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@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}
}
@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}
}
@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}
}
@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
