Volume 11; Issue 8

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PLoS Computational Biology
Volume 11; Issue 8

PLoS Computational Biology

Volume 11; Issue 8

1

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

King, Zachary A., Dräger, Andreas, Ebrahim, Ali, Sonnenschein, Nikolaus, Lewis, Nathan E., Palsson, Bernhard O., Gardner, Paul P

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.62 MB

english, 2015

2

Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations

Rockah-Shmuel, Liat, Tóth-Petróczy, Ágnes, Tawfik, Dan S., Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.48 MB

english, 2015

3

Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations

Harrison, Paul M., Badel, Laurent, Wall, Mark J., Richardson, Magnus J. E., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.52 MB

english, 2015

4

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets

Lu, Songjian, Lu, Kevin N., Cheng, Shi-Yuan, Hu, Bo, Ma, Xiaojun, Nystrom, Nicholas, Lu, Xinghua, Beerenwinkel, Niko

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

5

Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit

Bharioke, Arjun, Chklovskii, Dmitri B., Kording, Konrad P.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.00 MB

english, 2015

6

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Gritsenko, Alexey A., Hulsman, Marc, Reinders, Marcel J. T., de Ridder, Dick, Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.15 MB

english, 2015

7

Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009

Tamerius, James, Viboud, Cécile, Shaman, Jeffrey, Chowell, Gerardo, Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.30 MB

english, 2015

8

An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division

Xiong, Liping, Lan, Ganhui, Kruse, Karsten

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

9

Structure Learning in Bayesian Sensorimotor Integration

Genewein, Tim, Hez, Eduard, Razzaghpanah, Zeynab, Braun, Daniel A., Berniker, Max

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.55 MB

english, 2015

10

Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast

Chen, Po-Wei, Fonseca, Luis L., Hannun, Yusuf A., Voit, Eberhard O., Stelling, Jorg

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 6.54 MB

english, 2015

11

Correction: The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 119 KB

english, 2015

12

Flexible Modeling of Epidemics with an Empirical Bayes Framework

Brooks, Logan C., Farrow, David C., Hyun, Sangwon, Tibshirani, Ryan J., Rosenfeld, Roni, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

13

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

Griffith, Malachi, Walker, Jason R., Spies, Nicholas C., Ainscough, Benjamin J., Griffith, Obi L., Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.73 MB

english, 2015

14

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

Paulsen, Jonas, Gramstad, Odin, Collas, Philippe, Tanay, Amos

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.78 MB

english, 2015

15

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

Yang, Pengyi, Zheng, Xiaofeng, Jayaswal, Vivek, Hu, Guang, Yang, Jean Yee Hwa, Jothi, Raja, Iakoucheva, Lilia M.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.55 MB

english, 2015

16

Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers

Sanders, Shaun S., Martin, Dale D. O., Butland, Stefanie L., Lavallée-Adam, Mathieu, Calzolari, Diego, Kay, Chris, Yates, John R., Hayden, Michael R., Ben-Tal, Nir

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.91 MB

english, 2015

17

A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases

Xue, Chuan, Shtylla, Blerta, Brown, Anthony, Mofrad, Mohammad R. K.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.24 MB

english, 2015

18

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

Tsai, Zing Tsung-Yeh, Shiu, Shin-Han, Tsai, Huai-Kuang, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.39 MB

english, 2015

19

Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

Bennett, James E. M., Bair, Wyeth, Doiron, Brent

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.89 MB

english, 2015

20

The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans

Striegel, Deborah A., Hara, Manami, Periwal, Vipul, Pedersen, Morten Gram

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 6.18 MB

english, 2015

21

Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions

Amitai, Assaf, Toulouze, Mathias, Dubrana, Karine, Holcman, David, Morozov, Alexandre V

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.98 MB

english, 2015

22

A Bayesian Attractor Model for Perceptual Decision Making

Bitzer, Sebastian, Bruineberg, Jelle, Kiebel, Stefan J., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.21 MB

english, 2015

23

Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations

Kenzaki, Hiroo, Takada, Shoji, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 6.12 MB

english, 2015

24

Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling

Ponce-Alvarez, Adrián, He, Biyu J., Hagmann, Patric, Deco, Gustavo, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.69 MB

english, 2015

25

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

Yuan, Shuai, Johnston, H. Richard, Zhang, Guosheng, Li, Yun, Hu, Yi-Juan, Qin, Zhaohui S., Gardner, Paul P

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.59 MB

english, 2015

26

Formation and Dynamics of Waves in a Cortical Model of Cholinergic Modulation

Roach, James P., Ben-Jacob, Eshel, Sander, Leonard M., Zochowski, Michal R., Sporns, Olaf

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.73 MB

english, 2015

27

Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity

Breit, Marc, Netzer, Michael, Weinberger, Klaus M., Baumgartner, Christian, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.62 MB

english, 2015

28

Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks

Newberry, Mitchell G, Ennis, Daniel B, Savage, Van M, Weitz, Joshua S

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 733 KB

english, 2015

29

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks

Schillings, Claudia, Sunnåker, Mikael, Stelling, Jörg, Schwab, Christoph, Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

30

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses

Ocker, Gabriel Koch, Litwin-Kumar, Ashok, Doiron, Brent, Latham, Peter E.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 2.79 MB

english, 2015

31

Functional Basis of Microorganism Classification

Zhu, Chengsheng, Delmont, Tom O., Vogel, Timothy M., Bromberg, Yana, Orengo, Christine A.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.75 MB

english, 2015

32

Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees

Lykov, Kirill, Li, Xuejin, Lei, Huan, Pivkin, Igor V., Karniadakis, George Em, Feng, James

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.83 MB

english, 2015