Arvutiteaduse instituut
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  2. 2012/13 kevad
  3. Bioinformaatika seminar (MTAT.03.242)
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Bioinformaatika seminar 2012/13 kevad

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Calendar

  • 20.02 - Balaji Rajashekar
  • 06.03 - Raivo Kolde
  • 20.03 - Sten Ilmjärv
  • 27.03 - Priit Adler
  • 03.04 - Tauno Metsalu (Jaak Vilo)
  • 10.04 - Vijayachitra Modhukur (Sten Ilmjärv)
  • 17.04 - Kristjan Korjus (Sven Laur)
  • 24.04 - Elena Nikolaeva (Priit Adler)
  • 08.05 - Aleksei Panarin (Konstantin Tretjakov)
  • 15.05 - Prashanth Suravajhala (Guest speaker)
  • 22.05 - Gerli Viikmaa (Balaji Rajashekar)
  • 29.05 - Atilio Rrenja (Raivo Kolde)
  • 05.06 - Jordan Valdma (Balaji Rajashekar)

Details

  • 20.02 - Balaji
    Course Introduction | Introduction.pdf
  • 06.03 - Raivo Kolde | Article
  @article{hansen2012bsmooth,
  title={BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions},
  author={Hansen, Kasper D and Langmead, Benjamin and Irizarry, Rafael A and others},
  journal={Genome Biol},
  volume={13},
  pages={R83},
  year={2012}
  }
  • 20.03 - Sten Ilmjärv | Article
  @article{kelly2012genome,
  title={Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules},
  author={Kelly, Theresa K and Liu, Yaping and Lay, Fides D and Liang, Gangning and Berman, Benjamin P and Jones, Peter A},
  journal={Genome Research},
  year={2012},
  publisher={Cold Spring Harbor Lab}
  }
  • 27.03 - Priit Adler | Article
  @article{chen2013powerful,
  title={A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies},
  author={Chen, Min and Zang, Miao and Wang, Xinlei and Xiao, Guanghua},
  journal={Bioinformatics},
  year={2013},
  publisher={Oxford Univ Press}
  }
  • 03.04 - Tauno Metsalu | Detecting imprinted genes from RNA-seq data | Article1, Article2
  @article{rozowsky2011alleleseq,
  title={AlleleSeq: analysis of allele-specific expression and binding in a network framework},
  author={Rozowsky, Joel and Abyzov, Alexej and Wang, Jing and Alves, Pedro and Raha, Debasish and Harmanci, Arif and Leng, Jing and Bjornson, Robert and Kong, Yong and Kitabayashi, Naoki and others},
  journal={Molecular systems biology},
  volume={7},
  number={1},
  year={2011},
  publisher={Nature Publishing Group}
  }
  @article{skelly2011powerful,
  title={A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data},
  author={Skelly, Daniel A and Johansson, Marnie and Madeoy, Jennifer and Wakefield, Jon and Akey, Joshua M},
  journal={Genome research},
  volume={21},
  number={10},
  pages={1728--1737},
  year={2011},
  publisher={Cold Spring Harbor Lab}
  }
  • 10.04 - Vijayachitra Modhukur | Article
  @article{dong2012modeling,
  title={Modeling gene expression using chromatin features in various cellular contexts},
  author={Dong, Xianjun and Greven, Melissa C and Kundaje, Anshul and Djebali, Sarah and Brown, James B and Cheng, Chao and Gingeras, Thomas R and Gerstein, Mark and Guig{\'o}, Roderic and Birney, Ewan and others},
  journal={Genome Biol},
  volume={13},
  pages={R53},
  year={2012}
  }
  • 17.04 - Kristjan Korjus | Diffusion Maps and Coarse-Graining: A Unified Framework for Dimensionality Reduction, Graph Partitioning, and Data Set Parameterization
  • 24.04 - Elena Nikolaeva | Article
  @article{flottmann2012stochastic,
  title={A stochastic model of epigenetic dynamics in somatic cell reprogramming},
  author={Fl{\"o}ttmann, Max and Scharp, Till and Klipp, Edda},
  journal={Frontiers in physiology},
  volume={3},
  year={2012},
  publisher={Frontiers Media SA}
  }
  • 08.05 - Aleksei Panarin | Article
  @article{goldberg2012loctree2,
  title={LocTree2 predicts localization for all domains of life},
  author={Goldberg, Tatyana and Hamp, Tobias and Rost, Burkhard},
  journal={Bioinformatics},
  volume={28},
  number={18},
  pages={i458--i465},
  year={2012},
  publisher={Oxford Univ Press}
  }
  • 15.05 - Prashanth Suravajhala | Hypothetical proteins in Human: emphasis on proteins targeted to Mitochondria
  • 22.05 - Gerli Viikmaa | Clustering large data: Acceleration of sequence clustering for next-generation sequencing data
  • 29.05 - Atilio Rrenja | Article
  @article{haynes2013differential,
  title={Differential Expression Analysis for Pathways},
  author={Haynes, Winston A and Higdon, Roger and Stanberry, Larissa and Collins, Dwayne and Kolker, Eugene},
  journal={PLOS Computational Biology},
  volume={9},
  number={3},
  pages={e1002967},
  year={2013},
  publisher={Public Library of Science}
  }
  • 05.06 - Jordan Valdma | Global visualization of pathways
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