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Items: 1 to 20 of 190

1.

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system.

Salzberg SL, Breitwieser FP, Kumar A, Hao H, Burger P, Rodriguez FJ, Lim M, Quiñones-Hinojosa A, Gallia GL, Tornheim JA, Melia MT, Sears CL, Pardo CA.

Neurol Neuroimmunol Neuroinflamm. 2016 Jun 13;3(4):e251. doi: 10.1212/NXI.0000000000000251. eCollection 2016 Aug.

2.

Databases: Reminder to deposit DNA sequences.

Salzberg SL.

Nature. 2016 May 11;533(7602):179. doi: 10.1038/533179a. No abstract available.

PMID:
27172038
3.

Reminder to deposit DNA sequences.

Blaxter M, Danchin A, Savakis B, Fukami-Kobayashi K, Kurokawa K, Sugano S, Roberts RJ, Salzberg SL, Wu CI.

Science. 2016 May 13;352(6287):780. doi: 10.1126/science.aaf7672. Epub 2016 May 11. No abstract available.

PMID:
27169596
4.

Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships.

Booher NJ, Carpenter SC, Sebra RP, Wang L, Salzberg SL, Leach JE, Bogdanove AJ.

Microb Genom. 2015 Oct;1(4). doi: 10.1099/mgen.0.000032. Epub 2015 Oct 13.

5.

The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols.

Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB.

Plant J. 2016 May 3. doi: 10.1111/tpj.13207. [Epub ahead of print]

PMID:
27145194
6.

Use and mis-use of supplementary material in science publications.

Pop M, Salzberg SL.

BMC Bioinformatics. 2015 Nov 3;16:237. doi: 10.1186/s12859-015-0668-z.

7.

Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection.

Breitwieser FP, Pardo CA, Salzberg SL.

Version 2. F1000Res. 2015 Jul 2 [revised 2015 Jul 13];4:180. doi: 10.12688/f1000research.6743.2. eCollection 2015.

8.

Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms.

Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT.

Genome Res. 2015 Sep;25(9):1401-9. doi: 10.1101/gr.193607.115.

9.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G.

Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.

10.

The genomes of two key bumblebee species with primitive eusocial organization.

Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC.

Genome Biol. 2015 Apr 24;16:76. doi: 10.1186/s13059-015-0623-3.

11.

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.

12.

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.

13.

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

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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