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Items: 18

1.

AKT: ancestry and kinship toolkit.

Arthur R, Schulz-Trieglaff O, Cox AJ, O'Connell J.

Bioinformatics. 2017 Jan 1;33(1):142-144. doi: 10.1093/bioinformatics/btw576. Epub 2016 Sep 14.

PMID:
27634946
2.

Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions.

Arthur R, O'Connell J, Schulz-Trieglaff O, Cox AJ.

Bioinformatics. 2016 Aug 1;32(15):2306-12. doi: 10.1093/bioinformatics/btw097. Epub 2016 Mar 9.

PMID:
27153730
3.

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, Cox AJ, Kruglyak S, Saunders CT.

Bioinformatics. 2016 Apr 15;32(8):1220-2. doi: 10.1093/bioinformatics/btv710. Epub 2015 Dec 8.

PMID:
26647377
4.

NxRepair: error correction in de novo sequence assembly using Nextera mate pairs.

Murphy RR, O'Connell J, Cox AJ, Schulz-Trieglaff O.

PeerJ. 2015 Jun 2;3:e996. doi: 10.7717/peerj.996. eCollection 2015.

5.

NxTrim: optimized trimming of Illumina mate pair reads.

O'Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ.

Bioinformatics. 2015 Jun 15;31(12):2035-7. doi: 10.1093/bioinformatics/btv057. Epub 2015 Feb 5.

PMID:
25661542
6.

BEETL-fastq: a searchable compressed archive for DNA reads.

Janin L, Schulz-Trieglaff O, Cox AJ.

Bioinformatics. 2014 Oct;30(19):2796-801. doi: 10.1093/bioinformatics/btu387. Epub 2014 Jun 20.

PMID:
24950811
7.

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.

Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ.

BMC Bioinformatics. 2013;14 Suppl 5:S2. doi: 10.1186/1471-2105-14-S5-S2. Epub 2013 Apr 10.

8.

Genomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients.

Chung JC, Becq J, Fraser L, Schulz-Trieglaff O, Bond NJ, Foweraker J, Bruce KD, Smith GP, Welch M.

J Bacteriol. 2012 Sep;194(18):4857-66. doi: 10.1128/JB.01050-12. Epub 2012 Jun 29.

9.

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.

Köser CU, Holden MT, Ellington MJ, Cartwright EJ, Brown NM, Ogilvy-Stuart AL, Hsu LY, Chewapreecha C, Croucher NJ, Harris SR, Sanders M, Enright MC, Dougan G, Bentley SD, Parkhill J, Fraser LJ, Betley JR, Schulz-Trieglaff OB, Smith GP, Peacock SJ.

N Engl J Med. 2012 Jun 14;366(24):2267-75. doi: 10.1056/NEJMoa1109910.

10.

Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer.

Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, Bauer MJ, Fu B, Hims M, Ding Z, Ivakhno S, Stewart C, Ng BL, Wong W, Aken B, White S, Alsop A, Becq J, Bignell GR, Cheetham RK, Cheng W, Connor TR, Cox AJ, Feng ZP, Gu Y, Grocock RJ, Harris SR, Khrebtukova I, Kingsbury Z, Kowarsky M, Kreiss A, Luo S, Marshall J, McBride DJ, Murray L, Pearse AM, Raine K, Rasolonjatovo I, Shaw R, Tedder P, Tregidgo C, Vilella AJ, Wedge DC, Woods GM, Gormley N, Humphray S, Schroth G, Smith G, Hall K, Searle SM, Carter NP, Papenfuss AT, Futreal PA, Campbell PJ, Yang F, Bentley DR, Evers DJ, Stratton MR.

Cell. 2012 Feb 17;148(4):780-91. doi: 10.1016/j.cell.2011.11.065.

11.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

12.

A comprehensive catalogue of somatic mutations from a human cancer genome.

Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, Mudie LJ, Ning Z, Royce T, Schulz-Trieglaff OB, Spiridou A, Stebbings LA, Szajkowski L, Teague J, Williamson D, Chin L, Ross MT, Campbell PJ, Bentley DR, Futreal PA, Stratton MR.

Nature. 2010 Jan 14;463(7278):191-6. doi: 10.1038/nature08658. Epub 2009 Dec 16.

13.

Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments.

Schulz-Trieglaff O, Machtejevas E, Reinert K, Schlüter H, Thiemann J, Unger K.

BioData Min. 2009 Apr 7;2(1):4. doi: 10.1186/1756-0381-2-4.

14.

LC-MSsim--a simulation software for liquid chromatography mass spectrometry data.

Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K.

BMC Bioinformatics. 2008 Oct 8;9:423. doi: 10.1186/1471-2105-9-423.

15.

Computational quantification of peptides from LC-MS data.

Schulz-Trieglaff O, Hussong R, Gröpl C, Leinenbach A, Hildebrandt A, Huber C, Reinert K.

J Comput Biol. 2008 Sep;15(7):685-704. doi: 10.1089/cmb.2007.0117.

PMID:
18707556
16.

OpenMS - an open-source software framework for mass spectrometry.

Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O.

BMC Bioinformatics. 2008 Mar 26;9:163. doi: 10.1186/1471-2105-9-163.

17.

A geometric approach for the alignment of liquid chromatography-mass spectrometry data.

Lange E, Gröpl C, Schulz-Trieglaff O, Leinenbach A, Huber C, Reinert K.

Bioinformatics. 2007 Jul 1;23(13):i273-81.

PMID:
17646306
18.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091

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