@incollection{Amir-Zuk/11,
AUTHOR = {Amir, Amnon and Zuk, Or},
TITLE = {Bacterial community reconstruction using compressed sensing},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {1-15},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/t7161816v572221w/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bhatia-Kil-Ueberheide-Chait-Tayo-Cruz-Lu-Yates-Bern/11,
AUTHOR = {Bhatia, Swapnil and Kil, Yong J. and Ueberheide, Beatrix and Chait, Brian and Tayo, Lemmuel L. and Cruz, Lourdes J. and Lu, Bingwen and Yates III, John R. and Bern, Marshall},
TITLE = {Constrained de novo sequencing of peptides with application to conotoxins},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {16-30},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/g3g4m1263734u502/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chindelevitch-Regev-Berger/11,
AUTHOR = {Chindelevitch, Leonid and Regev, Aviv and Berger, Bonnie},
TITLE = {Metabolic network analysis demystified},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {31-33},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/w37hv77q164104h0/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chindelevitch-Ziemek-Enayetallah-Randhawa-Sidders-Brockel-Huang/11,
AUTHOR = {Chindelevitch, Leonid and Ziemek, Daniel and Enayetallah, Ahmed and Randhawa, Ranjit and Sidders, Ben and Brockel, Christoph and Huang, Enoch},
TITLE = {Causal reasoning on biological networks: Interpreting transcriptional changes},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {34-37},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/j1369ww72674q043/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Donmez-Brudno/11,
AUTHOR = {Donmez, Nilgun and Brudno, Michael},
TITLE = {Hapsembler: An assembler for highly polymorphic genomes},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {38-52},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/k25q1323158x45hw/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ernst-Kellis/11,
AUTHOR = {Ernst, Jason and Kellis, Manolis},
TITLE = {Discovery and characterization of chromatin states for systematic annotation of the human genome},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {53-53},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/t577355314254640/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Erten-Bebek-Koyuturk/11,
AUTHOR = {Erten, Sinan and Bebek, Gurkan and Koyut{\"u}rk, Mehmet},
TITLE = {Disease gene prioritization based on topological similarity in protein-protein interaction networks},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {54-68},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/u7814561xn188u60/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gat-Viks-Meller-Kupiec-Shamir/11,
AUTHOR = {Gat-Viks, Irit and Meller, Renana and Kupiec, Martin and Shamir, Ron},
TITLE = {Understanding gene sequence variation in the context of transcription regulation in yeast},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {69-69},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/lj77x2h71230uw20/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Heath-Bennett-Kavraki/11,
AUTHOR = {Heath, Allison P. and Bennett, George N. and Kavraki, Lydia E.},
TITLE = {Identifying branched metabolic pathways by merging linear metabolic pathways},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {70-84},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/d4h72wn53681382j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hickey-Blanchette/11,
AUTHOR = {Hickey, Glenn and Blanchette, Mathieu},
TITLE = {A probabilistic model for sequence alignment with context-sensitive indels},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {85-103},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/6h6281332118148j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hormozdiari-Hajirasouliha-McPherson-Eichler-Sahinalp/11,
AUTHOR = {Hormozdiari, Fereydoun and Hajirasouliha, Iman and McPherson, Andrew and Eichler, Evan E. and Sahinalp, S. Cenk},
TITLE = {Simultaneous structural variation discovery in multiple paired-end sequenced genomes},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {104-105},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/78j32u356061242m/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huang-Jojic/11,
AUTHOR = {Huang, Jim C. and Jojic, Nebojsa},
TITLE = {Variable selection through correlation sifting},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {106-123},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/p305513108350658/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Jiang-Alekseyev/11,
AUTHOR = {Jiang, Shuai and Alekseyev, Max A.},
TITLE = {Weighted genomic distance can hardly impose a bound on the proportion of transpositions},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {124-133},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/g62j4j7511891736/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kim-Ma/11,
AUTHOR = {Kim, Jaebum and Ma, Jian},
TITLE = {PSAR: Measuring multiple sequence alignment reliability by probabilistic sampling},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {134-135},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/133p805258720u6v/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Kirkpatrick-Li-Karp-Halperin/11,
AUTHOR = {Kirkpatrick, Bonnie and Li, Shuai Cheng and Karp, Richard M. and Halperin, Eran},
TITLE = {Pedigree reconstruction using identity by descent},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {136-152},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/9733hu3jrgkj6h1w/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{KuttyKrishnan-Sabina-Langton-Johnston-Brent/11,
AUTHOR = {KuttyKrishnan, Sooraj and Sabina, Jeffrey and Langton, Laura and Johnston, Mark and Brent, Michael R.},
TITLE = {A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {153-153},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/r33515316605g751/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Leiserson-Tatar-Cowen-Hescott/11,
AUTHOR = {Leiserson, Mark D.M. and Tatar, Diana and Cowen, Lenore J. and Hescott, Benjamin J.},
TITLE = {Inferring mechanisms of compensation from E-MAP and SGA data using local search algorithms for max cut},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {154-167},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/553027128r9850w7/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Li-Feng-Jiang/11,
AUTHOR = {Li, Wei and Feng, Jianxing and Jiang, Tao},
TITLE = {IsoLasso: A LASSO regression approach to RNA-Seq based transcriptome assembly},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {168-188},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/23732l708042nx82/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Li-Li/11,
AUTHOR = {Li, Xin and Li, Jing},
TITLE = {Haplotype reconstruction in large pedigrees with many untyped individuals},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {189-203},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/t8pj50556t152k6x/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lin-Bar-Joseph-Murphy/11,
AUTHOR = {Lin, Tien-ho and Bar-Joseph, Ziv and Murphy, Robert F.},
TITLE = {Learning cellular sorting pathways using protein interactions and sequence motifs},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {204-221},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/b517325434118r82/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Martin-Yan-Bailey-Kellogg-Zhou-Donald/11,
AUTHOR = {Martin, Jeffrey W. and Yan, Anthony K. and Bailey-Kellogg, Chris and Zhou, Pei and Donald, Bruce R.},
TITLE = {A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {222-237},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/l420221h5r8m5147/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Medvedev-Pham-Chaisson-Tesler-Pevzner/11,
AUTHOR = {Medvedev, Paul and Pham, Son and Chaisson, Mark and Tesler, Glenn and Pevzner, Pavel},
TITLE = {Paired de Bruijn Graphs: A novel approach for incorporating mate pair information into genome assemblers},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {238-251},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/v277282558288708/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Misra-Blelloch-Ravi-Schwartz/11,
AUTHOR = {Misra, Navodit and Blelloch, Guy and Ravi, R. and Schwartz, Russell},
TITLE = {An optimization-based sampling scheme for phylogenetic trees},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {252-266},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/d148332034780417/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Mohimani-Liu-Yang-Gaudencio-Fenical-Dorrestein-Pevzner/11,
AUTHOR = {Mohimani, Hosein and Liu, Wei-Ting and Yang, Yu-Liang and Gaud{\^e}ncio, Susana P. and Fenical, William and Dorrestein, Pieter C. and Pevzner, Pavel A.},
TITLE = {Multiplex de novo sequencing of peptide antibiotics},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {267-281},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/m3p7867204q2977h/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Nadeau/11a,
AUTHOR = {Nadeau, Joe},
TITLE = {Fractal and transgenerational genetic effects on phenotypic variation and disease risk},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {282-282},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/6712u65785780177/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Newkirk-Biesinger-Chon-Yokomori-Xie/11,
AUTHOR = {Newkirk, Daniel and Biesinger, Jacob and Chon, Alvin and Yokomori, Kyoko and Xie, Xiaohui},
TITLE = {AREM: Aligning short reads from ChIP-sequencing by expectation maximization},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {283-297},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/xp5150m40571287m/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ng-Amir-Pevzner/11,
AUTHOR = {Ng, Julio and Amir, Amihood and Pevzner, Pavel A.},
TITLE = {Blocked pattern matching problem and its applications in proteomics},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {298-319},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/m883121074j191v8/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Noble-Duan-Andronescu-Schutz-McIlwain-Kim-Lee-Shendure-Fields-Blau/11,
AUTHOR = {Noble, William and Duan, Zhi-jun and Andronescu, Mirela and Schutz, Kevin and McIlwain, Sean and Kim, Yoo Jung and Lee, Choli and Shendure, Jay and Fields, Stanley and Blau, C. Anthony},
TITLE = {A three-dimensional model of the yeast genome},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {320-320},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/p4862m3337704818/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Parker-Griswold-Bailey-Kellogg/11,
AUTHOR = {Parker, Andrew S. and Griswold, Karl E. and Bailey-Kellogg, Chris},
TITLE = {Optimization of combinatorial mutagenesis},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {321-335},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/78216w6662q85m1t/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Peng-Long/11,
AUTHOR = {Peng, Hanchuan and Long, Fuhui},
TITLE = {Seeing more is knowing more: V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {336-336},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/1767663617416244/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Peng-Leung-Yiu-Chin/11a,
AUTHOR = {Peng, Yu and Leung, Henry C.M. and Yiu, S.M. and Chin, Francis Y.L.},
TITLE = {T-IDBA: A de novo iterative de Bruijn graph assembler for transcriptome},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {337-338},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/ru28m0591t186404/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Petri-Kuffner-Zimmer/11,
AUTHOR = {Petri, Tobias and K{\"u}ffner, Robert and Zimmer, Ralf},
TITLE = {Experiment specific expression patterns},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {339-354},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/h725542467jv537j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Prat-Fromer-Linial-Linial/11a,
AUTHOR = {Prat, Yosef and Fromer, Menachem and Linial, Michal and Linial, Nathan},
TITLE = {Geometric interpretation of gene expression by sparse reconstruction of transcript profiles},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {355-357},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/b622562g827714p5/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Reuveni-Meilijson-Kupiec-Ruppin-Tuller/11,
AUTHOR = {Reuveni, Shlomi and Meilijson, Isaac and Kupiec, Martin and Ruppin, Eytan and Tuller, Tamir},
TITLE = {A ribosome flow model for analyzing translation elongation},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {358-360},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/j31u273628444050/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Roberts-Cushing-Boisguerin-Madden-Donald/11,
AUTHOR = {Roberts, Kyle E. and Cushing, Patrick R. and Boisguerin, Prisca and Madden, Dean R. and Donald, Bruce R.},
TITLE = {Design of protein-protein interactions with a novel ensemble-based scoring algorithm},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {361-376},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/3tv41426w7223361/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Scheubert-Hufsky-Rasche-Bocker/11,
AUTHOR = {Scheubert, Kerstin and Hufsky, Franziska and Rasche, Florian and B{\"o}cker, Sebastian},
TITLE = {Computing fragmentation trees from metabolite multiple mass spectrometry data},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {377-391},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/683x426823p0354p/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sefer-Kingsford/11,
AUTHOR = {Sefer, Emre and Kingsford, Carl},
TITLE = {Metric labeling and semi-metric embedding for protein annotation prediction},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {392-407},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/k3p63424kp6822rp/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Shenker-ODonnell-Devadas-Berger-Waldispuhl/11,
AUTHOR = {Shenker, Solomon and O'Donnell, Charles W. and Devadas, Srinivas and Berger, Bonnie and Waldisp{\"u}hl, J{\'e}r{\^o}me},
TITLE = {Efficient traversal of beta-sheet protein folding pathways using ensemble models},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {408-423},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/l04895135415qw33/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Silverbush-Elberfeld-Sharan/11,
AUTHOR = {Silverbush, Dana and Elberfeld, Michael and Sharan, Roded},
TITLE = {Optimally orienting physical networks},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {424-436},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/d686872117712087/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Gao-Nagarajan-Sung/11,
AUTHOR = {Gao, Song and Nagarajan, Niranjan and Sung, Wing-Kin},
TITLE = {Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {437-451},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/51100656mxq18614/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sul-Han-Eskin/11,
AUTHOR = {Sul, Jae Hoon and Han, Buhm and Eskin, Eleazar},
TITLE = {Increasing power of groupwise association test with likelihood ratio test},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {452-467},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/n7w372275rq47x27/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Tarpine-Lam-Istrail/11,
AUTHOR = {Tarpine, Ryan and Lam, Fumei and Istrail, Sorin},
TITLE = {Conservative extensions of linkage disequilibrium measures from pairwise to multi-loci and algorithms for optimal tagging SNP selection},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {468-482},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/x15w4415p254017n/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Tripathy-Zeng-Zhou-Donald/11,
AUTHOR = {Tripathy, Chittaranjan and Zeng, Jianyang and Zhou, Pei and Donald, Bruce Randall},
TITLE = {Protein loop closure using orientational restraints from NMR data},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {483-498},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/78mu4022246v0545/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Vandin-Upfal-Raphael/11,
AUTHOR = {Vandin, Fabio and Upfal, Eli and Raphael, Benjamin J.},
TITLE = {{\sc De Novo} discovery of mutated driver pathways in cancer},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {499-500},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/p37172493136h623/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Waldispuhl-Ponty/11,
AUTHOR = {Waldisp{\"u}hl, J{\'e}r{\^o}me and Ponty, Yann},
TITLE = {An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {501-515},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/g15248l332h470n3/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wauthier-Jordan-Jojic/11,
AUTHOR = {Wauthier, Fabian L. and Jordan, Michael I. and Jojic, Nebojsa},
TITLE = {Nonparametric combinatorial sequence models},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {516-530},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/wwv7491042728h06/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yu-Warnow-Nakhleh/11,
AUTHOR = {Yu, Yun and Warnow, Tandy and Nakhleh, Luay},
TITLE = {Algorithms for MDC-based multi-locus phylogeny inference},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {531-545},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/q4v5060836v84856/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zakov-Goldberg-Elhadad-Ziv-Ukelson/11,
AUTHOR = {Zakov, Shay and Goldberg, Yoav and Elhadad, Michael and Ziv-Ukelson, Michal},
TITLE = {Rich parameterization improves RNA structure prediction},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {546-562},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/h2380543713373k2/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zeng-Roberts-Zhou-Donald/11,
AUTHOR = {Zeng, Jianyang and Roberts, Kyle E. and Zhou, Pei and Donald, Bruce R.},
TITLE = {A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data},
BOOKTITLE = {Proceedings of the 15th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2011 (Vancouver, BC, Canada, March 28-31, 2011)},
SERIES = {LNCS/LNBI},
VOLUME = {6577},
PAGES = {563-578},
YEAR = {2011},
EDITOR = {Bafna, Vineet and Sahinalp, S. Cenk},
URL = {http://springerlink.metapress.com/content/113j531r6xr368x6/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}