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Literature DB >> 27054987

Compressive mapping for next-generation sequencing.

Deniz Yorukoglu¹, Yun William Yu^1,2, Jian Peng^1,2,3, Bonnie Berger^1,2.

Abstract

Entities: Species

Mesh：

Year: 2016 PMID： 27054987 PMCID： PMC5080835 DOI： 10.1038/nbt.3511

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

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23 in total

1. ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

Authors: Phuong Dao; Ibrahim Numanagić; Yen-Yi Lin; Faraz Hach; Emre Karakoc; Nilgun Donmez; Colin Collins; Evan E Eichler; S Cenk Sahinalp
Journal: Bioinformatics Date: 2013-10-15 Impact factor: 6.937

2. Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors: Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal: Nat Methods Date: 2008-05-30 Impact factor: 28.547

3. Fast gapped-read alignment with Bowtie 2.

Authors: Ben Langmead; Steven L Salzberg
Journal: Nat Methods Date: 2012-03-04 Impact factor: 28.547

Review 4. Repetitive DNA and next-generation sequencing: computational challenges and solutions.

Authors: Todd J Treangen; Steven L Salzberg
Journal: Nat Rev Genet Date: 2011-11-29 Impact factor: 53.242

5. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors: Bo Li; Colin N Dewey
Journal: BMC Bioinformatics Date: 2011-08-04 Impact factor: 3.307

6. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

Authors: David R Kelley; David G Hendrickson; Danielle Tenen; John L Rinn
Journal: Genome Biol Date: 2014-12-03 Impact factor: 13.583

7. HTSeq--a Python framework to work with high-throughput sequencing data.

Authors: Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal: Bioinformatics Date: 2014-09-25 Impact factor: 6.937

8. Fast and accurate read mapping with approximate seeds and multiple backtracking.

Authors: Enrico Siragusa; David Weese; Knut Reinert
Journal: Nucleic Acids Res Date: 2013-01-28 Impact factor: 16.971

9. Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection.

Authors: Claire Jubin; Alexandre Serero; Sophie Loeillet; Emmanuel Barillot; Alain Nicolas
Journal: G3 (Bethesda) Date: 2014-04-16 Impact factor: 3.154

10. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

Authors: Faraz Hach; Iman Sarrafi; Farhad Hormozdiari; Can Alkan; Evan E Eichler; S Cenk Sahinalp
Journal: Nucleic Acids Res Date: 2014-05-08 Impact factor: 16.971

13 in total

1. Statistical Binning for Barcoded Reads Improves Downstream Analyses.

Authors: Ariya Shajii; Ibrahim Numanagić; Christopher Whelan; Bonnie Berger
Journal: Cell Syst Date: 2018-08-22 Impact factor: 10.304

2. Fast genotyping of known SNPs through approximate k-mer matching.

Authors: Ariya Shajii; Deniz Yorukoglu; Yun William Yu; Bonnie Berger
Journal: Bioinformatics Date: 2016-09-01 Impact factor: 6.937

3. Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.

Authors: Michel Plüss; Anna M Kopps; Irene Keller; Janine Meienberg; Sylvan M Caspar; Nicolo Dubacher; Rémy Bruggmann; Manfred Vogel; Gabor Matyas
Journal: Proc Natl Acad Sci U S A Date: 2017-09-15 Impact factor: 11.205

Compressive mapping for next-generation sequencing.

1. ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms.

2. Mapping and quantifying mammalian transcriptomes by RNA-Seq.

3. Fast gapped-read alignment with Bowtie 2.

Review 4. Repetitive DNA and next-generation sequencing: computational challenges and solutions.

5. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

6. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

7. HTSeq--a Python framework to work with high-throughput sequencing data.

8. Fast and accurate read mapping with approximate seeds and multiple backtracking.

9. Sequence profiling of the Saccharomyces cerevisiae genome permits deconvolution of unique and multialigned reads for variant detection.

10. mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

1. Statistical Binning for Barcoded Reads Improves Downstream Analyses.

2. Fast genotyping of known SNPs through approximate k-mer matching.

3. Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.

4. False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors.

5. Seq: A High-Performance Language for Bioinformatics.

6. Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes.

7. Computational Biology in the 21st Century: Scaling with Compressive Algorithms.

8. Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.

9. Performance evaluation method for read mapping tool in clinical panel sequencing.

10. Levenshtein Distance, Sequence Comparison and Biological Database Search.