Volume 9; Issue 11

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PLoS Computational Biology
Volume 9; Issue 11

PLoS Computational Biology

Volume 9; Issue 11

1

Communication and Common Interest

Godfrey-Smith, Peter, MartÃnez, Manolo, Bergstrom, Carl T.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 813 KB

english, 2013

2

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein

Ortega, Davi R., Mo, Guoya, Lee, Kwangwoon, Zhou, Hongjun, Baudry, Jerome, Dahlquist, Frederick W., Zhulin, Igor B., Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.48 MB

english, 2013

3

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Bailey, Timothy, Krajewski, Pawel, Ladunga, Istvan, Lefebvre, Celine, Li, Qunhua, Liu, Tao, Madrigal, Pedro, Taslim, Cenny, Zhang, Jie, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 323 KB

english, 2013

4

Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis

Ray, Shayoni, Yuan, Daniel, Dhulekar, Nimit, Oztan, Basak, Yener, Bülent, Larsen, Melinda, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.27 MB

english, 2013

5

Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon

Valle, Denis, Clark, James, Fraser, Christophe

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.70 MB

english, 2013

6

Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations

Chapal-Ilani, Noa, Maruvka, Yosef E., Spiro, Adam, Reizel, Yitzhak, Adar, Rivka, Shlush, Liran I., Shapiro, Ehud, Wasserman, Wyeth W.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.25 MB

english, 2013

7

Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code

Micheyl, Christophe, Schrater, Paul R., Oxenham, Andrew J., Griffiths, Timothy D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 576 KB

english, 2013

8

Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection

Sullivan, Adam M., Zhao, Xiaopeng, Suzuki, Yasuhiro, Ochiai, Eri, Crutcher, Stephen, Gilchrist, Michael A., von Mering, Christian

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 578 KB

english, 2013

9

Predictive Coding of Dynamical Variables in Balanced Spiking Networks

Boerlin, Martin, Machens, Christian K., Denève, Sophie, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.52 MB

english, 2013

10

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Berestovsky, Natalie, Zhou, Wanding, Nagrath, Deepak, Nakhleh, Luay, Singh, Mona

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

11

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli

Dickson, Alex, Brooks, Charles L., Shakhnovich, Eugene I.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 828 KB

english, 2013

12

Dread and the Disvalue of Future Pain

Story, Giles W., Vlaev, Ivaylo, Seymour, Ben, Winston, Joel S., Darzi, Ara, Dolan, Raymond J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.65 MB

english, 2013

13

MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms

Ben-Hamo, Rotem, Efroni, Sol, Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 720 KB

english, 2013

14

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

Ung, Peter Man-Un, Thompson, Andrea D., Chang, Lyra, Gestwicki, Jason E., Carlson, Heather A., Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 4.17 MB

english, 2013

15

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

Ollikainen, Noah, Kortemme, Tanja, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.34 MB

english, 2013

16

A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection

Albergante, Luca, Timmis, Jon, Beattie, Lynette, Kaye, Paul M., Thieffry, Denis

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

17

Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals

Heldt, Frank S., Frensing, Timo, Pflugmacher, Antje, Gröpler, Robin, Peschel, Britta, Reichl, Udo, Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.73 MB

english, 2013

18

Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification

Theis, Lucas, Chagas, Andrè Maia, Arnstein, Daniel, Schwarz, Cornelius, Bethge, Matthias, Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 799 KB

english, 2013

19

Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

Ã‡etinbaÅŸ, Murat, Shakhnovich, Eugene I., Pande, Vijay S.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.00 MB

english, 2013

20

Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity

Wang, Kejian, Sun, Jiazhi, Zhou, Shufeng, Wan, Chunling, Qin, Shengying, Li, Can, He, Lin, Yang, Lun, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.91 MB

english, 2013

21

Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells

Mouri, Kazunari, Sako, Yasushi, Shvartsman, Stanislav

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.75 MB

english, 2013

22

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

Edwards, Hannah, Abeln, Sanne, Deane, Charlotte M., Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.00 MB

english, 2013

23

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Polles, Guido, Indelicato, Giuliana, Potestio, Raffaello, Cermelli, Paolo, Twarock, Reidun, Micheletti, Cristian, Schlessinger, Avner

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.73 MB

english, 2013

24

Leading a Statistical Bioinformatics Lab: It's All About Finding Balance

Vitek, Olga, Alexandrov, Theodore

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 874 KB

english, 2013

25

Learning How to Run a Lab: Interviews with Principal Investigators

Alexandrov, Theodore, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 118 KB

english, 2013

26

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

Hase, Takeshi, Ghosh, Samik, Yamanaka, Ryota, Kitano, Hiroaki, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.42 MB

english, 2013

27

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

Fuchs, Julian E., von Grafenstein, Susanne, Huber, Roland G., Kramer, Christian, Liedl, Klaus R., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.63 MB

english, 2013

28

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

Khazanov, Nickolay A., Carlson, Heather A., Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.71 MB

english, 2013

29

Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations

Metzger, Jakob J., Eule, Stephan, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 467 KB

english, 2013

30

Stochastic Computations in Cortical Microcircuit Models

Habenschuss, Stefan, Jonke, Zeno, Maass, Wolfgang, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.04 MB

english, 2013

31

Dynamical Adaptation in Photoreceptors

Clark, Damon A., Benichou, Raphael, Meister, Markus, Azeredo da Silveira, Rava, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.86 MB

english, 2013

32

In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids

Kempf, Harald, Hatzikirou, Haralampos, Bleicher, Marcus, Meyer-Hermann, Michael, Alber, Mark S.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.81 MB

english, 2013

33

A Computational Model of Liver Iron Metabolism

Mitchell, Simon, Mendes, Pedro, Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 821 KB

english, 2013

34

Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell

Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca, Soyer, Orkun S., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 493 KB

english, 2013

35

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

Patil, Ashwini, Kumagai, Yutaro, Liang, Kuo-ching, Suzuki, Yutaka, Nakai, Kenta, Saucerman, Jeffrey J.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.11 MB

english, 2013

36

A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions

Wang, Xiaoxia, Panchanathan, Sarada, Chowell, Gerardo, Salathé, Marcel

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

37

Mapping the Structural and Dynamical Features of Kinesin Motor Domains

Scarabelli, Guido, Grant, Barry J., Tajkhorshid, Emad

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.09 MB

english, 2013

38

Genetic Architecture Promotes the Evolution and Maintenance of Cooperation

Frénoy, Antoine, Taddei, François, Misevic, Dusan, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

39

Ten Simple Rules for Starting a Regional Student Group

Shanmugam, Avinash Kumar, Macintyre, Geoff, Michaut, Magali, Abeel, Thomas, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 132 KB

english, 2013

40

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

Sikora-Wohlfeld, Weronika, Ackermann, Marit, Christodoulou, Eleni G., Singaravelu, Kalaimathy, Beyer, Andreas, Ovcharenko, Ivan

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 459 KB

english, 2013

41

Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution

Persi, Erez, Horn, David, Fetrow, Jacquelyn S.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.38 MB

english, 2013

42

Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance

He, Biyu J., Zempel, John M., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.70 MB

english, 2013

43

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013

de Ridder, Jeroen, Bromberg, Yana, Michaut, Magali, Satagopam, Venkata P., Corpas, Manuel, Macintyre, Geoff, Alexandrov, Theodore

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 139 KB

english, 2013

44

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Portella, Guillem, Battistini, Federica, Orozco, Modesto, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.12 MB

english, 2013

45

Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector

Zenke, Friedemann, Hennequin, Guillaume, Gerstner, Wulfram, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.19 MB

english, 2013

46

About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium

Martens, Lennart, Alexandrov, Theodore

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 216 KB

english, 2013

47

Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution

Warnecke, Tobias, Becker, Erin A., Facciotti, Marc T., Nislow, Corey, Lehner, Ben, Tanay, Amos

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 979 KB

english, 2013

48

Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers

Szklarczyk, Oliwia M., González-Segredo, Nélido, Kukura, Philipp, Oppenheim, Ariella, Choquet, Daniel, Sandoghdar, Vahid, Helenius, Ari, Sbalzarini, Ivo F., Ewers, Helge, Nir, Ben-Tal

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.44 MB

english, 2013

49

Breaking the Ice and Forging Links: The Importance of Socializing in Research

Stobbe, Miranda, Mishra, Tarun, Macintyre, Geoff, Troyanskaya, Olga G.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 144 KB

english, 2013

50

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

Eksi, Ridvan, Li, Hong-Dong, Menon, Rajasree, Wen, Yuchen, Omenn, Gilbert S., Kretzler, Matthias, Guan, Yuanfang, Iakoucheva, Lilia M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.69 MB

english, 2013

51

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

Konc, Janez, Hodošček, Milan, Ogrizek, Mitja, Trykowska Konc, Joanna, Janežič, Dušanka, MacKerell, Alexander Donald

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.77 MB

english, 2013

52

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

Ruiz-Herrero, Teresa, Estrada, Javier, Guantes, Raúl, Miguez, David G., MacKerell, Alexander Donald

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.36 MB

english, 2013

53

A Neurocomputational Model of the Mismatch Negativity

Lieder, Falk, Stephan, Klaas E., Daunizeau, Jean, Garrido, Marta I., Friston, Karl J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.53 MB

english, 2013

54

Ten Quick Tips for Using the Gene Ontology

Blake, Judith A., Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 123 KB

english, 2013

55

Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins

Ganguly, Debabani, Zhang, Weihong, Chen, Jianhan, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 6.23 MB

english, 2013

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