September 2018

The bat-like autonomous Robat making its way through a novel environment, mapping it while doing so. The robat's emitter and two receivers acting as mouth and ears can be seen in its front.

Image Credit: Itamar Eliakim

Research Articles

Optimal multi-source forecasting of seasonal influenza

Zeynep Ertem, Dorrie Raymond, Lauren Ancel Meyers

PLOS Computational Biology: published September 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006236

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

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

PLOS Computational Biology: published September 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006378

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

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

PLOS Computational Biology: published September 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006454

A fully autonomous terrestrial bat-like acoustic robot

Itamar Eliakim, Zahi Cohen, Gabor Kosa, Yossi Yovel

PLOS Computational Biology: published September 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006406

Inter-nucleosomal communication between histone modifications for nucleosome phasing

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

PLOS Computational Biology: published September 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006416

Network mechanisms underlying the role of oscillations in cognitive tasks

Helmut Schmidt, Daniele Avitabile, Ernest Montbrió, Alex Roxin

PLOS Computational Biology: published September 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006430

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

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

PLOS Computational Biology: published September 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006409

Comparing two classes of biological distribution systems using network analysis

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

PLOS Computational Biology: published September 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006428

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

Fridolin Gross, Paolo Bonaiuti, Silke Hauf, Andrea Ciliberto

PLOS Computational Biology: published September 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006449

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

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

PLOS Computational Biology: published September 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006458

A Markov chain for numerical chromosomal instability in clonally expanding populations

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

PLOS Computational Biology: published September 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006447

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

Emelie Flood, Céline Boiteux, Toby W. Allen

PLOS Computational Biology: published September 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006398

Informational structures: A dynamical system approach for integrated information

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

PLOS Computational Biology: published September 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006154

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

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

PLOS Computational Biology: published September 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006439

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

Nikhil Bhagwat, Joseph D. Viviano, Aristotle N. Voineskos, M. Mallar Chakravarty, Alzheimer’s Disease Neuroimaging Initiative

PLOS Computational Biology: published September 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006376

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

Jan Poleszczuk, Malgorzata Debowska, Wojciech Dabrowski, Alicja Wojcik-Zaluska, Wojciech Zaluska, Jacek Waniewski

PLOS Computational Biology: published September 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006417

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

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

PLOS Computational Biology: published September 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006316

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

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

PLOS Computational Biology: published September 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006344

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

Rosanna Migliore, Carmen A. Lupascu, Luca L. Bologna, Armando Romani, Jean-Denis Courcol, Stefano Antonel, Werner A. H. Van Geit, Alex M. Thomson, Audrey Mercer, Sigrun Lange, Joanne Falck, Christian A. Rössert, Ying Shi, Olivier Hagens, Maurizio Pezzoli, Tamas F. Freund, Szabolcs Kali, Eilif B. Muller, Felix Schürmann, Henry Markram, Michele Migliore

PLOS Computational Biology: published September 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006423

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

Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li

PLOS Computational Biology: published September 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006436

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

Sean M. Cascarina, Eric D. Ross

PLOS Computational Biology: published September 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006256

Inferring decoding strategies for multiple correlated neural populations

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

PLOS Computational Biology: published September 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006371

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

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

PLOS Computational Biology: published September 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006492

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

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

PLOS Computational Biology: published September 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006486

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

Marcus A. Triplett, Lilach Avitan, Geoffrey J. Goodhill

PLOS Computational Biology: published September 28, 2018 | https://doi.org/10.1371/journal.pcbi.1006421

Correction

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

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

PLOS Computational Biology: published September 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006482

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