Ph.D., Computer Science, Harvard University, 1989 M.Phil., Computer Science, Yale University, 1984 M.S., Computer Science, Yale University, 1982 B.A. cum laude English, Yale University,1980

My group’s research focuses on the development of new computational methods for analysis of DNA from the latest sequencing technologies. Over the years we have developed and applied software to many problems in gene finding, genome assembly, comparative genomics, evolutionary genomics, and sequencing technology itself. Our current work emphasizes analysis of DNA and RNA sequenced with next-generation technology. My blogs and other writing cover topics on the impact of science on society including the effects of pseudoscience, the problems of alternative medicine, the anti-vaccination movement, gene patents, and the influence of sports on higher education. See the links on my lab home page for my scientific publications, my opinion pieces, and other news.

S.L. Salzberg. Horizontal gene transfer is not a hallmark of the human genome. Genome Biology 18:85 (2017). R. Luo, M.C. Schatz, and S.L. Salzberg. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. Gigascience (2017) gix045. A.J. Kandathil, F.P. Breitwieser, J. Sachithanandham, M. Robinson, S.H. Mehta, W. Timp, S.L. Salzberg, D.L. Thomas, and A. Balagopal. Presence of human hepegivirus-1 in a cohort of people who inject drugs. Annals of Internal Medicine, doi:10.7326/M17-0085, 6 June 2017. A.V. Zimin, D. Puiu, M.-C. Luo, T. Zhu, S. Koren, G. Marçais, J.A. Yorke, J. Dvorak, and S.L. Salzberg. Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm. Genome Research (2017). (preprint at bioRxiv) A.V. Zimin, K.A. Stevens, M.W. Crepeau, D. Puiu, J.L. Wegrzyn, J.A. Yorke, C.H. Langley, D.B. Neale, and S.L. Salzberg. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. Gigascience (2017) 6(1):1-4. J. Lu, F.P. Breitwieser, P. Thielen, and S.L. Salzberg. Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science 3:e104 (2017). D. Kim, L. Song, F.P. Breitwieser, and S.L. Salzberg. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research 26:12, 1721-29 (2016). M. Pertea, D. Kim, G. Pertea, J.T. Leek, and S.L. Salzberg. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown. Nature Protocols 11, 1650–1667 (2016). (Local PDF copy here) S.L. Salzberg, F.P. Breitwieser, A. Kumar, H. Hao, P. Burger, F.J. Rodriguez, M. Lim, A. Quiñones-Hinojosa, G.L. Gallia, J.A. Tornheim, M.T. Melia, C.L. Sears and C.A. Pardo. Next-generation sequencing in neuropathological diagnosis of infections of the nervous system. Neurology: Neuroimmunology & Neuroinflammation, 3:4 (2016), e251. V.L. Sork, S.T. Fitz-Gibbon, D. Puiu, M. Crepeau, P.F. Gugger, R. Sherman, K. Stevens, C. H. Langley, M. Pellegrini, and S.L. Salzberg. First draft assembly and annotation of the genome of a California endemic oak, Quercus lobata Née (Fagaceae). G3: Genes, Genomes, Genetics 6 (2016), 3485–3495 P.J. Martínez-García, et al. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols. The Plant Journal (2016), DOI: 10.1111/tpj.13207. M. Pertea, G.M. Pertea, C.M. Antonescu, T.C. Chang, J.T. Mendell, and S.L. Salzberg (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33 (3), 290-295. Publ. online 18 February 2015. D. Kim, B. Langmead, and S.L. Salzberg. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12, 357-360 (2015), publ. online 9 March 2015. A.C. Frazee, G. Pertea, A.E. Jaffe, B. Langmead, S.L. Salzberg, and J.T. Leek. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology 33, 243-246 (2015). K.M. Kapheim et al. Genomic signatures of evolutionary transitions from solitary to group living. Science 348:6239 (2015), 1139-43. 9. F.P. Breitwieser, C.A. Pardo, and S.L. Salzberg. Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection. F1000 Research, 2015, 4:180. 7. T.-C. Chang, M. Pertea, S. Lee, S.L. Salzberg, and J.T. Mendell. Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms. Genome Research 25, 1401-9 (2015). M. Pop and S.L. Salzberg. Use and mis-use of supplementary material in science publications. BMC Bioinformatics (2015), 16:237 B.M. Sadd et al. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biology 16:76 (2015). R. Wilton, T. Budavari, B. Langmead, S. Wheelan, S.L. Salzberg, and A.S. Szalay. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. PeerJ (2015) 3:e808, . K. Deng, M. Pertea, et al. Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations. Nature 517(7534), 381-385 (2015). N.J. Booher et al. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships. Microbial Genomics 1:4 (2015).