Meeting schedule

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  • The weekly meetings of the IBIVU Bioinformatics group are on Wednesdays at 11:00-12:15 in room T4.69, unless indicated otherwise below. Please find the meeting schedule below.
  • The literature scanning scheme will tell you who covers which journals.
  • Scheduled talks should be 25 minutes plus 20 minutes discussion.
  • Talks should not be about finished work (that goes into the big IBIVU meeting)
    • highlight methodology and open problems
  • The last 20 minutes are reserved for presenting breakthrough results (on the board).
  • If you want to schedule a presentation please contact Punto Bawono (p.bawono@vu.nl)
  • The first meeting of every month will be the IBIVU seminar, with selected talks of members of the IBIVU (Teusink and Heringa groups, or invited speakers)

Rotation:

Regular rotation:

  • Ali
  • Nicola
  • Annika
  • Qingzhen
  • Erik
  • Maurits
  • Bas
  • Ted

Sporadic rotation:

  • Reza
  • Sanne
  • Anton
  • Jaap

Schedule:


Past topics:

Date: Speaker: Subject:
2012-09-05 M2.12 Hannes Hettling
2012-06-28 M2.12 All Literature
2012-06-21 M2.12
  • Alumit Mannheim: final bachelor presentation
  • Qingzhen Hou: Plan "Sequence Analysis of Homodimer and Monomer Ortholog groups"
2012-06-14 M2.12
  • Mohammed El-Kebir
  • Marc Jan Bonder: mid-internship presentation
2012-06-07 F6.54 Bioinformatics & Systems Biology seminar Maria Daleke & Punto Bawono: "A general secretion signal for the mycobacterial type VII secretion pathway"
2012-05-31 No Group meeting (due to exams)
2012-05-24 M2.12 All Literature
2012-05-17 <ascension day>
2012-05-10 M2.12
  • Jaap: group research topics
  • Sanne & Anton: improvements, new developments and scheduling of Fundamentals of Bioinformatics (MSc) and Principles of Bioinformatics (BSc)
2012-04-26 M2.12 Nicola Bonzanni Object Oriented Gene Regulatory Networks
2012-04-19 M2.12 Ali May proposal defense
Anton Feenstra Talavera et al. JMB 2012 - Evolvability of Yeast Protein-Protein Interaction Interfaces
All Literature
2012-04-12 Sanne Abeln "The effect of denoising and clustering on 16S pyrosequencing datasets"
2012-04-05 Huub Hoefsloot Bioinformatics & Systems Biology seminar: Integrating multivariate statistics with knowledge
2012-03-29 All + Ali May in-depth literature discussion Media:nmeth.1376.pdf
2012-03-15 Anton Feenstra Calculating (effective) force profiles using umbrella sampling.
2012-03-08 Evert Bosdriesz Bioinformatics & Systems Biology seminar
"Optimal and robust regulation of gene expression".
2012-03-01 Hannes Hettling

Continued discussion of Retrieval, alignment, and clustering of computational models based on semantic annotations by Schulz, Krause, Le Novere, Klipp, and Liebermeister (Molecular Systems Biology 2011 7:512)

2012-02-23 Leonardos Mageiros mid/end internship talk "Environment-Specific Protein Structural Alignment"
All Literature
2012-02-09
  • Marlies van der Wees: mid-internship talk
  • Punto Bawono: "Motif-aware MSA + praline"
2012-02-02 Joost Boele IBIVU seminar "PAPD5 mediates isomiR-specific adenylation of oncomiR miR-21 to induce its degradation in a novel tumor suppression pathway"
2012-01-26
  • Danielle de Man: mid-internship talk "Evolving a gene Regulatory Network"
  • All + Hannes: in-depth literature discussion Media:MSB201141.pdf
2012-01-12 Hayssam Soueidan IBIVU seminar Network reconstruction from text mining
2012-01-05 Jaap Heringa New Year's speach
2011-12-15 Nicola Bonzanni
2011-12-08
  • Ali May: mid-internship talk
  • All: Literature - in-depth AND scanning
2011-12-01

IBIVU seminar:

  • Erik van Dijk "Introducing the Hydrophobic effect in Lattice Models of Protein Folding"
  • Sanne Abeln: "Self assembly into silk fibrils"
2011-11-24 Anton Feenstra Sequence Specificity, Conservation and Protein-Protein Interactions
2011-11-03 Herwig Bachmann IBIVU seminar "Privatization of public goods leads to increased microbial efficiency but decreases growth rates"
2011-10-27 Hannes Hettling
2011-10-20 All Literature MSAProbs - Liu Schmidt Maskell 2011
2011-10-20 Bianca Mladek IBIVU Seminar "Coarse graining DNA-coated colloids" abstract
2011-10-13 Mohammed El-Kebir
2011-10-06 Brett Olivier IBIVU seminar "Stochastic Modeling"
2011-09-22 Anton Feenstra Zenith Proposal: Petri-net modeling of b-Catenin signaling
2011-09-15 Punto Bawono
2011-09-08 Nicola Bonzanni IBIVU seminar "Why stochastic modeling?"
2011-09-01 Hannes Hettling
2011-06-23 All Literature: Non-adaptive origins of interactome complexity
2011-06-09 Bernd Brandt The Fanconi / ENFANC project
+ David Vossen (Mid-internship talk)
2011-05-26 All Hogeweg's paper.
+ Michiel Vegt (Mid-internship talk)
2011-05-12 RenĂ© Pool The Development of a Molecular Simulation Based Engine for the Quantification of Protein-Protein Interactions
2011-04-28 Nicola Bonzanni Google WebToolkit
2011-04-07 Pinar Ozturk
2011-03-17 All
2011-03-10 Anisha Goel
2011-03-03 Anton Feenstra SHMR: analyzing specificity in HIV disease progression and population evolution
2011-02-24 All Literature - in-depth AND scanning
2011-02-17 Sanne Protein solubility & aggregation with simple lattice models
2011-02-10 Douwe Molenaar "Probiotics"
2011-02-03 Hannes Hettling Once Again on the Functions of Creatine Kinase: the Shuttle Hypothesis
2011-01-13 Mohammed El-Kebir Network alignment
2011-01-06 Jaap Heringa New Year's speech
2010-12-02 Arjan van der Velde Distance-based alignment scoring
2010-11-25 René Pool Course-grained calculations of Protein-interaction PMF by grand-canonical MC
2010-11-18 All Shaw Science 330 15 Oct 2010 341
Science News Of The Week 330 15 Oct 2010 308
2010-11-11 Nicola Bonzanni The role of proteosome-mediated proteolysis in modulating the activity of potentially harmful transcription factor activity in Saccharomyces cerevisiae
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