news

March 2013

• 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.

February 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, USA, 2013.
• 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. 

January 2013

• The 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.
  

December 2012

• paper accepted: A. Stamatakis, A.J. Aberer: "Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference", IPDPS 2013.
  

Novemeber 2012

• 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.
  

September 2012

• paper accepted: N. Alachiotis, S. Berger, A. Stamatakis: "A Versatile UDP/IP based PC-FPGA Communication Platform", acccepted for publication at ReConFig 2012.
  

August 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.
  

July 2012

• Alexis was appointed as full professor at the department of computer science (in conjunction with his job at HITS) of the Karlsruhe Institute of Technology
  
• paper accepted: A.J. Aberer, D. Krompass, A. Stamatakis: "Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice", Systematic Biology, in press.
  

June 2012

• 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.

May 2012

• 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. Bentham Science.
  

February 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)

January 2012

• 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.
  

December 2011

• 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
  

November 2011

• 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.

October 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

September 2011

• 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 PLant Journal.
  
• 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

August 2011

• An easy to understand and very readable article about tree building was published in "The Scientist".
  

July 2011

• 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.

June 2011

• 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.

May 2011

• 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.

April 2011

• 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.
• The 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.

March 2011

• 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 2011.
• 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.

February 2011

• 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.

January 2011

• 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 2011.
• 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 Computing.
• 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 2011.
• 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.
• Paper 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)
• Paper 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
• The 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
• Paper with Nikos Alachiotis and Simon Berger on "Efficient PC-FPGA Communication over Gigabit Ethernet" accepted for publication at IEEE ICESS 2010.
• 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
• Paper 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
• John Cazes and BD from the Texas Advanced Computing Center will be visiting us in March to work on some NSF iPTOL project related issues
• On 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.

• Paper 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"
• Two papers accepted for publication at 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), Hammamet, Tunisia, May 2010:
• S.A. 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"
• Extended 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 Computational Biology.

• The 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
• Two PhD positions in phyloinformatics available at ETH Zurich in the group of Maria Anisimova, one of my favorite colleagues :-), more info here

• Paper on "Assessing the root of bilaterian animals with scalable phylogenomic methods"  accepted at Proceedings of the Royal Society  B.
• The iPTOL project web pages have been updated, including a detailed description of the working groups
• The DFG will kindly fund an additional PhD project that will deal with extremely large-scale tree reconstruction methods in conjunction with iPTOL
  

• 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
• Single 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 GAMMA.
  
• Prof. Apostolos Dollas, Nikos' former supervisor at the Technical University of Crete, will be visiting us on July 20

• New, significantly faster version of RAxML has been released that also includes some advanced search mechanisms for trees with thousands of taxa
• 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

1. "Load Balance in the Phylogenetic Likelihood Kernel" with Michael Ott
2. "Fine-grain parallelism using Multi-core, Cell/BE, and GPU systems: Accelerating the Phylogenetic Likelihood Function" with Frederico Pratas, Leonel Sousa, and Pedro Trancoso

• Alexis is now a member of the EES (Munich Graduate School for Evolution, Ecology, and Systematics) school curriculum commitee at the Ludwig Maximilians University of Munich (Biology Department)

• There are HiWi positions for CS/Bioinformatics students available at Gert Wörheides Lab
• 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 new features
• 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 lab :-)
• Together with Susanne Renner we just finalized the program of the Symposium on "Advances in Tree Reconstruction from Complex Data Matrices" we are organizing. It will take place at the 2009 evolution meeting in Darwin's 200th birthday year. Symposium Speakers are: Mike Sanderson, Nick Goldman, Olivier Gascuel, Alexis Stamatakis, Casey Dunn, Derrick Zwickl, and Stephen Smith
  

• Paper on mapping the phylogenetic likelihood function on FPGAs entitled "Exploring FPGAs for accelerating the Phylogenetic Likelihood Function" co-authored with Nikos Alaxiotis, Evripidis Sotiriades, and Apostolos Dollas accepted for publication at HICOMB 2009 (held in conjunction with IPDPS2009)
• Paper on a phylogenetic bootstrap convergence criterion "How Many Bootstrap Replicates are Necessary?" co-authored with Nick Pattengale, Masoud Alipour, Olaf Bininda-Emonds, and Bernard Moret accepted for publication at RECOMB 2009
• New beta-version of the CIPRES portal (offering RAxML and many other applications for phylogenetic analysis) that provides a full workbench 

• On March 02 2009 we will organize a "Joint Exelixis Lab (TUM) & Molecular Palaeobiology/GeoBioCenter (LMU) Phylogenomics Seminar" together with Prof. Gert Wörheide at the GeoBioCenter. Antonis Rokas (Vanderbilt University) and Casey Dunn (Brown University) will give invited talks.
• RAxML surpasses 4,000 source code downloads from distinct IP addresses (total > 11,000)
• Ziheng Yang (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
• SC08 cluster challenge article at insideHPC.com
• Szymon Seliga, an Erasmus student from Poland will join the lab as student programmer (HiWi)

• PRIB2008 paper was a finalist for the best paper award, Michael Ott presented this work at Melbourne, Australia
• The Exelixis Lab will move to the CS department of the Technical University of Munich
• Nikos 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 challenge