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Issue No. 06 - Nov.-Dec. (2012 vol. 9)
ISSN: 1545-5963
pp: 1553-1557
My four-year term as the Editor-in-Chief of TCBB is reaching its end. I want to thank all of the authors, editors, reviewers, Steering Committee members, and IEEE Computer Society staff who together have made TCBB a top venue for high-quality research in computational biology and bioinformatics. I thank the associate editors in particular for volunteering so much of their time and energy to TCBB, and the reviewers for their time and for the dedication they have shown together with the associate editors in keeping the review process as fair and useful to the authors as possible. I also thank the authors for the confidence they have kept putting in TCBB all through these years. Foremost, I would like to thank Dan Gusfield, who served as Editor-in-Chief for five years before me, and who with his vision, set a standard for TCBB that I hope to have been able to preserve. Thanks to him also for all of the help he provided at the time of transition—I still remember fondly the afternoon in Paris when he started explaining to me what I had in store for the next few years—and for his unfailing support as Chair of the Steering Committee since. The support and work of the IEEE Computer Society staff has also been crucial all through these four years, in particular but not exclusively, of those who have accompanied me since the beginning, Alicia Stickley, Hilda Carman, Jennifer Carruth, Pilar Hawthorne, and Kathleen Henry, as well as of the administrators of TCBB who have helped so much on a day-to-day basis. It has indeed been a great pleasure and honor working with all of you.
As one of my last official tasks, I am pleased to welcome seven new associate editors to TCBB, who are experts in a wide range of topics from biological networks, computational structural biology, computational proteomics, data mining and information retrieval, genomics, microarray data analysis, systems biology, machine learning, sequence and high-throughput biological data analysis, phylogenetics, and more: Alexander Bockmayr, Bruce Randall Donald, Mehmet Koyutürk, Hagit Shatkay, Russell Schwartz, Jean-Philippe Vert, and Lusheng Wang. Bios for each of these new editors can be found below.
In parallel to this, I announce the retirement of Dannie Durand, Bertram Ludäscher, Tao Jiang and Jörg Stelling. Dannie and Tao have been on the editorial board of TCBB since the beginning in 2004, Bertram since 2007 and Jörg since 2010. They have all contributed so much to making TCBB function and thrive. I would like to express my great appreciation for their service and support. Tao was also a member of the Steering Committee of TCBB from 2009 to 2011. His support of TCBB has been unfailing and I am most grateful to him for this.
New members have joined the Steering Committee recently. I extend my warm welcome to them: Mario Figueiredo, Stefano Lonardi, and Jeffrey S. Vitter from the IEEE Computer Society, Stephen Wong and Samuel K. Sia from the IEEE Engineering in Medicine & Biology Society, Clare Bates Congdon from the IEEE Computational Intelligence Society, Aidong Zhang from the ACM, and Francis J. Doyle III from the IEEE Control Systems Society. Bios for each of these new members can be found below.
Finally, I warmly welcome the incoming Editor-in-Chief, Ying Xu. Ying shares the conviction Dan and I have that the high quality and level of rigor of the papers in TCBB are its greatest asset. I know that TCBB is in excellent hands with Ying.
Thank you all again for your support of me and of TCBB during these four years.
Marie-France Sagot
Outgoing Editor-in-Chief

Ying Xu received the PhD degree in theoretical computer science from the University of Colorado at Boulder in 1991. He is the Regents and Georgia Research Alliance Eminent Scholar Chair Professor in the Department of Biochemistry and Molecular Biology, University of Georgia (UGA), and he is also the founding director of the UGA’s Institute of Bioinformatics (2004-2011). He started his bioinformatics career in 1993 when he joined Oak Ridge National Laboratory to work on the GRAIL gene finding project. In the past 20 years, he has published more than 300 papers and four books covering multiple areas in the fields of bioinformatics and computational and systems biology. As a bioinformatician working in a biology department, he is interested in both developing computational tools and in deriving new biological insights and understanding about complex systems using integrated computational and experimental techniques. His current research interests include cancer bioinformatics and systems biology and microbial bioinformatics and systems biology. He is now applying the knowledge that he learned about microbial systems to his study on cancer.

Mário A.T. Figueiredo, EE (1986), MSc (1990), PhD (1994), and “Agregação” (2004), is a full professor at the Instituto Superior Técnico (IST), Technical University of Lisbon. He is a fellow of the IEEE, and a fellow of the IAPR. His research interests include signal processing/analysis, computer vision, pattern recognition, and machine learning. He has served as an associate editor of several journals (including the IEEE Transactions on Pattern Analysis and Machine Intelligence, Pattern Recognition Letters, and the IEEE Transactions on Image Processing), as a guest editor of several journal special issues, and as a technical committee member of many conferences.

Stefano Lonardi received the Laurea degree (cum laude) from the University of Pisa in 1994 and the PhD degree in the summer of 2001 from the Department of Computer Sciences, Purdue University, West Lafayette, Indiana. He also received the doctorate degree in electrical and information engineering from the University of Padua in 1999. During the summer of 1999, he was an intern at Celera Genomics, Department of Informatics Research, Rockville, Maryland. He is a professor and vice chair of the Department of Computer Science and Engineering at University of California, Riverside. He is also a faculty member of the Graduate Program in Genetics, Genomics, and Bioinformatics, the Center for Plant Cell Biology, the Institute for Integrative Genome Biology, and the Graduate Program in Cell, Molecular and Developmental Biology. His recent research interests include design of algorithms, computational molecular biology, data compression, and data mining. He has published more than 40 papers in major theoretical computer science and computational biology journals and more than 50 publications in refereed international conferences. In 2005, he received the CAREER award from the US National Science Foundation (NSF). He has received funding from the NSF, NIH, DARPA, and USDA.

Jeffrey Vitter received the BS degree with highest honors in mathematics in 1977 from the University of Notre Dame, the PhD degree in computer science in 1980 from Stanford University, and the MBA degree in 2002 from Duke University. He is the provost and executive vice chancellor and the Roy A. Roberts Distinguished Professor at the University of Kansas (KU). As provost, Dr. Vitter is the chief academic and operations officer for the Lawrence and Edwards campuses. Before coming to KU, Dr. Vitter held a similar post at Texas A&M University. He served as the Frederick L. Hovde Dean of the College of Science and as a professor of computer science at Purdue University. He held a distinguished professorship at Duke University, and served at Duke as chair of the Department of Computer Science. Before that, he progressed through the faculty ranks and in leadership roles at Brown University. He serves on the Board of Advisors for the School of Science and Engineering at Tulane University, as well as on the Advisory Committee of the National Science Foundation Directorate for Computer & Information Science & Engineering. He served on the Board of Directors of the Computing Research Association, where he continues to cochair the Government Affairs Committee. He has served as chair of ACM SIGACT, the Special Interest Group on Algorithms and Computation Theory, and the ACM. His research deals with the algorithmic aspects of processing, compressing, and communicating massive amounts of information. He has been elected a fellow of the Guggenheim Foundation, the American Association for the Advancement of Science, the ACM, and the IEEE. He was named a US National Science Foundation Presidential Young Investigator and is a Fulbright Scholar. He has more than 280 book, journal, conference, and patent publications.

Stephen Wong, PhD, PE, is the founding chairman of the Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute (TMHRI), Weill Cornell Medical College. He holds the John S. Dunn Distinguished Endowed Chair in Biomedical Engineering. He is a professor of radiology, neurosciences, pathology, and laboratory medicine at Cornell University, associate director of translational research at the Methodist Cancer Center, and vice chair of radiology, chief of medical physics, and chief research information officer at The Methodist Hospital. In addition, he serves as the director of the TT and WF Chao Center for BRAIN and of the NCI Center for Modeling Cancer Development at TMHRI. His career highlights include leading teams that automated the first VLSI 1MB DRAM production, developed the largest web brokerage trading system, architected the first hospital-wide image management system (PACS) in US academic medical centers, and implemented one of the largest enterprise radiology information systems in Europe. He founded two research centers while at Harvard, the HCNR Center for Bioinformatics at Harvard Medical School and the Functional and Molecular Imaging Center at Brigham and Women’s Hospital (BWH), including the first cyclotron and optical imaging facilities at BWH. He has more than 25 years of experience in industry and academia, including Hewlett-Packard, Bell Laboratories, ICOT-the Japanese Fifth Generation Computer Systems Project, Philips Medical Systems, Charles Schwab, UCSF, Harvard, and The Methodist Hospital. He has published more than 300 peer-reviewed papers, four books, and nine patents.

Samuel Sia received the BS degree in biochemistry from the University of Alberta, the PhD degree in biophysics from Harvard University, and completed a postdoctoral fellowship in chemistry at Harvard University. He is an associate professor in the Department of Biomedical Engineering at Columbia University. His lab focuses on using microfluidics for global health diagnostics and for 3D tissue biology. He was a Howard Hughes Medical Institute Predoctoral Fellow, a National Science and Engineering Council of Canada Predoctoral Fellow, and a Canadian Institute of Health Postdoctoral Fellow. Since 2005, he has been a faculty member of Columbia University’s Biomedical Engineering Department. His lab’s work has been supported by the NIH (NHLBI and NINR), US National Science Foundation, Wallace H. Coulter Foundation, American Heart Association, and World Health Organization. He has been named one of the world’s top young innovators by MIT Technology Review, and one of 10 innovators in human health and sustainability by NASA. His research has been covered by NPR, the Washington Post, CBS, NBC, BBC, CBC, Voice of America, and Agence France Presse. He is a founder of Claros Diagnostics, a venture capital-backed company that is developing novel point-of-care diagnostics products; the company’s first microfluidics product for monitoring prostate cancer growth received European Union regulatory approval in 2010.

Clare Bates Congdon received the BA degree in mathematics from Wesleyan University and the MS and PhD degrees in computer science and engineering from the University of Michigan. She is an associate professor of computer science at the University of Southern Maine. She also is an adjunct associate professor at the Mount Desert Island Biological Lab, where she does research in the summers. Her area of specialization is in machine learning and data mining, and especially evolutionary computation, with particular application to both bioinformatics and intelligent agents.

Aidong Zhang is UB Distinguished Professor and Chair in the Department of Computer Science and Engineering at State University of New York at Buffalo. Her research interests include bioinformatics, data mining, multimedia and database systems, and content-based image retrieval. She is an author of more than 200 research publications in these areas. She has chaired or served on more than 100 program committees of international conferences and workshops, and currently serves on several journal editorial boards. She has published two books Protein Interaction Networks: Computational Analysis (Cambridge University Press, 2009) and Advanced Analysis of Gene Expression Microarray Data (World Scientific Publishing Co., Inc. 2006). Dr. Zhang is a recipient of the US National Science Foundation CAREER award and State University of New York (SUNY) Chancellor’s Research Recognition award. Dr. Zhang is an IEEE Fellow.

Francis J. Doyle III received the BSE degree from Princeton University in 1985, CPGS degree from Cambridge University, in 1986, and the PhD degree from the The California Institute of Technology in 1991, all in chemical engineering. He is the associate dean of research in the College of Engineering at the University of California, Santa Barbara (UCSB), and director of the Army Institute for Collaborative Biotechnologies. He holds the Duncan and Suzanne Mellichamp Chair in Process Control in the Department of Chemical Engineering, as well as appointments in the Electrical Engineering Department and the Biomolecular Science and Engineering Program. Prior to his appointment at UCSB, he held faculty appointments at Purdue University and the University of Delaware, and visiting positions at DuPont, Weyerhaeuser, and Stuttgart University. He is the recipient of several research awards (including the US National Science Foundation National Young Investigator, ONR Young Investigator, and Humboldt Research Fellowship) as well as teaching awards (including the Purdue Potter Award, the ASEE Ray Fahien Award, and the ASEE Chemstations Lectureship Award). He is a fellow of multiple professional societies, including the IEEE, IFAC, AIMBE, and AAAS. He served as the editor-in-chief of the IEEE Transactions on Control Systems Technology from 2004-2009, and has held associate editor positions with the Journal of Process Control, the SIAM Journal on Applied Dynamical Systems, and Royal Society’s Interface. In 2005, he was awarded the Computing in Chemical Engineering Award from the American Institute of Chemical Engineers for his innovative work in systems biology. His research interests are in systems biology, network science, modeling and analysis of circadian rhythms, drug delivery for diabetes, model-based control, and control of particulate processes.

Alexander Bockmayr received the diploma degree in mathematics from the Technical University Munich in 1985, the doctoral degree from the University of Karlsruhe in 1990, and the Habilitation from Saarland University in 1996. Since 2004, he has been a full professor at Freie Universität Berlin and the DFG Research Center Matheon. He holds the Chair for Mathematics in Life Sciences. From 1998 to 2004, he was a professor at the University Henri Poincare, Nancy, France, and head of the MODBIO (Computational Models in Molecular Biology) project-team at LORIA and INRIA. His current research focuses on new approaches for mathematical and computational modeling of metabolic and regulatory networks, with special emphasis on constraint-based methods. His mathematical background lies in discrete mathematics, including constraint and integer programming, combinatorial optimization, and computational logic.

Bruce Randall Donald is a full professor of computer science at Duke University, and of biochemistry at the Duke University Medical Center, Durham, North Carolina. His main areas of interest in the field of computational biology are in structural molecular biology, proteomics, and rational drug design.

Mehmet Koyutürk received the PhD degree in computer science from Purdue University in 2006. He is the T. & D. Schroeder Associate Professor in the Department of Electrical Engineering and Computer Science at Case Western Reserve University. He also holds a secondary appointment at the Center for Proteomics and Bioinformatics at Case School of Medicine. His research mainly focuses on analysis of biological networks, systems biology of complex diseases, and computational genomics. Dr. Koyutürk has published more than 50 papers in various computational and biological journals and conferences, has served on the program committees of many conferences on bioinformatics and computational biology, and received the US NSF early career development (CAREER) Award in 2010.

Hagit Shatkay received the BSc and MSc degrees in computer science from the Hebrew University of Jerusalem in 1988 and 1991, respectively, and the PhD degree in computer science from Brown University in 1999. She is an associate professor in the Department of Computer and Information Sciences at the University of Delaware, with cross-appointments in the Department of Biomedical Engineering, and at the Delaware Biotechnology Institute. Prior to joining the University of Delaware (2010), she was an associate professor at Queen’s University in Kingston, Ontario, where she still holds an adjunct position. Before moving to academia, she was an informatics research scientist with the Informatics Research group of Celera Genomics, and a postdoctoral fellow at NCBI. Her research is in the area of machine learning, particularly as it applies to biological and medical text and data mining. She has been an active member of the bio-text research community since its early days, and has recently coauthored (with Dr. Mark Craven) the book Mining the Biomedical Literature (MIT Press, 2012). She has published extensively, especially in the areas of biomedical text mining and biomedical data analysis. She has been active as a reviewer, program committee member, steering committee, and an editorial board member for a variety of conferences and journals in bioinformatics, including – among many others - the Text Mining Area Chair at ISMB multiple times, co-organizer of the BioLINK SIG workshop at ISMB since 2005, and an associate editor and deputy section editor for BMC Bioinformatics.

Russell Schwartz is a full professor in the Department of Biological Sciences and Lane Center for Computational Biology at Carnegie Mellon University, Pittsburgh, Pennsylvania. His main areas of interest are the analysis of genetic variations with specific application to inference of population subgroups and phylogenetics, and the modeling and simulation of biological systems.

Jean-Philippe Vert graduated from the Ecole Polytechnique in 1995, the Ecole des Mines de Paris in 1998, and received the PhD degree in mathematics from Paris 6 University in 2001. He is currently a senior researcher and director of the Centre for Computational Biology at Mines ParisTech, and the deputy director of the Laboratory for Bioinformatics and Computational Systems Biology of Cancer at the Institut Curie. His research interest focuses on statistics, machine learning, and their applications to computational and systems biology.

Lusheng Wang received the PhD degree in computational biology from McMaster University and completed a postdoctoral fellowship at UC Davis. He is a full professor in the Department of Computer Science at the City University of Hong Kong. His interests cover a wide range of areas, from sequences (motifs, duplication, and history inference), phylogeny, gene expression analysis, and haplotype studies.

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