Volume 8; Issue 3

PLoS Computational Biology

Volume 8; Issue 3

1

Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?

Craddock, Travis J. A., Tuszynski, Jack A., Hameroff, Stuart, Bernroider, Gustav

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.56 MB

english, 2012

2

Collective Dynamics Differentiates Functional Divergence in Protein Evolution

Glembo, Tyler J., Farrell, Daniel W., Gerek, Z. Nevin, Thorpe, M. F., Ozkan, S. Banu, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 837 KB

english, 2012

3

AutoClickChem: Click Chemistry in Silico

Durrant, Jacob D., McCammon, J. Andrew, Lapp, Hilmar

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 233 KB

english, 2012

4

Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb

Chow, Siu-Fai, Wick, Stuart D., Riecke, Hermann, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 663 KB

english, 2012

5

A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons

Vavoulis, Dimitrios V., Straub, Volko A., Aston, John A. D., Feng, Jianfeng, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.22 MB

english, 2012

6

Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity

Pantazatos, Spiro P., Talati, Ardesheer, Pavlidis, Paul, Hirsch, Joy, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.19 MB

english, 2012

7

Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics

Coen-Cagli, Ruben, Dayan, Peter, Schwartz, Odelia, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.62 MB

english, 2012

8

Entropic Tension in Crowded Membranes

Lindén, Martin, Sens, Pierre, Phillips, Rob, Tajkhorshid, Emad

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 334 KB

english, 2012

9

How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility

Marée, Athanasius F. M., Grieneisen, Verônica A., Edelstein-Keshet, Leah, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

10

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

Reboul, Cyril F., Meyer, Grischa R., Porebski, Benjamin T., Borg, Natalie A., Buckle, Ashley M., De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 4.38 MB

english, 2012

11

Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains

Mostarda, Stefano, Gfeller, David, Rao, Francesco, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.61 MB

english, 2012

12

The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion

Lehe, Rémi, Hallatschek, Oskar, Peliti, Luca, Neher, Richard A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 579 KB

english, 2012

13

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

Verma, Deeptak, Jacobs, Donald J., Livesay, Dennis R., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.20 MB

english, 2012

14

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

Calis, Jorg J. A., de Boer, Rob J., Keşmir, Can, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 497 KB

english, 2012

15

Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor

Duarte, A., Scholtens, E., Weissing, F. J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.77 MB

english, 2012

16

Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

Furnham, Nicholas, Sillitoe, Ian, Holliday, Gemma L., Cuff, Alison L., Laskowski, Roman A., Orengo, Christine A., Thornton, Janet M., Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.52 MB

english, 2012

17

Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction

Deco, Gustavo, Hugues, Etienne, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 893 KB

english, 2012

18

State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data

Shimazaki, Hideaki, Amari, Shun-ichi, Brown, Emery N., Grün, Sonja, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

19

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

Johnston, Iain G., Gaal, Bernadett, Neves, Ricardo Pires das, Enver, Tariq, Iborra, Francisco J., Jones, Nick S., Haugh, Jason M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 874 KB

english, 2012

20

Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus

Hafner, Marc, Koeppl, Heinz, Gonze, Didier, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.16 MB

english, 2012

21

The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

Jiang, Ying-Ying, Kong, De-Xin, Qin, Tao, Li, Xiao, Caetano-Anollés, Gustavo, Zhang, Hong-Yu, Valas, Ruben

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 508 KB

english, 2012

22

A Common Model for Cytokine Receptor Activation: Combined Scissor-Like Rotation and Self-Rotation of Receptor Dimer Induced by Class I Cytokine

Pang, Xiaodong, Zhou, Huan-Xiang, Feig, Michael

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.49 MB

english, 2012

23

Hemodynamic Traveling Waves in Human Visual Cortex

Aquino, Kevin M., Schira, Mark M., Robinson, P. A., Drysdale, Peter M., Breakspear, Michael, Kriegeskorte, Nikolaus

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.99 MB

english, 2012

24

Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion

Dieck Kattas, Graciano, Xu, Xiao-Ke, Small, Michael, Lu, Jinhu

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

25

Cell Shape Dynamics: From Waves to Migration

Driscoll, Meghan K., McCann, Colin, Kopace, Rael, Homan, Tess, Fourkas, John T., Parent, Carole, Losert, Wolfgang, Haugh, Jason M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.34 MB

english, 2012

26

Gradients and Modulation of K+ Channels Optimize Temporal Accuracy in Networks of Auditory Neurons

Kaczmarek, Leonard K., Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

27

Ten Simple Rules for Starting a Company

Fletcher, Anthony C., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 68 KB

english, 2012

28

Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery

Lörincz, András, Palotai, Zsolt, Szirtes, Gábor, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.82 MB

english, 2012

29

Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections

Burbank, Kendra S., Kreiman, Gabriel, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

30

Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees

Huys, Quentin J. M., Eshel, Neir, O'Nions, Elizabeth, Sheridan, Luke, Dayan, Peter, Roiser, Jonathan P., Maloney, Laurence T.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.63 MB

english, 2012

31

Inferring Epidemic Contact Structure from Phylogenetic Trees

Leventhal, Gabriel E., Kouyos, Roger, Stadler, Tanja, von Wyl, Viktor, Yerly, Sabine, Böni, Jürg, Cellerai, Cristina, Klimkait, Thomas, Günthard, Huldrych F., Bonhoeffer, Sebastian, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

32

Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB

Korkmaz, Elif Nihal, Nussinov, Ruth, Haliloğlu, Türkan, Teichmann, Sarah A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 616 KB

english, 2012

33

Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria

Richards, David M., Hempel, Antje M., Flärdh, Klas, Buttner, Mark J., Howard, Martin, Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 413 KB

english, 2012

34

Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza

Eames, Ken T. D., Tilston, Natasha L., Brooks-Pollock, Ellen, Edmunds, W. John, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 172 KB

english, 2012

35

Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations

Morra, Giulia, Potestio, Raffaello, Micheletti, Cristian, Colombo, Giorgio, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

36

Influence of the Fibroblastic Reticular Network on Cell-Cell Interactions in Lymphoid Organs

Graw, Frederik, Regoes, Roland R., De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 644 KB

english, 2012

37

Dynamic Effective Connectivity of Inter-Areal Brain Circuits

Battaglia, Demian, Witt, Annette, Wolf, Fred, Geisel, Theo, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.69 MB

english, 2012

38

Traffic Instabilities in Self-Organized Pedestrian Crowds

Moussaïd, Mehdi, Guillot, Elsa G., Moreau, Mathieu, Fehrenbach, Jérôme, Chabiron, Olivier, Lemercier, Samuel, Pettré, Julien, Appert-Rolland, Cécile, Degond, Pierre, Theraulaz, Guy, Ben-Jacob, Eshel

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.61 MB

english, 2012

39

Topic Pages: PLoS Computational Biology Meets Wikipedia

Wodak, Shoshana J., Mietchen, Daniel, Collings, Andrew M., Russell, Robert B., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 61 KB

english, 2012

40

Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures

Song, Hongyan, Parkinson, John, Elofsson, Arne

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.06 MB

english, 2012

41

Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses

Lemay, Mathieu, de Lange, Enno, Kucera, Jan P., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.82 MB

english, 2012

42

Thermodynamic State Ensemble Models of cis-Regulation

Sherman, Marc S., Cohen, Barak A., Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 417 KB

english, 2012

43

Living on Three Time Scales: The Dynamics of Plasma Cell and Antibody Populations Illustrated for Hepatitis A Virus

Andraud, Mathieu, Lejeune, Olivier, Musoro, Jammbe Z., Ogunjimi, Benson, Beutels, Philippe, Hens, Niel, Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 607 KB

english, 2012

44

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

Gillis, Jesse, Pavlidis, Paul, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 415 KB

english, 2012

45

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Melián, Carlos J., Alonso, David, Allesina, Stefano, Condit, Richard S., Etienne, Rampal S., Engelstädter, Jan

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.00 MB

english, 2012

46

Ensemble Models of Neutrophil Trafficking in Severe Sepsis

Song, Sang O. K., Hogg, Justin, Peng, Zhi-Yong, Parker, Robert, Kellum, John A., Clermont, Gilles, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.43 MB

english, 2012

47

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

Macalalad, Alexander R., Zody, Michael C., Charlebois, Patrick, Lennon, Niall J., Newman, Ruchi M., Malboeuf, Christine M., Ryan, Elizabeth M., Boutwell, Christian L., Power, Karen A., Brackney, Doug

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 463 KB

english, 2012

48

System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

Jol, Stefan J., Kümmel, Anne, Terzer, Marco, Stelling, Jörg, Heinemann, Matthias, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.58 MB

english, 2012

49

Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin?

Keck, Christian, Savin, Cristina, Lücke, Jörg, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.66 MB

english, 2012

50

Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation

Tseng, Yu-Yao, Hunt, Suzanne M., Heintzen, Christian, Crosthwaite, Susan K., Schwartz, Jean-Marc, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.29 MB

english, 2012

51

Network Evolution: Rewiring and Signatures of Conservation in Signaling

Sun, Mark G. F., Sikora, Martin, Costanzo, Michael, Boone, Charles, Kim, Philip M., von Mering, Christian

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 566 KB

english, 2012

52

Impact of Network Structure and Cellular Response on Spike Time Correlations

Trousdale, James, Hu, Yu, Shea-Brown, Eric, Josić, Krešimir, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 624 KB

english, 2012

53

Circular Permutation in Proteins

Bliven, Spencer, Prlić, Andreas, Wodak, Shoshana

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 327 KB

english, 2012