Before joining Johns Hopkins School of Medicine in 2011, he was the Director of the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park, where he was also the Horvitz Professor of Computer Science. From 1998–2005, he was the head of the Bioinformatics department at The Institute for Genomic Research, one of the world's largest genome sequencing centers, and prior to that he was a computer science professor at Johns Hopkins University. In 2013, Salzberg won the Benjamin Franklin award in bioinformatics. In 2014, 2015, 2016, and 2017, Salzberg was selected for inclusion in HighlyCited.com, a ranking compiled by the Institute for Scientific Information of scientists who are among the top 1% most cited for their subject field during the previous ten years. He was also chosen for this list when it was first created in 2001. In March 2015, he was named a Bloomberg Distinguished Professor at Johns Hopkins University for his accomplishments as an interdisciplinary researcher and excellence in teaching the next generation of scholars. The Bloomberg Distinguished Professorships were established in 2013 by a gift from Michael Bloomberg. Salzberg holds joint appointments in the Johns Hopkins Whiting School of Engineering, Johns Hopkins School of Medicine, and the Johns Hopkins Bloomberg School of Public Health. Salzberg has been a prominent scientist in the field of bioinformatics and computational biology since the 1990s. He has made many contributions to gene finding algorithms, notably the GLIMMER program for bacterial gene finding as well as several related programs for finding genes in animals, plants, and other organisms. He has also been a leader in genome assembly research and is one of the initiators of the open source AMOS project. He was a participant in the human genome project as well as many other genome projects, including the malaria genome and the genome of the model plant Arabidopsis thaliana. In 2001–2002, he and his colleagues sequenced the anthrax that was used in the 2001 anthrax attacks. They published their results in the journal Science in 2002. These findings helped the FBI track the source of the attacks to a single vial at Ft. Detrick in Frederick, Maryland. Salzberg together with David Lipman started the Influenza Genome Sequencing Project in 2003, a project to sequence and make available the genomes of thousands of influenza virus isolates. Soon after the advent of next-generation sequencing in the mid-2000s, Salzberg's research lab and his collaborators developed a suite of highly efficient, accurate programs for alignment of NGS sequences to large genomes and for assembly of sequences from RNA-Seq experiments. These include the "Tuxedo" suite, comprising the Bowtie, TopHat, and Cufflinks programs, which have been cited tens of thousands of times in the years since their publication. Salzberg has also been a vocal advocate against pseudoscience and in favor of the teaching of evolution in schools, and has authored editorials and appeared in print media on this topic. He writes a widely read column at Forbes magazine on science, medicine, and pseudoscience. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking.. In 2018, he was elected a Fellow of the American Academy of Arts and Sciences. His doctoral students and postdoctoral researchers include Cole Trapnell, Ben Langmead, and Olga Troyanskaya.
