Senior Scientist Accomplishment Award

The Senior Scientist Accomplishment Award recognizes members of the computational biology community who are more than 12 to 15 years post-degree and have made major contributions to the field of computational biology through research, education, service, or a combination of the three.

2009 ISCB Senior Scientist Accomplishment Award Winner - Webb Miller

Picture: 2009 SSAA Winner, Webb Miller

Ten years ago, Webb Miller was already well known to bioinformaticians worldwide for two very highly cited classic papers on the BLAST algorithms for searching sequence databases. Today Miller's name is equally well known for the alignment, comparison, and analysis of complete vertebrate genomes. Much of the code written in his group is embedded in the University of California Santa Cruz (UCSC) Genome Browser.

Miller's initial training was in mathematics. In the mid-1960s, at Whitman College in Walla Walla, Washington, he found a book in the library on the theoretical limits of what is computable, and he decided that he could undertake real, publishable research in this field. This led to graduate work in Computer Science, to his Ph.D. in Mathematics, and, by 1969, to an assistant professorship in Computer Science at The Pennsylvania State University (Penn State). At this time he still had no experience of practical computing or writing code.

In 1980, Miller was looking around for new challenges and applications of his computational knowledge. He found them through a most unexpected source. “My mother started sending me newspaper clippings about the beginnings of the Human Genome Project,” he says. “This fascinated me, although I knew no biology at the time.”

Soon after entering bioinformatics, Miller turned his attention from general sequence alignment algorithms to the specific problem of aligning long DNA sequences. “Most bioinformaticians spent the 1990s waiting for the human genome sequence,” he said. “My question was: How soon would the second vertebrate genome come out, so I could try a genome-wide sequence alignment?” That second genome—of the mouse—was published in 2002. “I originally anticipated that we would have two vertebrate genomes by the time I reached retirement age in 2008. Instead, thanks to improvements in sequencing technology, we now have over forty.”

He and his collaborators have now taken on a new challenge: sequencing the genomes and understanding the biology of rare, endangered, and even extinct species. He has published sequences of the nuclear genome of the woolly mammoth and the mitochondrial genome of the Tasmanian tiger (Thylacinus cynocephalus), which became extinct in 1936. Miller says he is hoping that similar sequencing techniques will help preserve endangered species from extinction. One of these is the so-called Tasmanian devil, a ferocious marsupial that is now under threat from a mysterious, contagious tumor: Devil Facial Tumor Disease. “We are sequencing two specimens, one with the disease and another that seems immune, and hope to use the differences to guide a breeding program,” he says.

Miller acknowledges that he owes much of his success to “great” collaborators, from Gene Myers (Howard Hughes Medical Institute, USA) and David Lipman (National Cancer Biotechnology Information, USA) in the late 1980s to David Haussler (UCSC, USA) and Haussler’s colleagues Jim Kent and Tom Pringle. And it may be that great collaborators make each other. “Time and time again, Webb has made major contributions and taken little credit for himself, preferring to put younger researchers in the limelight, whether or not they were his students. I've never worked with a more generous collaborator,” says Haussler.

In respect for his ISCB 2009 Accomplishment by a Senior Scientist Award, Miller offers his “10 Steps to Success in Bioinformatics” (click here).

This article is excerpted from the April 2009 issue of PLoS Computational Biology. To link to the full journal article please visit http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000375.

Picture: 2008 SSAA Winner, David Haussler

Picture: 2007 SSAA Winner, Temple F. Smith

“Professor Smith’s contributions go well beyond those for which he is best known,” says Thomas Lengauer, chair of the ISCB Awards Committee. Lengauer continued, “He is a towering figure in bioinformatics, one of the founders of the discipline. In addition to starting GenBank and being the Smith of the Smith-Waterman algorithm, he has done seminal work on the entropy of the genetic code and on pattern-directed protein structure prediction.” Other influential work includes research on gene prediction, molecular phylogenies, multiple sequence alignments and the analysis of sequence patterns.“ His results have had a tremendous impact on the field. And his BioMolecular Engineering Research Center at the Boston University College of Engineering is a superlative resource for a wide variety of endeavors.”

Smith obtained his doctorate in nuclear physics from the University of Colorado in 1969 and was at NIH as a postdoctoral fellow with Stanislaw Ulam, T. T. Puck, and John R. Sadler, studying bacterial genetic regulation. He then took an appointment as professor of physics at Northern Michigan University, spending summers as a visiting staff member in applied mathematics and theoretical biology at Los Alamos Scientific Laboratory where he helped to organize GenBank.

Moving to Boston University in 1991, Smith became a professor in the departments of bioengineering and pharmacology and director of The BioMolecular Engineering Research Center (BMERC) . His center is currently working under NIH and NSF grants on activation of inflammation stress response pathways, cellularsignaling problems (with the Alliance for Cellular Signaling), the generation of automated models of protein folds, and the core genomics of the origin of eukaryotes.

A science writer at Boston University, Michael Seele, writes of how Smith and Michael Waterman came to write his only geology paper as follows:

“As the pair walked to lunch, they passed through the geology department lobby, where two large core samples on display stopped them in their tracks. Similar sequences of strata on different columns were connected by strings. Smith and Waterman immediately saw the columns as strands of DNA and the comparable strata as the short protein sequences they were trying to align. “We now faced the possibility that a geologist had solved the problem before us,” Smith said. Resigned, Smith and Waterman visited the geology chairman and asked how the sequence alignment had been done. Their mood elevated when the chairman informed them that visual observation and string were as far as anyone had advanced with a solution. “Lo and behold! This was an unsolved problem in geology,” Smith said. “This resulted in our first geology paper, basically written over the next couple of days.” With a fresh perspective, the team returned to bioinformatics work and published the Smith-Waterman sequence alignment algorithm the following year. It remains one of the most referenced papers in molecular biology.

Of his award, Smith says, “I’m truly honored to join my longtime friend and colleague Mike Waterman, who preceded me in winning this award last year, as well as the distinguished company of previous winners.”

The Accomplishment by a Senior Scientist Award will be presented in Vienna followed by a keynote address, titled “Computational Biology. What’s next?” to close the conference on July 25, 2007. To read additional biographical information and an abstract of Smith’s keynote address see www.iscb.org/ismbeccb2007/keynotespresentations/#smith.

Citation: Maisel M (2007) ISCB Honors Temple F. Smith and Eran Segal. PLoS Comput Biol 3(6): e128 doi:10.1371/journal.pcbi.0030128

2006 ISCB Senior Scientist Accomplishment Award Winner - Professor Michael Waterman

Picture: 2006 SSAA Winner, Michael S. Waterman

Dr. Michael S. Waterman, Professor of Biological Sciences, Computer Sciences, and Mathematics at the University of Southern California, is the 2006 recipient of the Senior Scientist Accomplishment Award of the International Society for Computational Biology (ISCB).

Waterman is best known as the developer, with Temple F. Smith, of the Smith-Waterman algorithm for determining the degree of similarity (homology) of amino acid sequences from DNA, RNA, or proteins. In their famous three-page paper in the Journal of Molecular Biology in 1981, Waterman and Smith changed the face of molecular biology and helped launch the bioinformatics revolution.

"Ever since, Mike Waterman has contributed work of prime importance in half a dozen fields of computational biology," says Professor Thomas Lengauer of the Max-Planck-Institut für Informatik and chair of the ISCB Awards Committee. "In addition to the Smith-Waterman algorithm and its follow-ons, Waterman introduced the dynamic programming approach to RNA structure prediction; and he supplied the mathematical, probabilistic, and statistical underpinning that supports BLAST and similar alignment search and evaluation tools. In 1988, he and Eric Lander derived the fundamental formulae to enable the correct assembly of genome sequences. His recent software for genome assembly, written with computational scientist Pavel Pevzner of UCSD and mathematician Haixu Tang of USC, promises to become the standard for the field."

Lengauer adds, "Waterman has had enormous impact on the fields of bioinformatics, computational genomics, and phylogeny, combining vision with technical depth, and his influence goes beyond research." Waterman has trained many prominent computational geneticists, has served on virtually all the panels and committees advising government and evaluating major grants and fellowships, and has generally guided the development of computational biology. "He wrote one of the first textbooks in this field." Lengauer says," and his latest text, Computational Genome Analysis: An Introduction, written with Richard C. Deonier and Simon Tavaré, is unique in successfully addressing the needs of students with very little background in either biology or computing. With Pavel Pevzner and Sorin Istrail, Waterman founded RECOMB, the conference on research in computational molecular biology, which held its tenth conference in April 2006."

Waterman is a founding editor of the Journal of Computational Biology and serves on the editorial boards of six other journals. He was named a Guggenheim Fellow (1995), was elected to the American Academy of Arts and Sciences (1995) and to the National Academy of Sciences (2001), and is a Fellow of AAAS and the Institute of Mathematical Statistics. In 2005, he was elected to the French Académie des Sciences. In addition to his posts as University Professor and USC Associates Chair in Natural Sciences, he is professor-at-large in the Keck Graduate Institute of Life Sciences and master of USC's Parkside International Residence College.

The Senior Scientist Achievement Award will be presented to Professor Waterman on August 10 at the ISCB annual meeting, Intelligent Systems for Molecular Biology, in Fortaleza, Brazil. Waterman will deliver the final keynote lecture, "Whole genome optical mapping," for the conference.

Picture: 2005 SSAA Winner, Dr. Janet Thornton

2005 ISCB Senior Scientist Accomplishment Award-
Dr. Janet Thornton

Dr. Janet Thornton, Director of the EMBL European Bioinformatics Institute (EBI), was named the winner of the annual Senior Scientist Accomplishment Award. Dr. Thornton is the third scientist to have earned the honor.

Dr. Thomas Lengauer, member of the ISCB Awards Committee and professor at the Max Planck Institute said, "Janet Thornton could be described as 'Miss Structural Bioinformatics'. She has made outstanding and seminal research contributions to her field and, as Director of the EBI and the coordinator of the BioSapiens Network of Excellence, has selflessly dedicated herself to developing the research landscape in computational biology."

Dr. Thornton has published many predictive and explanatory models of protein function; protein-protein, protein-ligand and protein-dna interactions, and, more recently, protein catalytic sites. In the 1990's, she created the CATH classification system for protein structures and the associated database, now vital tools for understanding protein chemistry and evolution.

"In addition to her deep scientific contributions, Dr. Thornton has directed the European Bioinformatics Institute since October of 2001, dramatically expanding its research mission while continuing to provide its vital and unique databases to the molecular biology community," said Dr. Lawrence Hunter of the University of Colorado Health Sciences Center, the ISCB's founder and chair of the ISCB Awards Committee.

The prize was awarded at the ISCB's annual meeting, Intelligent Systems for Molecular Biology (ISMB) in Detroit, Michigan, on June 29, at which time Dr. Thornton delivered the annual Senior Scientist Accomplishment Award keynote lecture as the finale to a very successful conference.

For more details on the career and accomplishments of Dr. Thornton, please see the ISCB newsletter article at www.iscb.org/newsletter8-2/thornton.html.

Picture: 2004 SSAA Winner, Dr. David Lipman

2004 ISCB Senior Scientist Accomplishment Award-
Dr. David Lipman

The The International Society for Computational Biology (ISCB) named the second winner of its annual Senior Scientist Accomplishment Award, Dr. David Lipman, director of the National Center for Biotechnology Information (NCBI). The prize was awarded at the ISCB's annual meeting, Intelligent Systems for Molecular Biology (ISMB), held in conjunction with the European Conference on Computational Biology (ECCB), in Glasgow, Scotland, on August 4, 2004. Dr. Lipman delivered an informative and entertaining keynote lecture entitled "Message and meaning in sequence comparison: is systems biology possible?"

In "Over the course of his distinguished career, Dr. Lipman contributed to several of the most important tools used in the analysis of gene sequence data, and managed the growth of many of the most essential public scientific databases. His vision and leadership of the NIH's National Center for Biotechnology Information has not only altered the course of computational biology, but of science as a whole," said Larry Hunter of the University of Colorado Health Sciences Center, chair of the ISCB award committee.

Since 1989, Dr. Lipman has been the Director of the NCBI, a leading research center in computational biology, the creators of PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. He still remains active in research, most recently publishing a paper comparing mRNAs in eukaryotes in Nucleic Acids Research. He has received numerous awards in his career, including three Public Health Service Outstanding Service Medals and the National Institutes of Health Director's Award. He is also a member of a number of prestigious associations including the National Academy of Sciences.

For more information on the selection of Dr. Lipman for this award see the ISCB newsletter article at www.iscb.org/newsletter7-3/ssaa.html

Picture: 2003 SSAA Winner, David Sankoff

2003 ISCB Senior Scientist Accomplishment Award-
David Sankoff

The ISCB will present the first-ever ISCB Senior Scientist Accomplishment Award to David Sankoff, Canada Research Chair in Mathematical Genomics at the University of Ottawa and a member of the Centre de Recherches Mathématiques at the Université de Montréal. The prize will be awarded to Sankoff at ISMB2003, where he will present a keynote lecture on July 2, 2003.

In sequence comparison, he introduced the quadratic version of the Needleman-Wunsch algorithm, developed the first statistical test for alignments, initiated the study of the limit behavior of random sequences with Vaclav Chvatal and described the multiple alignment problem, based on minimum evolution over a phylogenetic tree. In the study of RNA secondary structure, he developed algorithms based on general energy functions for multiple loops and for simultaneous folding and alignment, and performed the earliest studies of parametric folding and automated phylogenetic filtering.

Sankoff and Robert Cedergren collaborated on the first studies of the evolution of the genetic code based on tRNA sequences. His contributions to phylogenetics include early models for horizontal transfer, a general approach for optimizing the nodes of a given tree, a method for rapid bootstrap calculations, a generalization of the nearest neighbor interchange heuristic, various constraint, consensus and supertree problems, the computational complexity of several phylogeny problems with William Day, and a general technique for phylogenetic invariants with Vincent Ferretti. Over the last fifteen years he has focused on the evolution of genomes as the result of chromosomal rearrangement processes. Here he introduced the computational analysis of genomic edit distances, including parametric versions, the distribution of gene numbers in conserved segments in a random model with Joseph Nadeau, phylogeny based on gene order with Mathieu Blanchette and David Bryant, generalizations to include multi-gene families, including algorithms for analyzing genome duplication and hybridization with Nadia El-Mabrouk, and the statistical analysis of gene clusters with Dannie Durand. Sankoff is also well known in linguistics for his methods of studying grammatical variation and change in speech communities, the quantification of discourse analysis and production models of bilingual speech.

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