Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 180

1.

Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space.

Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS.

PeerJ. 2015 Mar 3;3:e808. doi: 10.7717/peerj.808. eCollection 2015.

2.

HISAT: a fast spliced aligner with low memory requirements.

Kim D, Langmead B, Salzberg SL.

Nat Methods. 2015 Apr;12(4):357-60. doi: 10.1038/nmeth.3317. Epub 2015 Mar 9.

PMID:
25751142
3.

Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT.

Nat Biotechnol. 2015 Mar 6;33(3):243-6. doi: 10.1038/nbt.3172. No abstract available.

PMID:
25748911
4.

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL.

Nat Biotechnol. 2015 Mar;33(3):290-5. doi: 10.1038/nbt.3122. Epub 2015 Feb 18.

PMID:
25690850
5.

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations.

Deng K, Pertea M, Rongvaux A, Wang L, Durand CM, Ghiaur G, Lai J, McHugh HL, Hao H, Zhang H, Margolick JB, Gurer C, Murphy AJ, Valenzuela DM, Yancopoulos GD, Deeks SG, Strowig T, Kumar P, Siliciano JD, Salzberg SL, Flavell RA, Shan L, Siliciano RF.

Nature. 2015 Jan 15;517(7534):381-5. doi: 10.1038/nature14053. Epub 2015 Jan 7.

PMID:
25561180
6.

Unexpected cross-species contamination in genome sequencing projects.

Merchant S, Wood DE, Salzberg SL.

PeerJ. 2014 Nov 20;2:e675. doi: 10.7717/peerj.675. eCollection 2014.

7.

A new rhesus macaque assembly and annotation for next-generation sequencing analyses.

Zimin AV, Cornish AS, Maudhoo MD, Gibbs RM, Zhang X, Pandey S, Meehan DT, Wipfler K, Bosinger SE, Johnson ZP, Tharp GK, Marçais G, Roberts M, Ferguson B, Fox HS, Treangen T, Salzberg SL, Yorke JA, Norgren RB Jr.

Biol Direct. 2014 Oct 14;9(1):20. doi: 10.1186/1745-6150-9-20.

8.

Genomic features of a bumble bee symbiont reflect its host environment.

Martinson VG, Magoc T, Koch H, Salzberg SL, Moran NA.

Appl Environ Microbiol. 2014 Jul;80(13):3793-803. doi: 10.1128/AEM.00322-14. Epub 2014 Apr 18.

9.

Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

10.

Sequencing and assembly of the 22-gb loblolly pine genome.

Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, Koriabine M, Marçais G, Puiu D, Roberts M, Wegrzyn JL, de Jong PJ, Neale DB, Salzberg SL, Yorke JA, Langley CH.

Genetics. 2014 Mar;196(3):875-90. doi: 10.1534/genetics.113.159715.

11.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

12.

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Wood DE, Salzberg SL.

Genome Biol. 2014 Mar 3;15(3):R46. doi: 10.1186/gb-2014-15-3-r46.

13.

Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues.

Florea L, Song L, Salzberg SL.

Version 2. F1000Res. 2013 Sep 16 [revised 2013 Nov 21];2:188. doi: 10.12688/f1000research.2-188.v2. eCollection 2013.

14.

Genome-guided transcriptome assembly in the age of next-generation sequencing.

Florea LD, Salzberg SL.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1234-40. Review.

15.

DIAMUND: direct comparison of genomes to detect mutations.

Salzberg SL, Pertea M, Fahrner JA, Sobreira N.

Hum Mutat. 2014 Mar;35(3):283-8. doi: 10.1002/humu.22503.

16.

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Wegrzyn JL, Lin BY, Zieve JJ, Dougherty WM, Martínez-García PJ, Koriabine M, Holtz-Morris A, deJong P, Crepeau M, Langley CH, Puiu D, Salzberg SL, Neale DB, Stevens KA.

PLoS One. 2013 Sep 4;8(9):e72439. doi: 10.1371/journal.pone.0072439. eCollection 2013.

17.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

18.

The MaSuRCA genome assembler.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA.

Bioinformatics. 2013 Nov 1;29(21):2669-77. doi: 10.1093/bioinformatics/btt476. Epub 2013 Aug 29.

19.

Open access to tree genomes: the path to a better forest.

Neale DB, Langley CH, Salzberg SL, Wegrzyn JL.

Genome Biol. 2013 Jun 24;14(6):120. doi: 10.1186/gb-2013-14-6-120.

20.

GAGE-B: an evaluation of genome assemblers for bacterial organisms.

Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL.

Bioinformatics. 2013 Jul 15;29(14):1718-25. doi: 10.1093/bioinformatics/btt273. Epub 2013 May 10.

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk