Volume 10; Issue 2

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PLoS Computational Biology
Volume 10; Issue 2

PLoS Computational Biology

Volume 10; Issue 2

1

A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses

Matsen, Frederick A., Small, Christopher T., Soliven, Khanh, Engel, Gregory A., Feeroz, Mostafa M., Wang, Xiaoxing, Craig, Karen L., Hasan, M. Kamrul, Emerman, Michael, Linial, Maxine L., Jones-Engel,

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 923 KB

english, 2014

2

Optimal Recall from Bounded Metaplastic Synapses: Predicting Functional Adaptations in Hippocampal Area CA3

Savin, Cristina, Dayan, Peter, Lengyel, Máté, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1003 KB

english, 2014

3

Mathematical Modeling of the Phoenix Rising Pathway

Liu, Chad, Li, Chuan-Yuan, Yuan, Fan, Gabhann, Feilim Mac

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.16 MB

english, 2014

4

A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes

Riba, Andrea, Bosia, Carla, El Baroudi, Mariama, Ollino, Laura, Caselle, Michele, Zhou, Xianghong Jasmine

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.06 MB

english, 2014

5

Correction: Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 103 KB

english, 2014

6

A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain

Srinivasan, Shyam, Hu, Jia Sheng, Currle, D. Spencer, Fung, Ernest S., Hayes, Wayne B., Lander, Arthur D., Monuki, Edwin S., Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 5.01 MB

english, 2014

7

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor

Pierce, Brian G., Hellman, Lance M., Hossain, Moushumi, Singh, Nishant K., Vander Kooi, Craig W., Weng, Zhiping, Baker, Brian M., Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 601 KB

english, 2014

8

Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement

Nurhonen, Markku, Auranen, Kari, Cohen, Ted

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.12 MB

english, 2014

9

A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood

Hünniger, Kerstin, Lehnert, Teresa, Bieber, Kristin, Martin, Ronny, Figge, Marc Thilo, Kurzai, Oliver, De Boer, Rob J.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.04 MB

english, 2014

10

Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint

Enciso, Germán, Kellogg, Douglas R., Vargas, Arturo, Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 759 KB

english, 2014

11

Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations

Lesaint, Florian, Sigaud, Olivier, Flagel, Shelly B., Robinson, Terry E., Khamassi, Mehdi, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 600 KB

english, 2014

12

A Network Characteristic That Correlates Environmental and Genetic Robustness

Shreif, Zeina, Periwal, Vipul, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.88 MB

english, 2014

13

Ten Simple Rules for Running Interactive Workshops

Pavelin, Katrina, Pundir, Sangya, Cham, Jennifer A., Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 706 KB

english, 2014

14

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Chowdhury, Anupam, Zomorrodi, Ali R., Maranas, Costas D., Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.16 MB

english, 2014

15

Correction: Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 160 KB

english, 2014

16

GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans

Lao, Oscar, Liu, Fan, Wollstein, Andreas, Kayser, Manfred, Pasaniuc, Bogdan

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.05 MB

english, 2014

17

The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer

Acuner Ozbabacan, Saliha Ece, Gursoy, Attila, Nussinov, Ruth, Keskin, Ozlem, Xia, Yu

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.33 MB

english, 2014

18

The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes

Hu, Yu, Zylberberg, Joel, Shea-Brown, Eric, Pillow, Jonathan W.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.48 MB

english, 2014

19

Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups

Garcia, Thomas, Brunnet, Leonardo Gregory, De Monte, Silvia, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.27 MB

english, 2014

20

Workshops: A Great Way to Enhance and Supplement a Degree

Fatumo, Segun, Shome, Sayane, Macintyre, Geoff, Troyanskaya, Olga G.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 141 KB

english, 2014

21

A Unified View of “How Allostery Works”

Tsai, Chung-Jung, Nussinov, Ruth, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.00 MB

english, 2014

22

Learning Gene Networks under SNP Perturbations Using eQTL Datasets

Zhang, Lingxue, Kim, Seyoung, Chen, Kevin

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.57 MB

english, 2014

23

Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms

Bilsland, Alan E., Stevenson, Katrina, Liu, Yu, Hoare, Stacey, Cairney, Claire J., Roffey, Jon, Keith, W. Nicol, Miyano, Satoru

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.69 MB

english, 2014

24

Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism

Noor, Elad, Bar-Even, Arren, Flamholz, Avi, Reznik, Ed, Liebermeister, Wolfram, Milo, Ron, Beard, Daniel A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 611 KB

english, 2014

25

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations

Gumbart, James C., Beeby, Morgan, Jensen, Grant J., Roux, Benoît, Alber, Mark S.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.74 MB

english, 2014

26

Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration

Santra, Tapesh, Kolch, Walter, Kholodenko, Boris N., Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 358 KB

english, 2014

27

In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

Carrivain, Pascal, Barbi, Maria, Victor, Jean-Marc, Chen, Shi-Jie

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 948 KB

english, 2014

28

tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria

Amrine, Katherine C. H., Swingley, Wesley D., Ardell, David H., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.56 MB

english, 2014

29

Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

Pitkänen, Esa, Jouhten, Paula, Hou, Jian, Syed, Muhammad Fahad, Blomberg, Peter, Kludas, Jana, Oja, Merja, Holm, Liisa, Penttilä, Merja, Rousu, Juho, Arvas, Mikko, Nielsen, Jens

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.66 MB

english, 2014

30

Combining Experiments and Simulations Using the Maximum Entropy Principle

Boomsma, Wouter, Ferkinghoff-Borg, Jesper, Lindorff-Larsen, Kresten, Levitt, Michael

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

31

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

Jia, Peilin, Zhao, Zhongming, Radivojac, Predrag

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.05 MB

english, 2014

32

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery

Peng, Lili X., Hsu, Monica T., Bonomi, Massimiliano, Agard, David A., Jacobson, Matthew P., Alber, Mark S.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.17 MB

english, 2014

33

A Unified Model of Heading and Path Perception in Primate MSTd

Layton, Oliver W., Browning, N. Andrew, Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.77 MB

english, 2014

34

Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia

Sheppard, Patrick W., Sun, Xiaoyun, Khammash, Mustafa, Giffard, Rona G., Mac Gabhann, Feilim

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

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