Steven Salzberg | |
---|---|
Born | Steven Lloyd Salzberg 1960 (age 63–64) |
Alma mater | Yale University Harvard University |
Known for | GLIMMER [1] MUMmer [2] AMOS assembler [3] Bowtie [4] TopHat [5] |
Spouse | Claudia Pasche [6] |
Awards | Ben Franklin Award (2013) |
Scientific career | |
Institutions | University of Maryland, College Park The Institute for Genomic Research Johns Hopkins University |
Thesis | Learning with nested generalized exemplars (1989) |
Doctoral advisor | William Aaron Woods [7] |
Doctoral students | |
Other notable students | Olga Troyanskaya [8] |
Website | salzberg-lab |
Steven Lloyd Salzberg (born 1960) is an American computational biologist and computer scientist who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at Johns Hopkins University, where he is also Director of the Center for Computational Biology.
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. [9] Salzberg did his undergraduate studies at Yale University where he received his Bachelor of Arts degree in English in 1980. In 1981 he returned to Yale, and he received his Master of Science and Master of Philosophy degrees in Computer Science in 1982 and 1984, respectively. After several years in a startup company, he enrolled at Harvard University, where he earned a Ph.D. in Computer Science in 1989. [10]
After obtaining his undergraduate degree, he worked for a local power company in South Carolina, where he gained programming experience using IBM mainframe. [11] He also learned COBOL and IBM Assembler. He then joined a Boston-based AI startup upon completion of his masters degree in Computer Science. [11]
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 department at The Institute for Genomic Research, one of the world's largest genome sequencing centers. Salzberg then joined the Department of Computer Science at the University of Maryland, College Park, where he was the Horvitz Professor of Computer Science 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. [6] [12] [13]
In 2013, Salzberg won the Benjamin Franklin award [14] in bioinformatics.
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. [15] The Bloomberg Distinguished Professorships were established in 2013 by a gift from Michael Bloomberg. [16] 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 [17] 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 [18] as well as many other genome projects, including the malaria genome ( Plasmodium falciparum ) 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. [19] 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 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. [20] [21]
Soon after the advent of next-generation sequencing (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 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 has authored editorials and appeared in print media on this topic. Since 2010, he has written a column at Forbes magazine [22] on science, medicine, and pseudoscience, where he has published hundreds of articles that have received tens of millions of views. His work at Forbes won the 2012 Robert P. Balles Prize in Critical Thinking. [23]
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) and the likelihood of an accidental lab release. [24]
Salzberg has authored or co-authored over 300 scientific publications. [25] He has more than 300,000 citations in Google Scholar and an h-index of 159. [26] In 2014 and every year since (through at least 2022), 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. This list of highly cited researchers continues under Clarivate, and Salzberg was also included in the list in 2018, 2019, 2020, 2021, 2022, and 2023. [27]
Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
Comparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences in the aligned genomes and checking to what extent those sequences are conserved. Based on these, genome and molecular evolution are inferred and this may in turn be put in the context of, for example, phenotypic evolution or population genetics.
Michael Ashburner was an English biologist and Professor in the Department of Genetics at University of Cambridge. He was also the former joint-head and co-founder of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL) and a Fellow of Churchill College, Cambridge.
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 genes". GLIMMER was the first system that used the interpolated Markov model to identify coding regions. The GLIMMER software is open source and is maintained by Steven Salzberg, Art Delcher, and their colleagues at the Center for Computational Biology at Johns Hopkins University. The original GLIMMER algorithms and software were designed by Art Delcher, Simon Kasif and Steven Salzberg and applied to bacterial genome annotation in collaboration with Owen White.
Webb Colby Miller is an American bioinformatician who is professor in the Department of Biology and the Department of Computer Science and Engineering at The Pennsylvania State University.
MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure. It has been used for comparing different genomes assemblies to one another, which allows scientists to determine how a genome has changed. The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs.
RNA-Seq is a technique that uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome.
Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.
Lincoln David Stein is a scientist and Professor in bioinformatics and computational biology at the Ontario Institute for Cancer Research.
Bowtie is a software package commonly used for sequence alignment and sequence analysis in bioinformatics. The source code for the package is distributed freely and compiled binaries are available for Linux, macOS and Windows platforms. As of 2017, the Genome Biology paper describing the original Bowtie method has been cited more than 11,000 times. Bowtie is open-source software and is currently maintained by Johns Hopkins University.
Mathieu Daniel Blanchette is a computational biologist and Director of the School of Computer Science at McGill University. His research focuses on developing new algorithms for the detection of functional regions in DNA sequences.
Bonnie Anne Berger is an American mathematician and computer scientist, who works as the Simons professor of mathematics and professor of electrical engineering and computer science at the Massachusetts Institute of Technology. Her research interests are in algorithms, bioinformatics and computational molecular biology.
Lior Samuel Pachter is a computational biologist. He works at the California Institute of Technology, where he is the Bren Professor of Computational Biology. He has widely varied research interests including genomics, combinatorics, computational geometry, machine learning, scientific computing, and statistics.
TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat aligns RNA-Seq reads to mammalian-sized genomes.
Ben Langmead is a computational biologist and associate professor in the Computational Biology & Medicine Group at Johns Hopkins University.
Owen R. White is a bioinformatician and director of the Institute For Genome Sciences at the University of Maryland School of Medicine, United States. He is known for his work on the bioinformatics tools GLIMMER and MUMmer.
Jeffrey Tullis Leek is an American biostatistician and data scientist working as a Vice President, Chief Data Officer, and Professor at Fred Hutchinson Cancer Research Center. He is an author of the Simply Statistics blog, and runs several online courses through Coursera, as part of their Data Science Specialization. His most popular course is The Data Scientist's Toolbox, which he instructed along with Roger Peng and Brian Caffo. Leek is best known for his contributions to genomic data analysis and critical view of research and the accuracy of popular statistical methods.
Bruce Colston Trapnell Jr. is an assistant professor in the Department of Genome Sciences at the University of Washington. He was awarded the Overton Prize by the International Society for Computational Biology (ISCB) for “outstanding accomplishment in the early to mid stage of his career” in 2018.