Volume 8; Issue 6

PLoS Computational Biology

Volume 8; Issue 6

1

Computing with Neural Synchrony

Brette, Romain, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.89 MB

english, 2012

2

A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts

Onken, Arno, Dragoi, Valentin, Obermayer, Klaus, Brown, Emery N.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 764 KB

english, 2012

3

Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses

Pawelek, Kasia A., Huynh, Giao T., Quinlivan, Michelle, Cullinane, Ann, Rong, Libin, Perelson, Alan S., Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

4

MC EMiNEM Maps the Interaction Landscape of the Mediator

Niederberger, Theresa, Etzold, Stefanie, Lidschreiber, Michael, Maier, Kerstin C., Martin, Dietmar E., Fröhlich, Holger, Cramer, Patrick, Tresch, Achim, Siepel, Adam

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 769 KB

english, 2012

5

Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase

Reboul, C. F., Porebski, B. T., Griffin, M. D. W., Dobson, R. C. J., Perugini, M. A., Gerrard, J. A., Buckle, A. M., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.60 MB

english, 2012

6

Spine Calcium Transients Induced by Synaptically-Evoked Action Potentials Can Predict Synapse Location and Establish Synaptic Democracy

Sterratt, David C., Groen, Martine R., Meredith, Rhiannon M., van Ooyen, Arjen, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.75 MB

english, 2012

7

Deceleration of Fusion–Fission Cycles Improves Mitochondrial Quality Control during Aging

Figge, Marc Thilo, Reichert, Andreas S., Meyer-Hermann, Michael, Osiewacz, Heinz D., Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

8

A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis

Aandahl, R. Zachariah, Reyes, Josephine F., Sisson, Scott A., Tanaka, Mark M., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 342 KB

english, 2012

9

Location-Dependent Effects of Inhibition on Local Spiking in Pyramidal Neuron Dendrites

Jadi, Monika, Polsky, Alon, Schiller, Jackie, Mel, Bartlett W., Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.89 MB

english, 2012

10

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abubucker, Sahar, Segata, Nicola, Goll, Johannes, Schubert, Alyxandria M., Izard, Jacques, Cantarel, Brandi L., Rodriguez-Mueller, Beltran, Zucker, Jeremy, Thiagarajan, Mathangi, Henrissat, Bernard, W

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 785 KB

english, 2012

11

Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery

Arneodo, Ezequiel M., Perl, Yonatan Sanz, Goller, Franz, Mindlin, Gabriel B., Ayers, Joseph

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 472 KB

english, 2012

12

What Can Systems Theory of Networks Offer to Biology?

Rajapakse, Indika, Groudine, Mark, Mesbahi, Mehran, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 118 KB

english, 2012

13

Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology

Moss, Robert, Grosse, Thibault, Marchant, Ivanny, Lassau, Nathalie, Gueyffier, François, Thomas, S. Randall, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.40 MB

english, 2012

14

Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases

Ruau, David, Dudley, Joel T., Chen, Rong, Phillips, Nicholas G., Swan, Gary E., Lazzeroni, Laura C., Clark, J. David, Butte, Atul J., Angst, Martin S., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 640 KB

english, 2012

15

Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation

Holmes, William R., Lin, Benjamin, Levchenko, Andre, Edelstein-Keshet, Leah, Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 674 KB

english, 2012

16

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

Volz, Erik M., Koopman, James S., Ward, Melissa J., Brown, Andrew Leigh, Frost, Simon D. W., Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 961 KB

english, 2012

17

A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks

De Martino, Daniele, Figliuzzi, Matteo, De Martino, Andrea, Marinari, Enzo, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 710 KB

english, 2012

18

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

Capra, John A., Williams, Alexander G., Pollard, Katherine S., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 661 KB

english, 2012

19

Learning with Slight Forgetting Optimizes Sensorimotor Transformation in Redundant Motor Systems

Hirashima, Masaya, Nozaki, Daichi, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

20

Complementarity of Spike- and Rate-Based Dynamics of Neural Systems

Wilson, M. T., Robinson, P. A., O'Neill, B., Steyn-Ross, D. A., Jirsa, Viktor K.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 4.68 MB

english, 2012

21

Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling

Kahm, Matthias, Navarrete, Clara, Llopis-Torregrosa, Vicent, Herrera, Rito, Barreto, Lina, Yenush, Lynne, Ariño, Joaquin, Ramos, Jose, Kschischo, Maik, Elofsson, Arne

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 610 KB

english, 2012

22

Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity

Hoyle, Rebecca B., Avitabile, Daniele, Kierzek, Andrzej M., Reed, Jennifer L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 807 KB

english, 2012

23

Structural Drift: The Population Dynamics of Sequential Learning

Crutchfield, James P., Whalen, Sean, Bergstrom, Carl T.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 719 KB

english, 2012

24

Visualization and Analysis of 3D Microscopic Images

Long, Fuhui, Zhou, Jianlong, Peng, Hanchuan, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 3.07 MB

english, 2012

25

Viral Perturbations of Host Networks Reflect Disease Etiology

Gulbahce, Natali, Yan, Han, Dricot, Amélie, Padi, Megha, Byrdsong, Danielle, Franchi, Rachel, Lee, Deok-Sun, Rozenblatt-Rosen, Orit, Mar, Jessica C., Calderwood, Michael A., Baldwin, Amy, Zhao, Bo, Sa

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.57 MB

english, 2012

26

Fast Coding of Orientation in Primary Visual Cortex

Shriki, Oren, Kohn, Adam, Shamir, Maoz, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.72 MB

english, 2012

27

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

Keegan, Kevin P., Trimble, William L., Wilkening, Jared, Wilke, Andreas, Harrison, Travis, D'Souza, Mark, Meyer, Folker, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 497 KB

english, 2012

28

Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems

Chan, Carlo, Liu, Xinfeng, Wang, Liming, Bardwell, Lee, Nie, Qing, Enciso, Germán, Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 932 KB

english, 2012

29

Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue

Raudies, Florian, Hasselmo, Michael E., Maloney, Laurence T.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.23 MB

english, 2012

30

Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer

Rosenbaum, Robert, Rubin, Jonathan, Doiron, Brent, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 539 KB

english, 2012

31

Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach

Garcia-Seisdedos, Hector, Ibarra-Molero, Beatriz, Sanchez-Ruiz, Jose M., Elofsson, Arne

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.93 MB

english, 2012

32

Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction

Michaut, Magali, Bader, Gary D., von Mering, Christian

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 609 KB

english, 2012

33

Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees

Pnevmatikakis, Eftychios A., Kelleher, Keith, Chen, Rebecca, Saggau, Petter, Josi, Krešimir, Paninski, Liam, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.47 MB

english, 2012

34

A Report of the Curriculum Task Force of the ISCB Education Committee

Welch, Lonnie R., Schwartz, Russell, Lewitter, Fran, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 82 KB

english, 2012

35

Bringing Molecules Back into Molecular Evolution

Wilke, Claus O., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 79 KB

english, 2012

36

Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism

König, Matthias, Bulik, Sascha, Holzhütter, Hermann-Georg, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.99 MB

english, 2012

37

From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm

Tiedemann, Hendrik B., Schneltzer, Elida, Zeiser, Stefan, Hoesel, Bastian, Beckers, Johannes, Przemeck, Gerhard K. H., de Angelis, Martin Hrabě, Lubensky, David K.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 2.50 MB

english, 2012

38

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation

Ionescu, Crina-Maria, Svobodová Vařeková, Radka, Prehn, Jochen H. M., Huber, Heinrich J., Koča, Jaroslav, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 757 KB

english, 2012

39

Sarcomeric Pattern Formation by Actin Cluster Coalescence

Friedrich, Benjamin M., Fischer-Friedrich, Elisabeth, Gov, Nir S., Safran, Samuel A., Ono, Shoichiro

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 803 KB

english, 2012

40

Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches

Wodarz, Dominik, Hofacre, Andrew, Lau, John W., Sun, Zhiying, Fan, Hung, Komarova, Natalia L., Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.03 MB

english, 2012

41

The Role of Non-Native Interactions in the Folding of Knotted Proteins

Škrbić, Tatjana, Micheletti, Cristian, Faccioli, Pietro, Jernigan, Robert L.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1009 KB

english, 2012

42

Standing Genetic Variation and the Evolution of Drug Resistance in HIV

Pennings, Pleuni Simone, De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 369 KB

english, 2012

43

Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign

Carrera, Javier, Fernández del Carmen, Asun, Fernández-Muñoz, Rafael, Rambla, Jose Luis, Pons, Clara, Jaramillo, Alfonso, Elena, Santiago F., Granell, Antonio, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 857 KB

english, 2012

44

The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion

Gerlee, Philip, Nelander, Sven, Alber, Mark S.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 540 KB

english, 2012

45

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations

Wang, Xin, Castro, Mauro A., Mulder, Klaas W., Markowetz, Florian, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

46

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

Matsunaga, Yasuhiro, Fujisaki, Hiroshi, Terada, Tohru, Furuta, Tadaomi, Moritsugu, Kei, Kidera, Akinori, Pande, Vijay S.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.33 MB

english, 2012

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