Volume 10; Issue 9

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PLoS Computational Biology
Volume 10; Issue 9

PLoS Computational Biology

Volume 10; Issue 9

1

Torsion-Mediated Interaction between Adjacent Genes

Meyer, Sam, Beslon, Guillaume, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.39 MB

english, 2014

2

Synchronization of Isolated Downstates (K-Complexes) May Be Caused by Cortically-Induced Disruption of Thalamic Spindling

Mak-McCully, Rachel A., Deiss, Stephen R., Rosen, Burke Q., Jung, Ki-Young, Sejnowski, Terrence J., Bastuji, Hélène, Rey, Marc, Cash, Sydney S., Bazhenov, Maxim, Halgren, Eric, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.18 MB

english, 2014

3

The Structural Basis of ATP as an Allosteric Modulator

Lu, Shaoyong, Huang, Wenkang, Wang, Qi, Shen, Qiancheng, Li, Shuai, Nussinov, Ruth, Zhang, Jian, Wei, Guanghong

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

4

Mathematical Modeling of Bacterial Kinetics to Predict the Impact of Antibiotic Colonic Exposure and Treatment Duration on the Amount of Resistant Enterobacteria Excreted

Nguyen, Thu Thuy, Guedj, Jeremie, Chachaty, Elisabeth, de Gunzburg, Jean, Andremont, Antoine, Mentré, France, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.31 MB

english, 2014

5

Allele-Specific Network Reveals Combinatorial Interaction That Transcends Small Effects in Psoriasis GWAS

Climer, Sharlee, Templeton, Alan R., Zhang, Weixiong, Wu, Michael Chiao-An

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.03 MB

english, 2014

6

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

Suratanee, Apichat, Schaefer, Martin H., Betts, Matthew J., Soons, Zita, Mannsperger, Heiko, Harder, Nathalie, Oswald, Marcus, Gipp, Markus, Ramminger, Ellen, Marcus, Guillermo, Männer, Reinhard, Rohr

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.66 MB

english, 2014

7

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

Pettit, Jean-Baptiste, Tomer, Raju, Achim, Kaia, Richardson, Sylvia, Azizi, Lamiae, Marioni, John, Morris, Quaid

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.50 MB

english, 2014

8

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design

Dunbar, James, Knapp, Bernhard, Fuchs, Angelika, Shi, Jiye, Deane, Charlotte M., Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

9

Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo

Hogan, Thea, Kadolsky, Ulrich, Tung, Sim, Seddon, Benedict, Yates, Andrew, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.70 MB

english, 2014

10

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

Li, Jinyu, Rossetti, Giulia, Dreyer, Jens, Raugei, Simone, Ippoliti, Emiliano, Lüscher, Bernhard, Carloni, Paolo, MacKerell, Alexander Donald

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.87 MB

english, 2014

11

Correction: Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 139 KB

english, 2014

12

Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method

Vincenzi, Simone, Mangel, Marc, Crivelli, Alain J., Munch, Stephan, Skaug, Hans J., Levin, Simon A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

13

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

Nam, Hojung, Campodonico, Miguel, Bordbar, Aarash, Hyduke, Daniel R., Kim, Sangwoo, Zielinski, Daniel C., Palsson, Bernhard O., Ofran, Yanay

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.39 MB

english, 2014

14

Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma

Bernardo-Faura, Marti, Massen, Stefan, Falk, Christine S., Brady, Nathan R., Eils, Roland, Tucker-Kellogg, Greg

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.93 MB

english, 2014

15

Emergence of Assortative Mixing between Clusters of Cultured Neurons

Teller, Sara, Granell, Clara, De Domenico, Manlio, Soriano, Jordi, Gómez, Sergio, Arenas, Alex, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.15 MB

english, 2014

16

Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations

Stuckey, Erin M., Smith, Thomas, Chitnis, Nakul, Ferguson, Neil M.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.14 MB

english, 2014

17

The Time Scale of Evolutionary Innovation

Chatterjee, Krishnendu, Pavlogiannis, Andreas, Adlam, Ben, Nowak, Martin A., Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.33 MB

english, 2014

18

eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models

Brylinski, Michal, Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.96 MB

english, 2014

19

Ten Simple Rules for Better Figures

Rougier, Nicolas P., Droettboom, Michael, Bourne, Philip E.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.71 MB

english, 2014

20

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Hepler, N. Lance, Scheffler, Konrad, Weaver, Steven, Murrell, Ben, Richman, Douglas D., Burton, Dennis R., Poignard, Pascal, Smith, Davey M., Kosakovsky Pond, Sergei L., Murphy, Robert F.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 578 KB

english, 2014

21

Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA

Chu, Xiakun, Liu, Fei, Maxwell, Brian A., Wang, Yong, Suo, Zucai, Wang, Haijun, Han, Wei, Wang, Jin, MacKerell, Alexander Donald

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 5.02 MB

english, 2014

22

SANTA: Quantifying the Functional Content of Molecular Networks

Cornish, Alex J., Markowetz, Florian, Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 929 KB

english, 2014

23

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

Blair, David R., Wang, Kanix, Nestorov, Svetlozar, Evans, James A., Rzhetsky, Andrey, Cohen, K. Bretonnel

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.24 MB

english, 2014

24

Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data

Simeone, Angela, Marsico, Giovanni, Collinet, Claudio, Galvez, Thierry, Kalaidzidis, Yannis, Zerial, Marino, Beyer, Andreas, Morris, Quaid

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.05 MB

english, 2014

25

PTEN Hopping on the Cell Membrane Is Regulated via a Positively-Charged C2 Domain

Yasui, Masato, Matsuoka, Satomi, Ueda, Masahiro, Falke, Joseph

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.29 MB

english, 2014

26

Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies

Chang, Diana, Keinan, Alon, Benson, Mikael

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 996 KB

english, 2014

27

Evolution of the F0F1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes

Koumandou, Vassiliki Lila, Kossida, Sophia, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.69 MB

english, 2014

28

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

Ghosh, Amit, Nilmeier, Jerome, Weaver, Daniel, Adams, Paul D., Keasling, Jay D., Mukhopadhyay, Aindrila, Petzold, Christopher J., Martín, Héctor García, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.71 MB

english, 2014

29

Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression

Norström, Melissa M., Veras, Nazle M., Huang, Wei, Proper, Mattia C. F., Cook, Jennifer, Hartogensis, Wendy, Hecht, Frederick M., Karlsoon, Annika C., Salemi, Marco, Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.04 MB

english, 2014

30

NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles

Kosugi, Shunichi, Yanagawa, Hiroshi, Terauchi, Ryohei, Tabata, Satoshi, Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.98 MB

english, 2014

31

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

Xie, Qing, Liu, Qi, Mao, Fengbiao, Cai, Wanshi, Wu, Honghu, You, Mingcong, Wang, Zhen, Chen, Bingyu, Sun, Zhong Sheng, Wu, Jinyu, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

32

Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages

Székely, Tamás, Burrage, Kevin, Mangel, Marc, Bonsall, Michael B., Santos, Francisco C.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.98 MB

english, 2014

33

Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks

Luccioli, Stefano, Ben-Jacob, Eshel, Barzilai, Ari, Bonifazi, Paolo, Torcini, Alessandro, Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.65 MB

english, 2014

34

Environmental Statistics and Optimal Regulation

Sivak, David A., Thomson, Matt, Listgarten, Jennifer

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

35

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products

Medema, Marnix H., Paalvast, Yared, Nguyen, Don D., Melnik, Alexey, Dorrestein, Pieter C., Takano, Eriko, Breitling, Rainer, Gardner, Paul P.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 981 KB

english, 2014

36

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

Invernizzi, Gaetano, Tiberti, Matteo, Lambrughi, Matteo, Lindorff-Larsen, Kresten, Papaleo, Elena, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.48 MB

english, 2014

37

Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set

Hancock, Penelope A., Rehman, Yasmin, Hall, Ian M., Edeghere, Obaghe, Danon, Leon, House, Thomas A., Keeling, Matthew J., Ferrari, Matthew

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 927 KB

english, 2014

38

Inferring on the Intentions of Others by Hierarchical Bayesian Learning

Diaconescu, Andreea O., Mathys, Christoph, Weber, Lilian A. E., Daunizeau, Jean, Kasper, Lars, Lomakina, Ekaterina I., Fehr, Ernst, Stephan, Klaas E., Schrater, Paul

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 3.21 MB

english, 2014

39

Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability

Hraha, Thomas H., Westacott, Matthew J., Pozzoli, Marina, Notary, Aleena M., McClatchey, P. Mason, Benninger, Richard K. P., Glass, Leon

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.20 MB

english, 2014

40

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Chen, Yun-Ching, Douville, Christopher, Wang, Cheng, Niknafs, Noushin, Yeo, Grace, Beleva-Guthrie, Violeta, Carter, Hannah, Stenson, Peter D., Cooper, David N., Li, Biao, Mooney, Sean, Karchin, Rachel

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 686 KB

english, 2014

41

A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer

Huang, Sijia, Yee, Cameron, Ching, Travers, Yu, Herbert, Garmire, Lana X., Rzhetsky, Andrey

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 4.82 MB

english, 2014

42

Pupil-Linked Arousal Determines Variability in Perceptual Decision Making

Murphy, Peter R., Vandekerckhove, Joachim, Nieuwenhuis, Sander, O'Reilly, Jill X.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.67 MB

english, 2014

43

Geometry Shapes Evolution of Early Multicellularity

Libby, Eric, Ratcliff, William, Travisano, Michael, Kerr, Ben, Cordero, Otto X.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.61 MB

english, 2014

44

Multi-state Modeling of Biomolecules

Stefan, Melanie I., Bartol, Thomas M., Sejnowski, Terrence J., Kennedy, Mary B., Wodak, Shoshana

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 878 KB

english, 2014

45

Multidimensional Epistasis and the Transitory Advantage of Sex

Nowak, Stefan, Neidhart, Johannes, Szendro, Ivan G., Krug, Joachim, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.70 MB

english, 2014

46

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

Yang, Hong, Krumholz, Elias W., Brutinel, Evan D., Palani, Nagendra P., Sadowsky, Michael J., Odlyzko, Andrew M., Gralnick, Jeffrey A., Libourel, Igor G. L., Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 768 KB

english, 2014

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