Papers

Crystallizing short-read assemblies around seeds.

Hossain MS, Azimi N, Skiena S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S16.

PMID: 19208115 [PubMed - indexed for MEDLINE]


QSRA: a quality-value guided de novo short read assembler.

Bryant DW Jr, Wong WK, Mockler TC.

BMC Bioinformatics. 2009 Feb 24;10:69.

PMID: 19239711 [PubMed - indexed for MEDLINE]


De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.

Farrer RA, Kemen E, Jones JD, Studholme DJ.

FEMS Microbiol Lett. 2009 Feb;291(1):103-11. Epub 2008 Dec 9.

PMID: 19077061 [PubMed - indexed for MEDLINE]


ABySS: A parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Apr 21. [Epub ahead of print]

PMID: 19251739 [PubMed - as supplied by publisher]


A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.

Rausch T, Koren S, Denisov G, Weese D, Emde AK, Döring A, Reinert K.

Bioinformatics. 2009 May 1;25(9):1118-24. Epub 2009 Mar 5.

PMID: 19269990 [PubMed - in process]


Discovering genetic polymorphisms in next-generation sequencing data.

Imelfort M, Duran C, Batley J, Edwards D.

Plant Biotechnol J. 2009 May;7(4):312-7. Review.

PMID: 19386039 [PubMed - indexed for MEDLINE]


Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains.

Nelson W, Luo M, Ma J, Estep M, Estill J, He R, Talag J, Sisneros N, Kudrna D, Kim H, Ammiraju JS, Collura K, Bharti AK, Messing J, Wing RA, SanMiguel P, Bennetzen JL, Soderlund C.

BMC Genomics. 2008 Dec 19;9:621.

PMID: 19099592 [PubMed - indexed for MEDLINE]


Aggressive assembly of pyrosequencing reads with mates.

Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, Brownley A, Johnson J, Li K, Mobarry C, Sutton G.

Bioinformatics. 2008 Dec 15;24(24):2818-24. Epub 2008 Oct 24.

PMID: 18952627 [PubMed - indexed for MEDLINE]


Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404.

PMID: 18755037 [PubMed - indexed for MEDLINE]


ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. Epub 2008 Mar 13.

PMID: 18340039 [PubMed - indexed for MEDLINE]


Bioinformatics challenges of new sequencing technology.

Pop M, Salzberg SL.

Trends Genet. 2008 Mar;24(3):142-9. Epub 2008 Feb 11. Review.

PMID: 18262676 [PubMed - indexed for MEDLINE]


The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets.

Droege M, Hill B.

J Biotechnol. 2008 Aug 31;136(1-2):3-10. Epub 2008 Jun 21. Review.

PMID: 18616967 [PubMed - indexed for MEDLINE]


High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.

Aury JM, Cruaud C, Barbe V, Rogier O, Mangenot S, Samson G, Poulain J, Anthouard V, Scarpelli C, Artiguenave F, Wincker P.

BMC Genomics. 2008 Dec 16;9:603.

PMID: 19087275 [PubMed - indexed for MEDLINE]


Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.

PMID: 18083777 [PubMed - indexed for MEDLINE]


De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.

Genome Res. 2008 May;18(5):802-9. Epub 2008 Mar 10.

PMID: 18332092 [PubMed - indexed for MEDLINE]


Sequencing of natural strains of Arabidopsis thaliana with short reads.

Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.

PMID: 18818371 [PubMed - indexed for MEDLINE]


Applications of next-generation sequencing technologies in functional genomics.

Morozova O, Marra MA.

Genomics. 2008 Nov;92(5):255-64. Epub 2008 Aug 24. Review.

PMID: 18703132 [PubMed - indexed for MEDLINE]


Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. Epub 2008 Mar 18.

PMID: 18349386 [PubMed - indexed for MEDLINE]


Segment-based multiple sequence alignment.

Rausch T, Emde AK, Weese D, Döring A, Notredame C, Reinert K.

Bioinformatics. 2008 Aug 15;24(16):i187-92.

PMID: 18689823 [PubMed - indexed for MEDLINE]


Optimal spliced alignments of short sequence reads.

De Bona F, Ossowski S, Schneeberger K, Rätsch G.

Bioinformatics. 2008 Aug 15;24(16):i174-80.

PMID: 18689821 [PubMed - indexed for MEDLINE]


Paired-end diTagging for transcriptome and genome analysis.

Ng P, Wei CL, Ruan Y.

Curr Protoc Mol Biol. 2007 Jul;Chapter 21:Unit 21.12.

PMID: 18265396 [PubMed - indexed for MEDLINE]


Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

Dunn JJ, McCorkle SR, Everett L, Anderson CW.

Genet Eng (N Y). 2007;28:159-73. Review.

PMID: 17153938 [PubMed - indexed for MEDLINE]


Correcting base-assignment errors in repeat regions of shotgun assembly.

Zhi D, Keich U, Pevzner P, Heber S, Tang H.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):54-64.

PMID: 17277413 [PubMed - indexed for MEDLINE]


Whole-genome sequencing and assembly with high-throughput, short-read technologies.

Sundquist A, Ronaghi M, Tang H, Pevzner P, Batzoglou S.

PLoS ONE. 2007 May 30;2(5):e484.

PMID: 17534434 [PubMed]


SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing.

Dohm JC, Lottaz C, Borodina T, Himmelbauer H.

Genome Res. 2007 Nov;17(11):1697-706. Epub 2007 Oct 1.

PMID: 17908823 [PubMed - indexed for MEDLINE]


Assembling millions of short DNA sequences using SSAKE.

Warren RL, Sutton GG, Jones SJ, Holt RA.

Bioinformatics. 2007 Feb 15;23(4):500-1. Epub 2006 Dec 8.

PMID: 17158514 [PubMed - indexed for MEDLINE]


Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.

Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D.

Science. 2007 Jul 20;317(5836):338-42.

PMID: 17641193 [PubMed - indexed for MEDLINE]


Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y.

Nucleic Acids Res. 2006 Jul 13;34(12):e84.

PMID: 16840528 [PubMed - indexed for MEDLINE]


Drosophila melanogaster: a case study of a model genomic sequence and its consequences.

Ashburner M, Bergman CM.

Genome Res. 2005 Dec;15(12):1661-7. Review.

PMID: 16339363 [PubMed - indexed for MEDLINE]


A preprocessor for shotgun assembly of large genomes.

Roberts M, Hunt BR, Yorke JA, Bolanos RA, Delcher AL.

J Comput Biol. 2004;11(4):734-52.

PMID: 15579242 [PubMed - indexed for MEDLINE]


Fragment assembly with short reads.

Chaisson M, Pevzner P, Tang H.

Bioinformatics. 2004 Sep 1;20(13):2067-74. Epub 2004 Apr 1.

PMID: 15059830 [PubMed - indexed for MEDLINE]


Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana.

Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchell-Olds T, Weisshaar B.

Genome Res. 2003 Jun;13(6A):1250-7.

PMID: 12799357 [PubMed - indexed for MEDLINE]


Sequencing by hybridization (SBH): advantages, achievements, and opportunities.

Drmanac R, Drmanac S, Chui G, Diaz R, Hou A, Jin H, Jin P, Kwon S, Lacy S, Moeur B, Shafto J, Swanson D, Ukrainczyk T, Xu C, Little D.

Adv Biochem Eng Biotechnol. 2002;77:75-101. Review.

PMID: 12227738 [PubMed - indexed for MEDLINE]


Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana.

Bancroft I.

Yeast. 2000 Apr;17(1):1-5. Review.

PMID: 10797596 [PubMed - indexed for MEDLINE]