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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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
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
Your tags:
english, 2018
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