PLoS Computational Biology, Volume 5

Volume 5, Number 1, January 2009

Editorial

• 
  Evie Browne, Rosemary Dickin, Philip E. Bourne:
  A Review of 2008 for PLoS Computational Biology.

Message from ISCB

• 
  Neil F. W. Saunders, Pedro Beltrão, Lars Juhl Jensen, Daniel Jurczak, Roland Krause, Michael Kuhn, Shirley Wu:
  Microblogging the ISMB: A New Approach to Conference Reporting.

Education

• 
  Debopriya Das, Matteo Pellegrini, Joe W. Gray:
  A Primer on Regression Methods for Decoding cis-Regulatory Logic.

Research Articles

• 
  Patrick H. Bradley, Matthew J. Brauer, Joshua D. Rabinowitz, Olga G. Troyanskaya:
  Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae.
• 
  Sinisa Pajevic, Dietmar Plenz:
  Efficient Network Reconstruction from Dynamical Cascades Identifies Small-World Topology of Neuronal Avalanches.
• 
  Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart:
  A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations.
• 
  Like Fokkens, Berend Snel:
  Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes.
• 
  Dan S. Bolintineanu, Abdallah Sayyed-Ahmad, H. Ted Davis, Yiannis N. Kaznessis:
  Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore.
• 
  Mile Sikic, Sanja Tomic, Kristian Vlahovicek:
  Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests.
• 
  Dirk Müller, Jörg Stelling:
  Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures.
• 
  Stefan Engelen, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery, Alessandra Carbone:
  Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling.
• 
  Vijay Chickarmane, Tariq Enver, Carsten Peterson:
  Computational Modeling of the Hematopoietic Erythroid-Myeloid Switch Reveals Insights into Cooperativity, Priming, and Irreversibility.
• 
  Ivar Østby, Leiv Øyehaug, Gaute T. Einevoll, Erlend A. Nagelhus, Erik Plahte, Thomas Zeuthen, Catherine M. Lloyd, Ole Petter Ottersen, Stig W. Omholt:
  Astrocytic Mechanisms Explaining Neural-Activity-Induced Shrinkage of Extraneuronal Space.
• 
  Amos Ben-Zvi, Suzanne D. Vernon, Gordon Broderick:
  Model-Based Therapeutic Correction of Hypothalamic-Pituitary-Adrenal Axis Dysfunction.
• 
  Adam B. Barrett, Guy O. Billings, Richard G. M. Morris, Mark C. W. van Rossum:
  State Based Model of Long-Term Potentiation and Synaptic Tagging and Capture.
• 
  Adrian M. Altenhoff, Christophe Dessimoz:
  Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods.
• 
  Thorsten Lenser, Günter Theißen, Peter Dittrich:
  Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins.
• 
  Lucy J. Colwell, Michael P. Brenner:
  Action Potential Initiation in the Hodgkin-Huxley Model.
• 
  Wenxu Tong, Ying Wei, Leonel F. Murga, Mary Jo Ondrechen, Ronald J. Williams:
  Partial Order Optimum Likelihood (POOL): Maximum Likelihood Prediction of Protein Active Site Residues Using 3D Structure and Sequence Properties.
• 
  M. Kemal Sönmez, Naunihal T. Zaveri, Ilan A. Kerman, Sharon Burke, Charles R. Neal, Xinmin Xie, Stanley J. Watson, Lawrence Toll:
  Evolutionary Sequence Modeling for Discovery of Peptide Hormones.
• 
  Mun Ju Kim, Ivan V. Maly:
  Deterministic Mechanical Model of T-Killer Cell Polarization Reproduces the Wandering of Aim between Simultaneously Engaged Targets.
• 
  Katherine V. Wendelsdorf, Zhuo Song, Yang Cao, David C. Samuels:
  An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcription Inhibitors.
• 
  Todd A. Gibson, Debra Goldberg:
  Questioning the Ubiquity of Neofunctionalization.
• 
  Alain Mechulam, Konstantin G. Chernov, Elodie Mucher, Loic Hamon, Patrick A. Curmi, David Pastré:
  Polyamine Sharing between Tubulin Dimers Favours Microtubule Nucleation and Elongation via Facilitated Diffusion.
• 
  Adel Dayarian, Madalena Chaves, Eduardo D. Sontag, Anirvan M. Sengupta:
  Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks.
• 
  Edoardo M. Airoldi, Curtis Huttenhower, David Gresham, Charles Lu, Amy A. Caudy, Maitreya J. Dunham, James R. Broach, David Botstein, Olga G. Troyanskaya:
  Predicting Cellular Growth from Gene Expression Signatures.

Volume 5, Number 2, February 2009

Research Articles

• 
  Alexander M. Bailey, Michael B. Lawrence, Hulan Shang, Adam J. Katz, Shayn M. Peirce:
  Agent-Based Model of Therapeutic Adipose-Derived Stromal Cell Trafficking during Ischemia Predicts Ability To Roll on P-Selectin.
• 
  Barak Raveh, Angela Enosh, Ora Schueler-Furman, Dan Halperin:
  Rapid Sampling of Molecular Motions with Prior Information Constraints.
• 
  Kerry J. Kim, Vilaiwan M. Fernandes:
  Effects of Ploidy and Recombination on Evolution of Robustness in a Model of the Segment Polarity Network.
• 
  Maoz Shamir:
  The Temporal Winner-Take-All Readout.
• 
  Pär Bjelkmar, Perttu S. Niemelä, Ilpo Vattulainen, Erik Lindahl:
  Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel.
• 
  Yoram Burak, Ila R. Fiete:
  Accurate Path Integration in Continuous Attractor Network Models of Grid Cells.
• 
  Fan Li, Ines Thiele, Neema Jamshidi, Bernhard O. Palsson:
  Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling.
• 
  Michael D. Daily, Jeffrey J. Gray:
  Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins.
• 
  Samuel Feng, Philip Holmes, Alan Rorie, William T. Newsome:
  Can Monkeys Choose Optimally When Faced with Noisy Stimuli and Unequal Rewards?
• 
  Patrick F. Suthers, Madhukar S. Dasika, Vinay Satish Kumar, Gennady Denisov, John I. Glass, Costas D. Maranas:
  A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189.
• 
  Pragati Jain, Upinder S. Bhalla:
  Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch.
• 
  John M. Higgins, David T. Eddington, Sangeeta N. Bhatia, L. Mahadevan:
  Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing.
• 
  Joshua T. Dudman, Matthew F. Nolan:
  Stochastically Gating Ion Channels Enable Patterned Spike Firing through Activity-Dependent Modulation of Spike Probability.
• 
  Ana Perisic, Chris T. Bauch:
  Social Contact Networks and Disease Eradicability under Voluntary Vaccination.
• 
  Vincent A. Voelz, M. Scott Shell, Ken A. Dill:
  Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments.
• 
  Irit Gat-Viks, Martin Vingron:
  Evidence for Gene-Specific Rather Than Transcription Rate-Dependent Histone H3 Exchange in Yeast Coding Regions.
• 
  Kwang-il Lim, John Yin:
  Computational Fitness Landscape for All Gene-Order Permutations of an RNA Virus.

Volume 5, Number 3, March 2009

Review

• 
  Jason W. Bohland, Caizhi Wu, Helen Barbas, Hemant Bokil, Mihail Bota, Hans C. Breiter, Hollis T. Cline, John C. Doyle, Peter J. Freed, Ralph J. Greenspan, Suzanne N. Haber, Michael Hawrylycz, Daniel G. Herrera, Claus C. Hilgetag, Z. Josh Huang, Allan Jones, Edward G. Jones, Harvey J. Karten, David Kleinfeld, Rolf Kötter, Henry A. Lester, John M. Lin, Brett D. Mensh, Shawn Mikula, Jaak Panksepp, Joseph L. Price, Joseph Safdieh, Clifford B. Saper, Nicholas D. Schiff, Jeremy D. Schmahmann, Bruce W. Stillman, Karel Svoboda, Larry W. Swanson, Arthur W. Toga, David C. Van Essen, James D. Watson, Partha P. Mitra:
  A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale.

Research Articles

• 
  Sonia M. Leach, Hannah J. Tipney, Weiguo Feng, William A. Baumgartner Jr., Priyanka Kasliwal, Ronald P. Schuyler, Trevor Williams, Richard A. Spritz, Lawrence Hunter:
  Biomedical Discovery Acceleration, with Applications to Craniofacial Development.
• 
  Junghyo Jo, Oksana Gavrilova, Stephanie Pack, William Jou, Shawn Mullen, Anne E. Sumner, Samuel W. Cushman, Vipul Periwal:
  Hypertrophy and/or Hyperplasia: Dynamics of Adipose Tissue Growth.
• 
  Patrick Blomquist, Anna Devor, Ulf G. Indahl, István Ulbert, Gaute T. Einevoll, Anders M. Dale:
  Estimation of Thalamocortical and Intracortical Network Models from Joint Thalamic Single-Electrode and Cortical Laminar-Electrode Recordings in the Rat Barrel System.
• 
  Matthias S. Keil:
  "I Look in Your Eyes, Honey": Internal Face Features Induce Spatial Frequency Preference for Human Face Processing.
• 
  Alberto Pascual-García, David Abia, Angel R. Ortiz, Ugo Bastolla:
  Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures.
• 
  Allen W. Bryan Jr., Matthew Menke, Lenore J. Cowen, Susan Lindquist, Bonnie Berger:
  BETASCAN: Probable β-amyloids Identified by Pairwise Probabilistic Analysis.
• 
  Evangelia Petsalaki, Alexander Stark, Eduardo Garcia Urdiales, Robert B. Russell:
  Accurate Prediction of Peptide Binding Sites on Protein Surfaces.
• 
  Chun Ye, Simon J. Galbraith, James C. Liao, Eleazar Eskin:
  Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast.
• 
  Manfred G. Kitzbichler, Marie L. Smith, Søren R. Christensen, Ed Bullmore:
  Broadband Criticality of Human Brain Network Synchronization.
• 
  Oscar Westesson, Ian H. Holmes:
  Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments.
• 
  Pedro M. B. M. Coelho, Armindo Salvador, Michael A. Savageau:
  Quantifying Global Tolerance of Biochemical Systems: Design Implications for Moiety-Transfer Cycles.
• 
  Xionglei He, Jianzhi Zhang:
  On the Growth of Scientific Knowledge: Yeast Biology as a Case Study.
• 
  Yuqiao Gu, Philippe Lucas, Jean-Pierre Rospars:
  Computational Model of the Insect Pheromone Transduction Cascade.
• 
  Matthew A. Hibbs, Chad L. Myers, Curtis Huttenhower, David C. Hess, Kai Li, Amy A. Caudy, Olga G. Troyanskaya:
  Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis.
• 
  Giulia Morra, Gennady Verkhivker, Giorgio Colombo:
  Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer.
• 
  Barry J. Grant, Alemayehu A. Gorfe, James Andrew McCammon:
  Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics.
• 
  Gabriel Krouk, Daniel Tranchina, Laurence Lejay, Alexis A. Cruikshank, Dennis E. Shasha, Gloria M. Coruzzi, Rodrigo A. Gutiérrez:
  A Systems Approach Uncovers Restrictions for Signal Interactions Regulating Genome-wide Responses to Nutritional Cues in Arabidopsis.
• 
  Aidan MacNamara, Ulrich D. Kadolsky, Charles R. M. Bangham, Becca Asquith:
  T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules.
• 
  Javier Muñoz-García, Zoltan Neufeld, Boris N. Kholodenko:
  Positional Information Generated by Spatially Distributed Signaling Cascades.
• 
  Xin He, Xu Ling, Saurabh Sinha:
  Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution.
• 
  Manu, Svetlana Surkova, Alexander V. Spirov, Vitaly V. Gursky, Hilde Janssens, Ah-Ram Kim, Ovidiu Radulescu, Carlos E. Vanario-Alonso, David H. Sharp, Maria Samsonova, John Reinitz:
  Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors.
• 
  Gareth A. Palidwor, Sergey Shcherbinin, Matthew R. Huska, Tamas Rasko, Ulrich Stelzl, Anup Arumughan, Raphaele Foulle, Pablo Porras, Luis Sánchez-Pulido, Erich E. Wanker, Miguel A. Andrade-Navarro:
  Detection of Alpha-Rod Protein Repeats Using a Neural Network and Application to Huntingtin.
• 
  Pankhuri Arora, Narendra M. Dixit:
  Timing the Emergence of Resistance to Anti-HIV Drugs with Large Genetic Barriers.
• 
  Wolfram Stacklies, M. Cristina Vega, Matthias Wilmanns, Frauke Gräter:
  Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis.
• 
  Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid Eghbalnia:
  Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy.
• 
  Vinay Satish Kumar, Costas D. Maranas:
  GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions.
• 
  Vanessa Leone, Gianluca Lattanzi, Carla Molteni, Paolo Carloni:
  Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations.
• 
  Shin I. Nishimura, Masahiro Ueda, Masaki Sasai:
  Cortical Factor Feedback Model for Cellular Locomotion and Cytofission.
• 
  Ines Thiele, Neema Jamshidi, Ronan M. T. Fleming, Bernhard O. Palsson:
  Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization.
• 
  Boian S. Alexandrov, Vladimir Gelev, Sang Wook Yoo, Alan R. Bishop, Kim Ø. Rasmussen, Anny Usheva:
  Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter.
• 
  Stella Veretnik, Christopher Wills, Philippe Youkharibache, Ruben E. Valas, Philip E. Bourne:
  Sm/Lsm Genes Provide a Glimpse into the Early Evolution of the Spliceosome.
• 
  Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko:
  Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis.
• 
  Minghui Wang, Xiaohua Hu, Gang Li, Lindsey J. Leach, Elena Potokina, Arnis Druka, Robbie Waugh, Michael J. Kearsey, Zewei Luo:
  Robust Detection and Genotyping of Single Feature Polymorphisms from Gene Expression Data.
• 
  Guy Shinar, Joshua D. Rabinowitz, Uri Alon:
  Robustness in Glyoxylate Bypass Regulation.
• 
  Jeremy E. Purvis, Ravi Radhakrishnan, Scott L. Diamond:
  Steady-State Kinetic Modeling Constrains Cellular Resting States and Dynamic Behavior.
• 
  Schraga Schwartz, Nurit Gal-Mark, Nir Kfir, Ram Oren, Eddo Kim, Gil Ast:
  Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery.
• 
  Emili Balaguer-Ballester, Nicholas R. Clark, Martin Coath, Katrin Krumbholz, Susan L. Denham:
  Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation.
• 
  Taffeta M. Elliott, Frédéric E. Theunissen:
  The Modulation Transfer Function for Speech Intelligibility.

Volume 5, Number 4, April 2009

Editorial

• 
  Quentin Vicens, Philip E. Bourne:
  Ten Simple Rules To Combine Teaching and Research.

Message from ISCB

• 
  B. J. Morrison McKay, Clare Sansom:
  Webb Miller and Trey Ideker To Receive Top International Bioinformatics Awards for 2009 from the International Society for Computational Biology.

Review

• 
  David M. Shotton, Katie Portwin, Graham Klyne, Alistair Miles:
  Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article.

Research Articles

• 
  Yosef E. Maruvka, Nadav M. Shnerb:
  Polymorphism Data Can Reveal the Origin of Species Abundance Statistics.
• 
  Steffen Eikenberry, Craig J. Thalhauser, Yang Kuang:
  Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma.
• 
  Cheng Ly, Brent Doiron:
  Divisive Gain Modulation with Dynamic Stimuli in Integrate-and-Fire Neurons.
• 
  Srinivas Ramachandran, Adrian W. R. Serohijos, Le Xu, Gerhard Meissner, Nikolay V. Dokholyan:
  A Structural Model of the Pore-Forming Region of the Skeletal Muscle Ryanodine Receptor (RyR1).
• 
  Steven A. Niederer, Nicolas Smith:
  The Role of the Frank-Starling Law in the Transduction of Cellular Work to Whole Organ Pump Function: A Computational Modeling Analysis.
• 
  Curt Scharfe, Henry Horng-Shing Lu, Jutta K. Neuenburg, Edward A. Allen, Guan-Cheng Li, Thomas Klopstock, Tina M. Cowan, Gregory M. Enns, Ronald W. Davis:
  Mapping Gene Associations in Human Mitochondria using Clinical Disease Phenotypes.
• 
  Jesse D. Bloom, Matthew J. Glassman:
  Inferring Stabilizing Mutations from Protein Phylogenies: Application to Influenza Hemagglutinin.
• 
  Zheng Yang, Peter Májek, Ivet Bahar:
  Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL.
• 
  Chase L. Beisel, Christina D. Smolke:
  Design Principles for Riboswitch Function.
• 
  Dipak Barua, James R. Faeder, Jason M. Haugh:
  A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases.
• 
  Ian O'Sullivan, Etienne Burdet, Jörn Diedrichsen:
  Dissociating Variability and Effort as Determinants of Coordination.
• 
  Romulus Breban, John M. Drake, David E. Stallknecht, Pejman Rohani:
  The Role of Environmental Transmission in Recurrent Avian Influenza Epidemics.
• 
  Patrycja Vasilyev Missiuro, Kesheng Liu, Lihua Zou, Brian C. Ross, Guoyan Zhao, Jun S. Liu, Hui Ge:
  Information Flow Analysis of Interactome Networks.
• 
  Gitanjali Yadav, Rajesh S. Gokhale, Debasisa Mohanty:
  Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis.
• 
  James Robert White, Niranjan Nagarajan, Mihai Pop:
  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples.
• 
  César A. Hidalgo, Nicholas Blumm, Albert-László Barabási, Nicholas A. Christakis:
  A Dynamic Network Approach for the Study of Human Phenotypes.
• 
  Claudiu A. Giurumescu, Paul W. Sternberg, Anand R. Asthagiri:
  Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions.
• 
  Nadav Kashtan, Avi E. Mayo, Tomer Kalisky, Uri Alon:
  An Analytically Solvable Model for Rapid Evolution of Modular Structure.
• 
  Judith Legrand, Joseph R. Egan, Ian M. Hall, Simon Cauchemez, Steve Leach, Neil M. Ferguson:
  Estimating the Location and Spatial Extent of a Covert Anthrax Release.
• 
  Ping Jiang, Weixin Xu, Yuguang Mu:
  Amyloidogenesis Abolished by Proline Substitutions but Enhanced by Lipid Binding.
• 
  Orland R. Gonzalez, Susanne Gronau, Friedhelm Pfeiffer, Eduardo Mendoza, Ralf Zimmer, Dieter Oesterhelt:
  Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum.
• 
  Jan Eichhorn, Fabian H. Sinz, Matthias Bethge:
  Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
• 
  Florence Debarre, Thomas Lenormand, Sylvain Gandon:
  Evolutionary Epidemiology of Drug-Resistance in Space.
• 
  Xing Xu, Yongmei Ji, Gary D. Stormo:
  Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines.
• 
  Jakob M. A. Mauritz, Alessandro Esposito, Hagai Ginsburg, Clemens F. Kaminski, Teresa Tiffert, Virgilio L. Lew:
  The Homeostasis of Plasmodium falciparum-Infected Red Blood Cells.
• 
  Bree B. Aldridge, Julio Saez-Rodriguez, Jeremy Muhlich, Peter K. Sorger, Douglas A. Lauffenburger:
  Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling.
• 
  Mu Gao, Jeffrey Skolnick:
  From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions.
• 
  Se-Bum Paik, Tribhawan Kumar, Donald A. Glaser:
  Spontaneous Local Gamma Oscillation Selectively Enhances Neural Network Responsiveness.
• 
  Bosco K. Ho, David A. Agard:
  Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations.
• 
  Christina Toft, Tom A. Williams, Mario A. Fares:
  Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach.
• 
  Gregory W. Carter, David J. Galas, Timothy Galitski:
  Maximal Extraction of Biological Information from Genetic Interaction Data.

Volume 5, Number 5, May 2009

Messages from ISCB

• 
  Olga Vitek:
  Getting Started in Computational Mass Spectrometry-Based Proteomics.
• 
  Scott Markel:
  BioLINK Special Interest Group Session on the Future of Scientific Publishing.

Perspective

• 
  Steffen Klamt, Utz-Uwe Haus, Fabian J. Theis:
  Hypergraphs and Cellular Networks.

Review

• 
  Mark D. McDonnell, Derek Abbott:
  What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology.

Research Articles

• 
  Robert K. Bradley, Adam Roberts, Michael E. Smoot, Sudeep Juvekar, Jaeyoung Do, Colin N. Dewey, Ian H. Holmes, Lior Pachter:
  Fast Statistical Alignment.
• 
  Gregory D. Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme:
  A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family.
• 
  Axel R. Pries, Annemiek J. M. Cornelissen, Anoek A. Sloot, Marlene Hinkeldey, Matthew R. Dreher, Michael Höpfner, Mark W. Dewhirst, Timothy W. Secomb:
  Structural Adaptation and Heterogeneity of Normal and Tumor Microvascular Networks.
• 
  Yonghui Li, Yong Liu, Jun Li, Wen Qin, Kuncheng Li, Chunshui Yu, Tianzi Jiang:
  Brain Anatomical Network and Intelligence.
• 
  Stephen M. Rumble, Phil Lacroute, Adrian V. Dalca, Marc Fiume, Arend Sidow, Michael Brudno:
  SHRiMP: Accurate Mapping of Short Color-space Reads.
• 
  Smita Agrawal, Colin Archer, David V. Schaffer:
  Computational Models of the Notch Network Elucidate Mechanisms of Context-dependent Signaling.
• 
  Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur:
  How to Get the Most out of Your Curation Effort.
• 
  Li Xie, Jerry Li, Lei Xie, Philip E. Bourne:
  Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors.
• 
  Javad Golji, Robert Collins, Mohammad R. K. Mofrad:
  Molecular Mechanics of the α-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior.
• 
  Siebe B. van Albada, Pieter Rein ten Wolde:
  Differential Affinity and Catalytic Activity of CheZ in E. coli Chemotaxis.
• 
  Quentin J. M. Huys, Liam Paninski:
  Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings.
• 
  Yasser Roudi, Sheila Nirenberg, Peter E. Latham:
  Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't.
• 
  Stefano M. Marino, Vadim N. Gladyshev:
  A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues.
• 
  Christian I. Hong, Judit Zámborszky, Attila Csikász-Nagy:
  Minimum Criteria for DNA Damage-Induced Phase Advances in Circadian Rhythms.
• 
  Maoz Shamir, Oded Ghitza, Steven Epstein, Nancy Kopell:
  Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale.
• 
  Janneke F. M. Jehee, Dana H. Ballard:
  Predictive Feedback Can Account for Biphasic Responses in the Lateral Geniculate Nucleus.
• 
  Bálint Mészáros, István Simon, Zsuzsanna Dosztányi:
  Prediction of Protein Binding Regions in Disordered Proteins.
• 
  Joel O. Wertheim, Michael Worobey:
  Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2.
• 
  Damien A. Fair, Alexander Li Cohen, Jonathan D. Power, Nico U. F. Dosenbach, Jessica A. Church, Francis M. Miezin, Bradley L. Schlaggar, Steven E. Petersen:
  Functional Brain Networks Develop from a "Local to Distributed" Organization.
• 
  Nicholas J. Hudson, Antonio Reverter, Brian P. Dalrymple:
  A Differential Wiring Analysis of Expression Data Correctly Identifies the Gene Containing the Causal Mutation.

Volume 5, Number 6, June 2009

Editorials

• 
  Fran Lewitter, Michael Rebhan, Brent Richter, David P. Sexton:
  The Need for Centralization of Computational Biology Resources.
• 
  David B. Searls:
  Ten Simple Rules for Choosing between Industry and Academia.

Perspectives

• 
  Fran Lewitter, Michael Rebhan:
  Establishing a Successful Bioinformatics Core Facility Team.
• 
  Brent G. Richter, David P. Sexton:
  Managing and Analyzing Next-Generation Sequence Data.

Research Articles

• 
  Diego Prada-Gracia, Jesús Gómez-Gardeñes, Pablo Echenique, Fernando Falo:
  Exploring the Free Energy Landscape: From Dynamics to Networks and Back.
• 
  Nicholas J. Savill, William Chadwick, Sarah E. Reece:
  Quantitative Analysis of Mechanisms That Govern Red Blood Cell Age Structure and Dynamics during Anaemia.
• 
  Arne J. Nagengast, Daniel A. Braun, Daniel M. Wolpert:
  Optimal Control Predicts Human Performance on Objects with Internal Degrees of Freedom.
• 
  Zhang Zhang, Jeffrey P. Townsend:
  Maximum-Likelihood Model Averaging To Profile Clustering of Site Types across Discrete Linear Sequences.
• 
  Jes Frellsen, Ida Moltke, Martin Thiim, Kanti V. Mardia, Jesper Ferkinghoff-Borg, Thomas Hamelryck:
  A Probabilistic Model of RNA Conformational Space.
• 
  Yuanyuan Xiao, Mark R. Segal:
  Identification of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests.
• 
  Maria D. Chikina, Curtis Huttenhower, Coleen T. Murphy, Olga G. Troyanskaya:
  Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans.
• 
  Dennis A. Dean II, Daniel B. Forger, Elizabeth B. Klerman:
  Taking the Lag out of Jet Lag through Model-Based Schedule Design.
• 
  Stanca M. Ciupe, Blythe H. Devlin, M. Louise Markert, Thomas B. Kepler:
  The Dynamics of T-Cell Receptor Repertoire Diversity Following Thymus Transplantation for DiGeorge Anomaly.
• 
  Leonardo L. Gollo, Osame Kinouchi, Mauro Copelli:
  Active Dendrites Enhance Neuronal Dynamic Range.
• 
  Sangtae Ahn, Richard T. Wang, Christopher C. Park, Andy Lin, Richard M. Leahy, Kenneth Lange, Desmond J. Smith:
  Directed Mammalian Gene Regulatory Networks Using Expression and Comparative Genomic Hybridization Microarray Data from Radiation Hybrids.
• 
  Jeffrey Alstott, Michael Breakspear, Patric Hagmann, Leila Cammoun, Olaf Sporns:
  Modeling the Impact of Lesions in the Human Brain.
• 
  Gaëlle Lelandais, Yann Saint-Georges, Colette Geneix, Liza Al-Shikhley, Geneviève Dujardin, Claude Jacq:
  Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules.
• 
  Bas Teusink, Anne Wiersma, Leo Jacobs, Richard A. Notebaart, Eddy J. Smid:
  Understanding the Adaptive Growth Strategy of Lactobacillus plantarum by In Silico Optimisation.
• 
  Ankit Patel, William T. Gibson, Matthew C. Gibson, Radhika Nagpal:
  Modeling and Inferring Cleavage Patterns in Proliferating Epithelia.
• 
  Yu Xia, Eric A. Franzosa, Mark B. Gerstein:
  Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate.
• 
  Nobuyoshi Nagamine, Takayuki Shirakawa, Yusuke Minato, Kentaro Torii, Hiroki Kobayashi, Masaya Imoto, Yasubumi Sakakibara:
  Integrating Statistical Predictions and Experimental Verifications for Enhancing Protein-Chemical Interaction Predictions in Virtual Screening.
• 
  Josep M. Pujol, Joseph E. Eisenberg, Charles N. Haas, James S. Koopman:
  The Effect of Ongoing Exposure Dynamics in Dose Response Relationships.
• 
  Yossi Yovel, Mariana Laura Melcon, Matthias O. Franz, Annette Denzinger, Hans-Ulrich Schnitzler:
  The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls.
• 
  Anu Chakicherla, Carol L. Ecale Zhou, Martha Ligon Dang, Virginia Rodriguez, J. Norman Hansen, Adam T. Zemla:
  SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies.
• 
  Erwin P. Gianchandani, Andrew R. Joyce, Bernhard O. Palsson, Jason A. Papin:
  Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System.
• 
  Hiroshi Okamoto, Tomoki Fukai:
  Recurrent Network Models for Perfect Temporal Integration of Fluctuating Correlated Inputs.
• 
  Michal Brylinski, Jeffrey Skolnick:
  FINDSITE^LHM: A Threading-Based Approach to Ligand Homology Modeling.

Volume 5, Number 7, July 2009

Message from ISCB

• 
  Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein:
  Getting Started in Text Mining: Part Two.

Education

• 
  William Stafford Noble:
  A Quick Guide to Organizing Computational Biology Projects.

Review

• 
  Catia Pesquita, Daniel Faria, André O. Falcão, Phillip W. Lord, Francisco M. Couto:
  Semantic Similarity in Biomedical Ontologies.

Research Articles

• 
  Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng:
  Small RNAs Originated from Pseudogenes: cis- or trans-Acting?
• 
  Jiao Li, Xiaoyan Zhu, Jake Yue Chen:
  Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts.
• 
  Jennifer A. Flegg, Donald L. S. McElwain, Helen M. Byrne, Ian W. Turner:
  A Three Species Model to Simulate Application of Hyperbaric Oxygen Therapy to Chronic Wounds.
• 
  Lun Yang, Jian Chen, Lin He:
  Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome.
• 
  Yangle Wu, Xiaomeng Zhang, Jianglei Yu, Qi Ouyang:
  Identification of a Topological Characteristic Responsible for the Biological Robustness of Regulatory Networks.
• 
  Richard D. Rabbitt, Sarah Clifford, Kathryn D. Breneman, Brenda Farrell, William E. Brownell:
  Power Efficiency of Outer Hair Cell Somatic Electromotility.
• 
  Amy L. Bauer, Trachette L. Jackson, Yi Jiang:
  Topography of Extracellular Matrix Mediates Vascular Morphogenesis and Migration Speeds in Angiogenesis.
• 
  Andrew J. Olaharski, Nina Gonzaludo, Hans Bitter, David Goldstein, Stephan Kirchner, Hirdesh Uppal, Kyle Kolaja:
  Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors.
• 
  Ingmar Glauche, Kateri Moore, Lars Thielecke, Katrin Horn, Markus Loeffler, Ingo Roeder:
  Stem Cell Proliferation and Quiescence - Two Sides of the Same Coin.
• 
  Yongping Pan, Ruth Nussinov:
  Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View.
• 
  Chandramouli Chandrasekaran, Andrea Trubanova, Sébastien Stillittano, Alice Caplier, Asif A. Ghazanfar:
  The Natural Statistics of Audiovisual Speech.
• 
  Jun Zhang, Kent C. Berridge, Amy J. Tindell, Kyle S. Smith, J. Wayne Aldridge:
  A Neural Computational Model of Incentive Salience.
• 
  Taeyoon Kim, Wonmuk Hwang, Hyungsuk Lee, Roger D. Kamm:
  Computational Analysis of Viscoelastic Properties of Crosslinked Actin Networks.
• 
  Marialuisa Pellegrini-Calace, Tim Maiwald, Janet M. Thornton:
  PoreWalker: A Novel Tool for the Identification and Characterization of Channels in Transmembrane Proteins from Their Three-Dimensional Structure.
• 
  Daniel Geberth, Marc-Thorsten Hütt:
  Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation.
• 
  Flávio Codeço Coelho, Cláudia T. Codeço:
  Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs.
• 
  Daniel Bennequin, Ronit Fuchs, Alain Berthoz, Tamar Flash:
  Movement Timing and Invariance Arise from Several Geometries.
• 
  Lucy R. Allen, Sergei V. Krivov, Emanuele Paci:
  Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations.
• 
  Guido Gigante, Maurizio Mattia, Jochen Braun, Paolo Del Giudice:
  Bistable Perception Modeled as Competing Stochastic Integrations at Two Levels.
• 
  Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein:
  Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants.
• 
  Shigeru Shinomoto, Hideaki Kim, Takeaki Shimokawa, Nanae Matsuno, Shintaro Funahashi, Keisetsu Shima, Ichiro Fujita, Hiroshi Tamura, Taijiro Doi, Kenji Kawano, Naoko Inaba, Kikuro Fukushima, Sergei Kurkin, Kiyoshi Kurata, Masato Taira, Ken-Ichiro Tsutsui, Hidehiko Komatsu, Tadashi Ogawa, Kowa Koida, Jun Tanji, Keisuke Toyama:
  Relating Neuronal Firing Patterns to Functional Differentiation of Cerebral Cortex.
• 
  Susanne M. Rafelski, Jonathan B. Alberts, Garrett M. Odell:
  An Experimental and Computational Study of the Effect of ActA Polarity on the Speed of Listeria monocytogenes Actin-based Motility.
• 
  Olgun Guvench, Alexander D. MacKerell Jr.:
  Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation.
• 
  Mattia Zampieri, Giuseppe Legname, Claudio Altafini:
  Investigating the Conformational Stability of Prion Strains through a Kinetic Replication Model.
• 
  Sarah L. Kinnings, Nina Liu, Nancy Buchmeier, Peter J. Tonge, Lei Xie, Philip E. Bourne:
  Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis.
• 
  Felix Polyakov, Rotem Drori, Yoram Ben-Shaul, Moshe Abeles, Tamar Flash:
  A Compact Representation of Drawing Movements with Sequences of Parabolic Primitives.
• 
  Yossi Yovel, Peter Stilz, Matthias O. Franz, Arjan Boonman, Hans-Ulrich Schnitzler:
  What a Plant Sounds Like: The Statistics of Vegetation Echoes as Received by Echolocating Bats.
• 
  The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species.

Volume 5, Number 8, August 2009

Education

• 
  Stephen J. Eglen:
  A Quick Guide to Teaching R Programming to Computational Biology Students.

Perspectives

• 
  Azura M. H. Zeti, Mohd Shahir Shamsir, Khairina Tajul-Arifin, Amir F. Merican, Rahmah Mohamed, Sheila Nathan, Nor Muhammad Mahadi, Suhaimi Napis, Tin Wee Tan:
  Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges.
• 
  Daniel A. Beard, Martin J. Kushmerick:
  Strong Inference for Systems Biology.

Research Articles

• 
  Paola Causin, Giuseppe Facchetti:
  Autocatalytic Loop, Amplification and Diffusion: A Mathematical and Computational Model of Cell Polarization in Neural Chemotaxis.
• 
  Jochen S. Hub, Bert L. de Groot:
  Detection of Functional Modes in Protein Dynamics.
• 
  Robert K. Bradley, Ian H. Holmes:
  Evolutionary Triplet Models of Structured RNA.
• 
  Brian A. Kidd, David Baker, Wendy E. Thomas:
  Computation of Conformational Coupling in Allosteric Proteins.
• 
  Oliver Redfern, Benoit H. Dessailly, Timothy Dallman, Ian Sillitoe, Christine A. Orengo:
  FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies.
• 
  Yurie Okabe-Oho, Hiroki Murakami, Suguru Oho, Masaki Sasai:
  Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo.
• 
  Anshuman Dixit, Gennady Verkhivker:
  Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations.
• 
  Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan:
  Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production.
• 
  Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy:
  Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments.
• 
  Yuval Itan, Adam Powell, Mark A. Beaumont, Joachim Burger, Mark G. Thomas:
  The Origins of Lactase Persistence in Europe.
• 
  Frederik Graw, Roland R. Regoes:
  Investigating CTL Mediated Killing with a 3D Cellular Automaton.
• 
  Anne Cori, Pierre-Yves Boëlle, Guy Thomas, Gabriel M. Leung, Alain-Jacques Valleron:
  Temporal Variability and Social Heterogeneity in Disease Transmission: The Case of SARS in Hong Kong.
• 
  Wilfred Ndifon, Joshua B. Plotkin, Jonathan Dushoff:
  On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network.
• 
  Leighton Pritchard, Hui Liu, Clare Booth, Emma Douglas, Patrice François, Jacques Schrenzel, Peter E. Hedley, Paul R. J. Birch, Ian K. Toth:
  Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens.
• 
  James Corey Adams, Michael J. Keiser, Li Basuino, Henry F. Chambers, Deok-Sun Lee, Olaf G. Wiest, Patricia C. Babbitt:
  A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism.
• 
  Joost J. J. van Durme, Sebastian Maurer-Stroh, Rodrigo Gallardo, Hannah Wilkinson, Frederic Rousseau, Joost Schymkowitz:
  Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data.
• 
  Virginia Castillo, Salvador Ventura:
  Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases.
• 
  Naaman Kam, Yitzhak Pilpel, Mike Fainzilber:
  Can Molecular Motors Drive Distance Measurements in Injured Neurons?
• 
  Pu Liu, Fangqiang Zhu, Dmitrii N. Rassokhin, Dimitris K. Agrafiotis:
  A Self-Organizing Algorithm for Modeling Protein Loops.
• 
  Stefan Auer, Antonio Trovato, Michele Vendruscolo:
  A Condensation-Ordering Mechanism in Nanoparticle-Catalyzed Peptide Aggregation.
• 
  Dan Siegal-Gaskins, Joshua N. Ash, Sean Crosson:
  Model-Based Deconvolution of Cell Cycle Time-Series Data Reveals Gene Expression Details at High Resolution.
• 
  David Balduzzi, Giulio Tononi:
  Qualia: The Geometry of Integrated Information.
• 
  Shenghua Li, Paul Brazhnik, Bruno W. S. Sobral, John J. Tyson:
  Temporal Controls of the Asymmetric Cell Division Cycle in Caulobacter crescentus.
• 
  Stefan J. Kiebel, Katharina von Kriegstein, Jean Daunizeau, Karl J. Friston:
  Recognizing Sequences of Sequences.
• 
  Yuzhen Ye, Thomas G. Doak:
  A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes.
• 
  Daniel A. Braun, Pedro A. Ortega, Daniel M. Wolpert:
  Nash Equilibria in Multi-Agent Motor Interactions.
• 
  Jan Engelstädter, Sebastian Bonhoeffer:
  Red Queen Dynamics with Non-Standard Fitness Interactions.
• 
  Mati Cohen, Vladimir Potapov, Gideon Schreiber:
  Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction.
• 
  Goedele Roos, Nicolas Foloppe, Koen Van Laer, Lode Wyns, Lennart Nilsson, Paul Geerlings, Joris Messens:
  How Thioredoxin Dissociates Its Mixed Disulfide.
• 
  Regina Samaga, Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, Steffen Klamt:
  The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
• 
  Fabrizio Marinelli, Fabio Pietrucci, Alessandro Laio, Stefano Piana:
  A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations.
• 
  Steven Lemm, Klaus-Robert Müller, Gabriel Curio:
  A Generalized Framework for Quantifying the Dynamics of EEG Event-Related Desynchronization.
• 
  Oleksii Kuchaiev, Marija Rasajski, Desmond J. Higham, Natasa Przulj:
  Geometric De-noising of Protein-Protein Interaction Networks.
• 
  Jing Tang, William P. Hanage, Christophe Fraser, Jukka Corander:
  Identifying Currents in the Gene Pool for Bacterial Populations Using an Integrative Approach.
• 
  Eilen Nordlie, Marc-Oliver Gewaltig, Hans Ekkehard Plesser:
  Towards Reproducible Descriptions of Neuronal Network Models.

Volume 5, Number 9, September 2009

Editorial

• 
  Alex Bateman, Philip E. Bourne:
  Ten Simple Rules for Chairing a Scientific Session.

Perspective

• 
  Frank Eisenhaber, Chee Keong Kwoh, See-Kiong Ng, Wing-Kin Sung, Limsoon Wong:
  Brief Overview of Bioinformatics Activities in Singapore.

Research Articles

• 
  William Ritchie, Megha Rajasekhar, Stephane Flamant, John E. J. Rasko:
  Conserved Expression Patterns Predict microRNA Targets.
• 
  Yemin Shi, Hanbin Liu, Dahai Gai, Jianpeng Ma, Xiaojiang S. Chen:
  A Computational Analysis of ATP Binding of SV40 Large Tumor Antigen Helicase Motor.
• 
  Xueping Yu, Joseph Ivanic, Anders Wallqvist, Jaques Reifman:
  A Novel Scoring Approach for Protein Co-Purification Data Reveals High Interaction Specificity.
• 
  Stephen A. Stanhope, Srikumar Sengupta, Johan den Boon, Paul Ahlquist, Michael A. Newton:
  Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification.
• 
  Santhosh Palani, Casim A. Sarkar:
  Integrating Extrinsic and Intrinsic Cues into a Minimal Model of Lineage Commitment for Hematopoietic Progenitors.
• 
  Sami El Boustani, Olivier Marre, Sébastien Béhuret, Pierre Baudot, Pierre Yger, Thierry Bal, Alain Destexhe, Yves Frégnac:
  Network-State Modulation of Power-Law Frequency-Scaling in Visual Cortical Neurons.
• 
  Philippe Lemey, Andrew Rambaut, Alexei J. Drummond, Marc A. Suchard:
  Bayesian Phylogeography Finds Its Roots.
• 
  Jiguang Wang, Shi-Hua Zhang, Yong Wang, Luonan Chen, Xiang-Sun Zhang:
  Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases.
• 
  Deborah A. Striegel, Monica K. Hurdal:
  Chemically Based Mathematical Model for Development of Cerebral Cortical Folding Patterns.
• 
  Frank J. Bruggeman, Nils Blüthgen, Hans V. Westerhoff:
  Noise Management by Molecular Networks.
• 
  Michelle S. Scott, Fabio Avolio, Motoharu Ono, Angus I. Lamond, Geoffrey J. Barton:
  Human miRNA Precursors with Box H/ACA snoRNA Features.
• 
  Steven H. Wu, Michael A. Black, Robyn A. North, Kelly R. Atkinson, Allen G. Rodrigo:
  A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels.
• 
  Dusan Misevic, Roger D. Kouyos, Sebastian Bonhoeffer:
  Predicting the Evolution of Sex on Complex Fitness Landscapes.
• 
  Juen Guo, Kevin D. Hall:
  Estimating the Continuous-Time Dynamics of Energy and Fat Metabolism in Mice.
• 
  Rui-Ru Ji, Heshani de Silva, Yisheng Jin, Robert E. Bruccoleri, Jian Cao, Aiqing He, Wenjun Huang, Paul S. Kayne, Isaac Neuhaus, Karl-Heinz Ott, Becky Penhallow, Mark I. Cockett, Michael G. Neubauer, Nathan O. Siemers, Petra Ross-MacDonald:
  Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities.
• 
  Balázs Ujfalussy, Tamás Kiss, Péter Érdi:
  Parallel Computational Subunits in Dentate Granule Cells Generate Multiple Place Fields.
• 
  Cuong Than, Luay Nakhleh:
  Species Tree Inference by Minimizing Deep Coalescences.
• 
  Steve Hoffmann, Christian Otto, Stefan Kurtz, Cynthia M. Sharma, Philipp Khaitovich, Jörg Vogel, Peter F. Stadler, Jörg Hackermüller:
  Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures.
• 
  Jasmine Foo, Mark W. Drummond, Bayard Clarkson, Tessa Holyoake, Franziska Michor:
  Eradication of Chronic Myeloid Leukemia Stem Cells: A Novel Mathematical Model Predicts No Therapeutic Benefit of Adding G-CSF to Imatinib.
• 
  Simon Barthelmé, Pascal Mamassian:
  Evaluation of Objective Uncertainty in the Visual System.
• 
  Julie Baussand, Alessandra Carbone:
  A Combinatorial Approach to Detect Coevolved Amino Acid Networks in Protein Families of Variable Divergence.
• 
  Jiyong Park, Byungnam Kahng, Wonmuk Hwang:
  Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine.
• 
  Michiel W. H. Remme, Máté Lengyel, Boris S. Gutkin:
  The Role of Ongoing Dendritic Oscillations in Single-Neuron Dynamics.
• 
  Stefano Allesina, Mercedes Pascual:
  Googling Food Webs: Can an Eigenvector Measure Species' Importance for Coextinctions?
• 
  Pietro Berkes, Richard E. Turner, Maneesh Sahani:
  A Structured Model of Video Reproduces Primary Visual Cortical Organisation.
• 
  Timothy R. Lezon, Andrej Sali, Ivet Bahar:
  Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models.
• 
  Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac:
  Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins.
• 
  Samuel A. Danziger, Roberta Baronio, Lydia Ho, Linda Hall, Kirsty Salmon, G. Wesley Hatfield, Peter Kaiser, Richard H. Lathrop:
  Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning.
• 
  Jennifer L. Lahti, Adam P. Silverman, Jennifer R. Cochran:
  Interrogating and Predicting Tolerated Sequence Diversity in Protein Folds: Application to E. elaterium Trypsin Inhibitor-II Cystine-Knot Miniprotein.

Volume 5, Number 10, October 2009

Message from ISCB

• 
  Donna K. Slonim, Itai Yanai:
  Getting Started in Gene Expression Microarray Analysis.

Perspectives

• 
  Silvia Restrepo, Andrés Pinzón Velasco, Luis Miguel Rodriguez-Rojas, Roberto Sierra, Alejandro Grajales, Adriana Bernal, Emiliano Barreto, Pedro Moreno, Maria Mercedes Zambrano, Marco Cristancho, Andrés González, Harold E. Castro:
  Computational Biology in Colombia.
• 
  Eva C. Berglund, Björn Nystedt, Siv G. E. Andersson:
  Computational Resources in Infectious Disease: Limitations and Challenges.
• 
  Edward C. Holmes, Bryan T. Grenfell:
  Discovering the Phylodynamics of RNA Viruses.
• 
  Wesley C. Van Voorhis, Wim G. J. Hol, Peter J. Myler, Lance J. Stewart:
  The Role of Medical Structural Genomics in Discovering New Drugs for Infectious Diseases.

Research Articles

• 
  Ibrahim Baris, Aytug Tuncel, Natali Ozber, Ozlem Keskin, I. Halil Kavakli:
  Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase.
• 
  Mateusz Sikora, Joanna I. Sulkowska, Marek Cieplak:
  Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots.
• 
  Maksat Ashyraliyev, Ken Siggens, Hilde Janssens, Joke G. Blom, Michael Akam, Johannes Jaeger:
  Gene Circuit Analysis of the Terminal Gap Gene huckebein.
• 
  Katie Bentley, Giovanni Mariggi, Holger Gerhardt, Paul A. Bates:
  Tipping the Balance: Robustness of Tip Cell Selection, Migration and Fusion in Angiogenesis.
• 
  Takeshi Hase, Hiroshi Tanaka, Yasuhiro Suzuki, So Nakagawa, Hiroaki Kitano:
  Structure of Protein Interaction Networks and Their Implications on Drug Design.
• 
  François O. David, Etienne Hugues, Tristan Cenier, Nicolas Fourcaud-Trocmé, Nathalie Buonviso:
  Specific Entrainment of Mitral Cells during Gamma Oscillation in the Rat Olfactory Bulb.
• 
  Hédi Hegyi, László Buday, Peter Tompa:
  Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins.
• 
  Mark P. Little, Anna Gola, Ioanna Tzoulaki:
  A Model of Cardiovascular Disease Giving a Plausible Mechanism for the Effect of Fractionated Low-Dose Ionizing Radiation Exposure.
• 
  Thierry Mora, Howard Yu, Yoshiyuki Sowa, Ned S. Wingreen:
  Steps in the Bacterial Flagellar Motor.
• 
  Holly J. Atkinson, Patricia C. Babbitt:
  An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations.
• 
  Canan Atilgan, Ali Rana Atilgan:
  Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein.
• 
  Alon Zaslaver, Shai Kaplan, Anat Bren, Adrian Jinich, Avi E. Mayo, Erez Dekel, Uri Alon, Shalev Itzkovitz:
  Invariant Distribution of Promoter Activities in Escherichia coli.
• 
  Libin Rong, Alan S. Perelson:
  Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy.
• 
  Marc Hafner, Heinz Koeppl, Martin Hasler, Andreas Wagner:
  'Glocal' Robustness Analysis and Model Discrimination for Circadian Oscillators.
• 
  Alexander Lange, Neil M. Ferguson:
  Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens.
• 
  Bard Ermentrout, Daniel J. Simons, Peter W. Land:
  Subbarrel Patterns in Somatosensory Cortical Barrels Can Emerge from Local Dynamic Instabilities.
• 
  Vassilios N. Christopoulos, Paul R. Schrater:
  Grasping Objects with Environmentally Induced Position Uncertainty.
• 
  Nobuto Takeuchi, Paulien Hogeweg:
  Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization.
• 
  Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji:
  High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations.
• 
  Yizhi Cai, Matthew W. Lux, Laura Adam, Jean Peccoud:
  Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars.
• 
  Omar N. A. Demerdash, Michael D. Daily, Julie C. Mitchell:
  Structure-Based Predictive Models for Allosteric Hot Spots.
• 
  Dileep George, Jeff Hawkins:
  Towards a Mathematical Theory of Cortical Micro-circuits.
• 
  Jouhyun Jeon, Jae-Seong Yang, Sanguk Kim:
  Integration of Evolutionary Features for the Identification of Functionally Important Residues in Major Facilitator Superfamily Transporters.
• 
  José M. Peregrín-Alvarez, Xuejian Xiong, Chong Su, John Parkinson:
  The Modular Organization of Protein Interactions in Escherichia coli.
• 
  Penelope A. Hancock:
  Combining Fungal Biopesticides and Insecticide-Treated Bednets to Enhance Malaria Control.
• 
  Hsiao-Mei Lu, Jie Liang:
  Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES.
• 
  Jin Liu, Ruth Nussinov:
  The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation.

Volume 5, Number 11, November 2009

Perspectives

• 
  Mary Shimoyama, G. Thomas Hayman, Stanley J. F. Laulederkind, Rajni Nigam, Timothy Lowry, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob:
  The Rat Genome Database Curators: Who, What, Where, Why.

Review

• 
  Albert A. de Graaf, Andreas P. Freidig, Baukje De Roos, Neema Jamshidi, Matthias Heinemann, Johan A. C. Rullmann, Kevin D. Hall, Martin Adiels, Ben van Ommen:
  Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology.

Research Articles

• 
  Srivas Chennu, Patrick Craston, Bradley P. Wyble, Howard Bowman:
  Attention Increases the Temporal Precision of Conscious Perception: Verifying the Neural-ST² Model.
• 
  Arno Onken, Steffen Grünewälder, Matthias H. J. Munk, Klaus Obermayer:
  Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation.
• 
  Omer Dushek, Raibatak Das, Daniel Coombs:
  A Role for Rebinding in Rapid and Reliable T Cell Responses to Antigen.
• 
  Nicolas Pinto, David Doukhan, James J. DiCarlo, David D. Cox:
  A High-Throughput Screening Approach to Discovering Good Forms of Biologically Inspired Visual Representation.
• 
  Pål O. Westermark, David K. Welsh, Hitoshi Okamura, Hanspeter Herzel:
  Quantification of Circadian Rhythms in Single Cells.
• 
  Sergei L. Kosakovsky Pond, David Posada, Eric W. Stawiski, Colombe Chappey, Art F. Y. Poon, Gareth Hughes, Esther Fearnhill, Mike B. Gravenor, Andrew J. Leigh Brown, Simon D. W. Frost:
  An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1.
• 
  Congxin Li, Xiaofang Chen, Pengye Wang, Weichi Wang:
  Circadian KaiC Phosphorylation: A Multi-Layer Network.
• 
  Dominik M. Wittmann, Florian Blöchl, Dietrich Trümbach, Wolfgang Wurst, Nilima Prakash, Fabian J. Theis:
  Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary.
• 
  Tian Ge, Keith M. Kendrick, Jianfeng Feng:
  A Novel Extended Granger Causal Model Approach Demonstrates Brain Hemispheric Differences during Face Recognition Learning.
• 
  Carla S. Möller-Levet, Guy N. J. Betts, Adrian L. Harris, Jarrod J. Homer, Catharine M. West, Crispin J. Miller:
  Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis.
• 
  Suresh Kumar Poovathingal, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan:
  Stochastic Drift in Mitochondrial DNA Point Mutations: A Novel Perspective Ex Silico.
• 
  Eric A. Zilli, Motoharu Yoshida, Babak Tahvildari, Lisa M. Giocomo, Michael E. Hasselmo:
  Evaluation of the Oscillatory Interference Model of Grid Cell Firing through Analysis and Measured Period Variance of Some Biological Oscillators.
• 
  Wolfram Stacklies, Fei Xia, Frauke Gräter:
  Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis.
• 
  Gur Fabrikant, Suman Lata, James D. Riches, John A. G. Briggs, Winfried Weissenhorn, Michael M. Kozlov:
  Computational Model of Membrane Fission Catalyzed by ESCRT-III.
• 
  Kenneth S. Campbell:
  Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle.
• 
  Nicola J. van Rijsbergen, Philippe G. Schyns:
  Dynamics of Trimming the Content of Face Representations for Categorization in the Brain.
• 
  Eivind Valen, Albin Sandelin, Ole Winther, Anders Krogh:
  Discovery of Regulatory Elements is Improved by a Discriminatory Approach.
• 
  Asif U. Tamuri, Mario dos Reis, Alan J. Hay, Richard A. Goldstein:
  Identifying Changes in Selective Constraints: Host Shifts in Influenza.
• 
  Fabio Luciani, Samuel Alizon:
  The Evolutionary Dynamics of a Rapidly Mutating Virus within and between Hosts: The Case of Hepatitis C Virus.
• 
  Gary Chung Hon, Wei Wang, Bing Ren:
  Discovery and Annotation of Functional Chromatin Signatures in the Human Genome.
• 
  Mu Gao, Jeffrey Skolnick:
  A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome.
• 
  Nathan Salomonis, Brandon Nelson, Karen Vranizan, Alexander R. Pico, Kristina Hanspers, Allan Kuchinsky, Linda Ta, Mark Mercola, Bruce R. Conklin:
  Alternative Splicing in the Differentiation of Human Embryonic Stem Cells into Cardiac Precursors.
• 
  Russell S. A. Brinkworth, David C. O'Carroll:
  Robust Models for Optic Flow Coding in Natural Scenes Inspired by Insect Biology.
• 
  Raibatak Das, Christopher W. Cairo, Daniel Coombs:
  A Hidden Markov Model for Single Particle Tracks Quantifies Dynamic Interactions between LFA-1 and the Actin Cytoskeleton.
• 
  Jasmine Foo, Franziska Michor:
  Evolution of Resistance to Targeted Anti-Cancer Therapies during Continuous and Pulsed Administration Strategies.
• 
  Samuel Bandara, Johannes P. Schlöder, Roland Eils, Hans Georg Bock, Tobias Meyer:
  Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model.
• 
  Ivan Iossifov, Raul Rodriguez-Esteban, Ilya Mayzus, Kathleen J. Millen, Andrey Rzhetsky:
  Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans.

Volume 5, Number 12, December 2009

Education Articles

• 
  Joel Dudley, Atul J. Butte:
  A Quick Guide for Developing Effective Bioinformatics Programming Skills.
• 
  Raul Rodriguez-Esteban:
  Biomedical Text Mining and Its Applications.
• 
  Vebjorn Ljosa, Anne E. Carpenter:
  Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening.

Research Articles

• 
  Julijana Gjorgjieva, Taro Toyoizumi, Stephen J. Eglen:
  Burst-Time-Dependent Plasticity Robustly Guides ON/OFF Segregation in the Lateral Geniculate Nucleus.
• 
  Vitaly A. Selivanov, Tatyana V. Votyakova, Jennifer Zeak, Massimo Trucco, Josep Roca, Marta Cascante:
  Bistability of Mitochondrial Respiration Underlies Paradoxical Reactive Oxygen Species Generation Induced by Anoxia.
• 
  Xi Chen, Andrew D. Ellington:
  Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes.
• 
  Marianne O. Stefanini, Florence T. H. Wu, Feilim Mac Gabhann, Aleksander S. Popel:
  The Presence of VEGF Receptors on the Luminal Surface of Endothelial Cells Affects VEGF Distribution and VEGF Signaling.
• 
  Mattia Gazzola, Christoph J. Burckhardt, Basil Bayati, Martin Engelke, Urs F. Greber, Petros Koumoutsakos:
  A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus.
• 
  Khyati Kapoor, Mohd Rehan, Ajeeta Kaushiki, Ritu Pasrija, Andrew M. Lynn, Rajendra Prasad:
  Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach.
• 
  Pascal Chossat, Olivier D. Faugeras:
  Hyperbolic Planforms in Relation to Visual Edges and Textures Perception.
• 
  Jessica Cara Mar, John Quackenbush:
  Decomposition of Gene Expression State Space Trajectories.
• 
  Menachem Fromer, Julia M. Shifman:
  Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins.
• 
  Yoram Burak, Boris I. Shraiman:
  Order and Stochastic Dynamics in Drosophila Planar Cell Polarity.
• 
  Ian H. Stevenson, Hugo L. Fernandes, Iris Vilares, Kunlin Wei, Konrad P. Körding:
  Bayesian Integration and Non-Linear Feedback Control in a Full-Body Motor Task.
• 
  Ivan Puga-Gonzalez, Hanno Hildenbrandt, Charlotte K. Hemelrijk:
  Emergent Patterns of Social Affiliation in Primates, a Model.
• 
  Clémentine Dressaire, Christophe Gitton, Pascal Loubière, Véronique Monnet, Isabelle Queinnec, Muriel Cocaign-Bousquet:
  Transcriptome and Proteome Exploration to Model Translation Efficiency and Protein Stability in Lactococcus lactis.
• 
  Feng Hong, Fang Fang, Xuming He, Xiaoyi Cao, Hiram Chipperfield, Dan Xie, Wing Hung Wong, Huck H. Ng, Sheng Zhong:
  Dissecting Early Differentially Expressed Genes in a Mixture of Differentiating Embryonic Stem Cells.
• 
  Hongchao Lu, Lan Lin, Seiko Sato, Yi Xing, Christopher J. Lee:
  Predicting Functional Alternative Splicing by Measuring RNA Selection Pressure from Multigenome Alignments.
• 
  Kai J. Miller, Larry B. Sorensen, Jeffrey G. Ojemann, Marcel den Nijs:
  Power-Law Scaling in the Brain Surface Electric Potential.
• 
  Aristotelis Tsirigos, Isidore Rigoutsos:
  Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes.
• 
  Pulin Gong, Cees van Leeuwen:
  Distributed Dynamical Computation in Neural Circuits with Propagating Coherent Activity Patterns.
• 
  Brian J. Schmidt, Jason A. Papin, Michael B. Lawrence:
  Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation.
• 
  João F. Matias Rodrigues, Andreas Wagner:
  Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks.
• 
  Michael E. Wall, David A. Markowitz, Judah L. Rosner, Robert G. Martin:
  Model of Transcriptional Activation by MarA in Escherichia coli.
• 
  Charles G. Nathanson, Corina E. Tarnita, Martin A. Nowak:
  Calculating Evolutionary Dynamics in Structured Populations.
• 
  Kai Wang, Manikandan Narayanan, Hua Zhong, Martin Tompa, Eric E. Schadt, Jun Zhu:
  Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases.
• 
  Roland Schäfer, Eleni Vasilaki, Walter Senn:
  Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning.
• 
  Orly Noivirt-Brik, Amnon Horovitz, Ron Unger:
  Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real Proteins.
• 
  Florent E. Angly, Dana Willner, Alejandra Prieto-Davó, Robert A. Edwards, Robert Schmieder, Rebecca Vega-Thurber, Dionysios A. Antonopoulos, Katie Barott, Matthew T. Cottrell, Christelle Desnues, Elizabeth A. Dinsdale, Mike Furlan, Matthew Haynes, Matthew R. Henn, Yongfei Hu, David L. Kirchman, Tracey McDole, John D. McPherson, Folker Meyer, R. Michael Miller, Egbert Mundt, Robert K. Naviaux, Beltran Rodriguez-Mueller, Rick Stevens, Linda Wegley, Lixin Zhang, Baoli Zhu, Forest Rohwer:
  The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes.
• 
  Sean Ekins, Sandhya Kortagere, Manisha Iyer, Erica J. Reschly, Markus A. Lill, Matthew R. Redinbo, Matthew D. Krasowski:
  Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR.
• 
  Rebekka Schlatter, Kathrin Schmich, Ima Avalos Vizcarra, Peter Scheurich, Thomas Sauter, Christoph Borner, Michael Ederer, Irmgard Merfort, Oliver Sawodny:
  ON/OFF and Beyond - A Boolean Model of Apoptosis.
• 
  Jorge M. Pacheco, Flávio L. Pinheiro, Francisco C. Santos:
  Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation.
• 
  Daniel Ramsköld, Eric T. Wang, Christopher B. Burge, Rickard Sandberg:
  An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data.
• 
  Steven Phillips, William H. Wilson, Graeme S. Halford:
  What Do Transitive Inference and Class Inclusion Have in Common? Categorical (Co)Products and Cognitive Development.
• 
  Keith B. Godfrey, Stephen J. Eglen, Nicholas V. Swindale:
  A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth.
• 
  Gozde Kar, Attila Gürsoy, Ozlem Keskin:
  Human Cancer Protein-Protein Interaction Network: A Structural Perspective.
• 
  Shane Lee, Kamal Sen, Nancy Kopell:
  Cortical Gamma Rhythms Modulate NMDAR-Mediated Spike Timing Dependent Plasticity in a Biophysical Model.
• 
  Matthew J. Paszek, David Boettiger, Valerie M. Weaver, Daniel A. Hammer:
  Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate.
• 
  Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt:
  Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies.
• 
  Matthew D. Christensen, Wen Dun, Penelope A. Boyden, Mark E. Anderson, Peter J. Mohler, Thomas J. Hund:
  Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction: A Computational Analysis.
• 
  Rajagopal Sathyapriya, Jose M. Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe:
  Defining an Essence of Structure Determining Residue Contacts in Proteins.
• 
  John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser:
  Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.
• 
  Eleni Vasilaki, Nicolas Frémaux, Robert Urbanczik, Walter Senn, Wulfram Gerstner:
  Spike-Based Reinforcement Learning in Continuous State and Action Space: When Policy Gradient Methods Fail.
• 
  Gustavo Deco, Daniel Martí, Anders Ledberg, Ramon Reig, Maria V. Sanchez-Vives:
  Effective Reduced Diffusion-Models: A Data Driven Approach to the Analysis of Neuronal Dynamics.
• 
  Scott A. Sands, Bradley A. Edwards, Vanessa J. Kelly, Malcolm R. Davidson, Malcolm H. Wilkinson, Philip J. Berger:
  A Model Analysis of Arterial Oxygen Desaturation during Apnea in Preterm Infants.
• 
  Yue Zhao, David Granas, Gary D. Stormo:
  Inferring Binding Energies from Selected Binding Sites.
• 
  Alexander Mitsos, Ioannis N. Melas, Paraskeuas Siminelakis, Aikaterini D. Chairakaki, Julio Saez-Rodriguez, Leonidas G. Alexopoulos:
  Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data.