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Biocomputing 2008 - Proceedings Of The Pacific Symposium [Hardback]

Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Stanford Univ, Usa), Edited by (Indiana Univ, Usa), Edited by (Univ Of Colorado Health Sciences Center, Usa)
  • Formāts: Hardback, 684 pages
  • Izdošanas datums: 18-Dec-2007
  • Izdevniecība: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9812776087
  • ISBN-13: 9789812776082
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  • Cena: 357,72 €
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  • Bibliotēkām
  • Formāts: Hardback, 684 pages
  • Izdošanas datums: 18-Dec-2007
  • Izdevniecība: World Scientific Publishing Co Pte Ltd
  • ISBN-10: 9812776087
  • ISBN-13: 9789812776082
Citas grāmatas par šo tēmu:
The Pacific Symposium on Biocomputing (PSB) 2008 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2008 will be held on January 4-8, 2008 at the Fairmont Orchid, Big Island of Hawaii. Tutorials will be offered prior to the start of the conference.PSB 2008 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's hot topics. In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field.
Preface v
BEYOND GAP MODELS: RECONSTRUCTING ALIGNMENTS AND PHYLOGENIES UNDER GENOMIC-SCALE EVENTS
Session Introduction
1(2)
Michael Brudno
Bernard Moret
Randy Linder
Tandy Warnow
FRESCO: Flexible Alignment with Rectangle Scoring Schemes
3(12)
A.V. Dalca
M. Brudno
Local Reliability Measures from Sets of Co-Optimal Multiple Sequence Alignments
15(10)
Giddy Landan
Dan Graur
The Effect of the Guide Tree on Multiple Sequence Alignments and Subsequent Phylogenetic Analysis
25(12)
S. Nelesen
K. Liu
D. Zhao
C. R. Linder
T. Warnow
Sensitivity Analysis for Reversal Distance and Breakpoint Reuse in Genome Rearrangements
37(12)
Amit U. Sinha
Jaroslaw Meller
COMPUTATIONAL CHALLENGES IN THE STUDY OF SMALL REGULATORY RNAS
Session Introduction
49(3)
Doron Betel
Christina Leslie
Nikolaus Rajewsky
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMiR3
52(12)
J. C. Huang
B. J. Frey
Q. D. Morris
Analysis of MicroRNA-Target Interactions by a Target Structure Based Hybridization Model
64(11)
Dang Long
Chi Yu Chan
Ye Ding
A Probabilistic Model for Small RNA Flowgram Matching
75(12)
Vladimir Vacic
Hailing Jin
Jian-Kang Zhu
Stefano Lonardi
COMPUTATIONAL TOOLS FOR NEXT-GENERATION SEQUENCING APPLICATIONS
Session Introduction
87(3)
Francisco M. De La Vega
Gabor T. Marth
Granger Sutton
TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences Using Suffix Trees
90(12)
Benjarath Phoophakdee
Mohammed J. Zaki
Pash 2.0: Scaleable Sequence Anchoring for Next-Generation Sequencing Technologies
102(12)
Cristian Coarfa
Aleksandar Milosavljevic
Population Sequencing Using Short Reads: HIV as a Case Study
114(12)
Vladimir Jojic
Tomer Hertz
Nebojsa Jojic
Analysis of Large-Scale Sequencing of Small RNAs
126(11)
A. J. Olson
J. Brennecke
A. A. Aravin
G. J. Hannon
R. Sachidanandam
KNOWLEDGE-DRIVEN ANALYSIS AND DATA INTEGRATION FOR HIGH-THROUGHPUT BIOLOGICAL DATA
Session Introduction
137(4)
Michael F. Ochs
John Quackenbush
Ramana Davuluri
SGDI: System for Genomic Data Integration
141(12)
V. J. Carey
J. Gentry
D. Sarkar
R. Gentleman
S. Ramaswamy
Annotating Pathways of Interaction Networks
153(13)
Jayesh Pandey
Mehmet Koyuturk
Wojciech Szpankowski
Ananth Grama
Integrating Microarray and Proteomics Data to Predict the Response of Cetuximab in Patients with Rectal Cancer
166(12)
Anneleen Daeman
Olivier Gevaert
Tijl de Bie
Annelies Debucquoy
Jean-Pascal Machiels
Bart de Moor
Karin Haustermans
A Bayesian Framework for Data and Hypotheses Driven Fusion of High Throughput Data: Application to Mouse Organogenesis
178(12)
Madhuchhanda Bhattacharjee
Colin Pritchard
Peter Nelson
Gathering the Gold Dust: Methods for Assessing the Aggregate Impact of Small Effect Genes in Genomic Scans
190(11)
Michael A. Province
Ingrid B. Borecki
Multi-Scale Correlations in Continuous Genomic Data
201(15)
R. E. Thurman
W. S. Noble
J. A. Stamatoyannopoulos
Analysis of MALDI-TOF Spectrometry Data for Detection of Glycan Biomarkers
216(12)
Habtom W. Ressom
Rency S. Varghese
Lenka Goldman
Christopher A. Loffredo
Mohammed Abdel-Hamid
Zuzana Kyselova
Yehia Mechref
Milos Novotny
Radoslav Goldman
MOLECULAR BIOINFORMATICS FOR DISEASE: PROTEIN INTERACTIONS AND PHENOMICS
Session Introduction
228(3)
Yves A. Lussier
Younghee Lee
Predrag Radivojac
Yanay Ofran
Marco Punta
Atul Butte
Maricel Kann
System-Wide Peripheral Biomarker Discovery Using Information Theory
231(12)
Gil Alterovitz
Michael Xiang
Jonathan Liu
Amelia Chang
Marco F. Ramoni
Novel Integration of Hospital Electronic Medical Records and Gene Expression Measurements to Identify Genetic Markers of Maturation
243(12)
David P. Chen
Susan C. Weber
Philip S. Constantinou
Todd A. Ferris
Henry J. Lowe
Atul J. Butte
Networking Pathways Unveils Association Between Obesity and Non-Insulin Dependent Diabetes Mellitus
255(12)
Haiyan Hu
Xiaoman Li
Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma Using Simultaneous Nonnegative Matrix Factorization
267(12)
Liviu Badea
Integration of Microarray and Textual Data Improves the Prognosis Prediction of Breast, Lung and Ovarian Cancer Patients
279(12)
O. Gevaert
S. Van Vooren
B. De Moor
Mining Metabolic Networks for Optimal Drug Targets
291(12)
Padmavati Sridhar
Bin Song
Tamer Kahveci
Sanjay Ranka
Global Alignment of Multiple Protein Interaction Networks
303(12)
Rohit Singh
Jinbo Xu
Bonnie Berger
Predicting DNA Methylation Susceptibility Using CpG Flanking Sequences
315(12)
S. Kim
M. Li
H. Paik
K. Nephew
H. Shi
R. Kramer
D. Xu
T.-H. Huang
MULTISCALE MODELING AND SIMULATION SESSION: FROM MOLECULES TO CELLS TO ORGANISMS?
Session Introduction
327(5)
Jung-Chi Liao
Jeff Reinbolt
Roy Kerckhoffs
Anushka Michailova
Peter Arzberger
Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition
332(12)
Dariya S. Glazer
Randall J. Radmer
Russ B. Altman
Prediction of Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design
344(10)
Youyong Li
William A. Goddard III
Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations
354(12)
Hilary DeRemigio
Peter Kemper
M. Drew Lamar
Gregory D. Smith
Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle
366(12)
John Jeremy Rice
Yuhai Tu
Corrado Poggesi
Pieter P. De Tombe
Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular System Hemodynamics
378(12)
Joost Lumens
Tammo Delhaas
Borut Kirn
Theo Arts
Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging
390(12)
Frank B. Sachse
Eleonora Savio-Galimberti
Joshua I. Goldhaber
John H. B. Bridge
Efficient Multiscale Simulation of Circadian Rhythms Using Automated Phase Macromodelling Techniques
402(12)
Shatam Agarwal
Jaijeet Roychowdhury
Integration of Multi-Scale Biosimulation Models via Light-Weight Semantics
414(12)
John H. Gennari
Maxwell L. Neal
Brian E. Carlson
Daniel L. Cook
Comparisons of Protein Family Dynamics
426(12)
A. J. Rader
Joshua T. Harrell
PROTEIN-NUCLEIC ACID INTERACTIONS: INTEGRATING STRUCTURE, SEQUENCE, AND FUNCTION
Session Introduction
438(3)
Martha L. Bulyk
Alexander J. Hartemink
Ernest Fraenkel
Yael Mandel-Gutfreund
Functional Trends in Structural Classes of the DNA Binding Domains of Regulatory Transcription Factors
441(12)
Rachel Patton McCord
Martha L. Bulyk
Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery
453(12)
Raluca Gordan
Alexander J. Hartemink
A Parametric Joint Model of DNA-Protein Binding, Gene Expression and DNA Sequence Data to Detect Target Genes of a Transcription Factor
465(12)
Wei Pan
Peng Wei
Arkady Khodursky
An Analysis of Information Content Present in Protein-DNA Interactions
477(12)
Chris Kauffman
George Karypis
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)
Richard W. Lusk
Michael B. Eisen
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches
501(12)
Jae-Hyung Lee
Michael Hamilton
Colin Gleeson
Cornelia Caragea
Peter Zaback
Jeffrey D. Sander
Xue Li
Feihong Wu
Michael Terribilini
Vasant Honavar
Drena Dobbs
TILING MICROARRAY DATA ANALYSIS METHODS AND ALGORITHMS
Session Introduction
513(2)
Srinka Ghosh
Antonio Piccolboni
CMARRT: A Tool for the Analysis of ChIP-chip Data from Tiling Arrays by Incorporating the Correlation Structure
515(12)
Pei Fen Kuan
Hyonho Chun
Sunduz Keles
Transcript Normalization and Segmentation of Tiling Array Data
527(12)
Georg Zeller
Stefan R. Henz
Sascha Laubinger
Detlef Weigel
Gunnar Ratsch
GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data
539(12)
Timothy Danford
Alex Rolfe
David Gifford
TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK
Session Introduction
551(5)
K. Bretonnel Cohen
Hong Yu
Philip E. Bourne
Lynette Hirschman
Assisted Curation: Does Text Mining Really Help?
556(12)
Beatrice Alex
Claire Grover
Barry Haddow
Mijail Kabadjov
Ewan Klein
Michael Matthews
Stuart Roebuck
Richard Tobin
Xinglong Wang
Evidence for Showing Gene/Protein Name Suggestions in Bioscience Literature Search Interfaces
568(12)
Anna Divoli
Marti A. Hearst
Michael A. Wooldridge
Enabling Integrative Genomic Analysis of High-Impact Human Diseases Through Text Mining
580(12)
Joel Dudley
Atul J. Butte
Information Needs and the Role of Text Mining in Drug Development
592(12)
Phoebe M. Roberts
William S. Hayes
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location
604(12)
Scott Brady
Hagit Shatkay
Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example
616(12)
Yoshinobu Kano
Ngan Nguyen
Rune Sœtre
Kazuhiro Yoshida
Yusuke Miyao
Yoshimasa Tsuruoka
Yuichiro Matsubayashi
Sophia Ananiadou
Junichi Tsujii
Comparing Usability of Matching Techniques for Normalising Biomedical Named Entities
628(12)
Xinglong Wang
Michael Matthews
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks
640(12)
J. Gregory Caporaso
Nita Deshpande
J. Lynn Fink
Philip E. Bourne
K. Bretonnel Cohen
Lawrence Hunter
Banner: An Executable Survey of Advances in Biomedical Named Entity Recognition
652
Robert Leaman
Graciela Gonzalez