microarray spike-in data
,
2008,
Nucleic acids research.
[39]
Matthew E Ritchie,et al.
Spike-in validation of an Illumina-specific variance-stabilizing transformation
,
2008,
BMC Research Notes.
[40]
Mark D. Robinson,et al.
Moderated statistical tests for assessing differences in tag abundance
,
2007,
Bioinform..
[41]
Changqing Zeng,et al.
A six-nucleotide insertion-deletion polymorphism in the CASP8 promoter is associated with susceptibility to multiple cancers
,
2007,
Nature Genetics.
[42]
Hanlee P. Ji,et al.
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.
,
2006,
Nature biotechnology.
[43]
Maqc Consortium.
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
,
2006,
Nature Biotechnology.
[44]
Kathleen F. Kerr,et al.
The External RNA Controls Consortium: a progress report
,
2005,
Nature Methods.
[45]
Eugene W. Myers,et al.
Efficient q-Gram Filters for Finding All epsilon-Matches over a Given Length
,
2005,
RECOMB.
[46]
Kim R. Rasmussen,et al.
Efficient q-Gram Filters for Finding All-Matches Over a Given Length
,
2005
.
[47]
Rafael A Irizarry,et al.
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
,
2003,
Biostatistics.
[48]
Terence P. Speed,et al.
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
,
2003,
Bioinform..
[49]
Martin Vingron,et al.
q-gram based database searching using a suffix array (QUASAR)
,
1999,
RECOMB.
[50]
Eugene W. Myers,et al.
A fast bit-vector algorithm for approximate string matching based on dynamic programming
,
1998,
JACM.
[51]
E. Myers,et al.
Basic local alignment search tool.
,
1990,
Journal of molecular biology.
[52]
M S Waterman,et al.
Identification of common molecular subsequences.
,
1981,
Journal of molecular biology.
[53]
Christus,et al.
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
,
2022
.