Preface |
|
v | |
|
BEYOND GAP MODELS: RECONSTRUCTING ALIGNMENTS AND PHYLOGENIES UNDER GENOMIC-SCALE EVENTS |
|
|
|
|
1 | (2) |
|
|
|
|
|
FRESCO: Flexible Alignment with Rectangle Scoring Schemes |
|
|
3 | (12) |
|
|
|
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments |
|
|
15 | (10) |
|
|
|
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis |
|
|
25 | (12) |
|
|
|
|
|
|
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements |
|
|
37 | (12) |
|
|
|
COMPUTATIONAL CHALLENGES IN THE STUDY OF SMALL REGULATORY RNAS |
|
|
|
|
49 | (3) |
|
|
|
|
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMiR3 |
|
|
52 | (12) |
|
|
|
|
Analysis of MicroRNA-Target Interactions by a Target Structure Based Hybridization Model |
|
|
64 | (11) |
|
|
|
|
A Probabilistic Model for Small RNA Flowgram Matching |
|
|
75 | (12) |
|
|
|
|
|
COMPUTATIONAL TOOLS FOR NEXT-GENERATION SEQUENCING APPLICATIONS |
|
|
|
|
87 | (3) |
|
|
|
|
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees |
|
|
90 | (12) |
|
|
|
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies |
|
|
102 | (12) |
|
|
|
Population Sequencing Using Short Reads: HIV as a Case Study |
|
|
114 | (12) |
|
|
|
|
Analysis of Large-Scale Sequencing of Small RNAs |
|
|
126 | (11) |
|
|
|
|
|
|
KNOWLEDGE-DRIVEN ANALYSIS AND DATA INTEGRATION FOR HIGH-THROUGHPUT BIOLOGICAL DATA |
|
|
|
|
137 | (4) |
|
|
|
|
SGDI: System for Genomic Data Integration |
|
|
141 | (12) |
|
|
|
|
|
|
Annotating Pathways of Interaction Networks |
|
|
153 | (13) |
|
|
|
|
|
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer |
|
|
166 | (12) |
|
|
|
|
|
|
|
|
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis |
|
|
178 | (12) |
|
Madhuchhanda Bhattacharjee |
|
|
|
|
Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic Scans |
|
|
190 | (11) |
|
|
|
Multi-Scale Correlations in Continuous Genomic Data |
|
|
201 | (15) |
|
|
|
|
Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan Biomarkers |
|
|
216 | (12) |
|
|
|
|
|
|
|
|
|
|
MOLECULAR BIOINFORMATICS FOR DISEASE: PROTEIN INTERACTIONS AND PHENOMICS |
|
|
|
|
228 | (3) |
|
|
|
|
|
|
|
|
System-Wide Peripheral Biomarker Discovery Using Information Theory |
|
|
231 | (12) |
|
|
|
|
|
|
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation |
|
|
243 | (12) |
|
|
|
|
|
|
|
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus |
|
|
255 | (12) |
|
|
|
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization |
|
|
267 | (12) |
|
|
Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung and Ovarian Cancer Patients |
|
|
279 | (12) |
|
|
|
|
Mining Metabolic Networks for Optimal Drug Targets |
|
|
291 | (12) |
|
|
|
|
|
Global Alignment of Multiple Protein Interaction Networks |
|
|
303 | (12) |
|
|
|
|
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences |
|
|
315 | (12) |
|
|
|
|
|
|
|
|
|
MULTISCALE MODELING AND SIMULATION SESSION: FROM MOLECULES TO CELLS TO ORGANISMS? |
|
|
|
|
327 | (5) |
|
|
|
|
|
|
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition |
|
|
332 | (12) |
|
|
|
|
Prediction of Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design |
|
|
344 | (10) |
|
|
|
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations |
|
|
354 | (12) |
|
|
|
|
|
Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle |
|
|
366 | (12) |
|
|
|
|
|
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular System Hemodynamics |
|
|
378 | (12) |
|
|
|
|
|
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging |
|
|
390 | (12) |
|
|
Eleonora Savio-Galimberti |
|
|
|
|
Efficient Multiscale Simulation of Circadian Rhythms Using Automated Phase Macromodelling Techniques |
|
|
402 | (12) |
|
|
|
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics |
|
|
414 | (12) |
|
|
|
|
|
Comparisons of Protein Family Dynamics |
|
|
426 | (12) |
|
|
|
PROTEIN-NUCLEIC ACID INTERACTIONS: INTEGRATING STRUCTURE, SEQUENCE, AND FUNCTION |
|
|
|
|
438 | (3) |
|
|
|
|
|
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors |
|
|
441 | (12) |
|
|
|
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery |
|
|
453 | (12) |
|
|
|
A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor |
|
|
465 | (12) |
|
|
|
|
An Analysis of Information Content Present in Protein-DNA Interactions |
|
|
477 | (12) |
|
|
|
Use of an Evolutionary Model to Provide Evidence for a Wide Heterogeneity of Required Affinities Between Transcription Factors and Their Binding Sites in Yeast |
|
|
489 | (12) |
|
|
|
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches |
|
|
501 | (12) |
|
|
|
|
|
|
|
|
|
|
|
|
TILING MICROARRAY DATA ANALYSIS METHODS AND ALGORITHMS |
|
|
|
|
513 | (2) |
|
|
|
CMARRT: A Tool for the Analysis of ChIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure |
|
|
515 | (12) |
|
|
|
|
Transcript Normalization and Segmentation of Tiling Array Data |
|
|
527 | (12) |
|
|
|
|
|
|
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data |
|
|
539 | (12) |
|
|
|
|
TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK |
|
|
|
|
551 | (5) |
|
|
|
|
|
Assisted Curation: Does Text Mining Really Help? |
|
|
556 | (12) |
|
|
|
|
|
|
|
|
|
|
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces |
|
|
568 | (12) |
|
|
|
|
Enabling Integrative Genomic Analysis of High-Impact Human Diseases Through Text Mining |
|
|
580 | (12) |
|
|
|
Information Needs and the Role of Text Mining in Drug Development |
|
|
592 | (12) |
|
|
|
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location |
|
|
604 | (12) |
|
|
|
Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example |
|
|
616 | (12) |
|
|
|
|
|
|
|
|
|
|
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities |
|
|
628 | (12) |
|
|
|
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks |
|
|
640 | (12) |
|
|
|
|
|
|
|
Banner: An Executable Survey of Advances in Biomedical Named Entity Recognition |
|
|
652 | |
|
|