Steven Salzberg - Publications

Affiliations: 
Computer Science Johns Hopkins University, Baltimore, MD 

82 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Pallavajjala A, Kim D, Li T, Ghiaur G, Jones RJ, Burns KH, Salzberg SL, Ning Y. Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia. Leukemia & Lymphoma. 1-8. PMID 28882084 DOI: 10.1080/10428194.2017.1372577  0.48
2017 Luo R, Schatz MC, Salzberg SL. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. Gigascience. PMID 28637275 DOI: 10.1093/gigascience/gix045  0.52
2017 Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ. The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. Cancer. PMID 28081303 DOI: 10.1002/cncr.30510  0.48
2016 Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research. PMID 27852649 DOI: 10.1101/gr.210641.116  0.48
2016 Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nature Protocols. 11: 1650-1667. PMID 27560171 DOI: 10.1038/nprot.2016.095  0.48
2016 Salzberg SL. Databases: Reminder to deposit DNA sequences Nature. 533: 179. PMID 27172038 DOI: 10.1038/533179a  1
2016 Blaxter M, Danchin A, Savakis B, Fukami-Kobayashi K, Kurokawa K, Sugano S, Roberts RJ, Salzberg SL, Wu CI. Reminder to deposit DNA sequences. Science (New York, N.Y.). 352: 780. PMID 27169596 DOI: 10.1126/science.aaf7672  1
2015 Pop M, Salzberg SL. Use and mis-use of supplementary material in science publications. Bmc Bioinformatics. 16: 237. PMID 26525146 DOI: 10.1186/s12859-015-0668-z  1
2015 Chang TC, Pertea M, Lee S, Salzberg SL, Mendell JT. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Research. 25: 1401-9. PMID 26290535 DOI: 10.1101/gr.193607.115  1
2015 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, et al. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science (New York, N.Y.). 348: 1139-43. PMID 25977371 DOI: 10.1126/science.aaa4788  1
2015 Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. Peerj. 3: e808. PMID 25780763 DOI: 10.7717/peerj.808  1
2015 Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 12: 357-60. PMID 25751142 DOI: 10.1038/nmeth.3317  1
2015 Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology. 33: 243-6. PMID 25748911 DOI: 10.1038/nbt.3172  1
2015 Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 33: 290-5. PMID 25690850 DOI: 10.1038/nbt.3122  1
2015 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, ... ... Salzberg SL, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature. 517: 381-5. PMID 25561180 DOI: 10.1038/nature14053  1
2014 Merchant S, Wood DE, Salzberg SL. Unexpected cross-species contamination in genome sequencing projects. Peerj. 2: e675. PMID 25426337 DOI: 10.7717/peerj.675  1
2014 Martinson VG, Magoc T, Koch H, Salzberg SL, Moran NA. Genomic features of a bumble bee symbiont reflect its host environment. Applied and Environmental Microbiology. 80: 3793-803. PMID 24747890 DOI: 10.1128/AEM.00322-14  1
2014 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, ... ... Salzberg SL, et al. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics. 196: 891-909. PMID 24653211 DOI: 10.1534/genetics.113.159996  1
2014 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. Sequencing and assembly of the 22-gb loblolly pine genome. Genetics. 196: 875-90. PMID 24653210 DOI: 10.1534/genetics.113.159715  1
2014 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, ... ... Salzberg SL, et al. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biology. 15: R59. PMID 24647006 DOI: 10.1186/gb-2014-15-3-r59  1
2014 Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology. 15: R46. PMID 24580807 DOI: 10.1186/gb-2014-15-3-r46  1
2014 Salzberg SL, Pertea M, Fahrner JA, Sobreira N. DIAMUND: direct comparison of genomes to detect mutations. Human Mutation. 35: 283-8. PMID 24375697 DOI: 10.1002/humu.22503  1
2013 Florea LD, Salzberg SL. Genome-guided transcriptome assembly in the age of next-generation sequencing. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 10: 1234-40. PMID 24524156 DOI: 10.1109/TCBB.2013.140  1
2013 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. Insights into the loblolly pine genome: characterization of BAC and fosmid sequences. Plos One. 8: e72439. PMID 24023741 DOI: 10.1371/journal.pone.0072439  1
2013 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, ... ... Salzberg SL, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/journal.pbio.1001638  1
2013 Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics (Oxford, England). 29: 2669-77. PMID 23990416 DOI: 10.1093/bioinformatics/btt476  1
2013 Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biology. 14: 120. PMID 23796049 DOI: 10.1186/gb-2013-14-6-120  1
2013 Magoc T, Pabinger S, Canzar S, Liu X, Su Q, Puiu D, Tallon LJ, Salzberg SL. GAGE-B: an evaluation of genome assemblers for bacterial organisms. Bioinformatics (Oxford, England). 29: 1718-25. PMID 23665771 DOI: 10.1093/bioinformatics/btt273  1
2013 Leek JT, Salzberg SL. Sequestration: Inadvertently killing biomedical research to score political points Genome Biology. 14. PMID 23651812 DOI: 10.1186/gb-2013-14-3-109  1
2013 Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14: R36. PMID 23618408 DOI: 10.1186/gb-2013-14-4-r36  1
2013 Magoc T, Wood D, Salzberg SL. EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. Evolutionary Bioinformatics Online. 9: 127-36. PMID 23531787 DOI: 10.4137/EBO.S11250  1
2013 Salzberg SL. NIH funding: It does support innovators Nature. 493: 26. PMID 23282352 DOI: 10.1038/493026b  1
2013 Schatz MC, Phillippy AM, Sommer DD, Delcher AL, Puiu D, Narzisi G, Salzberg SL, Pop M. Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. Briefings in Bioinformatics. 14: 213-24. PMID 22199379 DOI: 10.1093/bib/bbr074  1
2012 Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biology Direct. 7: 37. PMID 23111013 DOI: 10.1186/1745-6150-7-37  1
2012 Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. Plos One. 7: e42680. PMID 22880081 DOI: 10.1371/journal.pone.0042680  1
2012 Salzberg S. A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo. Biotechniques. 53: 71. PMID 22873510 DOI: 10.2144/000113898  1
2012 Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2 Nature Methods. 9: 357-359. PMID 22388286 DOI: 10.1038/nmeth.1923  1
2012 Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols. 7: 562-78. PMID 22383036 DOI: 10.1038/nprot.2012.016  1
2012 Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Research. 22: 557-67. PMID 22147368 DOI: 10.1101/gr.131383.111  1
2012 Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: Computational challenges and solutions Nature Reviews Genetics. 13: 36-46. PMID 22124482 DOI: 10.1038/nrg3117  1
2012 Kelley DR, Liu B, Delcher AL, Pop M, Salzberg SL. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Research. 40: e9. PMID 22102569 DOI: 10.1093/nar/gkr1067  1
2011 Magoč T, Salzberg SL. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (Oxford, England). 27: 2957-63. PMID 21903629 DOI: 10.1093/bioinformatics/btr507  1
2011 Kim D, Salzberg SL. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biology. 12: R72. PMID 21835007 DOI: 10.1186/gb-2011-12-8-r72  1
2011 Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, ... ... Salzberg SL, et al. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology. 193: 5450-64. PMID 21784931 DOI: 10.1128/JB.05262-11  1
2011 Florea L, Souvorov A, Kalbfleisch TS, Salzberg SL. Genome assembly has a major impact on gene content: A comparison of annotation in two bos Taurus assemblies Plos One. 6. PMID 21731731 DOI: 10.1371/journal.pone.0021400  1
2011 Pertea M, Pertea GM, Salzberg SL. Detection of lineage-specific evolutionary changes among primate species Bmc Bioinformatics. 12. PMID 21726447 DOI: 10.1186/1471-2105-12-274  1
2011 Angiuoli SV, Dunning Hotopp JC, Salzberg SL, Tettelin H. Improving pan-genome annotation using whole genome multiple alignment. Bmc Bioinformatics. 12: 272. PMID 21718539 DOI: 10.1186/1471-2105-12-272  1
2011 Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths. Genome Biology. 12: R51. PMID 21627792 DOI: 10.1186/gb-2011-12-5-r51  1
2011 Brady A, Salzberg S. PhymmBL expanded: Confidence scores, custom databases, parallelization and more Nature Methods. 8: 367. PMID 21527926 DOI: 10.1038/nmeth0511-367  1
2011 Lipman D, Flicek P, Salzberg S, Gerstein M, Knight R. Closure of the NCBI SRA and implications for the long-term future of genomics data storage. Genome Biology. 12: 402. PMID 21418618 DOI: 10.1186/gb-2011-12-3-402  1
2011 Rasko DA, Worsham PL, Abshire TG, Stanley ST, Bannan JD, Wilson MR, Langham RJ, Decker RS, Jiang L, Read TD, Phillippy AM, Salzberg SL, Pop M, Van Ert MN, Kenefic LJ, et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proceedings of the National Academy of Sciences of the United States of America. 108: 5027-32. PMID 21383169 DOI: 10.1073/pnas.1016657108  1
2011 Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, ... ... Salzberg SL, et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 43: 109-16. PMID 21186353 DOI: 10.1038/ng.740  1
2011 Angiuoli SV, Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes Bioinformatics. 27: 334-342. PMID 21148543 DOI: 10.1093/bioinformatics/btq665  1
2011 Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, ... ... Salzberg SL, et al. COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Research. 39: D11-4. PMID 21097892 DOI: 10.1093/nar/gkq1168  1
2010 Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biology. 11: R116. PMID 21114842 DOI: 10.1186/gb-2010-11-11-r116  1
2010 Kelley DR, Salzberg SL. Clustering metagenomic sequences with interpolated Markov models. Bmc Bioinformatics. 11: 544. PMID 21044341 DOI: 10.1186/1471-2105-11-544  1
2010 Salzberg SL, Pertea M. Do-it-yourself genetic testing Genome Biology. 11. PMID 20932271 DOI: 10.1186/gb-2010-11-10-404  1
2010 Deng X, Phillippy AM, Li Z, Salzberg SL, Zhang W. Probing the pan-genome of Listeria monocytogenes: New insights into intraspecific niche expansion and genomic diversification Bmc Genomics. 11. PMID 20846431 DOI: 10.1186/1471-2164-11-500  1
2010 Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, ... ... Salzberg SL, et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. Plos Biology. 8. PMID 20838655 DOI: 10.1371/journal.pbio.1000475  1
2010 Miller TR, Delcher AL, Salzberg SL, Saunders E, Detter JC, Halden RU. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. Journal of Bacteriology. 192: 6101-2. PMID 20833805 DOI: 10.1128/JB.01030-10  1
2010 Schatz MC, Langmead B, Salzberg SL. Cloud computing and the DNA data race Nature Biotechnology. 28: 691-693. PMID 20622843 DOI: 10.1038/nbt0710-691  1
2010 Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing Genome Research. 20: 1165-1173. PMID 20508146 DOI: 10.1101/gr.101360.109  1
2010 Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology. 28: 511-5. PMID 20436464 DOI: 10.1038/nbt.1621  1
2010 Kelley DR, Salzberg SL. Detection and correction of false segmental duplications caused by genome mis-assembly. Genome Biology. 11: R28. PMID 20219098 DOI: 10.1186/gb-2010-11-3-r28  1
2010 Salzberg SL. Mind the gaps Nature Methods. 7: 105-106. PMID 20111034 DOI: 10.1038/nmeth0210-105  1
2009 Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biology. 10: R134. PMID 19930550 DOI: 10.1186/gb-2009-10-11-r134  1
2009 Phillippy AM, Deng X, Zhang W, Salzberg SL. Efficient oligonucleotide probe selection for pan-genomic tiling arrays Bmc Bioinformatics. 10: 293. PMID 19758451 DOI: 10.1186/1471-2105-10-293  1
2009 Brady A, Salzberg SL. Phymm and PhymmBL: Metagenomic phylogenetic classification with interpolated Markov models Nature Methods. 6: 673-676. PMID 19648916 DOI: 10.1038/nmeth.1358  1
2009 Kingsford C, Nagarajan N, Salzberg SL. 2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. Plos One. 4: e6402. PMID 19636415 DOI: 10.1371/journal.pone.0006402  1
2009 Eisen M, Salzberg S. Open access: the sooner the better. Science (New York, N.Y.). 325: 266; author reply 26. PMID 19608896 DOI: 10.1126/science.325_266c  1
2009 Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, Mashiyama ST, Al-Lazikani B, Andrade LF, Ashton PD, Aslett MA, Bartholomeu DC, Blandin G, Caffrey CR, Coghlan A, ... ... Salzberg SL, et al. The genome of the blood fluke Schistosoma mansoni. Nature. 460: 352-8. PMID 19606141 DOI: 10.1038/nature08160  1
2009 Trapnell C, Salzberg SL. How to map billions of short reads onto genomes Nature Biotechnology. 27: 455-457. PMID 19430453 DOI: 10.1038/nbt0509-455  1
2009 Phillippy AM, Ayanbule K, Edwards NJ, Salzberg SL. Insignia: a DNA signature search web server for diagnostic assay development. Nucleic Acids Research. 37: W229-34. PMID 19417071 DOI: 10.1093/nar/gkp286  1
2009 Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, Hanrahan F, Pertea G, Van Tassell CP, Sonstegard TS, Marçais G, Roberts M, Subramanian P, Yorke JA, Salzberg SL. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10: R42. PMID 19393038 DOI: 10.1186/gb-2009-10-4-r42  1
2009 Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England). 25: 1105-11. PMID 19289445 DOI: 10.1093/bioinformatics/btp120  1
2009 Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 10: R25. PMID 19261174 DOI: 10.1186/gb-2009-10-3-r25  1
2009 Salzberg SL, Puiu D, Sommer DD, Nene V, Lee NH. Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB. Journal of Bacteriology. 191: 1725. PMID 19114486 DOI: 10.1128/JB.01731-08  1
2009 Ravel J, Jiang L, Stanley ST, Wilson MR, Decker RS, Read TD, Worsham P, Keim PS, Salzberg SL, Fraser-Liggett CM, Rasko DA. The complete genome sequence of Bacillus anthracis Ames "Ancestor". Journal of Bacteriology. 191: 445-6. PMID 18952800 DOI: 10.1128/JB.01347-08  1
2009 Pertea M, Ayanbule K, Smedinghoff M, Salzberg SL. OperonDB: A comprehensive database of predicted operons in microbial genomes Nucleic Acids Research. 37. PMID 18948284 DOI: 10.1093/nar/gkn784  1
2008 Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove AJ. Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas. Plos One. 3: e3828. PMID 19043590 DOI: 10.1371/journal.pone.0003828  1
2008 Puiu D, Salzberg SL. Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18 Plos One. 3. PMID 18927608 DOI: 10.1371/journal.pone.0003427  1
2008 Carlton JM, Adams JH, Silva JC, Bidwell SL, Lorenzi H, Caler E, Crabtree J, Angiuoli SV, Merino EF, Amedeo P, Cheng Q, Coulson RM, Crabb BS, Del Portillo HA, Essien K, ... ... Salzberg SL, et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature. 455: 757-63. PMID 18843361 DOI: 10.1038/nature07327  1
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