Steven Lloyd Salzberg (born 1960) is an American computational biologist and

computer scientist A computer scientist is a scientist who specializes in the academic study of computer science. Computer scientists typically work on the theoretical side of computation. Although computer scientists can also focus their work and research on ...

who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at

Johns Hopkins University The Johns Hopkins University (often abbreviated as Johns Hopkins, Hopkins, or JHU) is a private university, private research university in Baltimore, Maryland, United States. Founded in 1876 based on the European research institution model, J ...

, where he is also Director of the Center for Computational Biology.

Early life and education

Salzberg was born in 1960 as one of four children to Herman Salzberg, a Distinguished Professor Emeritus of Psychology, and Adele Salzberg, a retired school teacher. Salzberg did his undergraduate studies at

Yale University Yale University is a Private university, private Ivy League research university in New Haven, Connecticut, United States. Founded in 1701, Yale is the List of Colonial Colleges, third-oldest institution of higher education in the United Stat ...

where he received his

Bachelor of Arts A Bachelor of Arts (abbreviated B.A., BA, A.B. or AB; from the Latin ', ', or ') is the holder of a bachelor's degree awarded for an undergraduate program in the liberal arts, or, in some cases, other disciplines. A Bachelor of Arts deg ...

degree in English in 1980. In 1981 he returned to Yale, and he received his

Master of Science A Master of Science (; abbreviated MS, M.S., MSc, M.Sc., SM, S.M., ScM or Sc.M.) is a master's degree. In contrast to the Master of Arts degree, the Master of Science degree is typically granted for studies in sciences, engineering and medici ...

and

Master of Philosophy A Master of Philosophy (MPhil or PhM; Latin ' or ') is a postgraduate degree. The name of the degree is most often abbreviated MPhil (or, at times, as PhM in other countries). MPhil are awarded to postgraduate students after completing at leas ...

degrees in Computer Science in 1982 and 1984, respectively. After several years in a startup company, he enrolled at

Harvard University Harvard University is a Private university, private Ivy League research university in Cambridge, Massachusetts, United States. Founded in 1636 and named for its first benefactor, the History of the Puritans in North America, Puritan clergyma ...

, where he earned a Ph.D. in

Computer Science Computer science is the study of computation, information, and automation. Computer science spans Theoretical computer science, theoretical disciplines (such as algorithms, theory of computation, and information theory) to Applied science, ...

in 1989.

Career

After obtaining his undergraduate degree, he worked for a local power company in

South Carolina South Carolina ( ) is a U.S. state, state in the Southeastern United States, Southeastern region of the United States. It borders North Carolina to the north and northeast, the Atlantic Ocean to the southeast, and Georgia (U.S. state), Georg ...

, where he gained programming experience on an

IBM mainframe IBM mainframes are large computer systems produced by IBM since 1952. During the 1960s and 1970s, IBM dominated the computer market with the 7000 series and the later System/360, followed by the System/370. Current mainframe computers in IBM' ...

, programming in

COBOL COBOL (; an acronym for "common business-oriented language") is a compiled English-like computer programming language designed for business use. It is an imperative, procedural, and, since 2002, object-oriented language. COBOL is primarily ...

and IBM assembly language. He then joined a

Boston Boston is the capital and most populous city in the Commonwealth (U.S. state), Commonwealth of Massachusetts in the United States. The city serves as the cultural and Financial centre, financial center of New England, a region of the Northeas ...

-based AI startup upon completion of his master's degree in computer science. After earning his Ph.D., Salzberg joined Johns Hopkins University as an assistant professor in the Department of Computer Science, and was promoted to associate professor in 1997. From 1998 to 2005, he was the head of the

Bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

department at

The Institute for Genomic Research The J. Craig Venter Institute (JCVI) is a non-profit genomics research institute founded by J. Craig Venter, Ph.D. in October 2006. The institute was the result of consolidating four organizations: the Center for the Advancement of Ge ...

, one of the world's largest genome sequencing centers. Salzberg then joined the Department of Computer Science at the

University of Maryland, College Park The University of Maryland, College Park (University of Maryland, UMD, or simply Maryland) is a public university, public Land-grant university, land-grant research university in College Park, Maryland, United States. Founded in 1856, UMD i ...

, where he was the Horvitz Professor of

as well as the Director of the Center for Bioinformatics and Computational Biology. In 2011, Salzberg returned to Johns Hopkins University as a professor in the McKusick-Nathans Institute of Genetic Medicine and in the Department of Medicine.ccb.jhu.edu
Brief biosketch In 2013, Salzberg won the Benjamin Franklin award in

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

. In 2014, he was named a Bloomberg Distinguished Professor at

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 Michael Rubens Bloomberg (born February 14, 1942) is an American businessman and politician. He is the majority owner and co-founder of Bloomberg L.P., and was its CEO from 1981 to 2001 and again from 2014 to 2023. He served as the 108th mayo ...

. Salzberg holds joint appointments in the Johns Hopkins Whiting School of Engineering,

Johns Hopkins School of Medicine The Johns Hopkins University School of Medicine (JHUSOM) is the medical school of Johns Hopkins University, a private research university in Baltimore, Maryland. Established in 1893 following the construction of the Johns Hopkins Hospital, th ...

, and the

Johns Hopkins Bloomberg School of Public Health The Johns Hopkins Bloomberg School of Public Health is the public health graduate school of Johns Hopkins University, a private university, private research university primarily based in Baltimore, Maryland. It was founded as the Johns Hopkins ...

Research

Salzberg has been a prominent scientist in the field of

and

computational biology Computational biology refers to the use of techniques in computer science, data analysis, mathematical modeling and Computer simulation, computational simulations to understand biological systems and relationships. An intersection of computer sci ...

since the 1990s. He has made many contributions to gene finding algorithms, notably the

GLIMMER In bioinformatics, GLIMMER (Gene Locator and Interpolated Markov ModelER) is used to gene prediction, find genes in prokaryotic DNA. "It is effective at finding genes in bacteria, archea, viruses, typically finding 98-99% of all relatively long ge ...

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 has led the assembly of dozens of genomes, both large and small. He was a participant in the

human genome project The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a ...

as well as many other genome projects, including the

malaria Malaria is a Mosquito-borne disease, mosquito-borne infectious disease that affects vertebrates and ''Anopheles'' mosquitoes. Human malaria causes Signs and symptoms, symptoms that typically include fever, Fatigue (medical), fatigue, vomitin ...

genome (''

Plasmodium falciparum ''Plasmodium falciparum'' is a Unicellular organism, unicellular protozoan parasite of humans and is the deadliest species of ''Plasmodium'' that causes malaria in humans. The parasite is transmitted through the bite of a female ''Anopheles'' mos ...

'') and the genome of the model plant ''

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...

''. In 2001–2002, he and his colleagues sequenced the

anthrax Anthrax is an infection caused by the bacterium '' Bacillus anthracis'' or ''Bacillus cereus'' biovar ''anthracis''. Infection typically occurs by contact with the skin, inhalation, or intestinal absorption. Symptom onset occurs between one ...

that was used in the

2001 anthrax attacks The 2001 anthrax attacks, also known as Amerithrax (a portmanteau of "United States, America" and "anthrax", from its FBI case name), occurred in the United States over the course of several weeks beginning on September 18, 2001, one week after th ...

. They published their results in the journal

Science Science is a systematic discipline that builds and organises knowledge in the form of testable hypotheses and predictions about the universe. Modern science is typically divided into twoor threemajor branches: the natural sciences, which stu ...

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 David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the INSDC, Internationa ...

and Lone Simonsen 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 Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...

(NGS) 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 RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...

experiments. These include the "Tuxedo" suite, comprising the

Bowtie The bow tie or dicky bow is a type of neckwear, distinguishable from a necktie because it does not drape down the shirt placket, but is tied just underneath a winged collar. A modern bow tie is tied using a common shoelace knot, which is also ...

, 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 Pseudoscience consists of statements, beliefs, or practices that claim to be both scientific and factual but are incompatible with the scientific method. Pseudoscience is often characterized by contradictory, exaggerated or unfalsifiable cl ...

and has authored editorials and appeared in print media on this topic. From 2010-2024, he wrote a column at ''Forbes'' magazine on science, medicine, and pseudoscience, where he published over 300 articles that collectively received tens of millions of views. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking. Since 2025, his columns have appeared on Substack at https://stevensalzberg.substack.com/, which includes all of his ''Forbes'' columns and others, nearly 500 articles in all. Salzberg was a charter member of the Cambridge Working Group in 2014, which was created to express alarm in the scientific community over the creation of highly transmissible and contagious viruses (also called

Gain-of-function research Gain-of-function research (GoF research or GoFR) is medical research that genetically alters an organism in a way that may enhance the biological functions of gene products. This may include an altered pathogenesis, transmissibility, or host ran ...

) and the likelihood of an accidental lab release.

Publications

Salzberg has authored or co-authored over 300 scientific publications. He has more than 350,000 citations in Google Scholar and an h-index of 167. In 2014 Salzberg was selected for inclusion in HighlyCited.com, a ranking compiled by the

Institute for Scientific Information The Institute for Scientific Information (ISI) was an academic publishing service, founded by Eugene Garfield in Philadelphia in 1956. ISI offered scientometric and bibliographic database services. Its specialty was citation indexing and analysis, ...

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. This list of highly cited researchers continues under

Clarivate Clarivate Plc is a British-American Public company, publicly traded analytics company that operates a collection of subscription business model, subscription-based services, in the areas of bibliometrics and scientometrics; business intelligenc ...

, and Salzberg was included in the list every year since 2014, through at least 2024.

Highly cited articles (more than 10,000 citations)

* 2012 with B Langmead, ''Fast gapped-read alignment with Bowtie 2'', in: '' Nature Methods''. Vol. 9, nº 4; 357. * 2009 With B Langmead, C Trapnell, M Pop, ''Ultrafast and memory-efficient alignment of short DNA sequences to the human genome'', in: ''

Genome Biology ''Genome Biology'' is a peer-reviewed open access scientific journal covering research in genomics. It was established in 2000 and is published by BioMed Central. The chief editor is currently Andrew Cosgrove ( BioMed Central, New York). Abstract ...

''. Vol. 10, nº 3; 1–10. * 2001 with JC Venter, MD Adams, EW Myers, PW Li, RJ Mural, et al., ''The sequence of the human genome'', in: ''

''. Vol. 291, nº 5507; 1304–1351. * 2015 with D Kim, B Langmead, ''HISAT: a fast spliced aligner with low memory requirements'', in: '' Nature Methods'' Vol. 12, 357–360. (2015) * 2010 with C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Van Baren, BJ Wold, L Pachter, ''Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation'', in: ''

Nature Biotechnology ''Nature Biotechnology'' is a monthly peer-reviewed scientific journal published by Nature Portfolio. The editor-in-chief is Barbara Cheifet who heads an in-house team of editors. The focus of the journal is biotechnology including research resu ...

''. Vol. 28, nº 5; 511–515. * 2009 with C Trapnell, L Pachter, ''TopHat: discovering splice junctions with RNA-Seq'', in: ''

''. Vol. 25, nº 9; 1105–1111. * 2013 with D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, ''TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions'', in: ''

''. Vol. 14, nº 4; 1–13. * 2012 with C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, JL Rinn, L Pachter. ''Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks'', in: ''Nature Protocols''. Vol. 7, nº 3; 562-578. * 2011 with T Magoč. ''FLASH: fast length adjustment of short reads to improve genome assemblies'', in: ''

''. Vol. 27, nº 21; 2957-2963. * 2000 with The Arabidopsis Genome Initiative. ''Analysis of the genome sequence of the flowering plant Arabidopsis thaliana'', in: ''

Nature Nature is an inherent character or constitution, particularly of the Ecosphere (planetary), ecosphere or the universe as a whole. In this general sense nature refers to the Scientific law, laws, elements and phenomenon, phenomena of the physic ...

''. Vol. 408, nº 6814; 796-815.

Awards

* 2020 Accomplishments by a Senior Scientist Award, International Society for Computational Biology * 2014-2024 Named Highly Cited Researcher, Thomson Reuters/Clarivate * 2018 Elected member of the

American Academy of Arts and Sciences The American Academy of Arts and Sciences (The Academy) is one of the oldest learned societies in the United States. It was founded in 1780 during the American Revolution by John Adams, John Hancock, James Bowdoin, Andrew Oliver, and other ...

* 2020 Elected Fellow,

Association for Computing Machinery The Association for Computing Machinery (ACM) is a US-based international learned society for computing. It was founded in 1947 and is the world's largest scientific and educational computing society. The ACM is a non-profit professional membe ...

(ACM) * 2013 Elected Fellow, International Society for Computational Biology * 2013 Robert G. Balles Prize in Critical Thinking * 2013 Benjamin Franklin Award (Bioinformatics) for Open Access in the Life Sciences * 2007 Hot 100 Authors, BioMed Central * 2004 Fellow, American Association for the Advancement of Science * 1996 NIH Career Award

References

External links

genome.fieldofscience.com
Salzberg's science blog
Salzberg's column at Forbes magazine

Duke Computer Science Colloquia Steven Salzberg - includes biography
Open source software from the Salzberg lab and other groups in the Hopkins Center for Computational Biology
{{DEFAULTSORT:Salzberg, Steven L Living people Yale University alumni Harvard John A. Paulson School of Engineering and Applied Sciences alumni Johns Hopkins University Department of Biomedical Engineering faculty University of Maryland, College Park faculty 21st-century American biologists American bioinformaticians Influenza researchers Jewish American scientists 1960 births Fellows of the American Association for the Advancement of Science Fellows of the International Society for Computational Biology