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Content
October 2007, Volume 3, Issue 10
- 1-8 Universally Sloppy Parameter Sensitivities in Systems Biology Models
by Ryan N Gutenkunst & Joshua J Waterfall & Fergal P Casey & Kevin S Brown & Christopher R Myers & James P Sethna - 1-8 A Statistical Framework for Modeling HLA-Dependent T Cell Response Data
by Jennifer Listgarten & Nicole Frahm & Carl Kadie & Christian Brander & David Heckerman - 1-10 Brightness and Darkness as Perceptual Dimensions
by Tony Vladusich & Marcel P Lucassen & Frans W Cornelissen - 1-11 Construction, Visualisation, and Clustering of Transcription Networks from Microarray Expression Data
by Tom C Freeman & Leon Goldovsky & Markus Brosch & Stijn van Dongen & Pierre Mazière & Russell J Grocock & Shiri Freilich & Janet Thornton & Anton J Enright - 1-12 Heat Shock Response in CHO Mammalian Cells Is Controlled by a Nonlinear Stochastic Process
by Ovidiu Lipan & Jean-Marc Navenot & Zixuan Wang & Lei Huang & Stephen C Peiper - 1-14 Landscape as a Model: The Importance of Geometry
by E Penelope Holland & James N Aegerter & Calvin Dytham & Graham C Smith
September 2007, Volume 3, Issue 9
- 1-5 From Pathways Databases to Network Models of Switching Behavior
by Baltazar D Aguda & Andrew B Goryachev - 1-7 Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
by Doron Betel & Kevin E Breitkreuz & Ruth Isserlin & Danielle Dewar-Darch & Mike Tyers & Christopher W V Hogue - 1-8 Bistability and Oscillations in the Huang-Ferrell Model of MAPK Signaling
by Liang Qiao & Robert B Nachbar & Ioannis G Kevrekidis & Stanislav Y Shvartsman - 1-11 Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
by Chakra Chennubhotla & Ivet Bahar - 1-12 Structural Reorganisation and Potential Toxicity of Oligomeric Species Formed during the Assembly of Amyloid Fibrils
by Mookyung Cheon & Iksoo Chang & Sandipan Mohanty & Leila M Luheshi & Christopher M Dobson & Michele Vendruscolo & Giorgio Favrin
August 2007, Volume 3, Issue 8
- 1-1 On State-Space Reduction in Multi-Strain Pathogen Models, with an Application to Antigenic Drift in Influenza A
by Sergey Kryazhimskiy & Ulf Dieckmann & Simon A Levin & Jonathan Dushoff - 1-4 Recent Evolutions of Multiple Sequence Alignment Algorithms
by Cédric Notredame - 1-8 A Primer on Learning in Bayesian Networks for Computational Biology
by Chris J Needham & James R Bradford & Andrew J Bulpitt & David R Westhead - 1-9 An Information-Theoretic Characterization of the Optimal Gradient Sensing Response of Cells
by Burton W Andrews & Pablo A Iglesias - 1-9 PERIOD–TIMELESS Interval Timer May Require an Additional Feedback Loop
by Robert S Kuczenski & Kevin C Hong & Jordi García-Ojalvo & Kelvin H Lee - 1-10 Functional Representation of Enzymes by Specific Peptides
by Vered Kunik & Yasmine Meroz & Zach Solan & Ben Sandbank & Uri Weingart & Eytan Ruppin & David Horn - 1-12 Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
by Sylvain V Costes & Artem Ponomarev & James L Chen & David Nguyen & Francis A Cucinotta & Mary Helen Barcellos-Hoff - 1-13 Automated Protein Subfamily Identification and Classification
by Duncan P Brown & Nandini Krishnamurthy & Kimmen Sjölander - 1-14 Design of Multi-Specificity in Protein Interfaces
by Elisabeth L Humphris & Tanja Kortemme - 1-15 Automated Discovery of Functional Generality of Human Gene Expression Programs
by Georg K Gerber & Robin D Dowell & Tommi S Jaakkola & David K Gifford - 1-15 A Numerical Approach to Ion Channel Modelling Using Whole-Cell Voltage-Clamp Recordings and a Genetic Algorithm
by Meron Gurkiewicz & Alon Korngreen - 1-16 Elucidating the Altered Transcriptional Programs in Breast Cancer using Independent Component Analysis
by Andrew E Teschendorff & Michel Journée & Pierre A Absil & Rodolphe Sepulchre & Carlos Caldas - 1-18 Slowness and Sparseness Lead to Place, Head-Direction, and Spatial-View Cells
by Mathias Franzius & Henning Sprekeler & Laurenz Wiskott
July 2007, Volume 3, Issue 7
- 1-8 Protein–Protein Interaction Hotspots Carved into Sequences
by Yanay Ofran & Burkhard Rost - 1-9 Chemotaxis Receptor Complexes: From Signaling to Assembly
by Robert G Endres & Joseph J Falke & Ned S Wingreen - 1-10 Introduction to Computational Proteomics
by Jacques Colinge & Keiryn L Bennett - 1-12 Natively Unstructured Loops Differ from Other Loops
by Avner Schlessinger & Jinfeng Liu & Burkhard Rost - 1-13 Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster
by Anastasia A Samsonova & Mahesan Niranjan & Steven Russell & Alvis Brazma - 1-18 Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
by Patricia A Ryan & Brian W Kirk & Chad W Euler & Raymond Schuch & Vincent A Fischetti
June 2007, Volume 3, Issue 6
- 1-3 The International Society for Computational Biology 10th Anniversary
by Lawrence Hunter & Russ B Altman & Philip E Bourne - 1-4 A View from the Dark Side
by David B Searls - 1-7 Digital Signal Processing Reveals Circadian Baseline Oscillation in Majority of Mammalian Genes
by Andrey A Ptitsyn & Sanjin Zvonic & Jeffrey M Gimble - 1-8 Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH
by Oscar M Rueda & Ramón Díaz-Uriarte - 1-9 Hierarchical Processing of Auditory Objects in Humans
by Sukhbinder Kumar & Klaas E Stephan & Jason D Warren & Karl J Friston & Timothy D Griffiths - 1-11 Machine Learning and Its Applications to Biology
by Adi L Tarca & Vincent J Carey & Xue-wen Chen & Roberto Romero & Sorin Drăghici - 1-13 Slowness: An Objective for Spike-Timing–Dependent Plasticity?
by Henning Sprekeler & Christian Michaelis & Laurenz Wiskott
May 2007, Volume 3, Issue 5
- 1-1 “Simple Rules for Editors”? Here is One Rule to Tackle Neglected Problems of Publishing
by Thomas C Erren & Michael Erren - 1-2 Ten Simple Rules for a Good Poster Presentation
by Thomas C Erren & Philip E Bourne - 1-10 Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions
by Tristan Ursell & Kerwyn Casey Huang & Eric Peterson & Rob Phillips - 1-11 Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites
by Timothy E Reddy & Charles DeLisi & Boris E Shakhnovich - 1-13 Integrated Mechanisms of Anticipation and Rate-of-Change Computations in Cortical Circuits
by Gabriel D Puccini & Maria V Sanchez-Vives & Albert Compte - 1-13 The Human Genomic Melting Map
by Fang Liu & Eivind Tøstesen & Jostein K Sundet & Tor-Kristian Jenssen & Christoph Bock & Geir Ivar Jerstad & William G Thilly & Eivind Hovig
April 2007, Volume 3, Issue 4
- 1-2 Ten Simple Rules for Making Good Oral Presentations
by Philip E Bourne - 1-7 Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
by Benjamin A Shoemaker & Anna R Panchenko
March 2007, Volume 3, Issue 3
- 1-9 Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees
by Barry G Hall & Stephen J Salipante - 1-10 Global Discriminative Learning for Higher-Accuracy Computational Gene Prediction
by Axel Bernal & Koby Crammer & Artemis Hatzigeorgiou & Fernando Pereira - 1-10 Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
by Oliver Sander & Tobias Sing & Ingolf Sommer & Andrew J Low & Peter K Cheung & P Richard Harrigan & Thomas Lengauer & Francisco S Domingues - 1-13 Potential Energy Landscape and Robustness of a Gene Regulatory Network: Toggle Switch
by Keun-Young Kim & Jin Wang - 1-14 DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
by Shaun Mahony & Philip E Auron & Panayiotis V Benos - 1-15 Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
by Eric P Nawrocki & Sean R Eddy
February 2007, Volume 3, Issue 2
- 1-10 Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology
by Stefano Ciliberti & Olivier C Martin & Andreas Wagner - 1-14 Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
by Rachel Karchin & Alvaro N A Monteiro & Sean V Tavtigian & Marcelo A Carvalho & Andrej Sali
January 2007, Volume 3, Issue 1
- 1-2 Moving Education Forward
by Fran Lewitter
December 2006, Volume 2, Issue 12
- 1-7 Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity
by Alon Kaufman & Gideon Dror & Isaac Meilijson & Eytan Ruppin - 1-8 Cooperation is Fleeting in the World of Transposable Elements
by Andreas Wagner - 1-9 Transcriptional Regulation by Competing Transcription Factor Modules
by Rutger Hermsen & Sander Tans & Pieter Rein ten Wolde
November 2006, Volume 2, Issue 11
- 1-2 Ten Simple Rules for Selecting a Postdoctoral Position
by Philip E Bourne & Iddo Friedberg - 1-7 Robustness and Fragility in Immunosenescence
by Sean P Stromberg & Jean Carlson - 1-8 Humans Can Adopt Optimal Discounting Strategy under Real-Time Constraints
by N Schweighofer & K Shishida & C E Han & Y Okamoto & S C Tanaka & S Yamawaki & K Doya - 1-10 Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle
by Jin Wang & Bo Huang & Xuefeng Xia & Zhirong Sun - 1-12 Optimal Noise Filtering in the Chemotactic Response of Escherichia coli
by Burton W Andrews & Tau-Mu Yi & Pablo A Iglesias - 1-12 Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set
by Clive H Glover & Michael Marin & Connie J Eaves & Cheryl D Helgason & James M Piret & Jennifer Bryan - 1-14 Computational Inference of Neural Information Flow Networks
by V Anne Smith & Jing Yu & Tom V Smulders & Alexander J Hartemink & Erich D Jarvis
October 2006, Volume 2, Issue 10
- 1-8 Cooperation Prevails When Individuals Adjust Their Social Ties
by Francisco C Santos & Jorge M Pacheco & Tom Lenaerts
September 2006, Volume 2, Issue 9
- 1-2 Ten Simple Rules for Reviewers
by Philip E Bourne & Alon Korngreen - 1-13 Sampling Realistic Protein Conformations Using Local Structural Bias
by Thomas Hamelryck & John T Kent & Anders Krogh - 1-14 Imitating Manual Curation of Text-Mined Facts in Biomedicine
by Raul Rodriguez-Esteban & Ivan Iossifov & Andrey Rzhetsky
August 2006, Volume 2, Issue 8
- 1-7 Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families
by Guohui Ding & Jiuhong Kang & Qi Liu & Tieliu Shi & Gang Pei & Yixue Li - 1-8 The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics
by Robert C Cannon & Giampaolo D'Alessandro
July 2006, Volume 2, Issue 7
- 1-1 On the Estimation of Intron Evolution
by Miklós Csűrös - 1-2 Authors' Reply
by Hung D Nguyen & Maki Yoshihama & Naoya Kenmochi - 1-11 Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems
by Marcus Kaiser & Claus C Hilgetag - 1-11 Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles
by Markus J Herrgård & Stephen S Fong & Bernhard Ø Palsson - 1-11 Complex Parameter Landscape for a Complex Neuron Model
by Pablo Achard & Erik De Schutter - 1-17 Wiggle—Predicting Functionally Flexible Regions from Primary Sequence
by Jenny Gu & Michael Gribskov & Philip E Bourne
June 2006, Volume 2, Issue 6
- 1-8 Assessing the Accuracy of Ancestral Protein Reconstruction Methods
by Paul D Williams & David D Pollock & Benjamin P Blackburne & Richard A Goldstein - 1-9 Parametric Alignment of Drosophila Genomes
by Colin N Dewey & Peter M Huggins & Kevin Woods & Bernd Sturmfels & Lior Pachter - 1-10 How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?
by Vitaly V Ganusov & Sergei S Pilyugin & Rafi Ahmed & Rustom Antia - 1-11 A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules
by Bjoern Peters & Huynh-Hoa Bui & Sune Frankild & Morten Nielsen & Claus Lundegaard & Emrah Kostem & Derek Basch & Kasper Lamberth & Mikkel Harndahl & Ward Fleri & Stephen S Wilson & John Sidney & Ole Lund & Soren Buus & Alessandro Sette
May 2006, Volume 2, Issue 5
- 1-8 Statistics of Knots, Geometry of Conformations, and Evolution of Proteins
by Rhonald C Lua & Alexander Y Grosberg - 1-10 Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays
by Rameen Beroukhim & Ming Lin & Yuhyun Park & Ke Hao & Xiaojun Zhao & Levi A Garraway & Edward A Fox & Ephraim P Hochberg & Ingo K Mellinghoff & Matthias D Hofer & Aurelien Descazeaud & Mark A Rubin & Matthew Meyerson & Wing Hung Wong & William R Sellers & Cheng Li - 1-10 Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach
by Christian L Barrett & Bernhard O Palsson - 1-12 Reverse Engineering the Gap Gene Network of Drosophila melanogaster
by Theodore J Perkins & Johannes Jaeger & John Reinitz & Leon Glass
April 2006, Volume 2, Issue 4
- 1-2 The Signal in the Genomes
by David Sankoff - 1-10 Practical Strategies for Discovering Regulatory DNA Sequence Motifs
by Kenzie D MacIsaac & Ernest Fraenkel - 1-13 Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation
by Eli S Groban & Arjun Narayanan & Matthew P Jacobson - 1-13 Codon Usage Domains over Bacterial Chromosomes
by Marc Bailly-Bechet & Antoine Danchin & Mudassar Iqbal & Matteo Marsili & Massimo Vergassola
March 2006, Volume 2, Issue 3
- 1-10 Circadian Clocks Are Resounding in Peripheral Tissues
by Andrey A Ptitsyn & Sanjin Zvonic & Steven A Conrad & L Keith Scott & Randall L Mynatt & Jeffrey M Gimble
February 2006, Volume 2, Issue 2
- 1-2 Ten Simple Rules for Getting Grants
by Philip E Bourne & Leo M Chalupa - 1-9 Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods
by Kai Puolamäki & Mikael Fortelius & Heikki Mannila
December 2005, Volume 1, Issue 7
- 1-8 New Maximum Likelihood Estimators for Eukaryotic Intron Evolution
by Hung D Nguyen & Maki Yoshihama & Naoya Kenmochi - 1-23 PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
by Rahul Siddharthan & Eric D Siggia & Erik van Nimwegen
November 2005, Volume 1, Issue 6
- 1-2 Bioinformatics Education—Perspectives and Challenges
by Shoba Ranganathan - 1-7 Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments
by Alon Kaufman & Alon Keinan & Isaac Meilijson & Martin Kupiec & Eytan Ruppin - 1-10 A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes
by Daniel H Haft & Jeremy Selengut & Emmanuel F Mongodin & Karen E Nelson - 1-13 Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection
by Rajeev K Azad & Jeffrey G Lawrence
October 2005, Volume 1, Issue 5
- 1-1 Protein Molecular Function Prediction by Bayesian Phylogenomics
by Barbara E Engelhardt & Michael I Jordan & Kathryn E Muratore & Steven E Brenner - 1-2 Ten Simple Rules for Getting Published
by Philip E Bourne - 1-6 The ISCB: Growing and Evolving in Step with Science
by Michael Gribskov - 1-13 Genomic Variability within an Organism Exposes Its Cell Lineage Tree
by Dan Frumkin & Adam Wasserstrom & Shai Kaplan & Uriel Feige & Ehud Shapiro
September 2005, Volume 1, Issue 4
- 1-1 Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family
by Carsten Rautengarten & Dirk Steinhauser & Dirk Büssis & Annick Stintzi & Andreas Schaller & Joachim Kopka & Thomas Altmann
July 2005, Volume 1, Issue 2
- 1-1 Recognition of Unknown Conserved Alternatively Spliced Exons
by Uwe Ohler & Noam Shomron & Christopher B Burge
June 2005, Volume 1, Issue 1
- 1-1 Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β -Hairpin
by Laxmi Parida & Ruhong Zhou