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Table of Contents

February 2019

This image is a 3D volume rendering of a confocal image stack showing an embryo with 16 cells (Orange), surrounded by seed tissues. Moukhtar et al. show in this issue that the division patterns during the first generation of embryogenesis in A. thaliana can be explained by a single rule linking cell geometry and division plane positioning.

Image Credit: Katia Belcram

Education

Bioinformatics calls the school: Use of smartphones to introduce Python for bioinformatics in high schools

Ana Julia Velez Rueda, Guillermo I. Benítez, Julia Marchetti, Marcia Anahí Hasenahuer, María Silvina Fornasari, Nicolas Palopoli, Gustavo Parisi

Research Articles

Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited

Dave Osthus, Ashlynn R. Daughton, Reid Priedhorsky

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion

Sabine Koch, Fabian Kohrs, Patrick Lahmann, Thomas Bissinger, Stefan Wendschuh, Dirk Benndorf, Udo Reichl, Steffen Klamt

Mapping DNA sequence to transcription factor binding energy in vivo

Stephanie L. Barnes, Nathan M. Belliveau, William T. Ireland, Justin B. Kinney, Rob Phillips

Noise-resistant developmental reproducibility in vertebrate somite formation

Honda Naoki, Ryutaro Akiyama, Dini Wahyu Kartika Sari, Shin Ishii, Yasumasa Bessho, Takaaki Matsui

Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks

Ahmed A. Metwally, Philip S. Yu, Derek Reiman, Yang Dai, Patricia W. Finn, David L. Perkins

DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network

Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine, Hsiao-Chun Wu, Michal Brylinski

Social evolution under demographic stochasticity

David V. McLeod, Troy Day

Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

Robert Marsland III, Wenping Cui, Joshua Goldford, Alvaro Sanchez, Kirill Korolev, Pankaj Mehta

A data-driven interactome of synergistic genes improves network-based cancer outcome prediction

Amin Allahyar, Joske Ubels, Jeroen de Ridder

Apollo: Democratizing genome annotation

Nathan A. Dunn, Deepak R. Unni, Colin Diesh, Monica Munoz-Torres, Nomi L. Harris, Eric Yao, Helena Rasche, Ian H. Holmes, Christine G. Elsik, Suzanna E. Lewis

A local measure of symmetry and orientation for individual spikes of grid cells

Simon N. Weber, Henning Sprekeler

Information integration in large brain networks

Daniel Toker, Friedrich T. Sommer

BioJava 5: A community driven open-source bioinformatics library

Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, Jose M. Duarte

How good are pathogenicity predictors in detecting benign variants?

Abhishek Niroula, Mauno Vihinen

Network-guided prediction of aromatase inhibitor response in breast cancer

Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph

A hierarchical sparse coding model predicts acoustic feature encoding in both auditory midbrain and cortex

Qingtian Zhang, Xiaolin Hu, Bo Hong, Bo Zhang

Correlation Structure in Micro-ECoG Recordings is Described by Spatially Coherent Components

Nicholas Rogers, John Hermiz, Mehran Ganji, Erik Kaestner, Kıvılcım Kılıç, Lorraine Hossain, Martin Thunemann, Daniel R. Cleary, Bob S. Carter, David Barba, Anna Devor, Eric Halgren, Shadi A. Dayeh, Vikash Gilja

Cell geometry determines symmetric and asymmetric division plane selection in Arabidopsis early embryos

Julien Moukhtar, Alain Trubuil, Katia Belcram, David Legland, Zhor Khadir, Aurélie Urbain, Jean-Christophe Palauqui, Philippe Andrey

Assessing the performance of real-time epidemic forecasts: A case study of Ebola in the Western Area region of Sierra Leone, 2014-15

Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind M. Eggo, W. John Edmunds

Maps of variability in cell lineage trees

Damien G. Hicks, Terence P. Speed, Mohammed Yassin, Sarah M. Russell

Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling

Nitzan Shahar, Tobias U. Hauser, Michael Moutoussis, Rani Moran, Mehdi Keramati, NSPN consortium, Raymond J. Dolan

Identifying the mechanism for superdiffusivity in mouse fibroblast motility

Giuseppe Passucci, Megan E. Brasch, James H. Henderson, Vasily Zaburdaev, M. Lisa Manning

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

Brandon Monier, Adam McDermaid, Cankun Wang, Jing Zhao, Allison Miller, Anne Fennell, Qin Ma

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher

Efficient neural decoding of self-location with a deep recurrent network

Ardi Tampuu, Tambet Matiisen, H. Freyja Ólafsdóttir, Caswell Barry, Raul Vicente

Identifying individual risk rare variants using protein structure guided local tests (POINT)

Rachel Marceau West, Wenbin Lu, Daniel M. Rotroff, Melaine A. Kuenemann, Sheng-Mao Chang, Michael C. Wu, Michael J. Wagner, John B. Buse, Alison A. Motsinger-Reif, Denis Fourches, Jung-Ying Tzeng

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes

Ivar Grytten, Knut D. Rand, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad, Geir K. Sandve

A numerical approach for a discrete Markov model for progressing drug resistance of cancer

Masayuki Maeda, Hideaki Yamashita

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

He Peng, Xiangxiang Zeng, Yadi Zhou, Defu Zhang, Ruth Nussinov, Feixiong Cheng

Multi-modality in gene regulatory networks with slow promoter kinetics

M. Ali Al-Radhawi, Domitilla Del Vecchio, Eduardo D. Sontag

Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis

Hongyu Zhou, Zheng Dong, Gennady Verkhivker, Brian D. Zoltowski, Peng Tao

Multiscale modeling of influenza A virus replication in cell cultures predicts infection dynamics for highly different infection conditions

Daniel Rüdiger, Sascha Young Kupke, Tanja Laske, Pawel Zmora, Udo Reichl

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas

David G. P. van IJzendoorn, Karoly Szuhai, Inge H. Briaire-de Bruijn, Marie Kostine, Marieke L. Kuijjer, Judith V. M. G. Bovée

Independent working memory resources for egocentric and allocentric spatial information

David Aagten-Murphy, Paul M. Bays

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models

Tyler Funnell, Allen W. Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P. Shah

Structure and variability of delay activity in premotor cortex

Nir Even-Chen, Blue Sheffer, Saurabh Vyas, Stephen I. Ryu, Krishna V. Shenoy

A computational model of epithelial solute and water transport along a human nephron

Anita T. Layton, Harold E. Layton

Controlling seizure propagation in large-scale brain networks

Simona Olmi, Spase Petkoski, Maxime Guye, Fabrice Bartolomei, Viktor Jirsa

Phylogenies from dynamic networks

Cornelia Metzig, Oliver Ratmann, Daniela Bezemer, Caroline Colijn

CoPhosK: A method for comprehensive kinase substrate annotation using co-phosphorylation analysis

Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance

Maximum entropy and population heterogeneity in continuous cell cultures

Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet

Learning the payoffs and costs of actions

Moritz Möller, Rafal Bogacz

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans Victor Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri

Predictability in process-based ensemble forecast of influenza

Sen Pei, Mark A. Cane, Jeffrey Shaman

Modeling and MEG evidence of early consonance processing in auditory cortex

Alejandro Tabas, Martin Andermann, Valeria Schuberth, Helmut Riedel, Emili Balaguer-Ballester, André Rupp

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics

Moritz Hoffmann, Christoph Fröhner, Frank Noé