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Serafim Batzoglou
Front matter
1-15
Searching Protein 3-D Structures in Linear Time
16-30
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
31-45
Boosting Protein Threading Accuracy
46-58
New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees
59-73
A Probabilistic Graphical Model for Ab Initio Folding
74-89
Topology-Free Querying of Protein Interaction Networks
90-107
Cross Species Expression Analysis of Innate Immune Response
108-120
Haplotype Inference in Complex Pedigrees
121-137
Storage and Retrieval of Individual Genomes
138-154
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
155-169
Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology
170-183
Spatial Clustering of Multivariate Genomic and Epigenomic Information
184-200
How Many Bootstrap Replicates Are Necessary?
201-216
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
217
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
218-219
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
220-235
Optimizing PCR Assays for DNA Based Cancer Diagnostics
236-252
The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory
253-269
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
270
Overlapping Pools for High Throughput Targeted Resequencing
271-284
Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction
285-301
Lifting Prediction to Alignment of RNA Pseudoknots
302-320
Detection of Locally Over-Represented GO Terms in Protein-Protein Interaction Networks
321-338
Protein Fragment Swapping: A Method for Asymmetric, Selective Site-Directed Recombination
339-355
Simultaneous Alignment and Folding of Protein Sequences
356-371
Shared Peptides in Mass Spectrometry Based Protein Quantification
372-385
Evaluating Between-Pathway Models with Expression Data
386-399
Sorting Signed Permutations by Inversions in O(nlogn) Time
400-417
Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information
418-433
Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data
434-450
On the Relationship between DNA Periodicity and Local Chromatin Structure
451-465
Phylogenies without Branch Bounds: Contracting the Short, Pruning the Deep Extended Abstract
466-481
Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples
482-495
An Adaptive and Memory Efficient Algorithm for Genotype Imputation
496-511
A Statistical Framework for the Functional Analysis of Metagenomes
512-531
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Back matter
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