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Items: 1 to 50 of 219

1.

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.

Pertea M, Shumate A, Pertea G, Varabyou A, Breitwieser FP, Chang YC, Madugundu AK, Pandey A, Salzberg SL.

Genome Biol. 2018 Nov 28;19(1):208. doi: 10.1186/s13059-018-1590-2.

2.

Assembly of a pan-genome from deep sequencing of 910 humans of African descent.

Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL.

Nat Genet. 2018 Nov 19. doi: 10.1038/s41588-018-0273-y. [Epub ahead of print]

PMID:
30455414
3.

KrakenUniq: confident and fast metagenomics classification using unique k-mer counts.

Breitwieser FP, Baker DN, Salzberg SL.

Genome Biol. 2018 Nov 16;19(1):198. doi: 10.1186/s13059-018-1568-0.

4.

Genomic architecture of complex traits in loblolly pine.

De La Torre AR, Puiu D, Crepeau MW, Stevens K, Salzberg SL, Langley CH, Neale DB.

New Phytol. 2018 Oct 14. doi: 10.1111/nph.15535. [Epub ahead of print]

PMID:
30318590
5.

Open questions: How many genes do we have?

Salzberg SL.

BMC Biol. 2018 Aug 20;16(1):94. doi: 10.1186/s12915-018-0564-x.

6.

The Terabase Search Engine: a large-scale relational database of short-read sequences.

Wilton R, Wheelan SJ, Szalay AS, Salzberg SL.

Bioinformatics. 2018 Jul 23. doi: 10.1093/bioinformatics/bty657. [Epub ahead of print]

PMID:
30052772
7.

Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics.

Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG, Carroll KC.

J Clin Microbiol. 2018 Aug 27;56(9). pii: e00472-18. doi: 10.1128/JCM.00472-18. Print 2018 Sep.

PMID:
29976594
8.

Removing contaminants from databases of draft genomes.

Lu J, Salzberg SL.

PLoS Comput Biol. 2018 Jun 25;14(6):e1006277. doi: 10.1371/journal.pcbi.1006277. eCollection 2018 Jun.

9.

Genomic Variation Among and Within Six Juglans Species.

Stevens KA, Woeste K, Chakraborty S, Crepeau MW, Leslie CA, Martínez-García PJ, Puiu D, Romero-Severson J, Coggeshall M, Dandekar AM, Kluepfel D, Neale DB, Salzberg SL, Langley CH.

G3 (Bethesda). 2018 Jul 2;8(7):2153-2165. doi: 10.1534/g3.118.200030.

10.

MUMmer4: A fast and versatile genome alignment system.

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A.

PLoS Comput Biol. 2018 Jan 26;14(1):e1005944. doi: 10.1371/journal.pcbi.1005944. eCollection 2018 Jan.

11.

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

Li Z, Breitwieser FP, Lu J, Jun AS, Asnaghi L, Salzberg SL, Eberhart CG.

Invest Ophthalmol Vis Sci. 2018 Jan 1;59(1):280-288. doi: 10.1167/iovs.17-21617.

12.

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.

Luo MC, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J.

Nature. 2017 Nov 23;551(7681):498-502. doi: 10.1038/nature24486. Epub 2017 Nov 15.

PMID:
29143815
13.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL.

Gigascience. 2017 Nov 1;6(11):1-7. doi: 10.1093/gigascience/gix097.

14.

A review of methods and databases for metagenomic classification and assembly.

Breitwieser FP, Lu J, Salzberg SL.

Brief Bioinform. 2017 Sep 23. doi: 10.1093/bib/bbx120. [Epub ahead of print]

PMID:
29028872
15.

Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Oct 1;6(10):1. doi: 10.1093/gigascience/gix072.

16.

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans).

Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL.

G3 (Bethesda). 2017 Nov 6;7(11):3831-3836. doi: 10.1534/g3.117.300107.

17.

Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia.

Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y.

Leuk Lymphoma. 2018 May;59(5):1231-1238. doi: 10.1080/10428194.2017.1372577. Epub 2017 Sep 7.

PMID:
28882084
18.

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL.

G3 (Bethesda). 2017 Sep 7;7(9):3157-3167. doi: 10.1534/g3.117.300078.

19.

16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model.

Luo R, Schatz MC, Salzberg SL.

Gigascience. 2017 Jul 1;6(7):1-4. doi: 10.1093/gigascience/gix045.

20.

Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs.

Kandathil AJ, Breitwieser FP, Sachithanandham J, Robinson M, Mehta SH, Timp W, Salzberg SL, Thomas DL, Balagopal A.

Ann Intern Med. 2017 Jul 4;167(1):1-7. doi: 10.7326/M17-0085. Epub 2017 Jun 6.

21.

Short Read Mapping: An Algorithmic Tour.

Canzar S, Salzberg SL.

Proc IEEE Inst Electr Electron Eng. 2017 Mar;105(3):436-458. doi: 10.1109/JPROC.2015.2455551. Epub 2015 Sep 7.

22.

Horizontal gene transfer is not a hallmark of the human genome.

Salzberg SL.

Genome Biol. 2017 May 8;18(1):85. doi: 10.1186/s13059-017-1214-2.

23.

An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

Zimin AV, Stevens KA, Crepeau MW, Puiu D, Wegrzyn JL, Yorke JA, Langley CH, Neale DB, Salzberg SL.

Gigascience. 2017 Jan 1;6(1):1-4. doi: 10.1093/gigascience/giw016. Erratum in: Gigascience. 2017 Oct 1;6(10):1.

24.

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm.

Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL.

Genome Res. 2017 May;27(5):787-792. doi: 10.1101/gr.213405.116. Epub 2017 Jan 27.

25.

The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus.

Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ.

Cancer. 2017 May 1;123(9):1507-1515. doi: 10.1002/cncr.30510. Epub 2017 Jan 12.

26.

Centrifuge: rapid and sensitive classification of metagenomic sequences.

Kim D, Song L, Breitwieser FP, Salzberg SL.

Genome Res. 2016 Dec;26(12):1721-1729. Epub 2016 Oct 17.

27.

Sequence of the Sugar Pine Megagenome.

Stevens KA, Wegrzyn JL, Zimin A, Puiu D, Crepeau M, Cardeno C, Paul R, Gonzalez-Ibeas D, Koriabine M, Holtz-Morris AE, Martínez-García PJ, Sezen UU, Marçais G, Jermstad K, McGuire PE, Loopstra CA, Davis JM, Eckert A, de Jong P, Yorke JA, Salzberg SL, Neale DB, Langley CH.

Genetics. 2016 Dec;204(4):1613-1626. Epub 2016 Oct 28.

28.

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae).

Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL.

G3 (Bethesda). 2016 Nov 8;6(11):3485-3495. doi: 10.1534/g3.116.030411.

29.

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL.

Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11.

30.

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.

31.

Databases: Reminder to deposit DNA sequences.

Salzberg SL.

Nature. 2016 May 12;533(7602):179. doi: 10.1038/533179a. No abstract available.

PMID:
27172038
32.

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
33.

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.

34.

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 Sep;87(5):507-32. doi: 10.1111/tpj.13207. Epub 2016 Jul 18.

35.

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.

36.

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 Jan 1];4:180. doi: 10.12688/f1000research.6743.2. eCollection 2015.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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