STATISTICAL MACHINE LEARNING AND BIOINFORMATICS GROUP: Bioinformatics Journal Club

NOTE: Machine Learning journal club and Bioinformatics journal club were merged at October 7, 2007. The new journal club site is located here.

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2007

 

• 7.10.2007 (Leo)
  Goeman, Jelle J. and Buhlmann, Peter: Analyzing gene expression data in terms of gene sets: methodological issues. In Bioinformatics 2007 23(8):980-987 . (pdf).
  
  
• 24.09.2007 (Sami)
  Motoki Shiga, Ichigaku Takigawa and Hiroshi Mamitsuka. Annotating gene function by combining expression data with a modular gene network. In ISMB/ECCB 2007 (Bioinformatics 2007 23(13):i468-i478). (pdf).
  
  
• 10.09.2007 (José)
  S. Madeira and A. Oliveira: An efficient Biclustering Algorithm for Finding Genes with Similar Patterns in Time-Series Expression Data. Technical Report. (pdf).
  
  
• 27.08.2007 (Ilkka)
  Gerber, Georg K. Dowell, Robin D. Jaakkola, Tommi S. Gifford, David K: Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression. Technical report. (pdf).
  
  
• 06.08.2007 (Merja and Leo)
  Best of ISMB/ECCB 2007: Proceedings.
  
  
• 25.06.2007 (Abhishek; A346)
  Ron M.A. Heeren Proteome imaging: A closer look at life's organization. In Proteomics 2005,5, 4316-4326. (pdf)
  
  
• 11.6.2007 postponed
  
  
• 28.5.2007 (Andrey; A346)
  Lu, Rosenfeld and Bar-Joseph: Identifying cycling genes by combining sequence homology and expression data. In Bioinformatics 2006 22(14):e314-e322. (abstract).
  
  
• 14.5.2007
  Guest lecture in Viikki Biocenter:
  John Quackenbush, Networks and stochastics in gene expression data analysis
  
  
• 30.4.2007 (Arto)
  M.J. Beal and P. Krishnamurthy: Gene expression time course clustering with countably infinite hidden Markov models. In UAI 2006. (pdf)
  
  
• 16.4.2007 (Jarkko)
  E.M. Conlon, J.J. Song, and A. Liu: Bayesian meta-analysis models for microarray data:a comparative study. In BMC Bioinformatics 8:80 (pdf).
  
  
• 2.4.2007 (Antti)
  T. Aittokallio and B. Schwikowski: Graph-based methods for analysing networks in cell biology. In Briefings in Bioinformatics 7(3):243-255, 2006.
  
  
• 19.3.2007 (Ilkka)
  A.-L. Boulesteix, K. Strimmer Partial Least Squares: A versatile tool for the analysis of high-dimensional genomic data. In Briefings in Bioinformatics 8(1):32-44. . (pdf).
  And
  Z. Li and C. Chan Integrating Gene expression and Metabolic profiles. In J Biol Chem, 2004 . (pdf).
  and
  T.D. Bie, N. Cristianini,R. Rosipal Eigenproblems in Pattern recognition. In Handbook of Computational Geometry for Pattern Recognition. , 2004 . (pdf).
  
  
• 5.3.2007 (Jaakko)
  A. V. Werhli, M. Grzegorczyk, and D. Husmeier: Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks. Bioinformatics 22:2523-2531, 2006. (abstract).
  
  
• 19.2.2007 (JanneN)
  Efron & Tibshirani On testing the significance of sets of genes Technical report , 2006. (pdf).
  
  
• 5.2.2007 (Merja)
  Interesting papers from the ECCB 2006 conference. (Proceedings, Program).
  
  
• 22.1.2007 (Leo)
  Olga G. Troyanskaya Putting microarrays in a context: Integrated analysis of diverse biological data. Briefings in Bioinformatics 6(1)34-43, 2005. (html, pdf).
  
  
• 8.1.2007 (Sami)
  Yeang, Ideker, Jaakkola: Physical network models. In Journal of Computational Biology, 11:243-262, 2004. (pdf).
  
  

2006

 

• 13.12.2006 (Abhishek)
  Jean-Philippe Vert Kernel methods in genomics and computational biology. In Technical Report HAL:ccsd-00012124, October 2005. (html).
  
  
• 29.11.2006 (Merja)
  K. MacIsaac, DB. Gordon, L. Nekludova, DT. Odom, J. Schreiber, DK. Gifford, RA. Young and E. Fraenkel:
  A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
  In Bioinformatics, 22(4):423-429, 2006. (html).
  
  
• 15.11.2006 (Arto)
  Momiao Xiong, Jun Li and Xiangzhong Fang: Identification of Genetic Networks. In Genetics, vol. 166, 1037-1052, February 2004. (html).
  
  
• 18.10.2006 (Ilkka)
  an overview of Mass Spectrometry & Chromatography methods. based on a Wikipedia chapter. (html).
  
  
• 4.10.2006 (Antti)
  Nir Friedman: Inferring Cellular Networks Using Probabilistic Graphical Models. In Science 303 (5659) pp. 799-805, 2004. (pdf).
  
  
• 20.9.2006 (Jaakko)
  Do et al.: CONTRAfold: RNA secondary structure prediction without physics-based models. In Bioinformatics 22 (14), pp. e90-e98, 2006. (pdf).
  
  
• 6.9.2006 (Janne)
  Segal et al.: A genomic code for nucleosome positioning. In Nature , vol.442, pp.772--778, 2006. (html).
  
  

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