Volume 14; Issue 11

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PLoS Computational Biology
Volume 14; Issue 11

PLoS Computational Biology

Volume 14; Issue 11

1

Motif-Aware PRALINE: Improving the alignment of motif regions

Dijkstra, Maurits, Bawono, Punto, Abeln, Sanne, Feenstra, K. Anton, Fokkink, Wan, Heringa, Jaap, Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.04 MB

english, 2018

2

Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter

Golan, Yarden, Alhadeff, Raphael, Glaser, Fabian, Ganoth, Assaf, Warshel, Arieh, Assaraf, Yehuda G., Papoian, Garegin A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.67 MB

english, 2018

3

Modeling driver cells in developing neuronal networks

Luccioli, Stefano, Angulo-Garcia, David, Cossart, Rosa, Malvache, Arnaud, Módol, Laura, Sousa, Vitor Hugo, Bonifazi, Paolo, Torcini, Alessandro, Giugliano, Michele

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.74 MB

english, 2018

4

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

Vorberg, Susann, Seemayer, Stefan, Söding, Johannes, Wallner, Björn

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.94 MB

english, 2018

5

A computational analysis of dynamic, multi-organ inflammatory crosstalk induced by endotoxin in mice

Zamora, Ruben, Korff, Sebastian, Mi, Qi, Barclay, Derek, Schimunek, Lukas, Zucca, Riccardo, Arsiwalla, Xerxes D., Simmons, Richard L., Verschure, Paul, Billiar, Timothy R., Vodovotz, Yoram, Androulaki

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.38 MB

english, 2018

6

Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

Zhao, Weilong, Sher, Xinwei, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.27 MB

english, 2018

7

The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history

Muthukrishna, Michael, Doebeli, Michael, Chudek, Maciej, Henrich, Joseph, Tarnita, Corina E

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.19 MB

english, 2018

8

Putting benchmarks in their rightful place: The heart of computational biology

Peters, Bjoern, Brenner, Steven E., Wang, Edwin, Slonim, Donna, Kann, Maricel G., Editor, An

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 226 KB

english, 2018

9

Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions

Pina, Jason E., Bodner, Mark, Ermentrout, Bard, Borisyuk, Roman

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.53 MB

english, 2018

10

Prediction and classification in equation-free collective motion dynamics

Fujii, Keisuke, Kawasaki, Takeshi, Inaba, Yuki, Kawahara, Yoshinobu, Gunji, Yukio

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.11 MB

english, 2018

11

Inferring interaction partners from protein sequences using mutual information

Bitbol, Anne-Florence, Wilke, Claus O.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.38 MB

english, 2018

12

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

Brandani, Giovanni B., Takada, Shoji, Onufriev, Alexey

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.83 MB

english, 2018

13

Visual physiology of the layer 4 cortical circuit in silico

Arkhipov, Anton, Gouwens, Nathan W., Billeh, Yazan N., Gratiy, Sergey, Iyer, Ramakrishnan, Wei, Ziqiang, Xu, Zihao, Abbasi-Asl, Reza, Berg, Jim, Buice, Michael, Cain, Nicholas, da Costa, Nuno, de Vrie

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.96 MB

english, 2018

14

Invasion and effective size of graph-structured populations

Giaimo, Stefano, Arranz, Jordi, Traulsen, Arne, Schreiber, Sebastian

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.73 MB

english, 2018

15

Functional mechanisms underlie the emergence of a diverse range of plasticity phenomena

Henderson, James A., Gong, Pulin, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

16

A regularity index for dendrites - local statistics of a neuron's input space

Anton-Sanchez, Laura, Effenberger, Felix, Bielza, Concha, Larrañaga, Pedro, Cuntz, Hermann, Morrison, Abigail

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.89 MB

english, 2018

17

Comparing Bayesian and non-Bayesian accounts of human confidence reports

Adler, William T., Ma, Wei Ji, Gershman, Samuel J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.96 MB

english, 2018

18

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Carvalho-Silva, Denise, Garcia, Leyla, Morgan, Sarah L., Brooksbank, Cath, Dunham, Ian, Markel, Scott

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 335 KB

english, 2018

19

Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions

Klughammer, Nils, Bischof, Johanna, Schnellbächer, Nikolas D., Callegari, Andrea, Lénárt, Péter, Schwarz, Ulrich S., Asthagiri, Anand R.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.20 MB

english, 2018

20

Correction: Assessment of ab initio models of protein complexes by molecular dynamics

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 273 KB

english, 2018

21

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

Xavier, Joana C., Patil, Kiran Raosaheb, Rocha, Isabel, Maranas, Costas D.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.19 MB

english, 2018

22

Bayesian phylodynamic inference with complex models

Volz, Erik M., Siveroni, Igor, Darling, Aaron E.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.61 MB

english, 2018

23

Rosetta FunFolDes – A general framework for the computational design of functional proteins

Bonet, Jaume, Wehrle, Sarah, Schriever, Karen, Yang, Che, Billet, Anne, Sesterhenn, Fabian, Scheck, Andreas, Sverrisson, Freyr, Veselkova, Barbora, Vollers, Sabrina, Lourman, Roxanne, Villard, Mélanie

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.38 MB

english, 2018

24

Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex

Hartung, Grant, Vesel, Claudia, Morley, Ryan, Alaraj, Ali, Sled, John, Kleinfeld, David, Linninger, Andreas, Ellis, Christopher Gerald

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 28.92 MB

english, 2018

25

Towards a molecular basis of ubiquitin signaling: A dual-scale simulation study of ubiquitin dimers

Berg, Andrej, Kukharenko, Oleksandra, Scheffner, Martin, Peter, Christine, Haliloglu, Turkan

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.43 MB

english, 2018

26

Ten simple rules for collaboratively writing a multi-authored paper

Frassl, Marieke A., Hamilton, David P., Denfeld, Blaize A., de Eyto, Elvira, Hampton, Stephanie E., Keller, Philipp S., Sharma, Sapna, Lewis, Abigail S. L., Weyhenmeyer, Gesa A., O’Reilly, Catherine M

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 582 KB

english, 2018

27

Adaptive feature detection from differential processing in parallel retinal pathways

Ozuysal, Yusuf, Kastner, David B., Baccus, Stephen A., Berens, Philipp

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.62 MB

english, 2018

28

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

Wick, Ryan R., Judd, Louise M., Holt, Kathryn E., Pertea, Mihaela

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 590 KB

english, 2018

29

Efficient pedigree recording for fast population genetics simulation

Kelleher, Jerome, Thornton, Kevin R., Ashander, Jaime, Ralph, Peter L., Kosakovsky Pond, Sergei L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.07 MB

english, 2018

30

Binding of the general anesthetic sevoflurane to ion channels

Stock, Letícia, Hosoume, Juliana, Cirqueira, Leonardo, Treptow, Werner, Wade, Rebecca C.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.82 MB

english, 2018

31

RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks

Li, Jun, Zhu, Wei, Wang, Jun, Li, Wenfei, Gong, Sheng, Zhang, Jian, Wang, Wei, Chen, Shi-Jie

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.77 MB

english, 2018

32

A Bayesian mixture modelling approach for spatial proteomics

Crook, Oliver M., Mulvey, Claire M., Kirk, Paul D. W., Lilley, Kathryn S., Gatto, Laurent, Vogel, Christine

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.41 MB

english, 2018

33

Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch

Meinecke, Lina, Sharma, Praveer P., Du, Huijing, Zhang, Lei, Nie, Qing, Schilling, Thomas F., Maini, Philip K.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.05 MB

english, 2018

34

Active dendrites regulate the spatiotemporal spread of signaling microdomains

Basak, Reshma, Narayanan, Rishikesh, Jedrzejewski-Szmek, Joanna

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 9.51 MB

english, 2018

35

Atlases of cognition with large-scale human brain mapping

Varoquaux, Gaël, Schwartz, Yannick, Poldrack, Russell A., Gauthier, Baptiste, Bzdok, Danilo, Poline, Jean-Baptiste, Thirion, Bertrand, Diedrichsen, Jörn

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.71 MB

english, 2018

36

powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire

Koch, Hillary, Starenki, Dmytro, Cooper, Sara J., Myers, Richard M., Li, Qunhua, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.55 MB

english, 2018

37

Mechanistic insight into spontaneous transition from cellular alternans to arrhythmia—A simulation study

Wang, Wei, Zhang, Shanzhuo, Ni, Haibo, Garratt, Clifford J., Boyett, Mark R., Hancox, Jules C., Zhang, Henggui, Panfilov, Alexander V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.96 MB

english, 2018

38

Strategies and opportunities for promoting bioinformatics in Zimbabwe

Shoko, Ryman, Manasa, Justen, Maphosa, Mcebisi, Mbanga, Joshua, Mudziwapasi, Reagan, Nembaware, Victoria, Sanyika, Walter T., Tinago, Tawanda, Chikwambi, Zedias, Mawere, Cephas, Matimba, Alice, Mugumb

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 966 KB

english, 2018

39

Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening

Jimenez-Carretero, Daniel, Abrishami, Vahid, Fernández-de-Manuel, Laura, Palacios, Irene, Quílez-Álvarez, Antonio, Díez-Sánchez, Alberto, del Pozo, Miguel A., Montoya, María C., Gallo, James

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.60 MB

english, 2018

40

How pupil responses track value-based decision-making during and after reinforcement learning

Van Slooten, Joanne C., Jahfari, Sara, Knapen, Tomas, Theeuwes, Jan, Einhäuser, Wolfgang

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.67 MB

english, 2018

41

Deterministic response strategies in a trial-and-error learning task

Mohr, Holger, Zwosta, Katharina, Markovic, Dimitrije, Bitzer, Sebastian, Wolfensteller, Uta, Ruge, Hannes, Inman, Cory

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.15 MB

english, 2018

42

Patterning the insect eye: From stochastic to deterministic mechanisms

Ebadi, Haleh, Perry, Michael, Short, Keith, Klemm, Konstantin, Desplan, Claude, Stadler, Peter F., Mehta, Anita, Johnston, Robert

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 4.07 MB

english, 2018

43

Modulation of voltage-dependent K+ conductances in photoreceptors trades off investment in contrast gain for bandwidth

Heras, Francisco J. H., Vähäsöyrinki, Mikko, Niven, Jeremy E., Bazhenov, Maxim

Journal:

PLoS Computational Biology

Year:

2018

File:

PDF, 4.22 MB

2018

44

Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs

Butler, Brandon M., Kazan, I. Can, Kumar, Avishek, Ozkan, S. Banu, Jernigan, Robert L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.71 MB

english, 2018

45

Determinants of early afterdepolarization properties in ventricular myocyte models

Huang, Xiaodong, Song, Zhen, Qu, Zhilin, McCulloch, Andrew D.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

46

Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle

Beul, Sarah F., Goulas, Alexandros, Hilgetag, Claus C., Marinazzo, Daniele

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.79 MB

english, 2018

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