| Searching Protein 3-D Structures in Linear Time / Tetsuo Shibuya |
| Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification / Zengyou He ; Chao Yang ; Can Yang ; Robert Z. Qi ; Jason Po-Ming Tam ; Weichuan Yu |
| Boosting Protein Threading Accuracy / Jian Peng ; Jinbo Xu |
| New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees / Cedric Chauve ; Nadia El-Mabrouk |
| A Probabilistic Graphical Model for Ab Initio Folding / Feng Zhao ; Joe DeBartolo ; Karl F. Freed ; Tobin R. Sosnick |
| Topology-Free Querying of Protein Interaction Networks / Sharon Bruckner ; Falk Huffner ; Richard M. Karp ; Ron Shamir ; Roded Sharan |
| Cross Species Expression Analysis of Innate Immune Response / Yong Lu ; Roni Rosenfeld ; Gerard J. Nau ; Ziv Bar-Joseph |
| Haplotype Inference in Complex Pedigrees / Bonnie Kirkpatrick ; Javier Rosa ; Eran Halperin |
| Storage and Retrieval of Individual Genomes / Veli Makinen ; Gonzalo Navarro ; Jouni Siren ; Niko Valimaki |
| An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations / Arvind Ramanathan ; Pratul K. Agarwal ; Maria Kurnikova ; Christopher J. Langmead |
| Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology / Alexandre Donze ; Gilles Clermont ; Axel Legay |
| Spatial Clustering of Multivariate Genomic and Epigenomic Information / Rami Jaschek ; Amos Tanay |
| How Many Bootstrap Replicates Are Necessary? / Nicholas D. Pattengale ; Masoud Alipour ; Olaf R.P. Bininda-Emonds ; Bernard M.E. Moret ; Alexandros Stamatakis |
| A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series / Oliver Stegle ; Katherine Denby ; David L. Wild ; Zoubin Ghahramani ; Karsten M. Borgwardt |
| Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation / Tali Raveh-Sadka ; Michal Levo ; Eran Segal |
| Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes / Fereydoun Hormozdiari ; Can Alkan ; Evan E. Eichler ; S. Cenk Sahinalp |
| Optimizing PCR Assays for DNA Based Cancer Diagnostics / Ali Bashir ; Qing Lu ; Dennis Carson ; Benjamin Raphael ; Yu-Tsueng Liu ; Vineet Bafna |
| The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory / Dan Gusfield |
| COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study / Xiang Zhang ; Feng Pan ; Yuying Xie ; Fei Zou ; Wei Wang |
| Overlapping Pools for High Throughput Targeted Resequencing / Snehit Prabhu ; Itsik Pe'er |
| Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction / Osvaldo Zagordi ; Lukas Geyrhofer ; Volker Roth ; Niko Beerenwinkel |
| Lifting Prediction to Alignment of RNA Pseudoknots / Mathias Mohl ; Sebastian Will ; Rolf Backofen |
| Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks / Mathieu Lavallee-Adam ; Benoit Coulombe ; Mathieu Blanchette |
| Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination / Wei Zheng ; Karl E. Griswold ; Chris Bailey-Kellogg |
| Simultaneous Alignment and Folding of Protein Sequences / Jerome Waldispuhl ; Charles W. O'Donnell ; Srinivas Devadas ; Bonnie Berger |
| Shared Peptides in Mass Spectrometry Based Protein Quantification / Banu Dost ; Nuno Bandeira ; Xiangqian Li ; Zhouxin Shen ; Steve Briggs |
| Evaluating Between-Pathway Models with Expression Data / Benjamin J. Hescott ; Maek D.M. Leiserson ; Lenore J. Cowen ; Donna K. Slonim |
| Sorting Signed Permutations by Inversions in O(n log n) Time / Krister M. Swenson ; Vaibhav Rajan ; Yu Lin |
| Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information / Saket Navlakha ; James White ; Niranjan Nagarajan ; Mihai Pop ; Carl Kingsford |
| Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data / Suzanne S. Sindi ; Benjamin J. Raphael |
| On the Relationship between DNA Periodicity and Local Chromatin Structure / Sheila M. Reynolds ; Jeff A. Bilmes ; William Stafford Noble |
| Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep (Extended Abstract) / Constantinos Daskalakis ; Elchanan Mossel ; Sebastien Roch |
| Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples / Eun Yong Kang ; Ilya Shpitser ; Chun Ye ; Eleazar Eskin |
| An Adaptive and Memory Efficient Algorithm for Genotype Imputation / Hyun Min Kang ; Noah A. Zaitlen ; Buhm Han |
| A Statistical Framework for the Functional Analysis of Metagenomes / Itai Sharon ; Amrita Pati ; Victor M. Markowitz ; Ron Y. Pinter |
| Learning Models for Aligning Protein Sequences with Predicted Secondary Structure / Eagu Kim ; Travis Wheeler ; John Kececioglu |
| Author Index |
| Searching Protein 3-D Structures in Linear Time / Tetsuo Shibuya |
| Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification / Zengyou He ; Chao Yang ; Can Yang ; Robert Z. Qi ; Jason Po-Ming Tam ; Weichuan Yu |
| Boosting Protein Threading Accuracy / Jian Peng ; Jinbo Xu |
ＥＢ
