Volume 11; Issue 2

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PLoS Computational Biology
Volume 11; Issue 2

PLoS Computational Biology

Volume 11; Issue 2

1

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Didelot, Xavier, Wilson, Daniel J., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.71 MB

english, 2015

2

Ten Simple Rules for Lifelong Learning, According to Hamming

Erren, Thomas C., Slanger, Tracy E., Groß, J. Valérie, Bourne, Philip E., Cullen, Paul, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 132 KB

english, 2015

3

Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies

Binder, Benjamin J., Sundstrom, Joanna F., Gardner, Jennifer M., Jiranek, Vladimir, Oliver, Stephen G., Lauffenburger, Douglas A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.09 MB

english, 2015

4

The Roles of Post-translational Modifications in the Context of Protein Interaction Networks

Duan, Guangyou, Walther, Dirk, Radivojac, Predrag

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

5

A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception

Bastien, Renaud, Douady, Stéphane, Moulia, Bruno, Alber, Mark S

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.59 MB

english, 2015

6

Ethical Challenges of Big Data in Public Health

Vayena, Effy, Salathé, Marcel, Madoff, Lawrence C., Brownstein, John S., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 134 KB

english, 2015

7

PathVisio 3: An Extendable Pathway Analysis Toolbox

Kutmon, Martina, van Iersel, Martijn P., Bohler, Anwesha, Kelder, Thomas, Nunes, Nuno, Pico, Alexander R., Evelo, Chris T., Murphy, Robert F.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.66 MB

english, 2015

8

Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial

Edlefsen, Paul T., Rolland, Morgane, Hertz, Tomer, Tovanabutra, Sodsai, Gartland, Andrew J., deCamp, Allan C., Magaret, Craig A., Ahmed, Hasan, Gottardo, Raphael, Juraska, Michal, McCoy, Connor, Larse

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.76 MB

english, 2015

9

Communication over the Network of Binary Switches Regulates the Activation of A2A Adenosine Receptor

Lee, Yoonji, Choi, Sun, Hyeon, Changbong, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 14.49 MB

english, 2015

10

Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions

Potapov, Vladimir, Kaplan, Jenifer B., Keating, Amy E., Russell, Robert B.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

11

Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding

Lowet, Eric, Roberts, Mark, Hadjipapas, Avgis, Peter, Alina, van der Eerden, Jan, De Weerd, Peter, Ermentrout, Bard

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.80 MB

english, 2015

12

Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle

Li, Ying, Li, Guang, Görling, Benjamin, Luy, Burkhard, Du, Jiulin, Yan, Jun, Hogenesch, John B.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 7.88 MB

english, 2015

13

How to Write a Presubmission Inquiry

Lengauer, Thomas, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 74 KB

english, 2015

14

Cell Cycle Control by a Minimal Cdk Network

Gérard, Claude, Tyson, John J., Coudreuse, Damien, Novák, Béla, Saucerman, Jeffrey J.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.51 MB

english, 2015

15

The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure

Allen, Benjamin, Sample, Christine, Dementieva, Yulia, Medeiros, Ruben C., Paoletti, Christopher, Nowak, Martin A., Bergstrom, Carl T.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.34 MB

english, 2015

16

Segment-Specific Adhesion as a Driver of Convergent Extension

Vroomans, Renske M. A., Hogeweg, Paulien, ten Tusscher, Kirsten H. W. J., Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.42 MB

english, 2015

17

When Less Is More: Non-monotonic Spike Sequence Processing in Neurons

Arnoldt, Hinrich, Chang, Shuwen, Jahnke, Sven, Urmersbach, Birk, Taschenberger, Holger, Timme, Marc, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.89 MB

english, 2015

18

Integrative Multi-omics Module Network Inference with Lemon-Tree

Bonnet, Eric, Calzone, Laurence, Michoel, Tom, Gardner, Paul P

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.64 MB

english, 2015

19

Protein Sectors: Statistical Coupling Analysis versus Conservation

Teşileanu, Tiberiu, Colwell, Lucy J., Leibler, Stanislas, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

20

Heterogeneous CD8+ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis

Banigan, Edward J., Harris, Tajie H., Christian, David A., Hunter, Christopher A., Liu, Andrea J., Asquith, Becca

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.03 MB

english, 2015

21

Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations

Johnson, David K., Karanicolas, John, Wade, Rebecca C.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 7.55 MB

english, 2015

22

Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion

Eckstein, Johannes, Berndt, Nikolaus, Holzhütter, Hermann-Georg, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.48 MB

english, 2015

23

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

Imam, Saheed, Noguera, Daniel R., Donohue, Timothy J., Leslie, Christina

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.68 MB

english, 2015

24

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination

González-Ramírez, Laura R., Ahmed, Omar J., Cash, Sydney S., Wayne, C. Eugene, Kramer, Mark A., Honey, Christopher J

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.00 MB

english, 2015

25

Embryonic Stem Cell Specific “Master” Replication Origins at the Heart of the Loss of Pluripotency

Julienne, Hanna, Audit, Benjamin, Arneodo, Alain, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.36 MB

english, 2015

26

Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble

Jolivet, Renaud, Coggan, Jay S., Allaman, Igor, Magistretti, Pierre J., Graham, Lyle

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 880 KB

english, 2015

27

Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis

Conlan, Andrew J. K., Brooks Pollock, Ellen, McKinley, Trevelyan J., Mitchell, Andrew P., Jones, Gareth J., Vordermeier, Martin, Wood, James L. N., Ferrari, Matthew (Matt)

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.37 MB

english, 2015

28

Developing a Molecular Roadmap of Drug-Food Interactions

Jensen, Kasper, Ni, Yueqiong, Panagiotou, Gianni, Kouskoumvekaki, Irene, Tan, Kai

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

29

Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds

Schweitzer, Yonatan, Kozlov, Michael M., Punta, Marco

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

30

Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli

Tartaglia, Elisa M., Brunel, Nicolas, Mongillo, Gianluigi, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.16 MB

english, 2015

31

Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells

García Münzer, David G., Kostoglou, Margaritis, Georgiadis, Michael C., Pistikopoulos, Efstratios N., Mantalaris, Athanasios, Beard, Daniel A

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 786 KB

english, 2015

32

Confronting the Ethical Challenges of Big Data in Public Health

Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 93 KB

english, 2015

33

HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects

Ferdinandy, Bence, Mones, Enys, Vicsek, Tamás, Müller, Viktor, Althaus, Christian L.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

34

Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage

Jain, Ishutesh, Inamdar, Mandar M., Padinhateeri, Ranjith, Sept, David

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.29 MB

english, 2015

35

Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum

Pacheco, Jorge M., Vasconcelos, Vítor V., Santos, Francisco C., Skyrms, Brian, Bergstrom, Carl T.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.40 MB

english, 2015

36

Protein Complexes in Bacteria

Caufield, J. Harry, Abreu, Marco, Wimble, Christopher, Uetz, Peter, Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.86 MB

english, 2015

37

PLOS Computational Biology 2014 Reviewer Thank You

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 74 KB

english, 2015

38

Critical Slowing Down Governs the Transition to Neuron Spiking

Meisel, Christian, Klaus, Andreas, Kuehn, Christian, Plenz, Dietmar, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.10 MB

english, 2015

39

Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information

Keenan, Daniel M., Quinkert, Amy W., Pfaff, Donald W., Maritan, Amos

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 7.59 MB

english, 2015

40

Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model

Malagarriga, Daniel, Villa, Alessandro E. P., Garcia-Ojalvo, Jordi, Pons, Antonio J., Hilgetag, Claus C.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

41

Correlations and Functional Connections in a Population of Grid Cells

Dunn, Benjamin, Mørreaunet, Maria, Roudi, Yasser, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.69 MB

english, 2015

42

DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates

Echeverria, Ignacia, Papoian, Garegin A., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.11 MB

english, 2015

43

Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment

Jorda, Julien, Liu, Yu, Bobik, Thomas A., Yeates, Todd O., Vajda, Sandor

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.46 MB

english, 2015

44

A Theoretical Justification for Single Molecule Peptide Sequencing

Swaminathan, Jagannath, Boulgakov, Alexander A., Marcotte, Edward M., Searls, David B.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.43 MB

english, 2015

45

Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity

Ponce-Alvarez, Adrián, Deco, Gustavo, Hagmann, Patric, Romani, Gian Luca, Mantini, Dante, Corbetta, Maurizio, Hilgetag, Claus C.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.17 MB

english, 2015

46

A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning

Lee, Mei Yan, Diamond, Scott L., Saucerman, Jeffrey J.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

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