Volume 7; Issue 10

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PLoS Computational Biology
Volume 7; Issue 10

PLoS Computational Biology

Volume 7; Issue 10

1

Teaching Bioinformatics at the Secondary School Level

Lewitter, Fran, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 58 KB

english, 2011

2

A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields

Zylberberg, Joel, Murphy, Jason Timothy, DeWeese, Michael Robert, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 486 KB

english, 2011

3

Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control

Salathé, Marcel, Khandelwal, Shashank, Meyers, Lauren Ancel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 368 KB

english, 2011

4

Integrated Information Increases with Fitness in the Evolution of Animats

Edlund, Jeffrey A., Chaumont, Nicolas, Hintze, Arend, Koch, Christof, Tononi, Giulio, Adami, Christoph, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 781 KB

english, 2011

5

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Hester, Susan D., Belmonte, Julio M., Gens, J. Scott, Clendenon, Sherry G., Glazier, James A., Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 9.49 MB

english, 2011

6

High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks

Ricci, Francesco, Vallée-Bélisle, Alexis, Plaxco, Kevin W., Fan, Chunhai

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 788 KB

english, 2011

7

A Neurodynamic Account of Spontaneous Behaviour

Namikawa, Jun, Nishimoto, Ryunosuke, Tani, Jun, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.38 MB

english, 2011

8

Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models

Fitzgerald, Jeffrey D., Rowekamp, Ryan J., Sincich, Lawrence C., Sharpee, Tatyana O., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 782 KB

english, 2011

9

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

Parnell, Laurence D., Lindenbaum, Pierre, Shameer, Khader, Dall'Olio, Giovanni Marco, Swan, Daniel C., Jensen, Lars Juhl, Cockell, Simon J., Pedersen, Brent S., Mangan, Mary E., Miller, Christopher A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.06 MB

english, 2011

10

Ten Simple Rules for Teaching Bioinformatics at the High School Level

Form, David, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 60 KB

english, 2011

11

Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics

Peng, Jyh-Ying, Lin, Chung-Chih, Chen, Yen-Jen, Kao, Lung-Sen, Liu, Young-Chau, Chou, Chung-Chien, Huang, Yi-Hung, Chang, Fang-Rong, Wu, Yang-Chang, Tsai, Yuh-Show, Hsu, Chun-Nan, Covert, Markus W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.84 MB

english, 2011

12

Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants

Demir, Özlem, Baronio, Roberta, Salehi, Faezeh, Wassman, Christopher D., Hall, Linda, Hatfield, G. Wesley, Chamberlin, Richard, Kaiser, Peter, Lathrop, Richard H., Amaro, Rommie E., Gilson, Michael

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 776 KB

english, 2011

13

Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs

van der Post, Daniel J., Semmann, Dirk, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.91 MB

english, 2011

14

Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling

Hall, Benjamin A., Armitage, Judith P., Sansom, Mark S. P., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.80 MB

english, 2011

15

Brain Rhythms Reveal a Hierarchical Network Organization

Steinke, G. Karl, Galán, Roberto F., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.20 MB

english, 2011

16

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

Maman, Yaakov, Nir-Paz, Ran, Louzoun, Yoram, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 474 KB

english, 2011

17

Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs

Rebaudo, François, Dangles, Olivier, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 887 KB

english, 2011

18

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization

Dalchau, Neil, Phillips, Andrew, Goldstein, Leonard D., Howarth, Mark, Cardelli, Luca, Emmott, Stephen, Elliott, Tim, Werner, Joern M., Chakraborty, Arup K.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.56 MB

english, 2011

19

Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks

Levy, Robert B., Reyes, Alex D., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.27 MB

english, 2011

20

Receptive Field Inference with Localized Priors

Park, Mijung, Pillow, Jonathan W., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

21

B Cell Activation Triggered by the Formation of the Small Receptor Cluster: A Computational Study

Hat, Beata, Kazmierczak, Bogdan, Lipniacki, Tomasz, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.38 MB

english, 2011

22

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis

Divoli, Anna, Mendonça, Eneida A., Evans, James A., Rzhetsky, Andrey, Cohen, Kevin Bretonnel

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.14 MB

english, 2011

23

Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation

Fitzpatrick, Anthony W., Knowles, Tuomas P. J., Waudby, Christopher A., Vendruscolo, Michele, Dobson, Christopher M., Pande, Vijay S.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 350 KB

english, 2011

24

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation

de Oliveira, César Augusto F., Grant, Barry J., Zhou, Michelle, McCammon, J. Andrew, Pande, Vijay S.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

25

Three People Can Synchronize as Coupled Oscillators during Sports Activities

Yokoyama, Keiko, Yamamoto, Yuji, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

26

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex

Sethi, Anurag, Goldstein, Byron, Gnanakaran, S., Hummer, Gerhard

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.66 MB

english, 2011

27

Chemical Basis of Metabolic Network Organization

Zhu, Qiang, Qin, Tao, Jiang, Ying-Ying, Ji, Cong, Kong, De-Xin, Ma, Bin-Guang, Zhang, Hong-Yu, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 237 KB

english, 2011

28

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

Ryba, Tyrone, Hiratani, Ichiro, Sasaki, Takayo, Battaglia, Dana, Kulik, Michael, Zhang, Jinfeng, Dalton, Stephen, Gilbert, David M., Teichmann, Sarah A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.09 MB

english, 2011

29

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

Yelton, Alexis P., Thomas, Brian C., Simmons, Sheri L., Wilmes, Paul, Zemla, Adam, Thelen, Michael P., Justice, Nicholas, Banfield, Jillian F., Eisen, Jonathan A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

30

Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning

Gustafson, Nicholas J., Daw, Nathaniel D., Kording, Konrad P.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.50 MB

english, 2011

31

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

Gerek, Z. Nevin, Ozkan, S. Banu, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 597 KB

english, 2011

32

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity

London, Nir, Lamphear, Corissa L., Hougland, James L., Fierke, Carol A., Schueler-Furman, Ora, Keating, Amy E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.58 MB

english, 2011

33

Metabolic Regulation in Progression to Autoimmune Diabetes

Sysi-Aho, Marko, Ermolov, Andrey, Gopalacharyulu, Peddinti V., Tripathi, Abhishek, Seppänen-Laakso, Tuulikki, Maukonen, Johanna, Mattila, Ismo, Ruohonen, Suvi T., Vähätalo, Laura, Yetukuri, Laxman, Hä

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.03 MB

english, 2011

34

The Dynamics of Supply and Demand in mRNA Translation

Brackley, Chris A., Romano, M. Carmen, Thiel, Marco, Schmittmann, Beate

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 499 KB

english, 2011

35

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

ten Tusscher, Kirsten H., Hogeweg, Paulien, van Nimwegen, Erik

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.92 MB

english, 2011

36

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

Yuan, Yinyin, Savage, Richard S., Markowetz, Florian, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.38 MB

english, 2011

37

Formation of Regulatory Modules by Local Sequence Duplication

Nourmohammad, Armita, Lässig, Michael, Tanay, Amos

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 413 KB

english, 2011

38

Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex

Battaglia, Demian, Hansel, David, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.27 MB

english, 2011

39

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

Dixit, Anshuman, Verkhivker, Gennady M., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.32 MB

english, 2011

40

Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs

Biess, Armin, Korkotian, Eduard, Holcman, David, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 3.18 MB

english, 2011

41

Neural Computation via Neural Geometry: A Place Code for Inter-whisker Timing in the Barrel Cortex?

Wilson, Stuart P., Bednar, James A., Prescott, Tony J., Mitchinson, Ben, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 585 KB

english, 2011

42

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

Provasi, Davide, Artacho, Marta Camacho, Negri, Ana, Mobarec, Juan Carlos, Filizola, Marta, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 646 KB

english, 2011

43

Accelerated Profile HMM Searches

Eddy, Sean R., Pearson, William R.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 925 KB

english, 2011

44

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer

Dewanji, Anup, Jeon, Jihyoun, Meza, Rafael, Luebeck, E. Georg, Kimmel, Marek

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 349 KB

english, 2011

45

Thousands of Rab GTPases for the Cell Biologist

Diekmann, Yoan, Seixas, Elsa, Gouw, Marc, Tavares-Cadete, Filipe, Seabra, Miguel C., Pereira-Leal, José B., Elofsson, Arne

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.41 MB

english, 2011

46

Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array

Tsitron, Julia, Ault, Addison D., Broach, James R., Morozov, Alexandre V., Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 751 KB

english, 2011

47

Conformation Regulation of the X Chromosome Inactivation Center: A Model

Scialdone, Antonio, Cataudella, Ilaria, Barbieri, Mariano, Prisco, Antonella, Nicodemi, Mario, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 361 KB

english, 2011

48

Ten Simple Rules for Getting Involved in Your Scientific Community

Michaut, Magali

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 61 KB

english, 2011

49

Representation of Dynamical Stimuli in Populations of Threshold Neurons

Tchumatchenko, Tatjana, Wolf, Fred, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.73 MB

english, 2011

50

NHE Inhibition Does Not Improve Na+ or Ca2+ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure

Roberts, Byron N., Christini, David J., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.38 MB

english, 2011

51

Ten Simple Rules for Developing a Short Bioinformatics Training Course

Via, Allegra, De Las Rivas, Javier, Attwood, Teresa K., Landsman, David, Brazas, Michelle D., Leunissen, Jack A. M., Tramontano, Anna, Schneider, Maria Victoria

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 69 KB

english, 2011

52

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release

Koldsø, Heidi, Noer, Pernille, Grouleff, Julie, Autzen, Henriette Elisabeth, Sinning, Steffen, Schiøtt, Birgit, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.06 MB

english, 2011

53

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers

Rands, Sean A., Sueur, Cédric

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 152 KB

english, 2011

54

Using Structure to Explore the Sequence Alignment Space of Remote Homologs

Kuziemko, Andrew, Honig, Barry, Petrey, Donald, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1012 KB

english, 2011

55

Evidence for Composite Cost Functions in Arm Movement Planning: An Inverse Optimal Control Approach

Berret, Bastien, Chiovetto, Enrico, Nori, Francesco, Pozzo, Thierry, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 989 KB

english, 2011

56

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Joo, Hyun, Chavan, Archana G., Day, Ryan, Lennox, Kristin P., Sukhanov, Paul, Dahl, David B., Vannucci, Marina, Tsai, Jerry, Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.65 MB

english, 2011

57

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

Mihalik, Ágoston, Csermely, Peter, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.74 MB

english, 2011

58

Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception

Gintautas, Vadas, Ham, Michael I., Kunsberg, Benjamin, Barr, Shawn, Brumby, Steven P., Rasmussen, Craig, George, John S., Nemenman, Ilya, Bettencourt, Luís M. A., Kenyon, Garret T., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.76 MB

english, 2011

59

Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach

Shirreff, George, Pellis, Lorenzo, Laeyendecker, Oliver, Fraser, Christophe, Müller, Viktor

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 566 KB

english, 2011

60

Identification of Potent EGFR Inhibitors from TCM Database@Taiwan

Yang, Shun-Chieh, Chang, Su-Sen, Chen, Hsin-Yi, Chen, Calvin Yu-Chian, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 3.69 MB

english, 2011

61

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks

Hallen, Mark, Li, Bochong, Tanouchi, Yu, Tan, Cheemeng, West, Mike, You, Lingchong, Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.26 MB

english, 2011

62

Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects

Berniker, Max, Kording, Konrad P., Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 957 KB

english, 2011

63

Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis

Mitchell, Kate M., Mutapi, Francisca, Savill, Nicholas J., Woolhouse, Mark E. J., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 2.82 MB

english, 2011

64

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

Venet, David, Dumont, Jacques E., Detours, Vincent, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 443 KB

english, 2011

65

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

Gallagher, Suzanne Renick, Coon, William, Donley, Kristin, Scott, Abby, Goldberg, Debra S., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 273 KB

english, 2011

66

LTS and FS Inhibitory Interneurons, Short-Term Synaptic Plasticity, and Cortical Circuit Dynamics

Hayut, Itai, Fanselow, Erika E., Connors, Barry W., Golomb, David, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.35 MB

english, 2011

67

Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing

Aitken, Stuart, Alexander, Ross D., Beggs, Jean D., Guigo, Roderic

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 471 KB

english, 2011

68

STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains

Gilson, Matthieu, Masquelier, Timothée, Hugues, Etienne, van Rossum, Mark C. W.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.73 MB

english, 2011

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