Volume 7; Issue 3

PLoS Computational Biology

Volume 7; Issue 3

1

Flexible Cognitive Strategies during Motor Learning

Taylor, Jordan A., Ivry, Richard B., Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 953 KB

english, 2011

2

Frequency-Invariant Representation of Interaural Time Differences in Mammals

Lüling, Hannes, Siveke, Ida, Grothe, Benedikt, Leibold, Christian, J. Friston, Karl

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 728 KB

english, 2011

3

Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain

Selivanov, Vitaly A., Votyakova, Tatyana V., Pivtoraiko, Violetta N., Zeak, Jennifer, Sukhomlin, Tatiana, Trucco, Massimo, Roca, Josep, Cascante, Marta, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.51 MB

english, 2011

4

Quantification of the Relative Importance of CTL, B Cell, NK Cell, and Target Cell Limitation in the Control of Primary SIV-Infection

Elemans, Marjet, Thiébaut, Rodolphe, Kaur, Amitinder, Asquith, Becca, De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 488 KB

english, 2011

5

Nucleotide Binding Switches the Information Flow in Ras GTPases

Raimondi, Francesco, Portella, Guillem, Orozco, Modesto, Fanelli, Francesca, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 5.93 MB

english, 2011

6

A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations

McKinley, Trevelyan J., Murcia, Pablo R., Gog, Julia R., Varela, Mariana, Wood, James L. N., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 495 KB

english, 2011

7

Human Leg Model Predicts Ankle Muscle-Tendon Morphology, State, Roles and Energetics in Walking

Krishnaswamy, Pavitra, Brown, Emery N., Herr, Hugh M., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 847 KB

english, 2011

8

Natural Selection on Functional Modules, a Genome-Wide Analysis

Serra, François, Arbiza, Leonardo, Dopazo, Joaquín, Dopazo, Hernán, von Mering, Christian

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 958 KB

english, 2011

9

The Roots of Bioinformatics in Theoretical Biology

Hogeweg, Paulien, Searls, David B.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 92 KB

english, 2011

10

Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation

Linaro, Daniele, Storace, Marco, Giugliano, Michele, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.63 MB

english, 2011

11

“Fluctuograms” Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution

Silvestre-Ryan, Jordi, Lin, Yuchun, Chu, Jhih-Wei, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.61 MB

english, 2011

12

A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity

Kim, Sanggyun, Putrino, David, Ghosh, Soumya, Brown, Emery N., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 870 KB

english, 2011

13

Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala

Vlachos, Ioannis, Herry, Cyril, Lüthi, Andreas, Aertsen, Ad, Kumar, Arvind, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.98 MB

english, 2011

14

Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards

Kouyos, Roger D., Abel zur Wiesch, Pia, Bonhoeffer, Sebastian, Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 647 KB

english, 2011

15

Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression

Sanchez, Alvaro, Garcia, Hernan G., Jones, Daniel, Phillips, Rob, Kondev, Jané, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.53 MB

english, 2011

16

Minimal Models of Multidimensional Computations

Fitzgerald, Jeffrey D., Sincich, Lawrence C., Sharpee, Tatyana O., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 704 KB

english, 2011

17

To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages

Joh, Richard I., Weitz, Joshua S., O. Wilke, Claus

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 686 KB

english, 2011

18

Animal Interactions and the Emergence of Territoriality

Giuggioli, Luca, Potts, Jonathan R., Harris, Stephen, Maloney, Laurence T.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.12 MB

english, 2011

19

Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations

Yu, Rilei, Craik, David J., Kaas, Quentin, Briggs, James

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.40 MB

english, 2011

20

Dynamic Phenotypic Clustering in Noisy Ecosystems

Ernebjerg, Morten, Kishony, Roy, Savage, Van

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

21

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

Shlomi, Tomer, Benyamini, Tomer, Gottlieb, Eyal, Sharan, Roded, Ruppin, Eytan, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 409 KB

english, 2011

22

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells

Cavill, Rachel, Kamburov, Atanas, Ellis, James K., Athersuch, Toby J., Blagrove, Marcus S. C., Herwig, Ralf, Ebbels, Timothy M. D., Keun, Hector C., Tucker-Kellogg, Greg

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.12 MB

english, 2011

23

No Need for a Cognitive Map: Decentralized Memory for Insect Navigation

Cruse, Holk, Wehner, Rüdiger, Friston, Karl

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 766 KB

english, 2011

24

Crawling Cells Can Close Wounds without Purse Strings or Signaling

Lee, Pilhwa, Wolgemuth, Charles W., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.35 MB

english, 2011

25

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

Kim, Yoo-Ah, Wuchty, Stefan, Przytycka, Teresa M., Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 794 KB

english, 2011

26

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

Morris, Melody K., Saez-Rodriguez, Julio, Clarke, David C., Sorger, Peter K., Lauffenburger, Douglas A., Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.90 MB

english, 2011

27

The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering

Osella, Matteo, Bosia, Carla, Corá, Davide, Caselle, Michele, Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.86 MB

english, 2011

28

A Compact Statistical Model of the Song Syntax in Bengalese Finch

Jin, Dezhe Z., Kozhevnikov, Alexay A., Friston, Karl J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.11 MB

english, 2011

29

Inferring Visuomotor Priors for Sensorimotor Learning

Turnham, Edward J. A., Braun, Daniel A., Wolpert, Daniel M., Körding, Konrad P.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 817 KB

english, 2011

30

CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data

Zhang, Kelvin Xi, Ouellette, B. F. Francis, Quackenbush, John

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 632 KB

english, 2011

31

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

Oberhardt, Matthew A., Puchałka, Jacek, Martins dos Santos, Vítor A. P., Papin, Jason A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 3.39 MB

english, 2011

32

Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations

Skjaerven, Lars, Grant, Barry, Muga, Arturo, Teigen, Knut, McCammon, J. Andrew, Reuter, Nathalie, Martinez, Aurora, Ma, Jianpeng

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.91 MB

english, 2011

33

Noise Driven Evolutionary Waves

Hallatschek, Oskar, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 297 KB

english, 2011

34

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Roberts, Elijah, Magis, Andrew, Ortiz, Julio O., Baumeister, Wolfgang, Luthey-Schulten, Zaida, Csermely, Peter

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.01 MB

english, 2011

35

Learning from Sensory and Reward Prediction Errors during Motor Adaptation

Izawa, Jun, Shadmehr, Reza, Körding, Konrad

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.25 MB

english, 2011

36

Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies

Metzger, Vincent T., Lloyd-Smith, James O., Weinberger, Leor S., De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.73 MB

english, 2011

37

PLoS Computational Biology Conference Postcard from PSB 2011

Eren, A. Murat, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 61 KB

english, 2011

38

Mechanisms of Magnetic Stimulation of Central Nervous System Neurons

Pashut, Tamar, Wolfus, Shuki, Friedman, Alex, Lavidor, Michal, Bar-Gad, Izhar, Yeshurun, Yosef, Korngreen, Alon, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.61 MB

english, 2011

39

On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems

Takeuchi, Nobuto, Hogeweg, Paulien, Koonin, Eugene V., O. Wilke, Claus

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 20.79 MB

english, 2011

40

Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts

Rocha, Luis E. C., Liljeros, Fredrik, Holme, Petter, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 819 KB

english, 2011

41

Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

Yang, Lun, Wang, Kejian, Chen, Jian, Jegga, Anil G., Luo, Heng, Shi, Leming, Wan, Chunling, Guo, Xizhi, Qin, Shengying, He, Guang, Feng, Guoyin, He, Lin, Altman, Russ B.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.06 MB

english, 2011

42

Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding

Bar-On, Dana, Nachliel, Esther, Gutman, Menachem, Ashery, Uri, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 4.57 MB

english, 2011

43

Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis

Xing, Heming, McDonagh, Paul D., Bienkowska, Jadwiga, Cashorali, Tanya, Runge, Karl, Miller, Robert E., DeCaprio, Dave, Church, Bruce, Roubenoff, Ronenn, Khalil, Iya G., Carulli, John, Crampin, Edmund

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.39 MB

english, 2011

44

Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction

López, Cesar A., de Vries, Alex H., Marrink, Siewert J., Berkowitz, Max

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 8.98 MB

english, 2011

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