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IBIVU - News Archive

• Our masters in Bioinformatics and Systems Biology has received a very favourable advice from the assessment panel (May 2016)
• We moved: our new rooms are S404, S406, T401 and T420 (13 July 2016)
Ted Meeds has joined the group (July 1, 2016)!



Old News
• Mohammed El-Kebir won the BioSB Young Investigator Award 2015!
Maurits Dijkstra (Feb 1, 2014), Bas Stringer (Apr 1, 2014) and Jochem Bijlard (Apr 1, 2014) have joined the group.
Seven students in our Bioinformatics and Systems Biology master have been selected based on motivation and excellence to participate in the STAR graduate programme. (Mar 13, 2014)
On Monday, November 5 at 13:45 Nicola Bonzanni will defended his PhD thesis "Towards Executable Biology" (Oct 16, 2012)

NWO Open Competitie grant awarded to Anton Feenstra
Formal methods yield insight into Leukemia and Blood transfusion.

Leukemia is caused by disruption of the cell division and differentiation of blood stem-cells. A complex network of genes that regulate each other, but also many other genes, normally ensures that this process is conducted in an orderly manner. By applying powerful modelling and analysis methods from theoretical computer science, we will gain a better understanding of how this network of genes functions. That will allow us to develop better treatment of leukemia, but also for example will enable safer and cheaper blood transfusion.

Within the project, the groups of Bioinformatics (Feenstra, Heringa, Bonzanni) and Theoretical Computer Science (Fokkink, Bonzanni) will work together. In collaboration with the groups of Receptor Biochemistry (Martine Smit, VU Faculty of Science, Chemistry) and Bertie Gƶttgens (Cambridge Institute for Medical Research), predictions from the models will be experimentally verified.

(July 6, 2012)
Open to researchers: Browsing the Human Genome by the Ensembl Outreach group

On Friday 27 May 2011 we will give a hands-on Ensembl/Vega browser workshop at the VU. This workshop is specifically targeted towards attendants of the ESHG 2011 conference, but is now also open for VU/VUmc, UvA/AMC staff and students. The workshop is free of costs. For more information and how to register, please have a look here.
With kind regards,
The Ensembl and Vega team
(May 27, 2011)
On Friday March 11, Thomas Binsl succesfully defended his PhD thesis "Fluxes of Life - Bioinformatics for Metabolic Flux Quantification in Isotopic Non-Steady-State" (March 14, 2011)
Today a large manifestation was organized in The Hague to protest against several proposed budget-cut measures by the Dutch governement that could severely cripple our Education and Research. A short photo impression of this 'Dag der Academische Treurnis' (Day of Academic Despondency). (Januari 21, 2011)
Symposium: ‘‘Bioinformatics for Metabolomics and Fluxomics’’ on Friday March 11, 9.00h-11.45h, VU University Amsterdam, room HG-07A02 (VU Main Building) (February 7, 2011)
Albert Kooistra (cum laude) and Frank Neezen graduated on December 15, 2010 as MSc bioinformatics.
(December 16, 2010)
Kees van Bochove and Mohammed El-Kebir graduated with honours on September 15, 2010 as MSc bioinformatics.
(September 24, 2010)
Fundamentals of Bioinformatics starting on September 6 at 9.30 (details).
(August 27, 2010)
Sonja Noback graduated on August 18, 2010 as a MSc bioinformatics.
(August 20, 2010)
Alexander de Ridder graduated with honours on June 16, 2010 as a MSc bioinformatics.
(June 24, 2010)
  • Walter Pirovano will defend his PhD Thesis Comparing building blocks of life in the Aula (VU main building) on January 15, 13.45h (Jan 5, 2010)
  • Symposium ‘Comparing Building Blocks of Life’ January 15 (Dec 23, 2009)
  • Seminar by Ruchira Datta from the Berkeley Phylogenomics Group on "PHOG phylogenomic orthology prediction", Wednesday June 24 at 13.30 in M2.12.
    (June 2, 2009)
  • Seminar by Dr. Ryan Gutenkunst from the LANL on "Sloppiness in biochemical modeling and evolution", Tuesday June 9 at 14.00 in M2.12.
    (June 3, 2009)
  • On September 29, 2008 Sandra Smit successfully defended her PhD thesis entitled: RNA in Formation - Computational Studies on RNA Structure and Evolution.
    (September 30, 2008).
  • Seminar by Dr. Curtis Huttenhower "Genomic data integration for regulatory and functional network inference", Tuesday Dec. 9, 15.30 in C6.68
    (December 5, 2008)
  • IBIVU project wins the NGI Venture Challenge 2008
    FLUXTRAX, the new venture of Hans van Beek (VU/VUmc), Koen Verhoef (VU/VUmc) and Thomas Binsl (IBIVU) had the most promising venture plan and will provide services to the pharmaceutical industry in terms of metabolite turnover quantification.
    (November 11, 2008)
  • On September 29, 2008 Sandra Smit successfully defended her PhD thesis entitled: RNA in Formation - Computational Studies on RNA Structure and Evolution.
    (September 30, 2008).
  • As of August 1st, 2008, a second group started within the IBIVU centre. The Systems Bioinformatics group is chaired by Prof. Dr. Bas Teusink.
  • Gerard Schaafsma graduated on September 17, 2008 as the fifth MSc bioinformatics.
    (September 18, 2008)
  • Peter den Harder graduated Wednesday June 18 as the fourth MSc bioinformatics. (June 20, 2008)
  • Vacancies:
  • Integrative Bioinformatics (Assistant Professor).
  • "Mesoscale PPI Modelling" (PostDoc),
  • Integrative Bioinformatics (Ph.D. student),
    (May 26, 2008)
  • PhD defence Radek Szklarczyk on Friday, November 23rd at 13:45 in the Aula of the VU main building. Title of the PhD thesis: "Information reuse in comparative genomics". (Nov 19, 2007)
  • Seminar by Dr. Kateryna Makova (Penn State University) on Thursday, November 22nd at 4pm in room C1.21. (Nov 19, 2007)
  • Vacancies for Ecogenomics: two PostDocs and one Research Assistant. (Nov 1, 2007)
  • LECTURE CANCELLED!!! The Computational Genomics & Proteomics lecture of Thursday September 6 at 9:00-10:45 is cancelled due to illness of the teacher. Our apologies for the inconvenience!
  • Vacancies for "Mesoscale PPI Modelling" (PostDoc), "Formal Cell Modeling" (Ph.D. student), Bioinformatics (Professor), "Pathway Analysis in Alzheimer" (Ph.D. student). (July 2, 2007)
  • Vacancies for "Mesoscale PPI Modelling" (PostDoc), "Formal Cell Modeling" (Ph.D. student), Bioinformatics (Professor), "Pathways" (Ph.D. student). (July 2, 2007)
  • Vacancies for "Mesoscale PPI Modelling" (PostDoc), "Ecogenomics" (PostDoc and Groupleader), Bioinformatics (Professor), "Pathways" (Ph.D.). (June 22, 2007)
  • We have all moved to our new rooms in the P1 corridor. (May 15, 2007)
  • This week we are preparing the move to our new rooms in the P1 corridor, that is scheduled to happen next week. (May 1, 2007)
  • Sjoerd Vosse is our second bioinformatics master student to graduate. (April 18, 2007)
  • Our new compute cluster arrived. (March 5, 2007)
  • New Ph.D. fellowship available on Mesoscale Modeling or protein-protein interactions (March 5, 2007) (more information to come)
  • Our website has moved to a new server. If all went well, this message should be the only noticeable change, if not please tell us. (Dec 1, 2006)
  • New Ph.D. fellowship available in Computational Pathway Analysis for Alzheimer's Disease and Metabolic Syndrome (November 8, 2006) More information
  • Seminar by Dr. Rob Knight (University of Colorado, Boulder) on Wednesday, September 27th, 2006 at 3:30 pm in Rm C6.23. (September 23, 2006) Abstract
  • First Bioinformatics MSc Josien Haan is our first bioinformatics master student to graduate. Here are a few nice pictures of the graduation. (December 14, 2005)

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