Volume 9; Issue 1

PLoS Computational Biology

Volume 9; Issue 1

1

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

Škunca, Nives, Bošnjak, Matko, Kriško, Anita, Panov, Panče, Džeroski, Sašo, Šmuc, Tomislav, Supek, Fran, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.85 MB

english, 2013

2

Evolutionary Optimization of Protein Folding

Debès, Cédric, Wang, Minglei, Caetano-Anollés, Gustavo, Gräter, Frauke, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 488 KB

english, 2013

3

The Effects of Temperature on the Stability of a Neuronal Oscillator

Rinberg, Anatoly, Taylor, Adam L., Marder, Eve, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 930 KB

english, 2013

4

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

Koren, Omry, Knights, Dan, Gonzalez, Antonio, Waldron, Levi, Segata, Nicola, Knight, Rob, Huttenhower, Curtis, Ley, Ruth E., Eisen, Jonathan A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.66 MB

english, 2013

5

An Integrative Model of Ion Regulation in Yeast

Ke, Ruian, Ingram, Piers J., Haynes, Ken, Price, Nathan D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.09 MB

english, 2013

6

Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex

Zheng, Pengsheng, Dimitrakakis, Christos, Triesch, Jochen, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 886 KB

english, 2013

7

The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks

Pujato, Mario, MacCarthy, Thomas, Fiser, Andras, Bergman, Aviv, Aitchison, John D.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 755 KB

english, 2013

8

Important miRs of Pathways in Different Tumor Types

Wuchty, Stefan, Arjona, Dolores, Bauer, Peter O., Singh, Mona

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.25 MB

english, 2013

9

How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns

Le Cunff, Yann, Baudisch, Annette, Pakdaman, Khashayar, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.44 MB

english, 2013

10

Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma

Volman, Vladislav, Bazhenov, Maxim, Sejnowski, Terrence J., Halassa, Michael M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 894 KB

english, 2013

11

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

Schaefer, Martin H., Lopes, Tiago J. S., Mah, Nancy, Shoemaker, Jason E., Matsuoka, Yukiko, Fontaine, Jean-Fred, Louis-Jeune, Caroline, Eisfeld, Amie J., Neumann, Gabriele, Perez-Iratxeta, Carol, Kawa

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.10 MB

english, 2013

12

Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin

Settanni, Giovanni, Serquera, David, Marszalek, Piotr E., Paci, Emanuele, Itzhaki, Laura S., Chen, Shi-Jie

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.72 MB

english, 2013

13

Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations

Lemmin, Thomas, Soto, Cinque S., Clinthorne, Graham, DeGrado, William F., Dal Peraro, Matteo, Livesay, Dennis R.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.18 MB

english, 2013

14

The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack

Joyce, Karen E., Hayasaka, Satoru, Laurienti, Paul J., Achard, Sophie

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.79 MB

english, 2013

15

Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy

Wilming, Niklas, Harst, Simon, Schmidt, Nico, König, Peter, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 3.09 MB

english, 2013

16

Identifying Transmission Cycles at the Human-Animal Interface: The Role of Animal Reservoirs in Maintaining Gambiense Human African Trypanosomiasis

Funk, Sebastian, Nishiura, Hiroshi, Heesterbeek, Hans, Edmunds, W. John, Checchi, Francesco, Pascual, Mercedes

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 714 KB

english, 2013

17

ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information

Cicek, A. Ercument, Bederman, Ilya, Henderson, Leigh, Drumm, Mitchell L., Ozsoyoglu, Gultekin, Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

18

Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics

Magiorkinis, Gkikas, Sypsa, Vana, Magiorkinis, Emmanouil, Paraskevis, Dimitrios, Katsoulidou, Antigoni, Belshaw, Robert, Fraser, Christophe, Pybus, Oliver George, Hatzakis, Angelos, Kosakovsky Pond, S

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.07 MB

english, 2013

19

Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective

Rockwell, Graham, Guido, Nicholas J., Church, George M., Papin, Jason A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 711 KB

english, 2013

20

Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images

Sinz, Fabian, Bethge, Matthias, Maloney, Laurence T.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 893 KB

english, 2013

21

The Effects of City Streets on an Urban Disease Vector

Barbu, Corentin M., Hong, Andrew, Manne, Jennifer M., Small, Dylan S., Quintanilla Calderón, Javier E., Sethuraman, Karthik, Quispe-Machaca, Víctor, Ancca-Juárez, Jenny, Cornejo del Carpio, Juan G., M

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 533 KB

english, 2013

22

Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins

Tyanova, Stefka, Cox, Jürgen, Olsen, Jesper, Mann, Matthias, Frishman, Dmitrij, Iakoucheva, Lilia M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 740 KB

english, 2013

23

Reward from Punishment Does Not Emerge at All Costs

Vukov, Jeromos, Pinheiro, Flávio L., Santos, Francisco C., Pacheco, Jorge M., Levin, Simon A.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 321 KB

english, 2013

24

How Sensitive Is the Human Visual System to the Local Statistics of Natural Images?

Gerhard, Holly E., Wichmann, Felix A., Bethge, Matthias, Kording, Konrad P.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.15 MB

english, 2013

25

Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics

Nowak-Lovato, Kristy, Alexandrov, Ludmil B., Banisadr, Afsheen, Bauer, Amy L., Bishop, Alan R., Usheva, Anny, Mu, Fangping, Hong-Geller, Elizabeth, Rasmussen, Kim Ø., Hlavacek, William S., Alexandrov,

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 2.65 MB

english, 2013

26

Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation

Kim, Yohan, Yewdell, Jonathan W., Sette, Alessandro, Peters, Bjoern, Antia, Rustom

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 451 KB

english, 2013

27

Visual Data Mining of Biological Networks: One Size Does Not Fit All

Pastrello, Chiara, Otasek, David, Fortney, Kristen, Agapito, Giuseppe, Cannataro, Mario, Shirdel, Elize, Jurisica, Igor, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 302 KB

english, 2013

28

Significance Analysis of Prognostic Signatures

Beck, Andrew H., Knoblauch, Nicholas W., Hefti, Marco M., Kaplan, Jennifer, Schnitt, Stuart J., Culhane, Aedin C., Schroeder, Markus S., Risch, Thomas, Quackenbush, John, Haibe-Kains, Benjamin, Tucker

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 578 KB

english, 2013

29

Approximate Bayesian Computation

Sunnåker, Mikael, Busetto, Alberto Giovanni, Numminen, Elina, Corander, Jukka, Foll, Matthieu, Dessimoz, Christophe, Wodak, Shoshana

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 415 KB

english, 2013

30

Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation

Ciandrini, Luca, Stansfield, Ian, Romano, M. Carmen, Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 993 KB

english, 2013

31

Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty

Lo Iacono, Giovanni, van den Bosch, Frank, Gilligan, Chris A., van Bruggen, Ariena

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 756 KB

english, 2013

32

Dynamic Finite Size Effects in Spiking Neural Networks

Buice, Michael A., Chow, Carson C., Ermentrout, Bard

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 982 KB

english, 2013

33

Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator

de Ridder, Jeroen, Abeel, Thomas, Michaut, Magali, Satagopam, Venkata P., Gehlenborg, Nils, Troyanskaya, Olga G.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 148 KB

english, 2013

34

Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures

Bennun, Sandra V., Yarema, Kevin J., Betenbaugh, Michael J., Krambeck, Frederick J., Tucker-Kellogg, Greg

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

35

Computational Analysis of Rho GTPase Cycling

Falkenberg, Cibele Vieira, Loew, Leslie M., Haugh, Jason M.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.05 MB

english, 2013

36

Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics

Chindapol, Nol, Kaandorp, Jaap A., Cronemberger, Carolina, Mass, Tali, Genin, Amatzia, Crampin, Edmund J.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 6.14 MB

english, 2013

37

Identification of a Functional Connectome for Long-Term Fear Memory in Mice

Wheeler, Anne L., Teixeira, Cátia M., Wang, Afra H., Xiong, Xuejian, Kovacevic, Natasa, Lerch, Jason P., McIntosh, Anthony R., Parkinson, John, Frankland, Paul W., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 5.12 MB

english, 2013

38

Metallochaperones Regulate Intracellular Copper Levels

Pang, W. Lee, Kaur, Amardeep, Ratushny, Alexander V., Cvetkovic, Aleksandar, Kumar, Sunil, Pan, Min, Arkin, Adam P., Aitchison, John D., Adams, Michael W. W., Baliga, Nitin S., Reed, Jennifer L.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 815 KB

english, 2013

39

Maximizing the Information Content of Experiments in Systems Biology

Liepe, Juliane, Filippi, Sarah, Komorowski, Michał, Stumpf, Michael P. H., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.62 MB

english, 2013

40

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

Yu, Hang, Schulten, Klaus, Grubmuller, Helmut

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 6.20 MB

english, 2013

41

Starling Flock Networks Manage Uncertainty in Consensus at Low Cost

Young, George F., Scardovi, Luca, Cavagna, Andrea, Giardina, Irene, Leonard, Naomi E., Bergstrom, Carl T.

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 974 KB

english, 2013

42

Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task

d'Acremont, Mathieu, Fornari, Eleonora, Bossaerts, Peter, Behrens, Tim

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 989 KB

english, 2013

43

Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation

Xu, Linan, Hasin, Naushaba, Shen, Manli, He, Jianwei, Xue, Youlin, Zhou, Xiaohong, Perrett, Sarah, Song, Youtao, Jones, Gary W., Legname, Giuseppe

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 562 KB

english, 2013

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