Volume 14; Issue 9

Main
PLoS Computational Biology
Volume 14; Issue 9

PLoS Computational Biology

Volume 14; Issue 9

1

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

Risso, Davide, Purvis, Liam, Fletcher, Russell B., Das, Diya, Ngai, John, Dudoit, Sandrine, Purdom, Elizabeth, Darling, Aaron E.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.44 MB

english, 2018

2

Optimal multi-source forecasting of seasonal influenza

Ertem, Zeynep, Raymond, Dorrie, Meyers, Lauren Ancel, Tanaka, Mark M.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.97 MB

english, 2018

3

A fully autonomous terrestrial bat-like acoustic robot

Eliakim, Itamar, Cohen, Zahi, Kosa, Gabor, Yovel, Yossi, Ayers, Joseph

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.62 MB

english, 2018

4

SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases

Titus, Alexander J., Flower, Audrey, Hagerty, Patrick, Gamble, Paul, Lewis, Charlie, Stavish, Todd, O’Connell, Kevin P., Shipley, Greg, Rogers, Stephanie M., Markel, Scott

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.77 MB

english, 2018

5

Co-evolution networks of HIV/HCV are modular with direct association to structure and function

Quadeer, Ahmed Abdul, Morales-Jimenez, David, McKay, Matthew R., Kouyos, Roger Dimitri

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.31 MB

english, 2018

6

Inter-nucleosomal communication between histone modifications for nucleosome phasing

Chen, Weizhong, Liu, Yi, Zhu, Shanshan, Chen, Guoyu, Han, Jing-Dong J., Yue, Feng

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 21.98 MB

english, 2018

7

Comparing two classes of biological distribution systems using network analysis

Papadopoulos, Lia, Blinder, Pablo, Ronellenfitsch, Henrik, Klimm, Florian, Katifori, Eleni, Kleinfeld, David, Bassett, Danielle S., Gershman, Samuel J.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 9.21 MB

english, 2018

8

Network mechanisms underlying the role of oscillations in cognitive tasks

Schmidt, Helmut, Avitabile, Daniele, Montbrió, Ernest, Roxin, Alex, Gutkin, Boris S.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.13 MB

english, 2018

9

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-timescale dynamics by atomistic molecular simulations and Markov state modeling

Pantsar, Tatu, Rissanen, Sami, Dauch, Daniel, Laitinen, Tuomo, Vattulainen, Ilpo, Poso, Antti, Nussinov, Ruth

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.67 MB

english, 2018

10

A Markov chain for numerical chromosomal instability in clonally expanding populations

Elizalde, Sergi, Laughney, Ashley M., Bakhoum, Samuel F., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.22 MB

english, 2018

11

Informational structures: A dynamical system approach for integrated information

Esteban, Francisco J., Galadí, Javier, Langa, José A., Portillo, José R., Soler-Toscano, Fernando, Jirsa, Viktor K

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.94 MB

english, 2018

12

Modeling and prediction of clinical symptom trajectories in Alzheimer’s disease using longitudinal data

Bhagwat, Nikhil, Viviano, Joseph D., Voineskos, Aristotle N., Chakravarty, M. Mallar, Jbabdi, Saad

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.51 MB

english, 2018

13

Patient-specific pulse wave propagation model identifies cardiovascular risk characteristics in hemodialysis patients

Poleszczuk, Jan, Debowska, Malgorzata, Dabrowski, Wojciech, Wojcik-Zaluska, Alicja, Zaluska, Wojciech, Waniewski, Jacek, Komarova, Natalia L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.86 MB

english, 2018

14

Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis

Stoianov, Ivilin Peev, Pennartz, Cyriel M. A., Lansink, Carien S., Pezzulo, Giovani, Daunizeau, Jean

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.89 MB

english, 2018

15

Emergent mechanics of actomyosin drive punctuated contractions and shape network morphology in the cell cortex

Miller, Callie J., Harris, Demetrius, Weaver, Robert, Ermentrout, G. Bard, Davidson, Lance A., Umulis, David

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 11.53 MB

english, 2018

16

Evolutionary footprint of epistasis

Pedruzzi, Gabriele, Barlukova, Ayuna, Rouzine, Igor M., Goldstein, Richard A.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.60 MB

english, 2018

17

Selective ion permeation involves complexation with carboxylates and lysine in a model human sodium channel

Flood, Emelie, Boiteux, Céline, Allen, Toby W., MacKerell, Alexander

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 22.49 MB

english, 2018

18

Transition state characteristics during cell differentiation

Brackston, Rowan D., Lakatos, Eszter, Stumpf, Michael P. H., Maini, Philip K

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 14.99 MB

english, 2018

19

Abstract concept learning in a simple neural network inspired by the insect brain

Cope, Alex J., Vasilaki, Eleni, Minors, Dorian, Sabo, Chelsea, Marshall, James A. R., Barron, Andrew B., Ayers, Joseph

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.37 MB

english, 2018

20

Implications of alternative routes to APC/C inhibition by the mitotic checkpoint complex

Gross, Fridolin, Bonaiuti, Paolo, Hauf, Silke, Ciliberto, Andrea, Thieffry, Denis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.68 MB

english, 2018

21

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli

Hädicke, Oliver, von Kamp, Axel, Aydogan, Timur, Klamt, Steffen, Sauro, Herbert

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.47 MB

english, 2018

22

Proteome-scale relationships between local amino acid composition and protein fates and functions

Cascarina, Sean M., Ross, Eric D., Schlessinger, Avner

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 12.13 MB

english, 2018

23

Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community

Hunt, Kristopher A., Jennings, Ryan M., Inskeep, William P., Carlson, Ross P., Hatzimanikatis, Vassily

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.73 MB

english, 2018

24

An information theoretic treatment of sequence-to-expression modeling

Khajouei, Farzaneh, Sinha, Saurabh, Morozov, Alexandre V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.04 MB

english, 2018

25

Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity

Fukushima, Makoto, Sporns, Olaf, Marinazzo, Daniele

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 8.08 MB

english, 2018

26

Quantitative single cell analysis uncovers the life/death decision in CD95 network

Buchbinder, Jörn H., Pischel, Dennis, Sundmacher, Kai, Flassig, Robert J., Lavrik, Inna N., Thieffry, Denis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.59 MB

english, 2018

27

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

Lyu, Yafei, Xue, Lingzhou, Zhang, Feipeng, Koch, Hillary, Saba, Laura, Kechris, Katerina, Li, Qunhua, Bar-Joseph, Ziv

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.89 MB

english, 2018

28

Emergence of spontaneous assembly activity in developing neural networks without afferent input

Triplett, Marcus A., Avitan, Lilach, Goodhill, Geoffrey J., Battaglia, Francesco P.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 10.21 MB

english, 2018

29

Robust spatial memory maps encoded by networks with transient connections

Babichev, Andrey, Morozov, Dmitriy, Dabaghian, Yuri, Hellyer, Peter

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 6.21 MB

english, 2018

30

Inferring decoding strategies for multiple correlated neural populations

Lakshminarasimhan, Kaushik J., Pouget, Alexandre, DeAngelis, Gregory C., Angelaki, Dora E., Pitkow, Xaq, Theunissen, Frédéric E.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 9.32 MB

english, 2018

31

The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh

Hill, Edward M., House, Thomas, Dhingra, Madhur S., Kalpravidh, Wantanee, Morzaria, Subhash, Osmani, Muzaffar G., Brum, Eric, Yamage, Mat, Kalam, Md. A., Prosser, Diann J., Takekawa, John Y., Xiao, Xi

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.71 MB

english, 2018

32

All-atom normal mode dynamics of HIV-1 capsid

Na, Hyuntae, Song, Guang, Zheng, Wenjun

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 13.66 MB

english, 2018

33

Individualised aspiration dynamics: Calculation by proofs

Wu, Bin, Zhou, Lei, Santos, Francisco C.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.53 MB

english, 2018

34

The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow

Migliore, Rosanna, Lupascu, Carmen A., Bologna, Luca L., Romani, Armando, Courcol, Jean-Denis, Antonel, Stefano, Van Geit, Werner A. H., Thomson, Alex M., Mercer, Audrey, Lange, Sigrun, Falck, Joanne,

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 23.20 MB

english, 2018

35

Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing

Jamalabadi, Hamidreza, Alizadeh, Sarah, Schönauer, Monika, Leibold, Christian, Gais, Steffen, Jbabdi, Saad

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.97 MB

english, 2018

36

Correction: A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling

Vedula, Vijay, Lee, Juhyun, Xu, Hao, Jay Kuo, C.-C., Hsiai, Tzung K., Marsden, Alison L.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 228 KB

english, 2018

37

Maintaining maximal metabolic flux by gene expression control

Planqué, Robert, Hulshof, Josephus, Teusink, Bas, Hendriks, Johannes C., Bruggeman, Frank J., Rao, Christopher V.

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 5.77 MB

english, 2018