@incollection{Alekseyev/07,
AUTHOR = {Alekseyev, Max A.},
TITLE = {Multi-break rearrangements: From circular to linear genomes},
BOOKTITLE = {Proceedings of the ...},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {1-15},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/5806r8tt00n2l161/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Angibaud-Fertin-Rusu-Thevenin-Vialette/07,
AUTHOR = {Angibaud, S{\'e}bastien and Fertin, Guillaume and Rusu, Irena and Th{\'e}venin, Annelyse and Vialette, St{\'e}phane},
TITLE = {A pseudo-Boolean programming approach for computing the breakpoint distance between two genomes with duplicate genes},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {16-29},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/v974512qnq683757/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Arndt-Tang/07,
AUTHOR = {Arndt, William and Tang, Jijun},
TITLE = {Improving inversion median computation using commuting reversals and cycle information},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {30-44},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/d1r77w1654740307/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chauve-Doyon-El-Mabrouk/07,
AUTHOR = {Chauve, Cedric and Doyon, Jean-Philippe and El-Mabrouk, Nadia},
TITLE = {Inferring a duplication, speciation and loss history from a gene tree},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {45-57},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/w812601622v37p60/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
PCOMMENT = {extended abstract},
}
@incollection{Gog-Bader/07,
AUTHOR = {Gog, Simon and Bader, Martin},
TITLE = {How to achieve an equivalent simple permutation in linear time},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {58-68},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/m367463x4q122141/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Goodman-Ollikainen-Sholley/07,
AUTHOR = {Goodman, Daniel and Ollikainen, Noah and Sholley, Chris},
TITLE = {Baculovirus phylogeny based on genome rearrangements},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {69-82},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/62660124881k0055/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Guo-Schuurmans/07,
AUTHOR = {Guo, Yuhong and Schuurmans, Dale},
TITLE = {Learning gene regulatory networks via globally regularized risk minimization},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {83-95},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/e182166432143064/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lajoie-Bertrand-El-Mabrouk/07,
AUTHOR = {Lajoie, Mathieu and Bertrand, Denis and El-Mabrouk, Nadia},
TITLE = {Evolution of tandemly arrayed genes in multiple species},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {96-109},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/nw867504tq860872/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Li-Ma-Zhang/07,
AUTHOR = {Li, Guoliang and Ma, Jian and Zhang, Louxin},
TITLE = {Selecting genomes for reconstruction of ancestral genomes},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {110-121},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/x200433110468l22/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ma-Ratan-Zhang-Miller-Haussler/07,
AUTHOR = {Ma, Jian and Ratan, Aakrosh and Zhang, Louxin and Miller, Webb and Haussler, David},
TITLE = {A heuristic algorithm for reconstructing ancestral gene orders with duplications},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {122-135},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/u531m71r72464p45/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Xia-Sharakhova-Sharakhov/07,
AUTHOR = {Xia, Ai and Sharakhova, Maria V. and Sharakhov, Igor V.},
TITLE = {Reconstructing an inversion history in the Anopheles gambiae complex},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {136-148},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/k463p4n4334g6110/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zhao-Bourque/07,
AUTHOR = {Zhao, Hao and Bourque, Guillaume},
TITLE = {Recovering true rearrangement events on phylogenetic trees},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {149-161},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/4530366v4867j034/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zheng-Zhu-Sankoff/07,
AUTHOR = {Zheng, Chunfang and Zhu, Qian and Sankoff, David},
TITLE = {Parts of the problem of polyploids in rearrangement phylogeny},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {162-176},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/c8hj7l3084137024/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zheng-Rogozin-Koonin-Przytycka/07,
AUTHOR = {Zheng, Jie and Rogozin, Igor B. and Koonin, Eugene V. and Przytycka, Teresa M.},
TITLE = {A rigorous analysis of the pattern of intron conservation supports the Coelomata clade of animals},
BOOKTITLE = {Proceedings of the International Workshop on Comparative Genomics, RECOMB-CG'2007 (San Diego, CA, USA, September 16-18, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4751},
PAGES = {177-191},
YEAR = {2007},
EDITOR = {Tesler, Glenn and Durand, Dannie},
URL = {http://springerlink.metapress.com/content/l7710804w3861163/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Hormozdiari-Berenbrink-Przulj-Sahinalp/07,
AUTHOR = {Hormozdiari, Fereydoun and Berenbrink, Petra and Pr{\v{z}}ulj, Nata{\v{s}}a and Sahinalp, Cenk},
TITLE = {Not all scale free networks are born equal: The role of the seed graph in PPI network emulation},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {1-13},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/y00515t76r847272/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huang-Zhang-Roth-Bader/07,
AUTHOR = {Huang, Hailiang and Zhang, Lan V. and Roth, Frederick P. and Bader, Joel S.},
TITLE = {Probabilistic paths for protein complex inference},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {14-28},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/pr2t604l85147861/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kaltenbach-Bocker-Rahmann/07,
AUTHOR = {Kaltenbach, Hans-Michael and B{\"o}cker, Sebastian and Rahmann, Sven},
TITLE = {Markov additive chains and applications to fragment statistics for peptide mass fingerprinting},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {29-41},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/01605n285x656248/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lefebvre-Lim-Basso-Favera-Califano/07,
AUTHOR = {Lefebvre, Celine and Lim, Wei Keat and Basso, Katia and Favera, Riccardo Dalla and Califano, Andrea},
TITLE = {A context-specific network of protein-DNA and protein-protein interactions reveals new regulatory motifs in human B cells},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {42-56},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/83440181j3x1n144/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ruan-Zhang/07,
AUTHOR = {Ruan, Jianhua and Zhang, Weixiong},
TITLE = {Identification and evaluation of functional modules in gene co-expression networks},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {57-76},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/gv784n60qx30620w/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Song-Liu/07,
AUTHOR = {Song, Mingzhou (Joe) and Liu, Z. Lewis},
TITLE = {A linear discrete dynamic system model for temporal gene interaction and regulatory network influence in response to bioethanol conversion inhibitor HMF for ethanologenic yeast},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {77-95},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/q247r247r28nkl86/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wu-Mechref-Klouckova-Novotny-Tang/07,
AUTHOR = {Wu, Yin and Mechref, Yehia and Klouckova, Iveta and Novotny, Milos V. and Tang, Haixu},
TITLE = {A computational approach for the identification of site-specific protein glycosylations through ion-trap mass spectrometry},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {96-107},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/125m55598r128r35/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ruths-Tseng-Nakhleh-Ram/07,
AUTHOR = {Ruths, Derek and Tseng, Jen-Te and Nakhleh, Luay and Ram, Prahlad T.},
TITLE = {De novo signaling pathway predictions based on protein-protein interaction, targeted therapy and protein microarray analysis},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {108-118},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/93gk07132r03l516/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Fasulo-Emde-Wang-Noy-Edwards/07,
AUTHOR = {Fasulo, Daniel and Emde, Anne-Katrin and Wang, Lu-Yong and Noy, Karin and Edwards, Nathan},
TITLE = {Alignment of mass spectrometry data by clique finding and optimization},
BOOKTITLE = {Proceedings of the Joint RECOMB 2006 Satellite Workshops on Systems Biology and on Computational Proteomics (San Diego, CA, USA, December 1-3, 2006)},
SERIES = {LNCS/LNBI},
VOLUME = {4532},
PAGES = {119-129},
YEAR = {2007},
EDITOR = {Ideker, Trey and Bafna, Vineet},
URL = {http://springerlink.metapress.com/content/h716314047k25505/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Dost-Shlomi-Gupta-Ruppin-Bafna-Sharan/07,
AUTHOR = {Dost, Banu and Shlomi, Tomer and Gupta, Nitin and Ruppin, Eytan and Bafna, Vineet and Sharan, Roded},
TITLE = {QNet: A tool for querying protein interaction networks},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {1-15},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/c533325614x1272v/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Singh-Xu-Berger/07,
AUTHOR = {Singh, Rohit and Xu, Jinbo and Berger, Bonnie},
TITLE = {Pairwise global alignment of protein interaction networks by matching neighborhood topology},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {16-31},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/x11r481g03660360/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bernard-Vaughn-Hartemink/07,
AUTHOR = {Bernard, Allister and Vaughn, David S. and Hartemink, Alexander J.},
TITLE = {Reconstructing the topology of protein complexes},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {32-46},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/146568q7q427216p/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Murali-Rivera/07,
AUTHOR = {Murali, T.M. and Rivera, Corban G.},
TITLE = {Network legos: Building blocks of cellular wiring diagrams},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {47-61},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/9u50g85478653456/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Garg-Xenarios-Mendoza-DeMicheli/07,
AUTHOR = {Garg, Abhishek and Xenarios, Ioannis and Mendoza, Luis and DeMicheli, Giovanni},
TITLE = {An efficient method for dynamic analysis of gene regulatory networks and insilico gene perturbation experiments},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {62-76},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/h01570u4120x3311/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sharon-Segal/07,
AUTHOR = {Sharon, Eilon and Segal, Eran},
TITLE = {A feature-based approach to modeling protein-DNA interactions},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {77-91},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/r01x6r68x5184j1v/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Grochow-Kellis/07,
AUTHOR = {Grochow, Joshua A. and Kellis, Manolis},
TITLE = {Network motif discovery using subgraph enumeration and symmetry-breaking},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {92-106},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/232p87x375r617m2/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Narlikar-Gordan-Hartemink/07,
AUTHOR = {Narlikar, Leelavati and Gord{\^a}n, Raluca and Hartemink, Alexander J.},
TITLE = {Nucleosome occupancy information improves de novo motif discovery},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {107-121},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/av526j7u275n1508/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ben-Dor-Lipson-Tsalenko-Reimers-Baumbusch-Barrett-Weinstein-Borresen-Dale-Yakhini/07,
AUTHOR = {Ben-Dor, Amir and Lipson, Doron and Tsalenko, Anya and Reimers, Mark and Baumbusch, Lars O. and Barrett, Michael T. and Weinstein, John N. and B{\o}rresen-Dale, Anne-Lise and Yakhini, Zohar},
TITLE = {Framework for identifying common aberrations in DNA copy number data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {122-136},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/j627358450r77722/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wang-Carvalho-Miller-Pevsner-Chakravarti-Irizarry/07,
AUTHOR = {Wang, Wenyi and Carvalho, Benilton and Miller, Nate and Pevsner, Jonathan and Chakravarti, Aravinda and Irizarry, Rafael A.},
TITLE = {Estimating genome-wide copy number using allele specific mixture models},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {137-150},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/t07246812328p527/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Shi-Guo-Wu-Xing/07,
AUTHOR = {Shi, Yanxin and Guo, Fan and Wu, Wei and Xing, Eric P.},
TITLE = {GIMscan: A new statistical method for analyzing whole-genome array CGH data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {151-165},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/3j5316255510j15v/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kuwahara-Myers/07,
AUTHOR = {Kuwahara, Hiroyuki and Myers, Chris},
TITLE = {Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {166-180},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/b483r11x85u78813/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zaitlen-Reyes-Gomez-Heckerman-Jojic/07,
AUTHOR = {Zaitlen, Noah and Reyes-Gomez, Manuel and Heckerman, David and Jojic, Nebojsa},
TITLE = {Shift-invariant adaptive double threading: Learning MHC II - peptide binding},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {181-195},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/k421p420j3r23624/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{ORourke-Zaitlen-Jojic-Eskin/07,
AUTHOR = {O'Rourke, Sean and Zaitlen, Noah and Jojic, Nebojsa and Eskin, Eleazar},
TITLE = {Reconstructing the phylogeny of mobile elements},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {196-210},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/t700n72173478657/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huson-Klopper/07,
AUTHOR = {Huson, Daniel H. and Kl{\"o}pper, Tobias H.},
TITLE = {Beyond galled trees --- Decomposition and computation of galled networks},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {211-225},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/3l7x004740545206/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wexler-Geiger/07,
AUTHOR = {Wexler, Ydo and Geiger, Dan},
TITLE = {Variational upper bounds for probabilistic phylogenetic models},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {226-237},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/b45v676227525561/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bansal-Burleigh-Eulenstein-Wehe/07,
AUTHOR = {Bansal, Mukul S. and Burleigh, J. Gordon and Eulenstein, Oliver and Wehe, Andr{\'e}},
TITLE = {Heuristics for the gene-duplication problem: A $\Theta(n)$ speed-up for the local search},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {238-252},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/kq72464458k13904/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yu-Joachims-Elber-Pillardy/07,
AUTHOR = {Yu, Chun-Nam John and Joachims, Thorsten and Elber, Ron and Pillardy, Jaroslaw},
TITLE = {Support vector training of protein alignment models},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {253-267},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/uh3x2j770618r445/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Tang-Thomas-Tapia-Amato/07,
AUTHOR = {Tang, Xinyu and Thomas, Shawna and Tapia, Lydia and Amato, Nancy M.},
TITLE = {Tools for simulating and analyzing RNA folding kinetics},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {268-282},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/433u3k75472v4542/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lu-Sze/07,
AUTHOR = {Lu, Yue and Sze, Sing-Hoi},
TITLE = {Multiple sequence alignment based on profile alignment of intermediate sequences},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {283-295},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/l6h716u4h2521227/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Pradines-Dancik-Ruttenberg-Farutin/07,
AUTHOR = {Pradines, Jo{\"e}l and Dan{\v{c}}{\'{i}}k, Vlado and Ruttenberg, Alan and Farutin, Victor},
TITLE = {Connectedness profiles in protein networks for the analysis of gene expression data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {296-310},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/v1r2005376020877/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Piccolboni/07,
AUTHOR = {Piccolboni, Antonio},
TITLE = {Multivariate segmentation in the analysis of transcription tiling array data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {311-324},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/u5r7553h67262643/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kannan-Emili-Frey/07,
AUTHOR = {Kannan, Anitha and Emili, Andrew and Frey, Brendan J.},
TITLE = {A Bayesian model that links microarray mRNA measurements to mass spectrometry protein measurements},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {325-338},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/509t01018w04467m/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Ozery-Flato-Shamir/07,
AUTHOR = {Ozery-Flato, Michal and Shamir, Ron},
TITLE = {Rearrangements in genomes with centromeres part I: Translocations},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {339-353},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/d335716667531663/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Corona-Raphael-Eskin/07,
AUTHOR = {Corona, Erik and Raphael, Benjamin and Eskin, Eleazar},
TITLE = {Identification of deletion polymorphisms from haplotypes},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {354-365},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/m56706t273363420/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kamisetty-Xing-Langmead/07,
AUTHOR = {Kamisetty, Hetunandan and Xing, Eric P. and Langmead, Christopher J.},
TITLE = {Free energy estimates of all-atom protein structures using generalized belief propagation},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {366-380},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/w135727272664390/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Yanover-Schueler-Furman-Weiss/07,
AUTHOR = {Yanover, Chen and Schueler-Furman, Ora and Weiss, Yair},
TITLE = {Minimizing and learning energy functions for side-chain prediction},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {381-395},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/6580j67688105283/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Nigham-Hsu/07,
AUTHOR = {Nigham, Anshul and Hsu, David},
TITLE = {Protein conformational flexibility analysis with noisy data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {396-411},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/e428770408168357/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Inbar-Schneidman-Duhovny-Dror-Nussinov-Wolfson/07,
AUTHOR = {Inbar, Yuval and Schneidman-Duhovny, Dina and Dror, Oranit and Nussinov, Ruth and Wolfson, Haim J.},
TITLE = {Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {412-429},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/n704738314q54067/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Philippakis-Qureshi-Berger-Bulyk/07,
AUTHOR = {Philippakis, Anthony A. and Qureshi, Aaron M. and Berger, Michael F. and Bulyk, Martha L.},
TITLE = {Design of compact, universal DNA microarrays for protein binding microarray experiments},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {430-443},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/71123839wv324h3u/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bern-Goldberg/07,
AUTHOR = {Bern, Marshall and Goldberg, David},
TITLE = {Improved ranking functions for protein and modification-site identifications},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {444-458},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/f01v2020017070x0/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Klammer-Yi-MacCoss-Noble/07,
AUTHOR = {Klammer, Aaron A. and Yi, Xianhua and MacCoss, Michael J. and Noble, William Stafford},
TITLE = {Peptide retention time prediction yields improved tandem mass spectrum identification for diverse chromatography conditions},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {459-472},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/p80405gnmnw30850/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Schulz-Trieglaff-Hussong-Gropl-Hildebrandt-Reinert/07,
AUTHOR = {Schulz-Trieglaff, Ole and Hussong, Rene and Gr{\"o}pl, Clemens and Hildebrandt, Andreas and Reinert, Knut},
TITLE = {A fast and accurate algorithm for the quantification of peptides from mass spectrometry data},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {473-487},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/y7n4593123531572/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wu/07a,
AUTHOR = {Wu, Yufeng},
TITLE = {Association mapping of complex diseases with ancestral recombination graphs: Models and efficient algorithms},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {488-502},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/026074q3723176j0/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sridhar-Rao-Halperin/07,
AUTHOR = {Sridhar, Srinath and Rao, Satish and Halperin, Eran},
TITLE = {An efficient and accurate graph-based approach to detect population substructure},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {503-517},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/86025611j06k771l/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lee-Sung/07,
AUTHOR = {Lee, Wah-Heng and Sung, Wing-Kin},
TITLE = {RB-Finder: An improved distance-based sliding window method to detect recombination breakpoints},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {518-532},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/g8mv7238378t1807/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Harmon-Ahammad-Hammonds-Weiszmann-Celniker-Sastry-Rubin/07,
AUTHOR = {Harmon, Cyrus L. and Ahammad, Parvez and Hammonds, Ann and Weiszmann, Richard and Celniker, Susan E. and Sastry, S. Shankar and Rubin, Gerald M.},
TITLE = {Comparative analysis of spatial patterns of gene expression in Drosophila melanogaster imaginal discs},
BOOKTITLE = {Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2007 (Oakland, CA, USA, April 21-25, 2007)},
SERIES = {LNCS/LNBI},
VOLUME = {4453},
PAGES = {533-547},
YEAR = {2007},
EDITOR = {Speed, Terry and Huang, Haiyan},
URL = {http://springerlink.metapress.com/content/q431j63103tp0585/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wu-Song-Jin-Chen/07,
AUTHOR = {Wu, Weihui and Song, Yongling and Jin, Shouguang and Chen, Su-Shing},
TITLE = {An interactive map of regulatory networks of Pseudomonas aeruginosa genome},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {1-10},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/m07225177th3g709/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Dill-Knapp-Gage-Talcott-Laderoute-Lincoln/07,
AUTHOR = {Dill, David L. and Knapp, Merrill A. and Gage, Pamela and Talcott, Carolyn and Laderoute, Keith and Lincoln, Patrick},
TITLE = {The pathalyzer: A tool for analysis of signal transduction pathways},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {11-22},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/16812166846362ru/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zotenko-Guimaraes-Jothi-Przytycka/07,
AUTHOR = {Zotenko, Elena and Guimar{\~a}es, Katia S. and Jothi, Raja and Przytycka, Teresa M.},
TITLE = {Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {23-38},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/93333867q0212418/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Suthram-Shlomi-Ruppin-Sharan-Ideker/07,
AUTHOR = {Suthram, Silpa and Shlomi, Tomer and Ruppin, Eytan and Sharan, Roded and Ideker, Trey},
TITLE = {Comparison of protein-protein interaction confidence assignment schemes},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {39-50},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/h1x607t5r6515573/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lapidot-Pilpel/07,
AUTHOR = {Lapidot, Michal and Pilpel, Yitzhak},
TITLE = {Characterization of the effects of TF binding site variations on gene expression towards predicting the functional outcomes of regulatory SNPs},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {51-61},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/r256p72325461557/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{de_Hoon-Vitkup/07,
AUTHOR = {de Hoon, Michiel and Vitkup, Dennis},
TITLE = {Comparative systems biology of the sporulation initiation network in prokaryotes},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {62-69},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/257408131338w77j/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kim-Lee-Park/07,
AUTHOR = {Kim, Haseong and Lee, Jae K. and Park, Taesung},
TITLE = {Improvement of computing times in Boolean networks using chi-square tests},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {70-79},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/a7013204h13v0727/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wang-Zhang/07,
AUTHOR = {Wang, Guandong and Zhang, Weixiong},
TITLE = {Build a dictionary, learn a grammar, decipher stegoscripts, and discover genomic regulatory elements},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {80-94},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/jj23222823381274/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Kulp-Jagalur/07,
AUTHOR = {Kulp, David and Jagalur, Manjunatha},
TITLE = {Causal inference of regulator-target pairs by gene mapping of expression phenotypes},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {95-106},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/thq7jq85n7814427/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Man-Sussman-Pilpel/07,
AUTHOR = {Man, Orna and Sussman, Joel L. and Pilpel, Yitzhak},
TITLE = {Examination of the tRNA adaptation index as a predictor of protein expression levels},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {107-118},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/310t41259168pl32/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Bebek-Berenbrink-Cooper-Friedetzky-Nadeau-Sahinalp/07,
AUTHOR = {Bebek, G{\"u}rkan and Berenbrink, Petra and Cooper, Colin and Friedetzky, Tom and Nadeau, Joseph H. and Sahinalp, S. Cenk},
TITLE = {Improved duplication models for proteome network evolution},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {119-137},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/b576u40305136384/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chen-Soo-Kuo/07,
AUTHOR = {Chen, Chih-Yu and Soo, Von-Wun and Kuo, Chi-Li},
TITLE = {Application of expectation maximization clustering to transcription factor binding positions for cDNA microarray analysis},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {138-149},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/k0877761567x1542/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Chesler-Langston/07,
AUTHOR = {Chesler, Elissa J. and Langston, Michael A.},
TITLE = {Combinatorial genetic regulatory network analysis tools for high throughput transcriptomic data},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {150-165},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/ut638ph1845x1768/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Huang-Fang-Tsai-Ng/07,
AUTHOR = {Huang, Chien-Hung and Fang, Jywe-Fei and Tsai, Jeffrey J.P. and Ng, Ka-Lok},
TITLE = {Topological robustness of the protein-protein interaction networks},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {166-177},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/47461j5322286h45/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Jonnalagadda-Srinivasan/07,
AUTHOR = {Jonnalagadda, Sudhakar and Srinivasan, Rajagopalan},
TITLE = {A Bayesian approach for integrating transcription regulation and gene expression: Application to Saccharomyces Cerevisiae Cell Cycle data},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {178-187},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/c77064803n49657l/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Lehrach-Husmeier-Williams/07,
AUTHOR = {Lehrach, Wolfgang and Husmeier, Dirk and Williams, Christopher K.I.},
TITLE = {Probabilistic in silico prediction of protein-peptide interactions},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {188-197},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/l6v7241k76148824/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Sze-Zhao/07,
AUTHOR = {Sze, Sing-Hoi and Zhao, Xiaoyan},
TITLE = {Improved pattern-driven algorithms for motif finding in DNA sequences},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {198-211},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/v830349400567307/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wang-Benham/07,
AUTHOR = {Wang, Huiquan and Benham, Craig J.},
TITLE = {Annotation of promoter regions in microbial genomes based on DNA structural and sequence properties},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {212-224},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/54h173668l1234q5/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Wang-Jensen-Hannenhalli/07,
AUTHOR = {Wang, Li-San and Jensen, Shane T. and Hannenhalli, Sridhar},
TITLE = {An interaction-dependent model for transcription factor binding},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {225-234},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/d3047082ht55g176/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Zhou-Ruan-Wang-Zhang/07,
AUTHOR = {Zhou, Xuefeng and Ruan, Jianhua and Wang, Guandong and Zhang, Weixiong},
TITLE = {Computational characterization and identification of core promoters of MicroRNA genes in C. elegans, H. sapiens and A. thaliana},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {235-248},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/w8644k4137863082/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}
@incollection{Mezer-Bosis-Ashery-Nachliel-Gutman/07,
AUTHOR = {Mezer, Aviv and Bosis, Eran and Ashery, Uri and Nachliel, Esther and Gutman, Menachem},
TITLE = {A comprehensive kinetic model of the exocytotic process: Evaluation of the reaction mechanism},
BOOKTITLE = {Proceedings of the Joint Annual RECOMB 2005 Satellite Workshops on Systems Biology and on Regulatory Genomics (San Diego, CA, USA, December 2-4, 2005)},
SERIES = {LNCS/LNBI},
VOLUME = {4023},
PAGES = {249-257},
YEAR = {2007},
EDITOR = {Eskin, Eleazar and Ideker, Trey and Raphael, Ben and Workman, Christopher},
URL = {http://springerlink.metapress.com/content/6w575037w1875354/fulltext.pdf},
PUBLISHER = {Springer-Verlag},
ADDRESS = {Berlin-Heidelberg},
}