Picture: 2006 Overton Prize Winner, Dr. Mathieu Blanchette

2006 Overton Prize Winner - Mathieu Blanchette

The International Society for Computational Biology (ISCB) awards the 2006 Overton Prize to Mathieu Blanchette, assistant professor in the School of Computer Science at McGill University in Montréal. The prize is awarded at the ISCB annual meeting, Intelligent Systems for Molecular Biology, held in Fortaleza, Brazil, on August 8, 2006 when Blanchette delivers the annual Overton keynote lecture entitled "What mammalian genomes tell us about our ancestors, and vice versa."

"Mathieu Blanchette is responsible for fundamental, highly cited contributions in several areas of bioinformatics," says Professor Thomas Lengauer of the Max-Planck-Institut für Informatik, who is chair of the ISCB Awards Committee.

"His doctoral thesis contained perhaps the first reasonable algorithm for gene-order phylogeny, based on a solution to the breakpoint median problem, and it also elaborated the now-famous concept of phylogenetic footprinting. As a postdoctoral researcher, he played a central role in working out algorithms for reconstructing ancestral mammalian genomes. His most recent work continues his interest in the inference of evolutionary scenarios and gene regulation. And he has been active in the bioinformatics community since his student days, presenting papers at the Computing and Combinatorics conferences and the Research in Computational Molecular Biology meetings, among others. He is currently organizing several workshops and conferences, has attracted many students to his new lab, and has been highly successful in obtaining funding in a competitive environment."

From 1994 through 1997, Blanchette was an undergraduate in the Mathematics and Computer Science departments of the Université de Montréal. After graduating, he did an M.Sc. there as well, writing a thesis on breakpoint phylogeny under the direction of David Sankoff. He then went to the University of Washington, obtaining a Ph.D. in Computer Science (2002) under the supervision of Martin Tompa. He spent the next year as a postdoctoral researcher at the Center for Biomolecular Science and Engineering of the University of California at Santa Cruz, where he worked with David Haussler. He took up his current position at McGill in 2003.

Blanchette says, "Chris Overton was one of the first explorers of the world of bioinformatics, before the name even existed, and he opened the area to young people like me. I am immensely grateful for the work he did and greatly honored to receive this award, created in his memory after his untimely death in 2000." The award is given annually to a scientist in the early to middle stage of his or her career who has contributed significantly to computational biology through research, education, service, or a combination of the three.

For an abstract of Blanchette's keynote address, please see
ismb2006.cbi.cnptia.embrapa.br/keynotes.html#blanchette.

>> Return to List of Overton Prize Recipients

Picture: 2005 Overton Prize Winner, Ewan Birney

2005 Overton Prize Winner - Ewan Birney

Dr. Ewan Birney of the EMBL European Bioinformatics Institute (EBI), was awarded the 2005 Overton Prize in honor of his advocacy of open source bioinformatics, and his generous contributions to the BioPerl community. Perhaps even more important to biology is his leadership of the Ensembl genome annotation project, providing rapid and accurate computational annotations for eukaryotic genomes.

"Dr. Birney follows his own advice, and credits the success of the Ensembl project to the open source development model," said Dr. Lawrence Hunter of the University of Colorado Health Sciences Center, the ISCB's founder and former chair of the ISCB Awards Committee. Hunter added, "Dr. Birney is not only a hugely productive scientist, but he started young: his first bioinformatics tools, Pairwise and Searchwise, were published when he was an undergraduate at Oxford, and their successor, GeneWise, is still in broad use more than a decade after its introduction."

The prize was awarded at the ISCB's annual meeting, Intelligent Systems for Molecular Biology (ISMB), in Detroit, Michigan, on June 29, where Dr. Birney then delivered the annual Overton keynote lecture on the final day of the conference.

For additional information on Dr. Birney’s many contributions to bioinformatics, please read the ISCB newsletter article at www.iscb.org/images/stories/newsletter/newsletter8-2/birney.html.

>> Return to List of Overton Prize Recipients

Picture: 2002 Overton Prize Winner, David Baker (photo credit: University of Washington/Mary Levin

2002 Overton Prize Winner - David Baker

The winner of this year’s Overton Prize, David Baker, associate professor at the University of Washington and Howard Hughes Medical Institute Investigator, delivered the Overton Lecture on the last day of ISMB2002. In the keynote talk, titled "Predication and design of protein structures and protein-protein interactions," Baker thanked the ISCB, "for this great honor." He then reviewed his research as well as explaining the contributions of his colleagues. Baker said, "It’s an exciting time because we can create new molecules that do all kinds of interesting things."

Larry Hunter, the founder of the ISCB and current Board member, introduced Baker. "David’s contributions to the field are many and excellent," he said. Hunter mentioned the CASP4 competition and said, "Thanks on behalf of the bioinformatics community for unraveling one of our most interesting problems."

The ISCB Awards Committee unanimously selected Baker to receive the Overton Prize for his work in applying computational science to drug design, genetics, and health care, and, in particular, the Rosetta algorithm, which predicts protein structure.

>> Return to List of Overton Prize Recipients

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.

------------

For more information, please contact:

This email address is being protected from spambots. You need JavaScript enabled to view it.
Executive Officer, ISCB
+1 858 822 0852

Note to Editors

The International Society for Computational Biology (ISCB) serves over 2500 members from nearly 70 countries around the world by addressing scientific policies, providing access to high quality publications, organizing regional and international conferences, and serving as a portal to information about training, education, employment and news from related fields.

TOP

ISCB Nominations Form

The ISCB Fellows nomination form will open soon.   Please check back within the next month if you wish to make a nomination.

Accomplishment by a Senior Scientist Award

The Accomplishment by a Senior Scientist Award recognizes a member of the computational biology community who is more than two decades post-degree (or equivalent professional experience) and has made major contributions to the field of computational biology.

2025 ISCB Accomplishments by a Senior Scientist Award: Amos Bairoch

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).

2025 ISCB Overton Prize: James Zou

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.

top
....................................................................................................................................................................
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.

top
....................................................................................................................................................................
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.

top
....................................................................................................................................................................
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.

top
....................................................................................................................................................................
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.

top
....................................................................................................................................................................
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.

top
....................................................................................................................................................................
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.

TOP

2016 Overton Prize Winner: Debora Marks

2016 ISCB Overton Prize: Debora Marks

The International Society for Computational Biology (ISCB) recognizes the achievements of an early- to mid-career scientist with the Overton Prize each year. The Overton Prize was established to honor the untimely loss of Dr. G. Christian Overton, a respected computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators in the early to middle phases of their careers who are selected because of their significant contributions to computational biology through research, teaching, and service.

ISCB is pleased to recognize Debora Marks, Assistant Professor of Systems Biology and director of the new the Raymond and Beverly Sackler Laboratory for Computational Biology at Harvard Medical School. She will accept this honor and present a keynote talk at ISMB 2016 in Orlando, Florida, on Sunday, July 10th.As a child and young adult, Marks never considered becoming any sort of scientist. She was fairly confident that she was either going to travel in time around the universe in the tardis with Dr. Who or be a professional political protester and save the world. However, math was a constant that captured Marks’s attention since she was a little girl and she recalls spending far too much time with math puzzle books, “math was one of the only activities that forced me to focus and calmed my brain”.

After school, Marks went to study medicine at the University of Bristol (in England) but left - now with some regret - after her 2nd MBChB degree as she was “more interested in theatre and politics than Latin names for bones”. Many years later, after babies and a variety of interesting jobs, Marks felt the pull back to academia and her first love, mathematics, and went on to complete an honors degree in mathematics at Manchester University. She recalled the focused scope of her mathematics studies during a time when students were not allowed to attend other courses, and interdisciplinary studies were not yet en vogue. “In England, when you did a math degree, it was a math degree and you were not supposed to dilute it with ‘lower value’ subjects like biology, computer science or even physics. I did however manage to attend an odd course on chaos and fractals that sparked my interest in the intersection of math and biology that continues to drive me today.”

Marks considers her introduction to computational biology somewhat unorthodox and recalled, “I came to computational biology by jumping in the deep end. After my math degree I won an award from the Wellcome Trust to research drug design for Leishmaniaand trypanosomiasis. I was given a Silicon Graphics machine and told to get to work. I hadn’t got a clue. I’d never used a computer. Because I had a math degree, they thought I was a computer scientist of sorts.”

In the wake of the Human Genome project, Marks went on to get a bioinformatics position at Harvard at a time when interest in the potential for computation in biological research intensified. MicroRNAs first captured her attention in mid-2000, and her work on these was eventually submitted as a PhD thesis at the Humboldt University in Berlin under the guidance of Reinhard Heinrich and, after Heinrich’s untimely passing, completed with Hanspeter Herzl as thesis mentor.

She recalled, “I accidently read an article in a biology journal lying around about what was then a semi-obscure discovery about small RNAs regulating development in worms. I couldn’t stop thinking about it. Do these little RNAs stick to more than one gene? Maybe humans have them?” MicroRNAs were obscure at the time, only two were known, not the category. The floodgates only opened after the discovery of tens (at the time) of the now named “microRNAs”, nearly identical in sequence across worms, flies and humans, published in three back-to-back papers in October 2001 and suggesting strong selection across many species. “So, what are they doing in all these organisms?” As more identified more and more of these microRNAs, it became obvious to Marks that a way needed a way to find out what processes they regulated. Unlike the much more complicated task of identifying targets of proteins, the chemistry of base-pairing suggested an obvious way to explore what microRNAs might stick to.”

Marks was the first, concurrently with the Cohen and Bartel labs, to publish genome-wide targeting by microRNAs, first in fly, then in human, having developed the miRanda algorithm that is still used today for target prediction. “Although many groups have now published papers on how to discover microRNA targets,” Marks said “At best, the science of microRNA target prediction is still imprecise, presenting an unmet challenge for the computational community”. These early papers highlighted the potential genomic scope of microRNA targeting across large pools of mRNAs and their many-to-many, cooperative and combinatorial regulation of protein expression, something we now take for granted. Struck by these indications of potential system-wide effects, Marks undertook work to investigate the function of small RNAs in the context of the cellular environment by using mathematical modeling, re-analysis of previously published experiments, and additional in vitro experiments.

She made several key findings that included demonstrating that mRNA half-life influences the effects of microRNA and siRNA targeting for thousands of gene targets and that mRNA and microRNA abundance impacts microRNA targeting (now thought of as the mRNA sponge effect, and, controversially, “ceRNAs”). She also showed that introducing siRNAs or microRNAs into cells results in attenuation of endogenously regulated genes. Marks explained, “This is a really important consideration for the interpretation of gene knock-down experiments and for therapeutic uses of small RNAs”. Her more recent work showed that for a given level of protein, adding microRNA regulation can reduce protein noise or fluctuations, especially for transcripts with low expression.

Quite by chance, Marks’s postdoctoral work shifted sharply away from microRNAs to the field of ab initio3D structure prediction of proteins. Together with Chris Sander, they revisited an older idea that had been advanced independently by the groups of Sander, Neher and Taylor in the mid-1990s of using covariation of residues in proteins across evolution to identify residues that might be in contact in 3D. They reasoned that if these inferred contacts were accurate enough, one should be able to fold a protein sequence using simple methods such as distance geometry and restrained molecular dynamics. The key advances were to use a statistically global model of covariation across the sequences that removes transitive correlations in the data, by using a probability model for entire proteins in the sequence family, not unlike a suggestion made by Gary Stormo and Alan Lapedes in 1999. She said, “We stumbled across statistical physics models that are used to determine inhomogeneous interactions in Ising models from observed data that contain transitive correlations. Listening to the team of Riccardo Zecchina, including Andrea Pagnani and Martin Weigt, in Torino, Italy made us think that their approaches to the analysis of correlated mutations could be important for the 3D structure-from-sequence problem. Working with their team in collaboration, I set off in the spring of 2010 to see if the maximum entropy method could work to find truly interacting co-evolved residues. If the computation was correct then co-evolved residue pairs should match contacts in known 3D structures, and they did nearly to the ceiling. I then cajoled a friend, Lucy Colwell who, like me, was also recent graduate, to join the project. What fun we had! Well, that is until it was time to try and publish it. Reviewers found it difficult to believe, but eventually we published the results at the end of 2011, and the EVfold community has grown ever since. Marks explained,

“The method is very democratic. It is fast and can be run on a laptop, even the folding, and relies only on gene sequences. Immediate applications were to proteins that are challenging experimentally such as large membrane proteins and to protein-protein complexes. More than five of the transmembrane proteins have since been crystallized and agree well with the predicted structures, such as the adiponectin receptor”. “A very effective mini-CASP,” she added with a smile.

After the protein folding breakthrough in the fall of 2010, implementation of similar methodology led her to the solution, published in 2016, of another hard and unsolved problem in computational biology, that of computing RNA 3D structures and of RNA-protein complexes just from sequence information.

Currently, Marks has a newly formed lab at Harvard Medical School and is building the Raymond and Beverly Sackler Laboratory for Computational Biology. She is continuing the “3D from sequence” work, including new types of biomolecular interactions and their conformational flexibility. The Marks lab is also going back to math and developing the core algorithms for sequences, and model inference for multidimensional biological data. At the same time, Marks is branching out with new applications that include the challenge of predicting the effects of genetic variation on disease risk and drug response, especially combinations of events, and particularly in antibiotic resistance “It may seem we are promiscuous in our choice of biological questions, but the underlying thread is one of solving problems that are hard to solve experimentally. One far-reaching question that I am increasingly less embarrassed to admit being interested in is: What makes us all different? With genomes in hand, surely we can now find out how much is nature, how much is nurture and how much is stochastic?”

Marks is grateful to her mentors and her “wonderful” Systems Biology department who have supported her throughout her unusual career path and feels greatly honored to be recognized with the Overton Prize. She is especially thankful to her new group members and her long-time scientific collaborator Chris Sander. She said, “I want to share the prize in spirit with all those who have tolerated and encouraged me despite the odds.”

Marks’s final message to young scientists (young in spirit, that is) is to “go big, go risky, and learn statistics (!)”

>> Return to List of Overton Prize Recipients

2016 ISCB Innovator Award Serafim Batzoglou

2016 ISCB Innovator Award: Serafim Batzoglou

2016 marks the awarding of the inaugural ISCB Innovator Award, which honors an ISCB scientist who is within two decades of receiving a graduate degree, and has consistently made outstanding contributions to the field and continues to forge new directions. The inaugural winner is Dr. Serafim Batzoglou, Professor in the Department of Computer Science at Stanford University. Batzoglou will receive his award and deliver a keynote address at ISMB 2016 in Orlando, Florida on July 12th, 2016 to mark this honor.

Batzoglou remembers having an early fascination with numbers and a sense of wonder about the universe around him as a young child. He recalled,“I was interested in math and science for as long as I can remember. Before going to preschool, I remember counting and adding large numbers, as well as wondering how big space is and where it ends.” Batzoglou’s curiosity was stoked by other cultural touchstones, including the novels of Jules Verne and Carl Sagan’s captivating Cosmos television series. These early experiences nurtured his interests in math, physics and computer science, and Batzoglou went on to earn two bachelor of science degrees in mathematics and computer science at the Massachusetts Institute of Technology (MIT). Batzoglou also encountered computational biology for the first time as an undergraduate. He said, “Upon entering college, I was deciding between two fields of study that had fascinated me during high school: astrophysics and artificial intelligence (AI). However, during the early nineties I felt that neither physics nor artificial intelligence was experiencing any exciting growth. At least that was my impression around 1995, when I had been admitted to a PhD program in computer science at MIT and was deciding on an area to focus on. I took Bonnie Berger and David Gifford’s class on computa-tional biology and felt that this was a research area with great potential where I could apply my computer science background to do science (rather than engineering).” Batzoglou credits his early mentors for giving him invaluable undergraduate research experiences, including Sorin Istrail, with whom he had a very enjoyable research summer during 1997, and his undergraduate research supervisor, David McAllester.

Batzoglou went on to earn his PhD in computer science at MIT under the mentorship of his advisor Bonnie Berger and co-mentor Eric Lander. During his early career, he was the lead algorithms designer and implementer of ARACHNE, one of the first programs for whole genome shotgun sequence assembly that was used for assembling several genomes including the mouse and dog genomes. Batzoglou’s early work included using comparative genomics for human gene identification. Together with his collaborators he developed multiple genome alignment tools, including LAGAN, and applied these tools to predict human genes from similar mouse genes. This work was significant to the emergence of the field of comparative genomics and its applications for identifying genes, regulatory regions, and evolutionary events, as well as other features across species.

Batzoglou and his lab focus currently on the development of algorithms, machine learning methods and systems for the analysis of genomic data. He recalls one of his more surprising research moments that stands out in his memory. “It was unexpectedly good news to me back in 2005 that Conditional Random Fields (CRFs) and similar flexible models that can learn very large parameter sets, could be so successful in a large variety of classic computational genomics problems including RNA secondary structure prediction, gene finding, and sequence alignment. My line of work on CRFs, together with my PhD students at the time, Chuong Do and Sam Gross, who led the effort, was when we began applying machine learning in earnest to genomics problems.”

Batzoglou aims to follow the example of his PhD mentor as he mentors students and post-docs in his lab. “I think I follow a similar style and philosophy as my PhD advisor, Bonnie Berger, in that I am supervising my students in a relatively hands-off, “first do no harm” manner, and to the extent possible allow them to define new research topics and directions.” He also looks forward to a time when more novel research can be supported through the grant system, and said, “The most talented and motivated students will do their best research when given freedom, encouragement and some resources. I would be supportive of a large fraction, say 25%, of the government funds to be earmarked for work on new directions – i.e., work on which the proposing PIs have no other funds and no related papers.”

Batzoglou’s novel research contributions have been recognized through several awards including being named among the Top 100 Young Technology Innovators in 2003 by MIT’s Technology Review Magazine and a 2004 NSF CAREER Award. His research publications alone also show his impact on the field, and his purely bioinformatics-based publications have been cited hundreds of times. Batzoglou has also served the computational biology community in numerous capacities, especially through his service as a member of the steering committee, program chair, session chair, and organizing committee member for various RECOMB and ISMB meetings.

Looking forward, he said, “The topic I am most fascinated by right now, although it hasn’t majorly influenced my research yet, is deep learning. Like many of my AI colleagues, I subscribe to the opinion that we are witnessing a major breakthrough in our ability to replicate (and improve on) a large fraction of the intellectual and perceptual capacity of humans. The victory of AlphaGo against Lee Sedol is a historic moment. From a personal perspective, I learned Go in 2003, and back then I considered it a midpoint in AI between where we were and full-blown human-level intellectual capacity (excluding emotions and human experiences, which AI hasn’t been focusing on as much). The significance of advances in AI cannot be overstated. I believe that AI will transform medicine, finance, construction, manufacturing, commuting and transport, and almost every other sector in society, over the next 20 years. I also believe that a large fraction of jobs in these fields will be made redundant. Re-education is great, but it is not clear at all what the new marketable human skills will be 20 years down the line. Perhaps anything involving human interaction, although that’s not clear. In terms of computational genomics and biomedicine, to the extent that we will be able to collect and agglomerate large genomic and biomedical datasets, application of AI will lead to breakthroughs that will start by vastly improving health care, agriculture and biotechnology, and continue to places that are hard to imagine today.”Batzoglou feels greatly honored to be selected as the inaugural winner of the ISCB Innovator Award, and said, “Innovation in computational biology – and in general – is largely a community process. I thank the committee for recognizing my work, and more importantly I thank my colleagues, mentors and foremost my students, with whom I should be sharing this Award.”

>> Return to Awards page