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Volume 9; Issue 8
Main
PLoS Computational Biology
Volume 9; Issue 8
PLoS Computational Biology
Volume 9; Issue 8
1
Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain
Babin, Volodymyr
,
Wang, Dongli
,
Rose, Robert B.
,
Sagui, Celeste
,
MacKerell, Alexander Donald
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.68 MB
Your tags:
english, 2013
2
The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients
Beerenwinkel, Niko
,
Montazeri, Hesam
,
Schuhmacher, Heike
,
Knupfer, Patrick
,
von Wyl, Viktor
,
Furrer, Hansjakob
,
Battegay, Manuel
,
Hirschel, Bernard
,
Cavassini, Matthias
,
Vernazza, Pietro
,
Bernasconi,
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 547 KB
Your tags:
english, 2013
3
Ultrasensitivity in Phosphorylation-Dephosphorylation Cycles with Little Substrate
Martins, Bruno M. C.
,
Swain, Peter S.
,
Mac Gabhann, Feilim
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 781 KB
Your tags:
english, 2013
4
Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
Tiemann, Christian A.
,
Vanlier, Joep
,
Oosterveer, Maaike H.
,
Groen, Albert K.
,
Hilbers, Peter A. J.
,
van Riel, Natal A. W.
,
Markel, Scott
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.47 MB
Your tags:
english, 2013
5
Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
Bauermeister, Christoph
,
Schwalger, Tilo
,
Russell, David F.
,
Neiman, Alexander B.
,
Lindner, Benjamin
,
Latham, Peter E.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.76 MB
Your tags:
english, 2013
6
Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
Manor, Ohad
,
Segal, Eran
,
Leslie, Christina
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 852 KB
Your tags:
english, 2013
7
International Society for Computational Biology Welcomes Its Newest Class of Fellows
Fogg, Christiana N.
,
Kovats, Diane E.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.14 MB
Your tags:
english, 2013
8
Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks
Sorek, Matan
,
Balaban, Nathalie Q.
,
Loewenstein, Yonatan
,
de Polavieja, Gonzalo G.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 970 KB
Your tags:
english, 2013
9
Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
Crevecoeur, Frédéric
,
Scott, Stephen H.
,
Diedrichsen, Jörn
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.01 MB
Your tags:
english, 2013
10
Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload
van Eunen, Karen
,
Simons, Sereh M. J.
,
Gerding, Albert
,
Bleeker, Aycha
,
den Besten, Gijs
,
Touw, Catharina M. L.
,
Houten, Sander M.
,
Groen, Bert K.
,
Krab, Klaas
,
Reijngoud, Dirk-Jan
,
Bakker, Barbara M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 588 KB
Your tags:
english, 2013
11
From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
Cocco, Simona
,
Monasson, Remi
,
Weigt, Martin
,
Wallner, Björn
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.05 MB
Your tags:
english, 2013
12
Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model
Lee, Jung H.
,
Whittington, Miles A.
,
Kopell, Nancy J.
,
Coombes, Stephen
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.53 MB
Your tags:
english, 2013
13
Host Mobility Drives Pathogen Competition in Spatially Structured Populations
Poletto, Chiara
,
Meloni, Sandro
,
Colizza, Vittoria
,
Moreno, Yamir
,
Vespignani, Alessandro
,
Tanaka, Mark M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 892 KB
Your tags:
english, 2013
14
A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
Zuckerman, Neta S.
,
Noam, Yair
,
Goldsmith, Andrea J.
,
Lee, Peter P.
,
Przytycka, Teresa M.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.67 MB
Your tags:
english, 2013
15
Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools
Reznik, Ed
,
Mehta, Pankaj
,
Segrè, Daniel
,
Maranas, Costas D.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.77 MB
Your tags:
english, 2013
16
Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses
Pavesi, Angelo
,
Magiorkinis, Gkikas
,
Karlin, David G.
,
Wilke, Claus O.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 614 KB
Your tags:
english, 2013
17
Software for Computing and Annotating Genomic Ranges
Lawrence, Michael
,
Huber, Wolfgang
,
Pagès, Hervé
,
Aboyoun, Patrick
,
Carlson, Marc
,
Gentleman, Robert
,
Morgan, Martin T.
,
Carey, Vincent J.
,
Prlic, Andreas
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 520 KB
Your tags:
english, 2013
18
Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
Shankaran, Harish
,
Zhang, Yi
,
Tan, Yunbing
,
Resat, Haluk
,
Gabhann, Feilim Mac
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.67 MB
Your tags:
english, 2013
19
Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
Heijman, Jordi
,
Zaza, Antonio
,
Johnson, Daniel M.
,
Rudy, Yoram
,
Peeters, Ralf L. M.
,
Volders, Paul G. A.
,
Westra, Ronald L.
,
McCulloch, Andrew D.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.87 MB
Your tags:
english, 2013
20
Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases
Mariani, Simona
,
Dell'Orco, Daniele
,
Felline, Angelo
,
Raimondi, Francesco
,
Fanelli, Francesca
,
Dunbrack, Roland L.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.75 MB
Your tags:
english, 2013
21
Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System
Zhu, Mengchen
,
Rozell, Christopher J.
,
Bethge, Matthias
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.03 MB
Your tags:
english, 2013
22
A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli
Gelens, Lendert
,
Hill, Lydia
,
Vandervelde, Alexandra
,
Danckaert, Jan
,
Loris, Remy
,
Covert, Markus W.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 2.15 MB
Your tags:
english, 2013
23
Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
Li, Chunhe
,
Wang, Jin
,
Sarkar, Casim A.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.64 MB
Your tags:
english, 2013
24
Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
Rodrigo, Guillermo
,
Landrain, Thomas E.
,
Majer, Eszter
,
Daròs, José-Antonio
,
Jaramillo, Alfonso
,
Arkin, Adam P.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.52 MB
Your tags:
english, 2013
25
Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
Zubler, Frederic
,
Hauri, Andreas
,
Pfister, Sabina
,
Bauer, Roman
,
Anderson, John C.
,
Whatley, Adrian M.
,
Douglas, Rodney J.
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.36 MB
Your tags:
english, 2013
26
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
Cataudella, Ilaria
,
Sneppen, Kim
,
Gerdes, Kenn
,
Mitarai, Namiko
,
Saucerman, Jeffrey J.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 858 KB
Your tags:
english, 2013
27
Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers
Ozonov, Evgeniy A.
,
van Nimwegen, Erik
,
Ioshikhes, Ilya
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.36 MB
Your tags:
english, 2013
28
Endogenous Cholinergic Inputs and Local Circuit Mechanisms Govern the Phasic Mesolimbic Dopamine Response to Nicotine
Graupner, Michael
,
Maex, Reinoud
,
Gutkin, Boris
,
Friston, Karl J.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.74 MB
Your tags:
english, 2013
29
Spike Triggered Hormone Secretion in Vasopressin Cells; a Model Investigation of Mechanism and Heterogeneous Population Function
MacGregor, Duncan J.
,
Leng, Gareth
,
Beck, Jeff
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.46 MB
Your tags:
english, 2013
30
On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins
Wong, Eric T. C.
,
Na, Dokyun
,
Gsponer, Jörg
,
Ben-Tal, Nir
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 3.53 MB
Your tags:
english, 2013
31
Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates
Szilágyi, András
,
Zachar, István
,
Szathmáry, Eörs
,
Wilke, Claus O.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.30 MB
Your tags:
english, 2013
32
Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics
Dehouck, Yves
,
Mikhailov, Alexander S.
,
Dunbrack, Roland L.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 3.27 MB
Your tags:
english, 2013
33
How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation
Poos, Kathrin
,
Smida, Jan
,
Nathrath, Michaela
,
Maugg, Doris
,
Baumhoer, Daniel
,
Korsching, Eberhard
,
Ioshikhes, Ilya
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 763 KB
Your tags:
english, 2013
34
Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides
Wu, Chun
,
Shea, Joan-Emma
,
Pande, Vijay S.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.48 MB
Your tags:
english, 2013
35
Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
Baldassi, Carlo
,
Alemi-Neissi, Alireza
,
Pagan, Marino
,
DiCarlo, James J.
,
Zecchina, Riccardo
,
Zoccolan, Davide
,
Einhäuser, Wolfgang
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.86 MB
Your tags:
english, 2013
36
Sensory Information and Encounter Rates of Interacting Species
Hein, Andrew M.
,
McKinley, Scott A.
,
Wilke, Claus O.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.06 MB
Your tags:
english, 2013
37
Causes and Consequences of Hyperexcitation in Central Clock Neurons
Diekman, Casey O.
,
Belle, Mino D. C.
,
Irwin, Robert P.
,
Allen, Charles N.
,
Piggins, Hugh D.
,
Forger, Daniel B.
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.16 MB
Your tags:
english, 2013
38
Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions
Teles, Jose
,
Pina, Cristina
,
Edén, Patrik
,
Ohlsson, Mattias
,
Enver, Tariq
,
Peterson, Carsten
,
Teichmann, Sarah A.
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.44 MB
Your tags:
english, 2013
39
Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems
Szekely, Pablo
,
Sheftel, Hila
,
Mayo, Avi
,
Alon, Uri
,
Rzhetsky, Andrey
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.86 MB
Your tags:
english, 2013
40
Sparse Coding Models Can Exhibit Decreasing Sparseness while Learning Sparse Codes for Natural Images
Zylberberg, Joel
,
DeWeese, Michael Robert
,
Sporns, Olaf
Journal:
PLoS Computational Biology
Year:
2013
Language:
english
File:
PDF, 1.34 MB
Your tags:
english, 2013
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