Volume 14; Issue 10

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PLoS Computational Biology
Volume 14; Issue 10

PLoS Computational Biology

Volume 14; Issue 10

1

Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing

Staddon, Michael F., Bi, Dapeng, Tabatabai, A. Pasha, Ajeti, Visar, Murrell, Michael P., Banerjee, Shiladitya, Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.37 MB

english, 2018

2

Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Handel, Andreas, Li, Yan, McKay, Brian, Pawelek, Kasia A., Zarnitsyna, Veronika, Antia, Rustom, Davenport, Miles P.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.02 MB

english, 2018

3

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays

Gelfman, Sahar, Wang, Quanli, Lu, Yi-Fan, Hall, Diana, Bostick, Christopher D., Dhindsa, Ryan, Halvorsen, Matt, McSweeney, K. Melodi, Cotterill, Ellese, Edinburgh, Tom, Beaumont, Michael A., Frankel,

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.70 MB

english, 2018

4

Ten simple rules for scientists: Improving your writing productivity

Peterson, Todd C., Kleppner, Sofie R., Botham, Crystal M., Markel, Scott

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 479 KB

english, 2018

5

A Kirchhoff-Nernst-Planck framework for modeling large scale extracellular electrodiffusion surrounding morphologically detailed neurons

Solbrå, Andreas, Bergersen, Aslak Wigdahl, van den Brink, Jonas, Malthe-Sørenssen, Anders, Einevoll, Gaute T., Halnes, Geir, Barreto, Ernest

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.32 MB

english, 2018

6

Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine

Cai, Francisco Y., Fussell, Thomas, Cobey, Sarah, Lipsitch, Marc, Viboud, Cecile

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.95 MB

english, 2018

7

Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals

Huh, Iksoo, Mendizabal, Isabel, Park, Taesung, Yi, Soojin V., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.97 MB

english, 2018

8

Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data

Soto, Fabian A., Vucovich, Lauren E., Ashby, F. Gregory, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.34 MB

english, 2018

9

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

Chen, Ling, Fish, Alexandra E., Capra, John A., Ma, Jian

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.95 MB

english, 2018

10

In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability

Vavourakis, Vasileios, Stylianopoulos, Triantafyllos, Wijeratne, Peter A., McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.62 MB

english, 2018

11

Ten quick tips for getting the most scientific value out of numerical data

Schwen, Lars Ole, Rueschenbaum, Sabrina, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.07 MB

english, 2018

12

Noise propagation in an integrated model of bacterial gene expression and growth

Kleijn, Istvan T., Krah, Laurens H. J., Hermsen, Rutger, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.83 MB

english, 2018

13

Seizure pathways: A model-based investigation

Karoly, Philippa J., Kuhlmann, Levin, Soudry, Daniel, Grayden, David B., Cook, Mark J., Freestone, Dean R., Marinazzo, Daniele

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.84 MB

english, 2018

14

Ten simple rules for developing good reading habits during graduate school and beyond

Méndez, Marcos, Lewitter, Fran

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 476 KB

english, 2018

15

Self-organized traffic via priority rules in leaf-cutting ants

Strömbom, Daniel, Dussutour, Audrey, Flack, Jessica C.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.74 MB

english, 2018

16

Modeling effects of voltage dependent properties of the cardiac muscarinic receptor on human sinus node function

Moss, Robin, Sachse, Frank B., Moreno-Galindo, Eloy G., Navarro-Polanco, Ricardo A., Tristani-Firouzi, Martin, Seemann, Gunnar, Marsden, Alison L

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.80 MB

english, 2018

17

Interactive reservoir computing for chunking information streams

Asabuki, Toshitake, Hiratani, Naoki, Fukai, Tomoki, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.52 MB

english, 2018

18

Internal but not external noise frees working memory resources

Tomić, Ivan, Bays, Paul M., van den Berg, Ronald

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.48 MB

english, 2018

19

Data-driven brain network models differentiate variability across language tasks

Bansal, Kanika, Medaglia, John D., Bassett, Danielle S., Vettel, Jean M., Muldoon, Sarah F., Jbabdi, Saad

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.16 MB

english, 2018

20

Predicting B cell receptor substitution profiles using public repertoire data

Dhar, Amrit, Davidsen, Kristian, Matsen, Frederick A., Minin, Vladimir N., Walczak, Aleksandra M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.32 MB

english, 2018

21

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

Wang, Hao, Marcišauskas, Simonas, Sánchez, Benjamín J., Domenzain, Iván, Hermansson, Daniel, Agren, Rasmus, Nielsen, Jens, Kerkhoven, Eduard J., Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.94 MB

english, 2018

22

Genomic data integration systematically biases interactome mapping

Skinnider, Michael A., Stacey, R. Greg, Foster, Leonard J., Iakoucheva, Lilia M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.56 MB

english, 2018

23

A k-mer-based method for the identification of phenotype-associated genomic biomarkers and predicting phenotypes of sequenced bacteria

Aun, Erki, Brauer, Age, Kisand, Veljo, Tenson, Tanel, Remm, Maido, Ouzounis, Christos A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.70 MB

english, 2018

24

Quantum chemistry reveals thermodynamic principles of redox biochemistry

Jinich, Adrian, Flamholz, Avi, Ren, Haniu, Kim, Sung-Jin, Sanchez-Lengeling, Benjamin, Cotton, Charles A. R., Noor, Elad, Aspuru-Guzik, Alán, Bar-Even, Arren, Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.40 MB

english, 2018

25

Modeling sensory-motor decisions in natural behavior

Zhang, Ruohan, Zhang, Shun, Tong, Matthew H., Cui, Yuchen, Rothkopf, Constantin A., Ballard, Dana H., Hayhoe, Mary M., Gershman, Samuel J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.37 MB

english, 2018

26

A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas

Schmidt, Maximilian, Bakker, Rembrandt, Shen, Kelly, Bezgin, Gleb, Diesmann, Markus, van Albada, Sacha Jennifer, Graham, Lyle J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 44.85 MB

english, 2018

27

An agent-based model for drug-radiation interactions in the tumour microenvironment: Hypoxia-activated prodrug SN30000 in multicellular tumour spheroids

Mao, Xinjian, McManaway, Sarah, Jaiswal, Jagdish K., Patel, Priyanka B., Wilson, William R., Hicks, Kevin O., Bogle, Gib, Cristini, Vittorio

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.60 MB

english, 2018

28

Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)

Chiang, Ying-Chih, Levsh, Olesya, Lam, Chun Kei, Weng, Jing-Ke, Wang, Yi, van der Spoel, David

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.90 MB

english, 2018

29

Computationally-guided drug repurposing enables the discovery of kinase targets and inhibitors as new schistosomicidal agents

Giuliani, Sandra, Silva, Arthur C., Borba, Joyce V. V. B., Ramos, Pablo I. P., Paveley, Ross A., Muratov, Eugene N., Andrade, Carolina Horta, Furnham, Nicholas, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.92 MB

english, 2018

30

Computational discovery of dynamic cell line specific Boolean Networks from multiplex time-course data

Razzaq, Misbah, Paulevé, Loïc, Siegel, Anne, Saez-Rodriguez, Julio, Bourdon, Jérémie, Guziolowski, Carito, Stelling, Joerg

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.93 MB

english, 2018

31

Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments

Kalfas, Ioannis, Vinken, Kasper, Vogels, Rufin, Kriegeskorte, Nikolaus

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.46 MB

english, 2018

32

Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions

Simpkins, Scott W., Nelson, Justin, Deshpande, Raamesh, Li, Sheena C., Piotrowski, Jeff S., Wilson, Erin H., Gebre, Abraham A., Safizadeh, Hamid, Okamoto, Reika, Yoshimura, Mami, Costanzo, Michael, Ya

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.75 MB

english, 2018

33

Modeling and subtleties of K-Ras and Calmodulin interaction

Garrido, Eduardo, Lázaro, Juan, Jaumot, Montserrat, Agell, Neus, Rubio-Martinez, Jaime, Dunbrack, Roland L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.64 MB

english, 2018

34

Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota

Henson, Michael A., Phalak, Poonam, Hatzimanikatis, Vassily

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.53 MB

english, 2018

35

Steered molecular dynamics simulations reveal critical residues for (un)binding of substrates, inhibitors and a product to the malarial M1 aminopeptidase

Moore, Daniel S., Brines, Conor, Jewhurst, Heather, Dalton, John P., Tikhonova, Irina G., de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.77 MB

english, 2018

36

Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis

Bismeijer, Tycho, Canisius, Sander, Wessels, Lodewyk F. A., Leslie, Christina S.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.04 MB

english, 2018

37

Wrangling distributed computing for high-throughput environmental science: An introduction to HTCondor

Erickson, Richard A., Fienen, Michael N., McCalla, S. Grace, Weiser, Emily L., Bower, Melvin L., Knudson, Jonathan M., Thain, Greg, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 572 KB

english, 2018

38

A Pareto approach to resolve the conflict between information gain and experimental costs: Multiple-criteria design of carbon labeling experiments

Nöh, Katharina, Niedenführ, Sebastian, Beyß, Martin, Wiechert, Wolfgang, Hatzimanikatis, Vassily

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.31 MB

english, 2018

39

Dilution and titration of cell-cycle regulators may control cell size in budding yeast

Heldt, Frank S., Lunstone, Reece, Tyson, John J., Novák, Béla, Sobie, Eric A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.43 MB

english, 2018

40

Predicting how and when hidden neurons skew measured synaptic interactions

Brinkman, Braden A. W., Rieke, Fred, Shea-Brown, Eric, Buice, Michael A., Beck, Jeff

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.27 MB

english, 2018

41

State dependence of stimulus-induced variability tuning in macaque MT

Lombardo, Joseph A., Macellaio, Matthew V., Liu, Bing, Palmer, Stephanie E., Osborne, Leslie C., Doiron, Brent

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.18 MB

english, 2018

42

Correction: Elucidation of molecular kinetic schemes from macroscopic traces using system identification

Fribourg, Miguel, Logothetis, Diomedes E., González-Maeso, Javier, Sealfon, Stuart C., Galocha-Iragüen, Belén, Las-Heras Andrés, Fernando, Brezina, Vladimir

Journal:

PLoS Computational Biology

Year:

2018

File:

PDF, 227 KB

2018

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