Volume 14; Issue 6

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PLoS Computational Biology
Volume 14; Issue 6

PLoS Computational Biology

Volume 14; Issue 6

1

Mechanical evolution of DNA double-strand breaks in the nucleosome

Cleri, Fabrizio, Landuzzi, Fabio, Blossey, Ralf, Wade, Rebecca C.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.13 MB

english, 2018

2

Changes in parasite traits, rather than intensity, affect the dynamics of infection under external perturbation

Ghosh, Suma, Ferrari, Matthew J., Pathak, Ashutosh K., Cattadori, Isabella M., Alizon, Samuel

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.94 MB

english, 2018

3

Classification of red blood cell shapes in flow using outlier tolerant machine learning

Kihm, Alexander, Kaestner, Lars, Wagner, Christian, Quint, Stephan, Pivkin, Igor V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.37 MB

english, 2018

4

3D morphology-based clustering and simulation of human pyramidal cell dendritic spines

Luengo-Sanchez, Sergio, Fernaud-Espinosa, Isabel, Bielza, Concha, Benavides-Piccione, Ruth, Larrañaga, Pedro, DeFelipe, Javier, Cuntz, Hermann

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 17.75 MB

english, 2018

5

A biophysical mechanism for preferred direction enhancement in fly motion vision

Borst, Alexander, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.76 MB

english, 2018

6

In vivo and in silico dynamics of the development of Metabolic Syndrome

Rozendaal, Yvonne J. W., Wang, Yanan, Paalvast, Yared, Tambyrajah, Lauren L., Li, Zhuang, Willems van Dijk, Ko, Rensen, Patrick C. N., Kuivenhoven, Jan A., Groen, Albert K., Hilbers, Peter A. J., van

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.31 MB

english, 2018

7

Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria

Mon Père, Nathaniel, Lenaerts, Tom, Pacheco, Jorge M., Dingli, David, Foo, Jasmine

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.38 MB

english, 2018

8

Modeling the functions of condensin in chromosome shaping and segregation

Sakai, Yuji, Mochizuki, Atsushi, Kinoshita, Kazuhisa, Hirano, Tatsuya, Tachikawa, Masashi, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.18 MB

english, 2018

9

Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer

Shin, Sung-Young, Müller, Anna-Katharina, Verma, Nandini, Lev, Sima, Nguyen, Lan K., Ma'ayan, Avi

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.62 MB

english, 2018

10

Evolution of chemokine receptors is driven by mutations in the sodium binding site

Taddese, Bruck, Deniaud, Madeline, Garnier, Antoine, Tiss, Asma, Guissouma, Hajer, Abdi, Hervé, Henrion, Daniel, Chabbert, Marie, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 27.34 MB

english, 2018

11

Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response

Tee, Wei-Ven, Guarnera, Enrico, Berezovsky, Igor N., Papaleo, Elena

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 50.59 MB

english, 2018

12

Cloud computing applications for biomedical science: A perspective

Navale, Vivek, Bourne, Philip E., Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 804 KB

english, 2018

13

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Henry, Nicolas, Krammer, Eva-Maria, Stengel, Florian, Adams, Quentin, Van Liefferinge, François, Hubin, Ellen, Chaves, Rui, Efremov, Rouslan, Aebersold, Ruedi, Vandenbussche, Guy, Prévost, Martine, Ra

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.83 MB

english, 2018

14

Control of neurite growth and guidance by an inhibitory cell-body signal

Bicknell, Brendan A., Pujic, Zac, Dayan, Peter, Goodhill, Geoffrey J., Maini, Philip K

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.22 MB

english, 2018

15

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

Medley, J. Kyle, Choi, Kiri, König, Matthias, Smith, Lucian, Gu, Stanley, Hellerstein, Joseph, Sealfon, Stuart C., Sauro, Herbert M., Prlic, Andreas

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.85 MB

english, 2018

16

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain

Jayaraman, Kumaresan, Morley, Alex N., Szöllősi, Daniel, Wassenaar, Tsjerk A., Sitte, Harald H., Stockner, Thomas, Schlessinger, Avner

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 36.76 MB

english, 2018

17

The impact of temporal sampling resolution on parameter inference for biological transport models

Harrison, Jonathan U., Baker, Ruth E., Nie, Qing

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 18.99 MB

english, 2018

18

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Zappia, Luke, Phipson, Belinda, Oshlack, Alicia, Schneidman, Dina

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.96 MB

english, 2018

19

Removing contaminants from databases of draft genomes

Lu, Jennifer, Salzberg, Steven L., Sun, Fengzhu

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.89 MB

english, 2018

20

Solving the RNA design problem with reinforcement learning

Eastman, Peter, Shi, Jade, Ramsundar, Bharath, Pande, Vijay S., Chen, Shi-Jie

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.34 MB

english, 2018

21

Transmission of temporally correlated spike trains through synapses with short-term depression

Bird, Alex D., Richardson, Magnus J. E., Nadim, Farzan

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.64 MB

english, 2018

22

Correction: A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems

Wilson, Robert C., Nassar, Matthew R., Tavoni, Gaia, Gold, Joshua I.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.04 MB

english, 2018

23

Age density patterns in patients medical conditions: A clustering approach

Alhasoun, Fahad, Aleissa, Faisal, Alhazzani, May, Moyano, Luis G., Pinhanez, Claudio, González, Marta C., Wang, Edwin

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 13.75 MB

english, 2018

24

Community interactions and spatial structure shape selection on antibiotic resistant lineages

Estrela, Sylvie, Brown, Sam P., Alizon, Samuel

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.13 MB

english, 2018

25

Assessment of ab initio models of protein complexes by molecular dynamics

Radom, Filip, Plückthun, Andreas, Paci, Emanuele, MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.56 MB

english, 2018

26

Mechanical positioning of multiple nuclei in muscle cells

Manhart, Angelika, Windner, Stefanie, Baylies, Mary, Mogilner, Alex, Igoshin, Oleg A

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.45 MB

english, 2018

27

Computation predicts rapidly adapting mechanotransduction currents cannot account for tactile encoding in Merkel cell-neurite complexes

Gerling, Gregory J., Wan, Lingtian, Hoffman, Benjamin U., Wang, Yuxiang, Lumpkin, Ellen A., Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.60 MB

english, 2018

28

Two critical positions in zinc finger domains are heavily mutated in three human cancer types

Munro, Daniel, Ghersi, Dario, Singh, Mona, Punta, Marco

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.92 MB

english, 2018

29

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions

Shi, Ya-Zhou, Jin, Lei, Feng, Chen-Jie, Tan, Ya-Lan, Tan, Zhi-Jie, Przytycka, Teresa M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.50 MB

english, 2018

30

Thalamocortical and intracortical laminar connectivity determines sleep spindle properties

Krishnan, Giri P., Rosen, Burke Q., Chen, Jen-Yung, Muller, Lyle, Sejnowski, Terrence J., Cash, Sydney S., Halgren, Eric, Bazhenov, Maxim, Battaglia, Francesco P.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 13.51 MB

english, 2018

31

Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir prophylaxis schemes

Duwal, Sulav, Dickinson, Laura, Khoo, Saye, von Kleist, Max, Koelle, Katia

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.44 MB

english, 2018

32

Bridging structure and function: A model of sequence learning and prediction in primary visual cortex

Klos, Christian, Miner, Daniel, Triesch, Jochen, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.91 MB

english, 2018

33

Latent environment allocation of microbial community data

Higashi, Koichi, Suzuki, Shinya, Kurosawa, Shin, Mori, Hiroshi, Kurokawa, Ken, Segata, Nicola

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.90 MB

english, 2018

34

Stochastic shielding and edge importance for Markov chains with timescale separation

Schmidt, Deena R., Galán, Roberto F., Thomas, Peter J., Gillespie, Dirk

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.68 MB

english, 2018

35

Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates

Werner, Benjamin, Sottoriva, Andrea, Komarova, Natalia L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.68 MB

english, 2018

36

Instance-based generalization for human judgments about uncertainty

Schustek, Philipp, Moreno-Bote, Rubén, Gershman, Samuel J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.67 MB

english, 2018

37

The effect of cell geometry on polarization in budding yeast

Trogdon, Michael, Drawert, Brian, Gomez, Carlos, Banavar, Samhita P., Yi, Tau-Mu, Campàs, Otger, Petzold, Linda R., Shahrezaei, Vahid

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.18 MB

english, 2018

38

φ-evo: A program to evolve phenotypic models of biological networks

Henry, Adrien, Hemery, Mathieu, François, Paul, Schneidman, Dina

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.58 MB

english, 2018

39

Identifying functional groups among the diverse, recombining antigenic var genes of the malaria parasite Plasmodium falciparum from a local community in Ghana

Rorick, Mary M., Baskerville, Edward B., Rask, Thomas S., Day, Karen P., Pascual, Mercedes, Regoes, Roland R.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.77 MB

english, 2018

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