Picture: 2011 ISCB ASSA Winner, Michael Ashburner Photo courtesy of European Molecular Biology Laborator

2011 ISCB Accomplishment by a Senior Scientist Award Winner:  Michael Ashburner

If computational biology seems challenging in the second decade of the 21st century, spare a thought for those who pioneered the discipline in the 1980s. Michael Ashburner at the University of Cambridge was one of them. “His work is now seen as a landmark and an achievement in technology,” says Alfonso Valencia, chair of the ISCB awards committee.

Ashburner began his career with a degree in genetics from the University of Cambridge in 1964. He stayed on to do a PhD, studying Drosophila and, in particular, polytene chromosomes, which form when certain specialised cells undergo repeated rounds of DNA replication. Polytene chromosomes have a characteristic banded structure. In Drosophila there are some 5,000 bands and a subset of these undergo, during development, a reversible structural modification as the result of transcription; this is known as puffing and can be considered an analog of gene activity. In the late 1960s and early 1970s, Ashburner studied puffing patterns and inferred the existence of a cascade of genetic controls under the influence of the hormone ecdysone during larval development.

In the late 1970s, Ashburner turned his attention to the study of the Alcohol dehydrogenase gene and its environs. By the mid-1980s, he had the most detailed analysis in full genetic terms of any small chromosome region of any multi-cellular organism, and had the Adh gene sequences from several different species of Drosophila. “That drew me into bioinformatics because we needed a way of comparing sequences,” he says. “There was almost no software available to help.”

Two people came to his aid. The first was Walter Bodmer, director of the Imperial Cancer Research Fund, who gave Ashburner the use of a DEC computer with access to the early network. “We could access this machine by dial-up and do some analysis,” he says. The second was Doug Brutlag at Stanford University, who was developing MOLGEN, an early bioinformatics system, which he allowed Ashburner to access.

That presented a significant obstacle, however. Getting a computer in the United Kingdom to speak to one in Stanford was not straightforward. Today, everybody uses the Internet, defined by the TCP/IP protocol. But in the early ‘80 s, the UK and United States used different systems. The US was pioneering TCP/IP while the UK had a standard called the Coloured Book protocols. “The only place that had an interface between the two protocols was University College, London, and they were very helpful,” says Ashburner, “giving us 5 kb of disk space.”

The process of connecting to Stanford was far from simple. “The way you did it was to dial up your local packet switching exchange at the Post Office and connect to the Rutherford Appleton Laboratory. You then typed in some code which connected you to UCL where you could use TCP/IP,” he says. The signal was routed via Goonhilly satellite station in Cornwall to Carnegie Mellon University and from there to Stanford. “I had a dumb terminal, that is a box with no memory, so everything had to be captured by a printer in parallel.” Ashburner was far from deterred, however.

At about that time, the European Molecular Biology Laboratory (EMBL) in Heidelberg and GenBank in the US released the first nucleotide sequence libraries in quick succession. Using his network access, Ashburner and his colleagues, collaboratively with MOLGEN, set up one of the first bulletin boards, called BioNet, to keep people informed of changes to the library and to software. “This became well used and things evolved from there,” he says.

As the field of bioinformatics grew, the need for an institution to house the data and conduct research increased. So in 1992, the EMBL decided to set up an institute of bioinformatics that would house this library and carry out research. This organisation became known as the European Bioinformatics Institute, based in Hinxton, UK, with Ashburner and John Sulston having led the UK bid to host it. “I was persuaded to become the first program coordinator and took half-time leave from Cambridge to do that,” he says. He eventually took over as joint-director, a post he held until 2001. “At first, the finances were sticky and the politics were horrendous. But it has since gone from strength to strength,” he says.

At the same time, Ashburner continued his interest in Drosophila genetics. This is a field with a rich and long history of collecting and sharing mutations. The first catalogue of mutations was published in 1925 and it was still being revised in paper form in the late 1980s. But the field was beginning to expand quickly and the books were out of date as soon as they were published. “It became clear to me that we couldn't carry on publishing in paper form every 10 or 20 years,” he recalls.

So in 1989 he proposed that the community set up an electronic database to take over the role of the printed one. In 1992, the NIH funded the project that became known as FlyBase, one of the first genetic and now genomic databases.

FlyBase was a crucial factor in triggering Ashburner's interest in a structured, controlled vocabulary, a formal representation of knowledge about genes and gene products. He began to define terms for gene products by their biological processes, such as wing development, and then defined the data structure in which these terms were related to each other. “It occurred to me that if you were able to do this for several model species, you'd have a fantastic tool,” he says.

But this insight initially met with little interest. “My first presentation, at ISMB in Greece in 1997, went down like a lead balloon,” he recalls. Eventually, he and three like-minded colleagues settled the matter in a bar at the Montreal ISMB in 1998.

Together, they decided to set up a cross-species ontology to be used by the Drosophila, yeast, and mouse databases. They called it the Gene Ontology, and it is now a major bioinformatics project that covers over 1,800 species. Their original paper on the idea in Nature Genetics is one of the most highly cited in the field. “His achievement is not just to have built this system but also to have organised the consortium behind it. It is now one of the most used resources in all of biology,” says Valencia.

He went on to collaborate with Gerry Rubin and Craig Venter in sequencing the Drosophila genome in 1999. “The process turned me into a nervous wreck,” he jokes. He published his account of this roller-coaster experience in a short but entertaining book called Won for All: How the Drosophila Genome was Sequenced (Cold Spring Harbor Laboratory Press, 2006).

“We're lucky to have such an inspirational figure in the community,” says Valencia. “This award has been well deserved for a number of years.”

This article is excerpted from the June 2011 issue of PLoS Computational Biology. To link to the full journal article please visit www.ploscompbiol.org/article/info%3Adoi/10.1371/journal.pcbi.1002081

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Picture: 2003 ISCB ASSA Winner, David Sankoff

2003 ISCB Accomplishment by a Senior Scientist Award Winner -
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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Picture: 2013 Accomplishment By A Senior Scientist Award Prize Winner, David Eisenberg

ISCB Congratulates 2013 Senior Scientist Award Winner: David Eisenberg

By Christiana N. Fogg, Freelance Science Writer, Kensington, MD

Each year, ISCB honors an esteemed member of the computational biology community with the Accomplishment by a Senior Scientist Award. This award recognizes an individual’s significant contributions to computational biology through research, service, and education. The winner of 2013 ISCB Accomplishment by a Senior Scientist Award is Dr. David Eisenberg, Professor of Chemistry and Biochemistry and Biological Chemistry at the University of California, Los Angeles.

David Eisenberg’s love of medicine and science was cultivated first during his childhood by his father, a gentle and beloved pediatrician. Eisenberg recalled, “Every night after dinner he would make house calls. I saw how appreciated—even loved— he was in our village.”

Eisenberg’s father also stoked his scientific curiosity by encouraging him to try some experiments in their basement, including attempts to petrify an egg and to grow worms in chocolate. Eisenberg reminisced, “None of these [experiments] worked, but they were fun.

Eisenberg strongly considered following in his father’s footsteps and pursuing a career in medicine. With that goal in mind, he focused his undergraduate studies on biochemical sciences at Harvard University. As a sophomore, he was assigned to Dr. John T. Edsall as a tutor.

Edsall was a pioneering researcher in the field of biophysical chemistry, and under his guidance, Eisenberg had his first encounter with laboratory research. “In my junior year, he assigned me to read scientific papers, most of which baffled me, and at the end of that year, I started a research project in his lab, which became the subject of my senior thesis.” Eisenberg recounted. “After graduation, Dr. Edsall turned my thesis into a short paper which was published in Science.”

In spite of Eisenberg’s eye-opening undergraduate research experiences, he applied and was accepted to medical school. Edsall was also trained as a medical doctor, but Eisenberg remembered how “Dr. Edsall convinced me that if my goal was to improve the health of mankind, I might have a greater impact working in biochemistry, than as a practicing physician.”

Eisenberg took Edsall’s advice to heart and “finessed making an immediate choice by going to Oxford to study theoretical chemistry under Dr. Charles Coulson, one of the founders of quantum chemistry.” Edsall’s guidance had also given him a strong foundation in math and physics, which served him well as a graduate student at Oxford as he recalled being “(just) able to work with Coulson on the energetics of hydrogen bonding.”

Eisenberg’s postdoctoral studies took him to Princeton in 1964 to work with Dr. Walter Kauzmann, well known for his discovery of the hydrophobic interaction. Eisenberg recollected his ambitious postdoctoral plan “to compute the energy of the hydrophobic interaction in myoglobin, the first protein with a known 3D structure. This plan now seems hopelessly naïve: computers were not yet up to such a calculation, potential functions and theory had not advanced to the point that this was a practical problem, and the early protein crystallographers were not eager to release their atomic coordinates.”

In light of these challenges, Eisenberg’s work with Kauzmann culminated in “a monograph on ice and water, which, incidentally, is still in print 44 years later.”

His failed postdoctoral research plan also opened his eyes. He knew if he wanted to pursue protein energetics, which required knowing protein coordinates, he had to learn X-ray crystallography. Eisenberg’s next postdoc took him “to Caltech to study X-ray crystallography with Richard Dickerson, who had been part of the team who had determined the structure of myoglobin.”

His X-ray crystallography training was pivotal to establishing his own lab at UCLA that focused on studying diverse protein structures. Melittin, a component of bee venom, was one of the first structures he determined with his then graduate student Tom Terwilliger. Eisenberg vividly recalled that, “At last I was able to get down to energetic calculations on a protein, and came up with the idea of the hydrophobic moment. This and related ideas gave me for the first time the feeling that I could make discoveries.”

Eisenberg also remembers the excitement of solving the structure of diphtheria toxin dimer, which he worked on with John Collier, Senyon Choe, and Melanie Bennett (Brewer). He recalled the excitement that stemmed from Bennett (Brewer)’s observation that “two monomers of the dimer swapped their third domains, and we called this phenomenon “3D domain swapping.” We explored the implications of 3D domain swapping, again calling on my background in energetics. Diphtheria toxin was the first structural example of 3D domain swapping; now there are hundreds.”

Eisenberg’s work on protein structures awakened his interest in how protein sequences relates to 3D structures. While on sabbatical at the Laboratory of Molecular Biology in Cambridge, he worked with Andrew McLachlan and Mike Gribskov to develop methods to examine protein sequences and use profile analysis to predict the presence of potential structural motifs. These studies led to his work on 3D profiles with Jim Bowie and Roland Luethy, which Eisenberg has now seen “applied to many protein problems.”

Burkhard Rost, president of the ISCB, considers Eisenberg’s work on hydrophobicity profiling as groundbreaking as it “describes an important feature of the constituents which] we found we could extract information on protein interactions from sequenced genomes.” These cutting edge studies resulted in several publications that showed how protein function and protein-protein interactions could be predicted from genome sequences.

Eisenberg has focused his research over the last decade on studying amyloid-forming proteins. Several neurodegenerative diseases are associated with amyloid-forming proteins, including Alzheimer’s, Parkinson’s and amyotrophic lateral sclerosis (Lou Gehrig’s) disease. “Just before the turn of the century, I realized that amyloid diseases represent the greatest unmet medical problem facing the world.” Eisenberg recounted. “And at the same time, I realized that structural and computational biology, which have illuminated other areas of biomedicine so well, have not been widely applied to the fundamental problems of amyloid disease. In particular, there had been almost no single crystal x-ray studies of amyloid-forming proteins.”

Eisenberg also acknowledges that, “Having several friends afflicted with amyloid disorders is a great inspiration. I would love to be able to help them, and others. If we can, it would validate Dr. Edsall advice that sometimes biochemists can do as much or more to help mankind than physicians.”

Eisenberg’s group has studied the structural basis of how normal proteins convert to amyloid fibrils. They have gained great insight into this conversion process by determining the atomic structures of the spines of many different types of amyloid fibrils. The use of computational biology with this structural data has helped support the definition of the “amyloid state” of proteins. “Bioinformatics and computational biology are great partners with structural biology. Using the tools together can be surprisingly powerful,” said Eisenberg.

Eisenberg remains humble about his accomplishments. When asked about being the recipient of the ISCB Senior Scientist Accomplishment Award, he felt “honored, but perhaps over-honored. There are many others who are equally or more deserving of this recognition.” But he also recognizes that this award helps highlight the importance of studying amyloid diseases, especially using the tools of computational biology. Eisenberg speaks warmly of the mentors that have guided and shaped his scientific training. “I was enormously fortunate to find myself in the research groups of four great mentors: John Edsall, Charles Coulson, Walter Kauzmann, and Richard Dickerson, not to mention my father. All were creative scientists, and also humanists. Watching them I saw their pleasure in scientific discovery, and also saw their insistence on fairness to all those involved in the process of science.”

Their examples have not only served him well as a scientist, but also as a mentor. Eisenberg delights in working with trainees because he loves “their eagerness to learn and to succeed, and their willingness to think freshly about hard problems.”

Eisenberg’s scientific curiosity remains insatiable, and when asked for advice to motivate young scientists, his sage answer was “work on fundamental problems, maintain your curiosity, and above all, persevere.”

This article is excerpted from the June 28, 2013, issue of PLOS Computational Biology. To link to the full journal article please visit: www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003116

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2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers

2014 ISCB ACCOMPLISHMENT BY A
SENIOR SCIENTIST AWARD: GENE MYERS

By Christiana N. Fogg¹, Diane E. Kovats²*

¹ Freelance Science Writer, Kensington, Maryland, United States of America,
² Executive Director, International Society for Computational Biology, La Jolla, California,
United States of America

* E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

The International Society for Computational Biology (ISCB; www.iscb.org) annually recognizes a senior
scientist for his or her outstanding achievements. The ISCB Accomplishment by a Senior Scientist Award honors a leader in the field of computational biology for his or her significant contributions to the community through research, service, and education. Dr. Eugene “Gene” Myers of the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden has been selected as the 2014 ISCB Accomplishment by a Senior Scientist Award winner.

Myers was selected by the ISCB's awards committee, which is chaired by Dr. Bonnie Berger of the Massachusetts Institute of Technology (MIT). Myers will receive his award and deliver a keynote address at ISCB's 22nd Annual Intelligent Systems for Molecular Biology (ISMB) meeting. This meeting is being held in Boston, Massachusetts, on July 11–15, 2014, at the John B. Hynes Memorial Convention Center (www.iscb.org/ismb2014).

Gene Myers: Coding and Decoding

Myers was captivated by computer programming as a young student. He remembered his fascination being stoked by a realization and recalls, “A computer is a programmable device, and once programmed, is a specific device for doing something that I conceived of. I found this magical.” He completed a BS in mathematics at the California Institute of Technology, but his interest in biology came during his PhD studies at the University of Colorado in the late 1970s. Myers recounted that he initially considered molecular
biology as “a source of interesting computational questions.” He was studying computer science under the guidance of his dissertation advisor, Andrzej Ehrenfeucht, who had eclectic interests that included molecular biology. Myers, along with fellow graduate students and future bioinformaticians Gary Stormo and David Haussler, was drawn by Ehrenfeucht's curiosity about such basic questions as how to compare DNA sequences and how to build evolutionary trees.

Myers landed his first faculty position in the Department of Computer Science at the University of Arizona. Throughout his research career, he has been interested in sequence assembly. He recollected. “While I developed many seminal algorithms for sequence comparison and search in the '80s and early '90s, including BLAST (Basic Local Alignment Search Tool), the problem that has and continues to fascinate me to this day is sequence assembly.” He is well-known for being one of the authors of the 1990 manuscript that first described BLAST, a groundbreaking algorithm that is still used today for sequence comparison. This paper is also one of the most cited papers in scientific literature.

Myers’s interest in sequence assembly led him to promote the idea that whole genome shotgun sequencing could be used on the large and unwieldy human genome. Craig Venter brought Myers to Celera Genomics in 1998 during their push to sequence the human genome. Myers recalled writing thousands of lines of code to build algorithms that could assemble the vast amounts of sequence data. He considers the success of this landmark sequencing project as a highlight of his career.

In 2002, Myers returned to academia in a position at the University of California, Berkeley's Center for Integrative Genomics. More recently, Myers headed a lab at the Howard Hughes Medical Institute (HHMI)'s Janelia Farm Research Campus. In 2012, he moved to Dresden, Germany to serve as a director at the Max Planck Institute of Molecular Cell Biology and Genetics and the Klaus-Tschira chair of the Systems Biology Center. Myers describes that his “latest focus all started because [he] wish[es], like many, to ‘decode’ the genome.” His work has evolved into building microscopic devices and image analysis tools that can be used to observe and model the inner workings of cells and biological systems. He sees this type of work as having the potential to revolutionize medicine. He said, “Really understanding (in molecular terms) what a cell can do and how what it does affects its role in a complex tissue or organ will greatly advance medicine and treatment as well as help us understand
variation across species and how organisms develop.”

Myers recounted the importance of key mentors in the success of his career. Myers met Webb Miller when he was a young faculty member at the University of Arizona in the early 1980s. The two struck up a fruitful collaboration that led to many early papers about sequence analysis. Myers explained, “Miller helped me greatly in the early part of my career in that he taught me, through example, that writing can be fun.” Myers gained a different sort of insight while working for Venter at Celera. He described Venter as “a master of the sound bite, and while this may sound trivial, it is actually more important than one might think.

"Much of one’s career success depends on the ability to present one’s ideas in powerful, succinct, clear ways.”

Myers believes that mentorship should be “about shaping the character of the individual and their understanding of their role within the research community.” He starts with himself as he aims to “do [his] best to be a good role model, to instill values of integrity, objectivity, and openness.” Myers has trained students from varied academic backgrounds throughout his career, and affirmed that, “there is no substitute for passion.”

Myers’s unique contributions to computational biology have been recognized by several awards, including election to the National Academy of Engineering (2003), the Association for Computing Machinery (ACM) Kannellakis Prize (2002), and the International Max Planck Research Prize (2004). Bonnie Berger (MIT), chair of the ISCB Nominating Committee, sees Myers as an exemplar of the Achievement by a Senior Scientist Award. Berger stated that, “Myers is one of the founders of the field, bringing his algorithmic expertise to the most fundamental problems in computational biology. From his role in creating the indispensable and widely used BLAST program for basic sequence search, to breaking the barrier of sequencing the human genome, to deciphering what is coded in DNA, he has launched our discipline. Myers has been a prominent member of the ISCB community, serving on the Board of
Directors, as an ISCB fellow, and as chair and area chair for numerous ISMB meetings.” Alfonso Valencia, leader of the Structural Computational Biology group at the Spanish National Cancer Research Center and president-elect of ISCB, also sees Myers as a stellar representative of the field. Valencia said of this year’s award winner, “I am particularly happy about the election of Gene Myers, since he represents the strong roots of computational biology in algorithmic and method development. The intensity with which he lives science, the originality of his approaches, and the attention he dedicates to the technical details are characteristics of his work and a great example for our new generations of bioinformaticians and computational biologists.”

Myers remains fervent and passionate about the work he does. He contends that his upbringing, which included traveling the globe with his family, as well as his innate passion for science and mathematics have helped make him “flexible, broad-minded, and curious.” He also prefers to keep his research group small while keeping his research vision large. He advises future and active scientists,

“Simultaneously be able to 'go deep' and yet continuously remain in an environment that keeps you in touch with the 'big picture.' And you always have to take on new challenges and new problems.” In the end, he cannot speak strongly enough about the importance of passion and states, “My overarching advice is to do what you are passionate about. Ours is not a career for security or wealth. You have to love it, absolutely love it.”

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Picture: 2004 Overton Prize Winner, Uri Alon

2004 Overton Prize Winner - Uri Alon

The International Society for Computational Biology (ISCB) awarded the 2004 Overton Prize to Uri Alon, senior scientist at the Weizmann Institute of Science. 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. Alon delivered the annual Overton keynote lecture, entitled "Design principles of biological networks."

"Uri Alon epitomizes the spirit of the Overton Prize. Despite being in a relatively early stage of his career, he has made significant contributions to computational biology, particularly in the areas of network motifs and the design principles of biological networks," said Larry Hunter of the University of Colorado Health Sciences Center, chair of the ISCB Awards Committee.

Alon received his PhD in theoretical physics from the Weizmann Institute, where he studied statistical mechanics and hydrodynamics. During Alon's graduate studies he became intrigued by the biological sciences after reading a biology textbook. Subsequently, he headed for his postdoctoral studies at Princeton determined to learn experimental biology.

For more information on Alon please see the ISCB newsletter article announcing his selection for this award at
www.iscb.org/images/stories/newsletter/newsletter7-3/overton.html

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Overton Prize

The Overton Prize was established by the ISCB in memory of G. Christian Overton, a major contributor to the field of bioinformatics and a member of the ISCB Board of Directors who died unexpectedly in 2000. The annual prize is awarded for outstanding accomplishment to a scientist in the early to mid-career stage (up to a decade post-degree or equivalent experience), who has already made a significant contribution to the field of computational biology.

ISCB recognizes that career paths may take many forms and that the definition of “early/mid-career” is fluid; supports researchers taking time off for maternity/paternity, care for a family member, an event of personal disability or other factors. A nominee may qualify for the Overton Prize even though their actual years since degree is above the set threshold. It is the responsibility of the nominator to indicate any time-off taken by the nominee when submitting the nomination form. ISCB may deduct the equivalent time for the maternity/paternity leave, care for a family member or personal disability from the set award thresholds using guidance established by the European Research Council (page 19, paragraph 5).

2024 ISCB Overton Prize: Martin Steinegger

ISCB Awards Policies & Procedures

ISCB is currently offering four annual awards, the Overton Prize, the Innovator Award, the ISCB Accomplishment by a Senior Scientist Award, and the Outstanding Contributions to ISCB Award.

Links within this page:

• Eligibility
• Committee Structure
• Nominations for the Awards
• Selection Process
• Award Elements
• Timeline
• Endowment

Eligibility for the Overton Prize:
The Overton Prize was established by the ISCB in memory of G. Christian Overton, a major contributor to the field of bioinformatics and a member of the ISCB Board of Directors who died unexpectedly in 2000. The annual prize is awarded for outstanding accomplishment to a scientist in the early to mid-career stage (up to a decade post-degree), who has already made a significant contribution to the field of computational biology.

Eligibility for the ISCB Innovator Award:
The ISCB Innovator Award is given to a leading scientist, 10-20 years post-degree, who consistently makes outstanding contributions to the field of computational biology and continues to forge new directions.

Eligibility for the ISCB Accomplishment by a Senior Scientist Award:
The Senior Scientist Accomplishment Award recognizes a member of the computational biology community who is more than two decades post-degree and has made major contributions to the field of computational biology.

Eligibility for the Outstanding Contributions to ISCB Award
The Outstanding Contributions to ISCB Award is in recognition of outstanding service contributions by any member toward the betterment of ISCB through exemplary leadership, education, service, or a combination of the three.

Nominees must be current ISCB members and application should detail the contributions to ISCB made through leadership, education, service, or a combination of the three, and provide examples of these contributions and service to the society. Nominations submitted to the system will be considered for two consecutive years (if they meet all eligibility criteria) if not selected as the awardee the year of submission.  After which, a new nomination must be submitted for consideration.

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Committee Structure:
The award selection is the responsibility of the Awards Committee, with approval from the ISCB President. (At the Chair’s discretion, a sub-committee can be charged with reviewing nominees and making a recommendation to the Awards Committee Chair regarding selection of a winner of each of the two annual awards.) The committee is composed of at least six members that are appointed by the Board of Directors of ISCB and the ISCB membership at large.  Previous award winners will be invited to propose nominees and to champion the nominees in the initial committee discussions, but will not be members of the Awards committee. Duration of terms is three years. After the three-year term membership will not be renewable as such but, every member will be re-electable by the Board of Directors.

Committee membership should be as representative of the ISCB membership as is possible and practical with respect to geographic and academic / institutional interest. All members of the Awards Committee are to be current members of ISCB.

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Nominations for the Awards:
A letter to the membership will be sent via email on behalf of either the Awards Committee Chair or ISCB President soliciting nominations for the Accomplishment by a Senior Scientist Award. This letter can be in conjunction with other Society news. Nominations should go to the Committee or Sub-Committee Chair and the ISCB Administrative Officer.

Scientific Award Nominations are requested to arrive with:

• A biosketch or curricular information that is sufficient to evaluate the candidate. In particular all graduation dates, all major career steps and the date of the last degree have to be given.
• A succinct but sufficiently detailed exposition of the major accomplishments
• List of up to ten key citations

Outstanding Contributions to ISCB Award Nominations are requested to arrive with:

• A detailed list of service to ISCB
• Area of service
• Up to 500 word motivation statement describing the members contributions

For a nominee to be given full consideration, the nomination should include as much of the requested information as possible, without being more than three pages long. The committee does not have the responsibility to add missing information.

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Selection Process:
The method of committee communication during the selection process is up to the Chair. However, unless a nominee has the overwhelming approval of all committee members, the process will likely require at least one conference call among the committee members.

Once a selection is made, the Chair must contact the ISCB President with news of the selection and a summary of the rationale behind the decision. Upon gaining approval of the selection from the President, the Committee Chair will contact the winner to share the news. Immediately upon acceptance, the Committee Chair must notify the ISCB Administrative Office to begin making arrangements regarding travel, ordering the medal, notifying the organizers of ISMB, etc.

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Award Elements:
The winner of either award will be awarded the following:

• Keynote presentation slot during ISMB Conference (ideally on first or last full day of conference)  **Scientific Awards Only**
• Travel and Hotel expenses to attend ISMB paid by ISCB
• A personalized award presented at the ISMB meeting

Conferral of the degree is contingent upon the candidate attending the next ISMB Conference and presenting his or her award lecture.

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Timeline:
In order to allow adequate time for review of nominations and notification to the winner in time to fit into his/her schedule to attend ISMB, the recommended nominations timeline is as follows:

• October of pre-conference year: Letter soliciting nominations
• December 2 of pre-conference year: Nominations cut-off
• end of pre-conference year: Selection of proposed winner and notification to ISCB President
• mid January of conference year: Notification to winner

Each of the above time references represent the latest recommended timing, and every effort should be made to work in advance of said deadlines. However, falling behind in any or all of the above activities will not necessarily prevent ISCB from presenting an Overton Prize, Innovator Award, or Accomplishment by a Senior Scientist Award for that year.

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Overton Prize Endowment:
ISCB must solicit contributions toward the endowment of the annual Overton Prize through corporate and institutional sponsorships, letters to the membership, newsletter articles, and ISCB membership renewal contribution options. Contributions at the level of $5,000.00 will be acknowledged as Principal Sponsors and all contributions at the level of $1,000.00 or more will be acknowledged as Supporting Sponsors in a brochure distributed at each year’s award of the prize. All contributions are tax deductible.

ISCB Accomplishment by a Senior Scientist Award Endowment:
ISCB must solicit contributions toward the endowment of the annual Accomplishment by a Senior Scientist Award through corporate and institutional sponsorships, letters to the membership, newsletter articles, and ISCB membership renewal contribution options. Contributions at the level of $5,000.00 will be acknowledged as Principal Sponsors and all contributions at the level of $1,000.00 or more will be acknowledged as Supporting Sponsors in a brochure distributed at each year’s award of the prize. All contributions are tax deductible.

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Webb Miller and Trey Ideker to Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology

The International Society for Computational Biology has named Webb Miller of Pennsylvania State University, USA as winner of its Accomplishment by a Senior Scientist Award for 2009, and the 2009 Overton Prize, for scientists in early- to mid-career, will go to Trey Ideker of the University of California, San Diego, USA.

Webb Miller began his career at Penn State in the late 1960’s as a computer scientist. By the time he entered the emerging field of bioinformatics in 1987 he was already a full professor there. Initially, his research revolved around developing algorithms for aligning pairs of DNA or protein sequences; he worked on the algorithms that were used in the BLAST program for searching databases for similar sequences, which is still one of the most widely used bioinformatics tools worldwide. His interests then changed to methods for aligning long DNA sequences and extracting functional information from them. Miller has made important contributions to the analysis of many vertebrate genomes including those of the mouse, chicken and rhesus macaque. He collaborated with David Haussler – his immediate predecessor as ISCB Senior Scientist Accomplishment Award winner – in the development of sequence-alignment software for the UCSC Genome Browser, which now provides access to about fifty complete genome sequences. Haussler praised Miller on being named for the 2009 award by saying, “Webb has played an essential role in nearly every vertebrate genome sequence project: he developed the first program capable of accurate comparative alignment for entire vertebrate-sized genomes.” Miller’s recent research interests include the bioinformatics of species extinction, and in November 2008 he published a paper in Nature that described a draft sequence for the woolly mammoth genome. In 2004 he was appointed to a chair in biology alongside the chair appointment he already held in computer science.

Established in 2003, ISCB’s Accomplishment by a Senior Scientist Award recognizes members of the computational biology community who have made major contributions to the field through research, education, service, or a combination of the three. Miller will be joining a prestigious group of previous winners, which includes David Sankoff (University of Ottawa, Canada), David Lipman (US National Center for Biotechnology Information, USA), Janet Thornton (European Bioinformatics Institute, UK), Mike Waterman (University of Southern California, USA), Temple Smith (Boston University, USA) and David Haussler (University of California, Santa Cruz, USA).

Trey Ideker also started his career as an engineer and computer scientist. A burgeoning interest in molecular biology led him to join a graduate program in molecular biology run by Leroy Hood, founder of the Institute of Systems Biology in Seattle, Washington. There, he began to model and analyse networks of molecular interactions using genome-scale measurements, an emerging field in which he became a pioneer. He was still a Ph.D. student when, in 2001, he published a classic paper demonstrating how biological networks are mapped and tested using a systems biology approach that has attracted well over 800 citations to date. He then took a fellowship at the prestigious Whitehead Institute for Biomedical Research in Cambridge, Massachusetts before joining the faculty at UCSD in 2003, where he is now an associate professor. In recent years, Ideker has developed a number of influential bioinformatics methods and resources including Cytoscape, a widely used open source program for visualising molecular networks. In 2003, his group was the first to demonstrate that protein networks can be aligned and compared across species, just like genome sequences. Since then, he has extended network comparison to incorporate many different interaction types, and used network-based methods to map the DNA damage response, compare host and pathogen networks, and classify diseases. He has already received many honours and was recognised as one of the top 10 innovators of 2006 by MIT’s Technology Review. Aviv Regev, the 2008 ISCB Overton Prize winner, commends the selection of Ideker for the 2009 award. "Trey's work has epitomized the power of integrating innovative computational methods with cutting-edge genomics. His pioneering work has set a model for doing systems biology that has been followed by numerous groups and has impacts for understanding the evolution of biological systems and for treating disease".

The Overton Prize was established in 2001 in memory of G. Christian Overton, a major contributor to the field of bioinformatics and member of the ISCB Board of Directors who died suddenly the previous year. The prize is awarded for outstanding accomplishment to a scientist in the early- to mid-career who has already made a significant contribution to the field of computational biology. Previous recipients are Christopher Burge (Massachusetts Institute of Technology, Boston, USA), David Baker (University of Washington, USA), W. James Kent (University of California, Santa Cruz, USA), Uri Alon (Weizmann Institute of Science, Israel), Ewan Birney (European Bioinformatics Institute, UK), Mathieu Blanchette (McGill University, Canada), Eran Segal (Weizmann Institute of Science, Israel), Aviv Regev (The Broad Institute of Harvard and MIT, USA).

ISCB Award recipients are selected from among nominations received from the computational biology community. The awards committee thoroughly reviews the merits of all nominees and unanimously decides on a recommendation of each award winner to be approved by the ISCB president. Both awards will be presented at the Society’s prestigious Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), being held jointly with the European Conference on Computational Biology (ECCB) in Stockholm, Sweden, June 29–July 2.

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