Laboratory for
  High-Performance Algorithm Engineering
  and Computational Molecular Biology

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Bernard M.E. Moret and David A. Bader

Departments of Computer Science and of Electrical and Computer Engineering

Founding Members of the CIPRES Project

Research Objective:

The design, development, implementation, and testing of high-performance computational solutions for complex discrete optimization problems in computational biology, especially those arising in the reconstruction of phylogenies from molecular data.

Ancillary goals include (i) the development of a methodology for the assessment of serial and parallel algorithms, (ii) the migration to shared-memory architectures of PRAM parallel algorithms, (iii) the refinement of models of genome evolution, and (iv) the study of the combinatorial problems arising from these models.


  • January 31, 2006  The lab will close at the end of this year, with the departure of founder and director Bernard Moret, who has accepted the chair of bioinformatics at the Swiss Federal Institute of Technology (EPFL) in Lausanne, starting this summer. It has been a great adventure with outstanding students and postdocs. Both David Bader at Georgia Tech and now Bernard Moret at EPFL will work on recreating the atmosphere and the success of this laboratory. Our sincere thanks go to the US National Science Foundation for its steady support of our work throughout the last 6 years.
  • August 1, 2005  Lab co-founder and co-director David Bader has left for a new position at the Georgia Institute of Technology in Atlanta, where he will, among many other things, work to develop a new emphasis in high-performance computational science. Our best wishes go with him -- he will be sorely missed!
  • May 6, 2005  Krister Swenson received the 2005 Outstanding Graduate Student award from the Department of Computer Science.
  • March 31, 2005  Lab member Nicholas Pattengale successfully defended his MS thesis today, in the presence of committee members David Bader and Tanya Berger-Wolf (U. Illinois-Chicago). He will continue in his job at Sandia National Laboratories.
  • March 8-10, 2005  The National Science Foundation, which funds our work, featured our activities poster for CIPRES at its ITR Committee of Visitors meeting.
  • February 18, 2005  Past lab member Mi Yan accepted a position with Linux Networx to perform research and development on their HPC systems, with a focus on computational biology applications.
  • November 4, 2004  Zak Betz successfully defended his MS thesis today, in the presence of committee members Bernard Moret, David Bader and Lance Williams; he will graduate this Christmas with his MS in CS.
  • October 29, 2004  Guojing Cong successfully defended his PhD dissertation today; his committee (David Bader, chair, with Bernard Moret, Arthur Maccabe, and Wennie Shu, all from UNM) unanimously awarded him distinction.
  • October 2004  Joel Earnest-DeYoung has been hired in his country of choice (Denmark); he will start work there for Foss Analytical A/S in a few weeks.
  • July 28, 2004  Tao Liu successfully defended his MS thesis today; he will receive his MS/CS at the end of August and will start work at Access Innovations Inc. (in Albuquerque) next month.
  • July 15, 2004  We welcome a new member in our lab: Lijuan Zhao joins us mid-summer. She will work on her Ph.D. with Bernard Moret, focusing on gene-order problems.
  • May 24, 2004  Joel Earnest-DeYoung successfully defended his MS thesis, entitled "Reversing gene erosion" -- and was granted distinction by his thesis committee, consisting of Bernard Moret and David Bader from UNM and Nancy Moran from U. Arizona; he will receive his MS degree in Computer Science this August.
  • May 7, 2004  Jijun Tang received the 2004 Outstanding Graduate Student award from the Department of Computer Science.
  • May 1, 2004  We are delighted to report that
  • April 5, 2004  Jijun Tang successfully defended his Ph.D. dissertation. Committee member Tandy Warnow (UT Austin and Harvard) joined us for the occasion, while committee member Robert Jansen (UT Austin) participated through a conference call and committee member Pavel Pevzner (UC San Diego) sent in his comments. The committe unanimously voted to award distinction to Jijun Tang for his work.
  • March 2004  We are very pleased to report that Tanya Berger-Wolf has accepted a one-year fellowship to work at DIMACS on topics in population genetics, while Tiffani Williams received and accepted a one-year fellowship at the Radcliffe Institute for Advanced Study to work on large-scale phylogenetic reconstruction and sequence alignment.
  • January 27, 2004  Mi Yan successfully defendend her Ph.D dissertation on fast and parallel implementations of algorithms in computational biology.
  • December 17, 2003  Monique Morin successfully defended her Ph.D. proposal; she will do her research on models, measures, and algorithms for phylogenetic network reconstruction.
  • November 10, 2003  Sukanya Sreshta successfully defended her MS thesis on parallel algorithms for shared-memory machines; she is graduating with an MS in Computer Engineering this Fall and leaving the lab for industry.
  • October 8, 2003  Our lab hosted a visit and talk by Richard Stallman (founder of the Free Software Foundation).
  • October, 2003  Past lab member Zhan Li started her new job as research programmer in bioinformatics at Penn. State U.
  • September 17, 2003  We received a major new grant from the National Science Foundation, in the Information Technology Research (ITR) program, large category. This is a 5-year, $11.6M, collaborative award to support the CIPRES project, with four other leading institutions (Florida State U., U. California at Berkeley, U. California at San Diego, and U. Texas at Austin) and a total of 13 participating institutions, which will support the construction of the computational infrastructure (algorithms, software, databases, and platforms) needed to attempt a reconstruction of the Tree of Life. Grant EF 03-31654 ITR: Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics
  • August, 2003  Sinan Al-Saffar is leaving our lab; he is continuing his PhD degree in Computer Science.
  • July, 2003  We received a new grant from IBM Corp., extending for three years, to collaborate with them on the development of the PERCS architecture, under a DARPA contract in their HPCS program.
  • July, 2003  Lab member Anna Tholse successfully defended her MS thesis, entitled "Phylogenetic Networks." Anna will leave us at the end of the summer, to start her new job at Microsoft in Redmond, WA.
  • July, 2003  David A. Bader is elected Chair of the IEEE Computer Society Technical Committee on Parallel Processing (TCPP), for a term from 2003 to 2005.
  • May, 2003  Zhan Li is leaving us after completing her MSCS degree; she is off to Penn. State U., where her husband will do his postdoc in biochemistry.
  • March, 2003  Emeline Picard, a fifth-year computer science undergraduate student from France, has joined our group for a six-month stay to perform research in high-performance computing.
  • January, 2003  Two new CS Ph.D. students are joining our group: Monique Morin (MS in CS), who spent the last year doing research at Los Alamos Lab with our collaborator Madhav Marathe; and Sinan Al-Saffar. Monique will focus on optimization algorithms in computational biology, while Sinan will focus on high-performance computing.
  • January, 2003  David A. Bader is selected as an IEEE Distinguished Speaker in its Distinguished Visitors Program (DVP). This prestigious program is a popular offering of first quality speakers serving IEEE Computer Society professional and student chapters, and speakers are recognized authorities in their respective fields. (2003-2005)
  • December, 2002  Lab member Zhan Li successfully defended her MS thesis, entitled "Implementing PRAM algorithms on shared-memory architectures."
  • December, 2002  Lab member Jingyi Dong is leaving us after completing his MSEE degree.
  • November, 2002  Lab member Guojing Cong successfully defended his Ph.D. proposal.
  • September, 2002  Lab member Jijun Tang successfully defended his Ph.D. proposal.
  • September 2002  The Division of Experimental and Integrative Activies (EIA) of the NSF, which funds our research, showcased our work on GRAPPA in its Research Highlights.
  • August 19, 2002  Two new graduate students are joining our group: Joel Earnest-DeYoung (MS in Biology) and Krister Swenson (BS in Math). Lab member Min Zhu is leaving us after completing her MSEE degree.
  • August 1, 2002  We received a new NSF grant, to support Dr. Berger-Wolf for her two years as an NSF Postdoctoral Associate.
  • July 31, 2002  New and much improved release of GRAPPA, our software suite for phylogeny reconstruction from gene-order data.
  • July 20, 2002  Lab member Bei Wang successfully defended her MSEE thesis and will start on her PhD at the University of Southern California.
  • July 1, 2002  A new researcher is joining our team: Dr. Tanya Berger-Wolf, who earned her Ph.D. in Computer Science from the University of Illinois at Urbana-Champaign.
  • July 1, 2002  Two new graduate students are joining our group: Zak Betz (BS in Computer Science, UNM, 2001) and Mark Marron (BS in Mathematics, UC Berkeley, 2002).
  • June 20, 2002  We have received a new grant from IBM Corp. as part of a large project under contract to DARPA to develop the next-generation computer for the Department of Defense. Our role in this project is to help IBM personnel ensure that this new architecture will support large-scale computations in computational biology.
  • June 1, 2002  Three new undergraduates are joining our laboratory and one is continuing in her second year with us, all with REU support from the National Science Foundation:
    • Diana Aranda is a sophomore in the Department of Biology.
    • Letisha Kaskaske is a junior in the Anderson School of Management.
    • Angeline Madrid-Ritchey is a second-degree student in the Department of Computer Science.
    • Laura Waymire returns for her second year with us, pursuing a dual major in Computer Science and Biochemistry.
  • May 1, 2002  Postdoctoral researcher Dr. Tiffani Williams was awarded a prestigious Sloan Foundation Postdoctoral Fellowship in Computational Molecular Biology -- see the UNM Press Release.


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This lab is a Microsoft-free zone -- all of our machines run Linux (on the Dell boxes) or Solaris (on the Sun boxes and the large Sun SMP) and none is dual-booted. If you are curious why, KMFMS has made an excellent list of the technical, sociological, moral, and other reasons why Microsoft (the original "evil empire") is the worst thing that ever happened to computing. For a humorous and fast-reading account of OS development, as well as another take on the Microsoft empire and its competition, you should definitely read "In The Beginning There Was The Command Line", by Neal Stephenson, the author of "Cryptonomicon".

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