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Results: 1 to 20 of 173

1.

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 1;80(13):3793-3803. Epub 2014 Apr 18.

PMID:
24747890
[PubMed - as supplied by publisher]
2.

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.

PMID:
24653211
[PubMed - in process]
3.

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.

PMID:
24653210
[PubMed - in process]
4.

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 20;15(3):R59. [Epub ahead of print]

PMID:
24647006
[PubMed - as supplied by publisher]
Free PMC Article
5.

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Wood DE, Salzberg SL.

Genome Biol. 2014 Mar 3;15(3):R46. [Epub ahead of print]

PMID:
24580807
[PubMed - as supplied by publisher]
Free PMC Article
6.

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.

PMID:
24555089
[PubMed]
Free PMC Article
7.

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.

PMID:
24524156
[PubMed - in process]
8.

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.

PMID:
24375697
[PubMed - in process]
9.

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.

PMID:
24023741
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
24013487
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
23990416
[PubMed - indexed for MEDLINE]
12.

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. [Epub ahead of print]

PMID:
23796049
[PubMed - as supplied by publisher]
Free PMC Article
13.

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.

PMID:
23665771
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Sequestration: inadvertently killing biomedical research to score political points.

Leek JT, Salzberg SL.

Genome Biol. 2013 Mar 27;14(3):109. [Epub ahead of print] No abstract available.

PMID:
23651812
[PubMed - as supplied by publisher]
Free PMC Article
15.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL.

Genome Biol. 2013 Apr 25;14(4):R36. [Epub ahead of print]

PMID:
23618408
[PubMed - as supplied by publisher]
Free PMC Article
16.

EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.

Magoc T, Wood D, Salzberg SL.

Evol Bioinform Online. 2013;9:127-36. doi: 10.4137/EBO.S11250. Epub 2013 Mar 10.

PMID:
23531787
[PubMed]
Free PMC Article
17.

NIH funding: It does support innovators.

Salzberg SL.

Nature. 2013 Jan 3;493(7430):26. doi: 10.1038/493026b. No abstract available.

PMID:
23282352
[PubMed - indexed for MEDLINE]
18.

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.

Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL.

Biol Direct. 2012 Oct 30;7:37. doi: 10.1186/1745-6150-7-37.

PMID:
23111013
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA.

PLoS One. 2012;7(8):e42680. doi: 10.1371/journal.pone.0042680. Epub 2012 Aug 3.

PMID:
22880081
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

The perils of gene patents.

Salzberg SL.

Clin Pharmacol Ther. 2012 Jun;91(6):969-71. doi: 10.1038/clpt.2012.6.

PMID:
22609909
[PubMed - indexed for MEDLINE]
Free PMC Article

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