Steven Lloyd Salzberg (born 1960) is an American

computational biologist Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...

and

computer scientist A computer scientist is a person who is trained in the academic study of computer science. Computer scientists typically work on the theoretical side of computation, as opposed to the hardware side on which computer engineers mainly focus (al ...

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

Johns Hopkins University Johns Hopkins University (Johns Hopkins, Hopkins, or JHU) is a private university, private research university in Baltimore, Maryland. Founded in 1876, Johns Hopkins is the oldest research university in the United States and in the western hem ...

, 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 research university in New Haven, Connecticut. Established in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and among the most prestigious in the wo ...

where he received his

Bachelor of Arts Bachelor of arts (BA or AB; from the Latin ', ', or ') is a bachelor's degree awarded for an undergraduate program in the arts, or, in some cases, other disciplines. A Bachelor of Arts degree course is generally completed in three or four years ...

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

Master of Science A Master of Science ( la, Magisterii Scientiae; abbreviated MS, M.S., MSc, M.Sc., SM, S.M., ScM or Sc.M.) is a master's degree in the field of science awarded by universities in many countries or a person holding such a degree. In contrast to ...

and

Master of Philosophy The Master of Philosophy (MPhil; Latin ' or ') is a postgraduate degree. In the United States, an MPhil typically includes a taught portion and a significant research portion, during which a thesis project is conducted under supervision. An MPhil m ...

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 Ivy League research university in Cambridge, Massachusetts. Founded in 1636 as Harvard College and named for its first benefactor, the Puritan clergyman John Harvard, it is the oldest institution of higher le ...

, where he earned a

Ph.D. A Doctor of Philosophy (PhD, Ph.D., or DPhil; Latin: or ') is the most common degree at the highest academic level awarded following a course of study. PhDs are awarded for programs across the whole breadth of academic fields. Because it is a ...

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

in 1989.

Career

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 1998–2005, he was the head of the

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

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 G ...

, 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 land-grant research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Mary ...

, 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 Department of Medicine. From 2014, he was a Professor in the Department of Biomedical Engineering in the School of Medicine; the Department of Computer Science in the Whiting School of Engineering; and in the Department of Biostatistics in the Bloomberg School of Public Health.ccb.jhu.edu
Brief biosketch In 2013, Salzberg won the Benjamin Franklin award in

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

. In March 2015, 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, politician, philanthropist, and author. He is the majority owner, co-founder and CEO of Bloomberg L.P. He was Mayor of New York City from 2002 to 2013, and was a ca ...

. Salzberg holds joint appointments in the Johns Hopkins

Whiting School of Engineering The G.W.C. Whiting School of Engineering is the engineering college of the Johns Hopkins University, a private research university in Baltimore, Maryland. History Engineering at Johns Hopkins was originally created in 1913 as an educational p ...

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. Founded in 1893, the School of Medicine shares a campus with the Johns Hopkins Hospi ...

, 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 research university in Baltimore, Maryland. As the second independent, degree-granting institution for research in epi ...

Research

Salzberg has been a prominent scientist in the field of

and

computational biology Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...

since the 1990s. He has made many contributions to

gene finding In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functio ...

algorithms, notably the

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

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 In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology might not be able to 'read' whole genomes in on ...

research and is one of the initiators of the open source AMOS project. 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 infectious disease that affects humans and other animals. Malaria causes symptoms that typically include fever, tiredness, vomiting, and headaches. In severe cases, it can cause jaundice, seizures, coma, or death. S ...

genome (''

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

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

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter a ...

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

anthrax Anthrax is an infection caused by the bacterium ''Bacillus anthracis''. It can occur in four forms: skin, lungs, intestinal, and injection. Symptom onset occurs between one day and more than two months after the infection is contracted. The sk ...

that was used in the

2001 anthrax attacks The 2001 anthrax attacks, also known as Amerithrax (a portmanteau of "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 the September 11 ...

. They published their results in the journal

Science Science is a systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the universe. Science may be as old as the human species, and some of the earliest archeological evidence for ...

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 International Sequ ...

and Lone Simonsen started the

Influenza Genome Sequencing Project The Influenza Genome Sequencing Project (IGSP), initiated in early 2004, seeks to investigate influenza evolution by providing a public data set of complete influenza genome sequences from collections of isolates representing diverse species distr ...

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 s ...

(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 sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing c ...

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

Bowtie The bow tie is a type of necktie. A modern bow tie is tied using a common shoelace knot, which is also called the bow knot for that reason. It consists of a ribbon of fabric tied around the collar of a shirt in a symmetrical manner so that the ...

, 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 falsifiability, unfa ...

and in favor of the teaching of

evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...

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. 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 ra ...

) and the likelihood of an accidental lab release.

Publications

Salzberg has authored or co-authored over 300 scientific publications. He has more than 290,000 citations in Google Scholar and an h-index of 156. In 2014, 2015, 2016, and 2017, 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 intelligence, ...

, and Salzberg was also included in the list in 2018, 2019, 2020, 2021, and 2022.

Highly cited articles (more than 10,000 citations)

* 2012 with B Langmead, ''Fast gapped-read alignment with Bowtie 2'', in: ''

Nature Methods ''Nature Methods'' is a monthly peer-reviewed scientific journal covering new scientific techniques. It was established in 2004 and is published by Springer Nature under the Nature Portfolio. Like other ''Nature'' journals, there is no external edi ...

''. 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). Abstracti ...

''. 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. * 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 chief editor heads an in-house team of editors. The focus of the journal is biotechnology including research results and the commercial busi ...

''. 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: ''Genome Biology''. Vol. 14, nº 4; 1-13. * 2015 with D Kim, B Langmead, ''HISAT: a fast spliced aligner with low memory requirements'', in: ''

'' Vol. 12, 357–360. (2015)

Awards

* 2020 Accomplishments by a Senior Scientist Award,

International Society for Computational Biology The International Society for Computational Biology (ISCB) is a scholarly society for researchers in computational biology and bioinformatics. The society was founded in 1997 to provide a stable financial home for the Intelligent Systems for Mole ...

* 2014-2020 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 (abbreviation: AAA&S) 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 ...

* 2013 Named Fellow,

* 2013 Robert G. Balles Prize in Critical Thinking * 2009 Genome Biology Award * 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 School of Engineering and Applied Sciences alumni Johns Hopkins Biomedical Engineering faculty University of Maryland, College Park faculty 21st-century American biologists American bioinformaticians Influenza researchers Jewish scientists 1960 births Fellows of the American Association for the Advancement of Science Fellows of the International Society for Computational Biology