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PLoS Computational Biology, Volume 5
Volume 5, Number 1, January 2009
- Evie Browne
, Rosemary Dickin, Philip E. Bourne:
A Review of 2008 for PLoS Computational Biology.
- 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.
- Debopriya Das, Matteo Pellegrini
, Joe W. Gray:
A Primer on Regression Methods for Decoding cis-Regulatory Logic.
- 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 P. 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
- 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
- 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.
- 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
- Quentin Vicens
, Philip E. Bourne:
Ten Simple Rules To Combine Teaching and Research.
- 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.
- David M. Shotton
, Katie Portwin, Graham Klyne, Alistair Miles
:
Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article.
- 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.