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Table of Contents

September 2018

Cover

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

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

A fully autonomous terrestrial bat-like acoustic robot

Itamar Eliakim, Zahi Cohen, Gabor Kosa, Yossi Yovel

Inter-nucleosomal communication between histone modifications for nucleosome phasing

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

Network mechanisms underlying the role of oscillations in cognitive tasks

Helmut Schmidt, Daniele Avitabile, Ernest Montbrió, Alex Roxin

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

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

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

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

Fridolin Gross, Paolo Bonaiuti, Silke Hauf, Andrea Ciliberto

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

A Markov chain for numerical chromosomal instability in clonally expanding populations

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

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

Emelie Flood, Céline Boiteux, Toby W. Allen

Informational structures: A dynamical system approach for integrated information

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

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

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

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

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

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

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

Evolutionary footprint of epistasis

Gabriele Pedruzzi, Ayuna Barlukova, Igor M. Rouzine

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

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

Robust spatial memory maps encoded by networks with transient connections

Andrey Babichev, Dmitriy Morozov, Yuri Dabaghian

All-atom normal mode dynamics of HIV-1 capsid

Hyuntae Na, Guang Song

Transition state characteristics during cell differentiation

Rowan D. Brackston, Eszter Lakatos, Michael P. H. Stumpf

Maintaining maximal metabolic flux by gene expression control

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

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

Inferring decoding strategies for multiple correlated neural populations

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

Individualised aspiration dynamics: Calculation by proofs

Bin Wu, Lei Zhou

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

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

An information theoretic treatment of sequence-to-expression modeling

Farzaneh Khajouei, Saurabh Sinha

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

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

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

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

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