- paper accepted: J. Hauser, F. Izquierdo-Carrasco, K. Meusemann, B. Misof, M. Gertz, A. Stamatakis:
"Heuristic Algorithms for the Protein Model Assignment Problem", ISBRA 2013, Charlotte, USA, May 2013.
- paper accepted: J. Fuller, P. Khoueiry, H. Dinkel, K. Forslund, A. Stamatakis,
J. Barry, A. Budd, T. Soldatos, K. Linssen, A. Rajput, and HUB
participants: "Biggest Challenges in Bioinformatics", accepted for
publication in EMBO reports, 2013.
- paper accepted: F. Izquierdo-Carrasco, N. Alachiotis, S. Berger, T. Flouri, S.P. Pissis, A. Stamatakis:
"A generic Vectorization Scheme and a GPU kernel for the Phylogenetic
Likelihood Library", accepted for publication at IPDPS 2013, Boston,
- paper accepted: D. Darriba, A.J. Aberer, T. Flouri, T.A. Heath, F. Izquierdo-Carrasco, A. Stamatakis:
"Boosting the performance of Bayesian divergence time estimation with
the Phylogenetic Likelihood Library", accepted for publication at IPDPS 2013, Boston, USA, 2013.
- paper accepted: A. Stamatakis, A. J. Aberer:
"Novel Parallelization Schemes for Large-Scale Likelihood-based
Phylogenetic Inference", accepted for publication at IPDPS 2013,
Boston, USA, 2013.
course evaluation by the students for the course: "Introduction to
Bioinformatics for Computer Scientists" which Alexis, Solon, Tomas,
Kassian, Andre, and Pavlos teach at the CS department of KIT was very
positive. We received a teaching quality index (Lehrqualitätsindex) of
100 out of 100.
- Simon Berger succesfully defended his PhD thesis on January
14 at the CS department of KIT. Prof. C. v. Mering, Prof. W. Karl,
Prof. H Meyerhenke and Alexis were on his committe which was kindly
headed by Prof. Beckert.
- paper accepted: N. Alachiotis, S. Berger, T. Flouri, S.P. Pissis, A. Stamatakis: "libgapmis: extending short-read alignments". Accepted for publiocation in BMC Bioinformatics, 2013.
- paper accepted: A. Stamatakis, A.J. Aberer: "Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference", IPDPS 2013.
- Nikos Alachiotis successfully defended his PhD thesis on
November 21 at the CS department of TU Munich. Prof. A. Bode, Prof. A.
Dollas, and Alexis were on the committee which was kindly headed by
Prof. B. Rost.
- paper accepted: N. Alachiotis, S. Berger, A. Stamatakis: "A Versatile UDP/IP based PC-FPGA Communication Platform", acccepted for publication at ReConFig 2012.
- Jörg Hauser
submitted his Master's thesis that deals with the protein model
assignment problem for multi-gene alignments of amino acid data.
- paper accepted: M. Christou, M. Crochemore, T. Flouri, C.S. Iliopoulos, J. Janousek, B. Melichar, S.P. Pissis: "Computing all subtree repeats in ordered trees", accepted for publication in Information Processing Letters, 2012.
- paper accepted: T. Flouri, K. Kobert, S.P. Pissis, A.
Stamatakis: "A simple method for computing all subtree repeats in
unordered trees in linear time", Festschrift for Borivoj
Melichar, Czech Technical University in Prague, 145-152, 2012.
- paper accepted: T. Flouri, C.S. Iliopoulos, T. Kociumaka, S.P. Pissis,
S.J. Puglisi, W. F. Smyth, W. Tyczynski: "New and efficient approaches
to the quasiperiodic characterisation of a string", In Proceedings of
the Prague Stringology Conference (PSC2012), pp.75-88, 2012.
- news item about Alexis appointment at KIT
- paper accepted: N. Alachiotis, S. Berger, T. Flouri, S. Pissis, A. Stamatakis:
"libgapmis: an ultrafast library for short-read single-gap alignment",
accepted for publication at Next Generation Sequencing workshop in
conjunction with IEEE BIBM 2012.
- paper published: N. Alachiotis, S. Berger, A. Stamatakis: "Coupling SIMD and SIMT Architectures to Boost Performance of a Phylogeny-aware Alignment Kernel" BMC Bioinformatics, OPEN ACCESS.
was appointed as full professor at the department of computer science
(in conjunction with his job at HITS) of the Karlsruhe Institute of
- paper accepted: A.J. Aberer, D. Krompass, A. Stamatakis: "Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice", Systematic Biology, in press.
- paper accepted: N. Alachiotis, A. Stamatakis, P. Pavlidis: ``OmegaPlus: A Scalable Tool for Rapid Detection of Selective Sweeps in Whole-Genome Datasets'', accepted for publication in Bioinformatics.
- paper accepted: N. Alachiotis, P. Pavlidis, A. Stamatakis:
``Exploiting Multi-grain Parallelism for efficient Selective Sweep
Detection'', accepted for publication at 12th International Conference
on Algorithms and Architectures for
Parallel Programming (ICA3PP-2012), Fukuoka, Japan, September 2012, to
appear in Springer LNCS.
- paper accepted: T. Flouri, C.S. Iliopoulos, K. Park, S.P. Pissis: "GapMis-OMP: pairwise short-read alignment on multi-core architectures."
In Proceedings of the 8th Artificial Intelligence Applications and
Innovations Conference (AIAI 2012), IFIP Advances in Information and
Communication Technology, 2012. Springer LNCS.
- paper accepted: C. Barton, C.S. Iliopoulos, L. Mouchard, S.P. Pissis, Thierry Lecroq, Mathieu Giraud: "Querying Highly Similar Sequences", accepted for publication at ICIBM'12.
- paper published: A. Stamatakis, A.J. Aberer, C. Goll, S.A. Smith, S.A. Berger, F. Izquierdo-Carrasco:
"RAxML-Light: A Tool for computing TeraByte Phylogenies", Bioinformatics 2012; doi: 10.1093/bioinformatics/bts309. On-Line Access PDF SUPPLEMENT
- paper published: P. Pavlidis, J.D. Jensen, W. Stephan, A. Stamatakis: "A
Critical Assessment of Story-Telling: Gene Ontology categories and
the importance of validating genomic scans", in press, Molecular Biology and Evolution, 2012. ADVANCE ON-LINE ACCESS
- paper accepted: T. Flouri, K. Frousios, C.S. Iliopoulos, K. Park, S.P. Pissis, G. Tischler: "GapMis: a tool for pairwise sequence
alignment with a single gap". Recent Patents on DNA and Gene Sequence
Journal: Pattern Finding in Computational Molecular Biology, 2012.
- paper accepted: S.A. Berger, N. Alachiotis, A. Stamatakis:
"An Optimized Reconfigurable System for Computing the Phylogenetic
Likelihood on DNA Data", accepted for publication at IEEE RAW workshop
(in conjunction with IPDPS 2012).
- paper accepted: H. Schabauer, M. Valle, C. Pacher, H. Stockinger, A. Stamatakis,
M. Robinson-Rechavi, Z. Yang, N. Salamin: "SlimCodeML: An Optimized
Version of CodeML for the Branch-Site Model", accepted at IEEE HICOMB
workshop 2012 (in conjunction with IPDPS 2012)
- paper accepted: J. Zhang, A. Stamatakis: "The Multi-Processor Scheduling Problem in Phylogenetics", accepted at IEEE HICOMB workshop 2012 (in conjunction with IPDPS)
- Antonis Rokas has written a nice chapter about hands-on phylogeny reconstruction that uses RAxML as example program
- paper accepted: F.A. Matsen, N. Hoffman, A. Gallagher, A. Stamatakis: " A format for phylogenetic placements", accepted for publication in PLOS One.
- 1Kite project started officially: Web-Site
- paper accpted: F. Izquierdo-Carrasco, S.A. Smith, A. Stamatakis:
"Algorithms, Data Structures, and Numerics for Likelihood-based
Phylogenetic Inference of Huge Trees" BMC Bioinformatics: OPEN ACCESS
- paper accepted: S.S. Saminadin-Peter, C. Kemkemer, P. Pavlidis,
J. Parsch: "Selective Sweep of a cis-Regulator y Sequence in a
Non-African Population of Drosophila melanogaster", accepted for
publication in Molecular Biology and Evolution, November 2011.
- SMBE 2012 symposium proposal with Carolin Kosiol and Reed
Cartwright on "Estimating and Simulating Models of Molecular Evolution"
has been accepted.
- Alexis has been included in a list of highly cited Greek scientists
- paper published: B.M. von Reumont, R.A. Jenner, M.A. Wills,
E. Dell’Ampio, G. Pass,I. Ebersberger, B. Meyer, S. Koenemann, T.M.
Iliffe, A. Stamatakis, O. Niehuis, K. Meusemann, B. Misof:
"Pancrustacean phylogeny in the light of new phylogenomic data: support
for Remipedia as the possible sister group of Hexapoda", Molecular
Biology and Evolution, advance on-line access, November 2011.
- Funding granted: The DFG will kindly fund an additional PostDoc or PhD position for three years.
- paper accepted: E. Lee, A. Cibrián-Jaramillo, S.-O. Kolokotronis, M. Katari, A.
Stamatakis, M. Ott, J. Chiu, D. Little, D. Stevenson, W.R. McCombie, R.
Martienssen, G. Coruzzi, R. DeSalle: "A Functional Phylogenomic View of the Seed Plants" PLOS Genetics.
- paper accepted: F. Izquierdo-Carrasco, J. Gagneur, A. Stamatakis:
"Trading Memory for Running Time in Phylogenetic Likelihood
Computations", Bioinformatics 2012 conference, Vilamoura, Portugal, February 2012.
- The GUI for the evolutionary placement algorithm developped by Denis Krompass and Simon Berger has been included into softpedia
- paper accepted: A. Bousios, Y. Kourmpetis, P. Pavlidis,
E. Minga, A. Tsaftaris, N. Darzentas: "The turbulent life of Sirevirus
retrotransposons and the evolution of the maize genome: more than ten
thousand elements tell the story", accepted for publication in The
- paper accepted: Aurélien Tellier, Stefan J.Y. Laurent, Hilde Lainer, Pavlos Pavlidis, Wolfgang Stephan: "Inference
of Seed Bank Parameters in Two Wild Tomato Species Using Ecological and
Genetic Data", accepted for publication in PNAS.
- short paper accepted: Andre J. Aberer, Alexandros Stamatakis: "A Simple and Accurate Method for Rogue Taxon Identification" at IEEE BIBM 2011, Atlanta, Georgia
- An easy to understand and very readable article about tree building was published in "The Scientist".
- paper accepted: Stephen A Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E
Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon,
Andrew Lenards, Andy Muir, Nirav Merchant, Sonya Lowry, Stephen Mock,
Matthew Helmke, Adam Kuback, Martha Narro, Nicole Hopkins, Uwe Hilgert,
Michael Gonzales, Chris Jordan, Edwin Skidmore, Rion Dooley, John
Cazes, Robert McLay, Zhenyuan Lu, Shiran Pasternak, Lars Koesterke,
William H Piel, Ruth Grene, Christos Noutsos, Karla Gendler, Xin Feng,
Chunglao Tang, Monica Lent, Seung-jin Kim, Val Tannen, Alexandros Stamatakis,
Michael Sanderson, Stephen M Welch, Karen Cranston, Pamela Soltis,
Douglas Soltis, Brian O'Meara, Cecile Ane, Tom Brutnell, Daniel J
Kleibenstein, Jeffrey W White, Jim Leebens-Mack, Michael J Donoghue,
Edgar P Spalding, Kristian Kvilekval, B.S. Manjunath, Todd J Vision,
Brian J Enquist, Brad Boyle, David Lowenthal, Ali Akoglu, David
Micklos, Greg Andrews, Sudha Ram, Doreen Ware, Lincoln Stein, Dan
Stanzione: "The iPlant Collaborative: Cyberinfrastructure for Plant
Biology". Frontiers in Plant Genetics and Genomics 2011 on-line access.
- paper accepted: Madeleine Seeland, Simon A. Berger, Alexandros Stamatakis, Stefan Kramer: "Parallel Structural Graph Clustering", accepted for publication at ECML PKDD 2011, to appear in Springer LNAI.
- paper accepted: Simon A. Berger, Alexandros Stamatakis: "Aligning short Reads to reference Alignments and Trees", accepted for publication in Bioinformatics.
- paper accepted: Nikos Alachiotis, Alexandros Stamatakis: "FPGA Acceleration of the Phylogenetic Parsimony Kernel?", accepted at FPL 2011.
- paper accepted: Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis,
Guochun Shi, Volodymyr Kindratenko: "Fine-grain Parallelism using
Multi-Core, Cell/BE, and GPU Systems", accepted for publication in Parallel Computing.
- paper accepted: Simon A. Berger, Alexandros Stamatakis,
Robert Lücking: "Morphology-based phylogenetic binning of the lichen
genera Graphis and Allographa (Ascomycota: Graphidaceae) using
molecular site weight calibration", accepted for publication in Taxon.
- press releases about 55,000 taxon plant tree English German
- paper accepted: Victoria I. Siarkou, Alexandros Stamatakis, Ilias Kappas, Paul Hadweh,
Karine Laroucau: "Evolutionary Relationships amond Chmlamydophila
abortus Variant Strains Inferred by rRNA Secondary Structure-based Phylogeny", accepted for publication in PLoS ONE, 2011.
2012 summer school on computational molecular evolution with Nick
Goldman, Aidan Budd, Ziheng Yang, and Giorgos Kotoulas will be funded
by EMBO. This will be the 4th time it will take place and the second
time that it will be located in Crete at the Hellenic Center for Marine
Research - Institute for Marine Biology and Genetics.
- paper accepted: Nikos Alachiotis, Simon A. Berger, Alexandros Stamatakis:
"Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs",
accepted for publication at IEEE FCCM 2011, Salt Lake City, Utah, USA, May
- The largest plant phylogeny that will be published soon (Stephen A. Smith, Jeremy Beaulieu, Alexandros Stamatakis,
Michael J Donoghue: "Understanding angiosperm diversification using
small and large phylogenetic trees", accepted for publication in American Journal of Botany, special issue on Biodiversity) can be browsed on-line here thanks to Karen Cranston at NESCENT. You will just need to select "BigPlanTree" in the menu.
- Alexis will be teaching at the EES summer school on "Phylogenetics - new applications, pitfalls and challenges"
- paper accepted: Stephen A. Smith, Jeremy Beaulieu, Alexandros Stamatakis,
Michael J Donoghue: "Understanding angiosperm diversification using
small and large phylogenetic trees", accepted for publication in American Journal of Botany, special issue on Biodiversity.
- paper accepted: Marc Gottschling, Markus Göker, Alexandros Stamatakis,
Olaf R.P. Bininda-Emonds, Ingo Nindl, Ignacio G. Bravo: "Quantifying
the phylodynamic forces driving papillomavirus evolution", accepted for
publication in Molecular Biology and Evolution.
- paper accepted: Nicholas D. Pattengale, Andre J. Aberer, Krister M. Swenson, Alexandros Stamatakis, Bernard M.E. Moret : "Uncovering Hidden Phylogenetic Consensus in Large Datasets" accepted for publication in IEEE/ACM Transactions on Computational Biology and Bioinformatics
- paper published: Robert K. Luecking, Brendan P. Hodkinson, Alexandros Stamatakis,
Reed A. Cartwright: "PICS-Ord: Unlimited Coding of Ambiguous Regions by
Pairwise Identity and Cost Scores Ordination". BMC Bioinformatics 12:10, 2011.
- paper accepted: Simon A. Berger, Denis Krompaß, Alexandros Stamatakis:
"Performance, Accuracy and Web-Server for Evolutionary Placement of
Short Sequence Reads under maximum-likelihood" accepted for publication
in Systematic Biology.
- paper accepted: Nikos Alachiotis, Alexandros Stamatakis:
"FPGA Optimizations for a Pipelined Floating-Point Exponential Unit",
accepted for publication, 7th International Symposium on Applied
Reconfigurable Computing (ARC 2011), Belfast, United Kingdom, March
- paper accepted: Kevin Liu, Tandy J. Warnow, Mark T. Holder, serita Nelesen, Jiaye Yu, Alexandros Stamatakis,
C. Randal Linder: "SATe-II: Very Fast and Accurate Simultaneous
Estimation of Multiple Sequence Alignments and Phylogenetic Trees"
accepted for publication
in Systematic Biology.
- paper accepted: Nikos Alachiotis, Alexandros Stamatakis:
"A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm",
accepted for publication in International Journal of Reconfigurable
- paper accepted: Fernando Izquierdo-Carrasco, Alexandros Stamatakis:
"Computing the Phylogenetic Likelihood Function Out-of-Core", HICOMB
workshop 2011, held in conjunction with IPDPS2011, Anchorage, USA, May
- Andre Aberer
submitted and presented his Master's thesis on: "Advanced Methods for
Phylogenetic Post-Analysis", TU Munich/HITS, January 2011.
- RAxML is now also available on softpedia for MACs
- Michael Ott succesfully defended his PhD thesis.
with Fernando on "Result Verification, Code Verification, and
Computation of Support Values in Phylogenetics" accepted for
publication in Briefings in Bioinformatics
- The Exelixis Lab moved to its new home at the Heidelberg Institute for Theoretical Studies, the lab is now part of a larger group that is called Scientific Computing
- An article was published in Genome Web that addresses High Performance Computing for Phylogenetics and some of the work conducted at the Exelixis Lab
- The work of the Exelixis lab is mentioned on pages 68-69 in the 2009 yearbook of the German Science Foundation (DFG)
with Manuel Stark, Simon Berger, and Christian von Mering on "MLTreeMap
- accurate Maximum Likelihood placement of environmental DNA sequences
into taxonomic and functional reference phylogenies" accepted for
publication in BMC Genomics.
- Paper with Simon Berger on "Assessment
of Barrier Implementions for Fine-Grain Parallel Regions on
Current Multi-core Architectures" accepted at IEEE Cluster workshop on
Parallel Programming and Applications on Accelerator Clusters,
Heraklion, Greece, September 2010.
- Alexis will be at the "Fast, Free Phylogenies: HPC for Phylogenetics Tutorial” Oct. 13-15, 2010, at NIMBioS, Knoxville, Tennessee
DAAD (German Academic Exchange Service) kindly granted us travel money
for a collaborative project with George Constantinides and his group at
the EE department of Imperial College, London
- The Exelixis lab is moving to the Heidelberg Institute for Theoretical Studies in October 2010
- Pavlos Pavlidis and Andre Aberer will join our lab in Heidelberg at the beginning of 2011
- Nick Pattengale who defended his PhD in March 2010 received the QForma
prize for the best dissertation in engineering and computation in the
academic year 2009-2010 at the University of New Mexico,
congratulations Nick :-)
- Alexis has been elected as a member of the council of the Society of Systematic Biologists
- Joint TUM/LRZ press release about integration of RAxML into the SPEC MPI 2007 benchmark
with Nikos Alachiotis and Simon Berger on "Efficient PC-FPGA
Communication over Gigabit Ethernet" accepted for publication at IEEE
- Paper with Nikos Poulakakis on "Recapitulating the evolution of
Afrotheria: 57 genes and rare genomic changes (RGCs) consolidate their
history" accepted for publication in Systematics and Biodiversity.
- Nick Pattengale succesufully defended his PhD thesis at the University of New Mexico
with Andre Aberer and Nick Pattengale on "Parallelized phylogenetic
post-analysis on multi-core architectures" accepted for publication in Elsevier Journal of Computational Science
- Paper with Nikos on "Time and memory efficient likelihood-based tree searches on gappy
phylogenomic alignments" accepted for publication at ISMB2010.
- The fine-grained MPI parallelization of RAxML is now part of the SPEC MPI 2007 version 2.0 benchmark suite
- Website of Workshop on Parallel Programming Applications on Accelerator Clusters (PPAAC 2010) to be held in conjunction with IEEE Cliuster 2010 in Heraklion, Crete, Greece is available
- Paper with Guido Grimm and Markus Göker on "Maximum Likelihood Analyses of 3,490 rbcL
Sequences: Scalability of Comprehensive Inference versus Group-Specific
Taxon Sampling", accepted for publication in Evolutionary Bioinformatics.
- Paper with Andre Aberer and Nick Pattengale on
"Parallel Computation of Phylogenetic Consensus Trees",
accepted for publication
at ICCS 2010 conference, Emerging Parallel Architectures Workshop
Cazes and BD from the Texas Advanced Computing Center will be visiting
us in March to work on some NSF iPTOL project related issues
March 19 we will carry out the inofficial 1st year PhD defense for
Nikos and Simon. Bernard Moret (EPFL) and Christian von Mering (Univ
Zurich) will visit us in Munich for their defenses. Fritz Sedlazek from
Arndt von Haeseler's lab in Vienna will also visit us again for his 2nd
year PhD defense.
with Wayne Pfeiffer (SDSC) on the hybrid MPI/Pthreads parallelization
of RAxML accepted for publication at HICOMB 2010 workshop which is held
in conjunction with IPDPS 2010
- Fernando Izquierdo joins the Exelixis Lab as PhD student :-)
- According to Scopus which is an ISI-like citation tool, Alexis' 2006 Bioinformatics paper on RAxML-VI ranks on place 4 of the 20 most cited papers in Computer Science in the last 5 years (2006-2010)
- Paper accepted at RAW workshop which is held in conjunction with IEEE IPDPS 2010 conference. N.
Alachiotis, A. Stamatakis: "Efficient Floating-Point
Logarithm Unit for FPGAs"
papers accepted for publication at 8th ACS/IEEE International
Conference on Computer Systems and Applications (AICCSA-10), Hammamet,
Tunisia, May 2010:
Berger, A. Stamatakis: "Accuracy of Morphology-based
Phylogenetic Fossil Placement under Maximum Likelihood"
- A. Stamatakis, Z. Komornik, S.A. Berger:
"Evolutionary Placement of Short
Sequence Reads on Multi-Core Architectures"
journal version of the RECOMB09 paper on "How many Bootstrap Replicates
are necessary?" with N. Pattengale, M. Alipour, O.R.P. Bininda-Emonds,
B.M.E. Moret, and E.J. Gottlieb accepted for publication at Journal of
joint EMBO summer school grant application with Aidan Budd, Ziheng
Yang, Nick Goldman, and Giorgos Kotoulas for organizing a 10-day school
on "Molecular Evolution" at the Hellenic Center for Marine Research in
Heraklion, Crete, Greece (May 2010) just got funded :-) more
details to follow soon.
- Prof. Ziheng Yang will be visiting us from
December 1 - December 7
PhD positions in phyloinformatics available at ETH Zurich in the group
of Maria Anisimova, one of my favorite colleagues :-), more info here
on "Assessing the root of bilaterian animals with scalable phylogenomic
methods" accepted at Proceedings of the Royal
- The iPTOL project web pages
have been updated, including a detailed description of the working
DFG will kindly fund an additional PhD project that will deal with
extremely large-scale tree reconstruction methods in conjunction with
- RAxML reaches over 6,000 source-code
downloads from distinct IPs, over 40,000 job submissions to the two
web-servers, and over 500
citations from the 2005 Bioinformatics, 2006 Bioinformatics,
and 2008 Systematic Biology papers
versus double precision arithmetics again:
I played around a bit more with RAxML to figure out the cases where it
is worth to use single precision. I ran the SSE3-vectorized Pthreads
version (16 threads on a Sun x4600) of RAxML on a protein dataset with
321,145 distinct alignment patterns and 232 taxa. The double-precision
runs were done under GAMMA and the single-precision runs under CAT.
This means that the memory footprint was at approx. 40GB for GAMMA
under double precision and only at approx. 5GB for CAT under single
precision. The CAT+single precision run was 3 times faster and also
returned a tree with a slightly better likelihood when scored under
- Prof. Apostolos Dollas, Nikos' former
supervisor at the Technical University of Crete, will be visiting us on
significantly faster version of RAxML has been released that also
includes some advanced search mechanisms for trees with thousands of
- Minh, a PostDoc at Arndt's lab in Vienna
will be visiting us on July 9 & 10
- Paper on "Accuracy
and Performance of Single versus Double Precision Arithmetics for
Maximum Likelihood Phylogeny Reconstruction" accepted for publication
at PBC09 workshop.
- Short paper accepted at FPL 2009 "A
Reconfigurable Architecture for the Phylogenetic Likelihood Function"
with Nikos Alachiotis, Apostolos Dollas, and Evripidis Sotoriades
- Two papers accepted at ICPP 2009
- "Load Balance in the Phylogenetic
Likelihood Kernel" with Michael Ott
parallelism using Multi-core, Cell/BE, and GPU systems: Accelerating
the Phylogenetic Likelihood Function" with Frederico Pratas,
Leonel Sousa, and Pedro Trancoso
- There are HiWi
positions for CS/Bioinformatics students available at Gert
- The NSF iPlant Collaborative
Grand Challenge Proposal (PDF)
received a very positive review. Alexis Stamatakis is a Co-PI on this
grant which is lead by Mike Sanderson together with Pam
Doug Soltis, Michael Donoghue, Todd Vision, and Val Tannen
- We moved to our new offices in finger
number 9, 1st floor of the CS building
- New version of RAxML released with many
- Antonis Rokas and Casey Dunn visited us at
Munich and gave very interetsing talks
- Fritz Sedlazeck, a PhD student from Arndt
von Haeseler's lab in Vienna visited us to defend his PhD proposal
- Zsolt Komornik, an Erasmus student from
France started working with us
- Nikos and Simon arrived at the Exelixis
with Susanne Renner we just finalized the program of the
Symposium on "Advances in Tree Reconstruction from Complex
Matrices" we are organizing. It will take place at the 2009
in Darwin's 200th birthday year. Symposium Speakers are: Mike
Sanderson, Nick Goldman, Olivier Gascuel, Alexis Stamatakis, Casey
Dunn, Derrick Zwickl, and Stephen Smith
- On March 02 2009 we
will organize a "Joint
Exelixis Lab (TUM) & Molecular
Palaeobiology/GeoBioCenter (LMU) Phylogenomics Seminar"
Prof. Gert Wörheide at the GeoBioCenter. Antonis Rokas (Vanderbilt
University) and Casey Dunn (Brown University) will give invited talks.
surpasses 4,000 source code downloads from distinct IP addresses (total
(University College London, Fellow of the Royal Society) will be
visiting the Exelixis lab once per year within the framework of
a BBSRC project on which we are collaborating, we are really looking
forward to his visits
cluster challenge article at
Seliga, an Erasmus student from Poland will join the lab as student
- PRIB2008 paper was a finalist for the best
paper award, Michael Ott presented this work at Melbourne,
Exelixis Lab will move to the CS department of the Technical University
succesfully defended his Diploma Thesis
- Simon Berger and Nikos Alahiotis will join
The Exelixis Lab as PhD students
- RAxML will be one of the test applications
for the IEEE/ACM 2008 Supercomputing Conference cluster