Selected Publications

see also my Google Scholar page


  1. 13.Fast gapped-read alignment with Bowtie 2.  B. Langmead and S.L. Salzberg.  Nature Methods 9 (2012), 357-359. (PDF reprint).

  2. 14.The perils of gene patents.  S.L. Salzberg. Clinical Pharmacology & Therapeutics 91:6 (2012), 969-971.

  3. 15.Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.  The Heliconius Genome Consortium. Nature 487 (2012), 94-98. (PDF reprint)

  4. 16.GAGE: A critical evaluation of genome assemblies and assembly algorithms. S.L. Salzberg, A.M. Phillippy, A.V. Zimin, D. Puiu, T. Magoc, S. Koren, T. Treangen, M.C. Schatz, A.L. Delcher, M. Roberts, G. Marcais, M. Pop, and J.A. Yorke. Genome Research 22:3 (2012), 557-567. (PDF reprint) (Supplementary material) (Suppl Figure 1) (Suppl Figure 2) (Suppl Table 1)

  5. 17.Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimental, S.L. Salzberg, J.L. Rinn, and L. Pachter.  Nature Protocols 7:3 (2012), 562-578.

  6. 18.Repetitive DNA and next-generation sequencing: computational challenges and solutions. T.J. Treangen and S.L. Salzberg. Nature Reviews Genetics 13 (2012), 557-567.

  7. 19.Mis-assembled segmental duplications in two versions of the Bos taurus genome. A.V. Zimin, D.R. Kelley, M. Roberts, S.L. Salzberg, and J.A. Yorke. PLoS ONE 7(8): e42680 (2012).

  8. 20.Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. D.R. Kelley, B. Liu, A.L. Delcher, M. Pop, and S.L. Salzberg.  Nucleic Acids Research (2012) 40 (1): e9. doi:10.1093/nar/gkr1067.

  9. 21.TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. D. Kim and S.L. Salzberg. Genome Biology 2011, 12:R72.

  10. 22.FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S.L. Salzberg. Bioinformatics 27:21 (2011), 2957-63.

  11. 23.PhymmBL expanded: confidence scores, custom databases, parallelization and more. A. Brady and S. Salzberg. Nature Methods 8, 367 (2011).

  12. 24.Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.. A.J. Bogdanove, R. Koebnik, H. Lu, ..., and S.L. Salzberg. J. Bacteriology 193:19 (2011), 5450-64.

  13. 25.Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.  J. Enk et al., Genome Biology 2011, 12:R51.

  14. 26.Detection of lineage-specific evolutionary changes among primate species.  M. Pertea, G.M. Pertea, and S.L. Salzberg.  BMC Bioinformatics 2011, 12:274.

  15. 27.Mugsy: Fast multiple alignment of closely related whole genomes.  S. V. Angiuoli and S.L. Salzberg.  Bioinformatics (2011), 27(3), 334-342.

  16. 28.Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.  D. Rasko et al.  Proc. National Acad. Sci. 108:12 (2011), 5027-32.

  17. 29.The genome of woodland strawberry (Fragaria vesca). V. Shulaev et al.  Nature Genetics 43(2011), 109-116.


  1. 30.Do-it-yourself genetic testing. S.L. Salzberg and M. Pertea. Genome Biology 2010, 11:404.

  2. 31.Cloud computing and the DNA data race.  M.C. Schatz, B. Langmead, and S.L. Salzberg.  Nature Biotechnology 28, 691-693 (2010).

  3. 32.Quake: quality-aware detection and correction of sequencing errors.  D.R. Kelley, M.C. Schatz, and S.L. Salzberg. Genome Biology 2010, 11:R116.

  4. 33.Between a chicken and a grape: estimating the number of human genes. M. Pertea and S.L. Salzberg. Genome Biology 2010, 11:206.

  5. 34.Assembly of large genomes using second-generation sequencing.  M.C. Schatz, A.L. Delcher, and S.L. Salzberg.  Genome Research 20 (2010), 1165-1173.

  6. 35.[The Cufflinks paper] Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter (2010). Nature Biotechnology 28, 511-515 (2010).

  7. 36.Recent advances in RNA sequence analysisF1000 Biology Reports 2010, 2:64.

  8. 37.Mind the gaps.  S.L. Salzberg, Nature Methods 7:2 (2010), 105-6.

  9. 38.[the turkey genome] Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. R.A. Dalloul et al.,PLoS Biology 8(9): e1000475 (2010).

  10. 39.Searching for SNPs with cloud computing.  B. Langmead, M.C. Schatz, J. Lin, M. Pop, and S.L. Salzberg.  Genome Biology 2009, 10:R134.

  11. 40.Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. A. Brady and S.L. Salzberg. Nature Methods, 6:673-676, 2009.

  12. 41.[The Bowtie paper] Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.  B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg. Genome Biology 2009, 10:R25. doi:10.1186/gb-2009-10-3-r25.

  13. 42.TopHat: discovering splice junctions with RNA-Seq.  C. Trapnell, L. Pachter, and S.L. Salzberg.  Bioinformatics, 25:1105-11, 2009.

  14. 43.A whole-genome assembly of the domestic cow, Bos taurus. A.V. Zimin, A.L. Delcher, L. Florea, D.R. Kelley, M.C. Schatz, D. Puiu, F. Hanrahan, G. Pertea, C.P. Van Tassell, T.S. Sonstegard, G. Marcais, M. Roberts, P. Subramanian, J.A. Yorke, and S.L. Salzberg. Genome Biology 2009, 10:R42.

  15. 44.How to map billions of short reads onto genomes.  C. Trapnell and S.L. Salzberg.  Nature Biotechnology 27:5 (2009), 455-7.

  16. 45.OperonDB: a comprehensive database of predicted operons in microbial genomes.  M. Pertea, K. Ayanbule, M. Smedinghoff, and S.L. Salzberg. Nucleic Acids Research 2009, 37:D479-482. doi:10.1093/nar/gkn784.


  1. 1.Kraken: ultrafast metagenomic sequence classification using exact alignments. D.E. Wood and S.L. Salzberg. Genome Biology 2014, 15:R46.

  2. 2.A new rhesus macaque assembly and annotation for next-generation sequencing analyses. A.V. Zimin et al., Biology Direct 9:20 (2014), 

  3. 3.Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. D.B. Neale et al., Genome Biology 2014, 15:R59.

  4. 4.Sequencing and assembly of the 22-Gb loblolly pine genome. A. Zimin et al., Genetics (2014) 196:3, 875-890.

  5. 5.DIAMUND: Direct comparison of genomes to detect mutations. S.L. Salzberg, M. Pertea, J.A. Fahrner, and N. Sobreira. Human Mutation 35:3 (2014), 283-288.

  6. 6.V.G. Martinson, T. Magoc, H. Koch, S.L. Salzberg, and N.A. Moran. Genomic features of a bumble bee symbiont reflect its host environment. Applied Environmental Microbiology 80:13 (2014), 3793-3803.

  7. 7.GAGE-B: An evaluation of genome assemblers for bacterial organisms.  T. Magoc, S. Pabinger, S. Canzar, X. Liu, Q. Su, D. Puiu, L.J. Tallon, and S.L. Salzberg.  Bioinformatics 29:14 (2013), 1718-1725.

  8. 8.The MaSuRCA genome assembler.  A.V. Zimin et al.  Bioinformatics 29(21), 2669-2677.

  9. 9.TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.  D. Kim, G. Pertea, C. Trapnell, H. Pimentel, R. Kelley, and S.L. Salzberg.  Genome Biology 2013, 14: R36.

  10. 10.NIH funding: It does support innovators.  S.L. Salzberg.  Nature (2013) 493, 26.

  11. 11.Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.  M.C. Schatz et al., Briefings in Bioinf. 14(2), 213-224.

  12. 12.Genome-guided transcriptome assembly in the age of next-generation sequencing. L.D. Florea and S.L. Salzberg. IEEE/ACM Trans. on Comp. Biology and Bioinf. 10:5 (2013), 1234-1240.

  13. 13.Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. L. Florea, L. Song, and S.L. Salzberg. F1000Research 2013, 2:188.

  14. 14.EDGE-pro: Estimated Degree of Gene Expression in prokaryotic genomes.  T. Magoc, D. Wood, and S.L. Salzberg. Evolutionary Bioinf. (2013), 9:127.