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ORCIDPLoS 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.