Laboratory for Computational
Biology and Bioinformatics
- December 2010
Alisa Yurovsky travelled to Hong Kong to present
a paper at the 4th Int'l Conf. on Bioinformatics & Biomedicine
- November 2010
Xiuwei Zhang travelled to New York to give a poster
and an invited oral presentation at the 7th RECOMB Conf. on
- August 23, 2010
Dr. Nicholas Pattengale, senior member of the technical staff
at Sandia National Laboratories, joins us for a week of joint
work on phylogenetic post-analysis, particularly tree
consensus and tree-to-tree distance measures.
- August 1, 2010
Prof. Jijun Tang, from the U. of South Carolina, joins us for two
weeks to work on rearrangement-based phylogenetic reconstruction.
- July 14, 2010
Prof. Tandy Warnow, from the U. of Texas, arrives today to spend
the rest of the summer working with our laboratory on research
in large-scale phylogenetic inference. Prof. Warnow is a long-time
collaborator; she was recently awarded a prestigious Guggenheim
Fellowship to spend part of 2010-2011 working with our laboratory,
so this is a first 7-week visit, to be followed by a longer one
- July 12, 2010
Congratulations to Alisa Yurovsky, who successfully defended her MS
thesis in front of an appreciative audience (great presentation)
and of external expert Prof. Steven Salzberg, director of the Center
for Bioinformatics and Computational Biology at the U. of Maryland.
- June 30, 2010
Congratulations to our "new" PhD students Slavica Dimitrieva,
Cristina Ghiurcuta, and Nishanth Nair: all three passed their
PhD Candidacy examinations over these past two days.
- June 11, 2010
Our summer student, Ms. Olga Ponomarova, has arrived. Ms. Ponomarova
comes from Ukraine and will work on the reverse engineering of
regulatory networks. We are all delighted to have her company for the
next three months.
- May 2010
Postdoctoral fellow Wei Xu has accepted an offer for a second
postdoctoral fellowship in the laboratory of Prof. Eric Xing
at Carnegie Mellon University
(the SAILING lab)
and so will be leaving our laboratory by the end of July.
At CMU, Wei will shift his research emphasis towards machine learning
and working with primary data, complementing the more theoretical work
he has done so far in his PhD and in our lab. Congratulations Wei!
- May 7, 2010
Further congratulations to Dr. Nicholas Pattengale, who just
received the QForma prize
for the best UNM dissertation in engineering and computation
in the 2009-2010 academic year!
- April 7, 2010
Congratulations to Panteleimon Zotos, who successfully defended
his MS thesis today, in the presence of his supervisor, Ms. Li Long,
and the external expert, Prof. Ioannis Xenarios. Pantelis did his
work at the Swiss Institute of Bioinformatics.
- March 29, 2010
Congratulations to Dr. Nicholas Pattengale, who successfully defended
his dissertation this afternoon at the University of New Mexico,
in the presence of committee members Jared Saia (UNM, committee chair),
Bernard Moret (EPFL, advisor), and Alexandros Stamatakis (TU Munich).
The committee unanimously awarded distinction (given to the top 5-10\%
- November 10, 2009
Congratulations to Dr. Krister Swenson, who successfully defended
his dissertation this afternoon, in the presence of jury members
Profs. Babak Falsafi (EPFL, jury president), Anastasia Ailamaki (EPFL),
Marie-France Sagot (U. Lyon and INRIA), David Sankoff (U. Ottawa),
and Bernard Moret. The jury unanimously nominated the work for the
annual EPFL Dissertation Award.
- October 2009
Cristina Ghiurcuta has joined our lab, completing our team for this
coming academic year. All of us at the lab are involved in the
Advanced Algorithms course for this fall, Nishanth and Cristina
taking the course, Bernard teaching it, and Vaibhav, Wei, Xiuwei,
Yann, and Yu working as TAs for it.
- September 2009
New faces, and missing old friends... Oana Jurj completed her summer
in our lab and returned to Timisoara, where she will start her MS
program; she leaves behind many friends and will be missed.
Krister Swenson left for Canada to start his postdoctoral studies
with David Sankoff at the University of Ottawa (and with Anne Bergeron
at the University of Montreal). We are all desolate -- Krister made
a lot of friends, had assumed quiet leadership in the lab, and had been
working with Bernard Moret since 2002 in New Mexico (learning how to
rock climb with him). We are also very proud of what Krister has
achieved and looking forward to continue working with him.
He will return for 10 days in early November for the formal defense of
his Ph.D. and suitable festivities!
Fortunately, in this time of separation, we were delighted to welcome
Nishanth Nair to our lab. Nishanth arrived on Sept. 14 and is already
a familiar figure in the lab. Cristina Ghiurcuta will arrive at the end
of the month and complete our new roster.
- July 2009
We are very happy to report that Cristina Ghiurcuta and Nishanth Nair
will join the EPFL PhD program this fall and work in our lab.
Cristina is completing her MS at the University of Timisoara
in Romania, while Nishanth finished his MS at the Indian Institute of
Science in Bangalore and is currently working for Microsoft Research.
We are looking forward to welcoming them both in the lab this fall.
- June 1, 2009
Ms. Oana Jurj joins our laboratory for a 3-month research summer;
she is finishing her degree at the University of Timisoara in
Romania and is interested in machine learning.
We are always looking
for another great Ph.D. student.
Prerequisites for an RA position are a 4-year BS degree or MS degree
in Computer Science or an MS in any of Mathematics, Biology, Physics,
and related areas, with a strong background in computing and theory.
A predilection for theory, algorithm development, programming,
simulation, and testing is a big plus.
In order to join our laboratory, you must first be admitted to the
PhD program in Computer Science, called EDIC. You can find information,
details on the application procedure, and deadlines at the
Please note that admission is very competitive; last year, we had
around 800 applicants to the program, for around 60 positions.
We also are happy to
discuss possible projects for MS students (I&C or Life
Please enquire directly with Prof. Moret.
Send email to Professor Moret (email@example.com).
This lab is a Microsoft-free zone -- all of our machines run Linux.
We are doing this for rather obvious technical as well as ethical
reasons, most of which are well documented in numerous sites
on the web.
(In particular, note that any documents sent to us in
Microsoft-proprietary formats, such as Word documents,
will be discarded without reading.)
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 (widely available online).
The pages on this site are best viewed with Mozilla (now called
Seamonkey) or any of its numerous derivatives, such as Iceape,
Camino, Epiphany, Firefox, Iceweasel, or Galeon), or Safari.
We are using two True Type fonts (Impact and Trebuchet MS), which
Microsoft's own IE (ironically, as these fonts were originally
released by Microsoft) does not render well, especially at small