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Table of Contents

December 2019

Most bio-sonar studies have focused on the reception of single target-echoes by echolocating bats. However, under natural conditions insect-targets often occur in swarms. Boonman et al. constructed life-like avatars of mosquitoes and placed them in constellations following natural statistics representing different densities and group sizes. Using a virtual acoustic paradigm they calculated the echoes received for 100 realizations of the swarm. To assess the contribution of insect-shape, they compared the responses to echoes of virtual clouds of point-targets. The authors found that, especially for dense clouds, modulating the emitted narrowband-signal by several kHz greatly enhances detection probability.

Image Credit: Mor Taub, Tel Aviv University.

Education

Nine quick tips for analyzing network data

Vincent Miele, Catherine Matias, Stéphane Robin, Stéphane Dray

Perspective

Establishment of computational biology in Greece and Cyprus: Past, present, and future

Anastasia Chasapi, Michalis Aivaliotis, Lefteris Angelis, Anastasios Chanalaris, Ioannis Iliopoulos, Ilias Kappas, Christos Karapiperis, Nikos C. Kyrpides, Evangelos Pafilis, Eleftherios Panteris, Pantelis Topalis, George Tsiamis, Ioannis S. Vizirianakis, Metaxia Vlassi, Vasilis J. Promponas, Christos A. Ouzounis

Research Articles

Statistics of correlated percolation in a bacterial community

Xiaoling Zhai, Joseph W. Larkin, Kaito Kikuchi, Samuel E. Redford, Ushasi Roy, Gürol M. Süel, Andrew Mugler

A cell-based probabilistic approach unveils the concerted action of miRNAs

Shelly Mahlab-Aviv, Nathan Linial, Michal Linial

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data

Kai Kang, Qian Meng, Igor Shats, David M. Umbach, Melissa Li, Yuanyuan Li, Xiaoling Li, Leping Li

CBNA: A control theory based method for identifying coding and non-coding cancer drivers

Vu V. H. Pham, Lin Liu, Cameron P. Bracken, Gregory J. Goodall, Qi Long, Jiuyong Li, Thuc D. Le

The effect of inhibition on rate code efficiency indicators

Tomas Barta, Lubomir Kostal

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Bin Du, Laurence Yang, Colton J. Lloyd, Xin Fang, Bernhard O. Palsson

Inferring reaction network structure from single-cell, multiplex data, using toric systems theory

Shu Wang, Jia-Ren Lin, Eduardo D. Sontag, Peter K. Sorger

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics

Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret M. Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher

Statistical inference in ensemble modeling of cellular metabolism

Tuure Hameri, Marc-Olivier Boldi, Vassily Hatzimanikatis

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard

Stability of spontaneous, correlated activity in mouse auditory cortex

Richard F. Betzel, Katherine C. Wood, Christopher Angeloni, Maria Neimark Geffen, Danielle S. Bassett

From energy to cellular forces in the Cellular Potts Model: An algorithmic approach

Elisabeth G. Rens, Leah Edelstein-Keshet

Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level

Simon Mathis Kønig, Vendela Rissler, Thilde Terkelsen, Matteo Lambrughi, Elena Papaleo

Molecular sampling at logarithmic rates for next-generation sequencing

Caroline Horn, Julia Salzman

NUFEB: A massively parallel simulator for individual-based modelling of microbial communities

Bowen Li, Denis Taniguchi, Jayathilake Pahala Gedara, Valentina Gogulancea, Rebeca Gonzalez-Cabaleiro, Jinju Chen, Andrew Stephen McGough, Irina Dana Ofiteru, Thomas P. Curtis, Paolo Zuliani

Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models

Colette Mair, Sema Nickbakhsh, Richard Reeve, Jim McMenamin, Arlene Reynolds, Rory N. Gunson, Pablo R. Murcia, Louise Matthews

Probing neural networks for dynamic switches of communication pathways

Holger Finger, Richard Gast, Christian Gerloff, Andreas K. Engel, Peter König

Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model

John E. Mittler, James T. Murphy, Sarah E. Stansfield, Kathryn Peebles, Geoffrey S. Gottlieb, Neil F. Abernethy, Molly C. Reid, Steven M. Goodreau, Joshua T. Herbeck

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling

Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini

ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest

Jiajin Li, Brandon Jew, Lingyu Zhan, Sungoo Hwang, Giovanni Coppola, Nelson B. Freimer, Jae Hoon Sul

Evidence for a multi-level trophic organization of the human gut microbiome

Tong Wang, Akshit Goyal, Veronika Dubinkina, Sergei Maslov

Motion prediction enables simulated MR-imaging of freely moving model organisms

Markus Reischl, Mazin Jouda, Neil MacKinnon, Erwin Fuhrer, Natalia Bakhtina, Andreas Bartschat, Ralf Mikut, Jan G. Korvink

Chemotaxis in external fields: Simulations for active magnetic biological matter

Agnese Codutti, Klaas Bente, Damien Faivre, Stefan Klumpp

Avoidance of non-localizable obstacles in echolocating bats: A robotic model

Carl Bou Mansour, Elijah Koreman, Jan Steckel, Herbert Peremans, Dieter Vanderelst

Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection

Jinyuan Yan, Henri Estanbouli, Chen Liao, Wook Kim, Jonathan M. Monk, Rayees Rahman, Mini Kamboj, Bernhard O. Palsson, Weigang Qiu, Joao B. Xavier

Regulatory context drives conservation of glycine riboswitch aptamers

Matt Crum, Nikhil Ram-Mohan, Michelle M. Meyer

The dynamics of motor learning through the formation of internal models

Camilla Pierella, Maura Casadio, Ferdinando A. Mussa-Ivaldi, Sara A. Solla

Benchmarking network algorithms for contextualizing genes of interest

Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy Jenkins, Melody K. Morris

Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways

Kirill E. Medvedev, Lisa N. Kinch, R. Dustin Schaeffer, Nick V. Grishin

Interkinetic nuclear movements promote apical expansion in pseudostratified epithelia at the expense of apicobasal elongation

Marina A. Ferreira, Evangeline Despin-Guitard, Fernando Duarte, Pierre Degond, Eric Theveneau

Protons in small spaces: Discrete simulations of vesicle acidification

Apeksha Singh, Frank V. Marcoline, Salome Veshaguri, Aimee W. Kao, Marcel Bruchez, Joseph A. Mindell, Dimitrios Stamou, Michael Grabe

A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation

Matthew C. Pharris, Neal M. Patel, Tyler G. VanDyk, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy, Melanie I. Stefan, Tamara L. Kinzer-Ursem

Overlap matrix completion for predicting drug-associated indications

Mengyun Yang, Huimin Luo, Yaohang Li, Fang-Xiang Wu, Jianxin Wang

A novel machine learning based approach for iPS progenitor cell identification

Haishan Zhang, Ximing Shao, Yin Peng, Yanning Teng, Konda Mani Saravanan, Huiling Zhang, Hongchang Li, Yanjie Wei

Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15

Akira Endo, Mitsuo Uchida, Adam J. Kucharski, Sebastian Funk

Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs

Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang

Neuronal population model of globular bushy cells covering unit-to-unit variability

Go Ashida, Helen T. Heinermann, Jutta Kretzberg