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Table of Contents

November 2020

Astrocytes influence cortical synaptic plasticity during postnatal development. The computational study by Manninen et al. links for the first time the interactions of complex molecular and cellular mechanisms of a fine astrocyte process (yellow) with neuronal presynaptic (red) and postsynaptic (cyan) sites to the time window of spike-timing-dependent long-term depression. The astrocyte is sensing the postsynaptic release of endocannabinoid and is modulating the presynaptic release of glutamate via astrocytic glutamate exocytosis affecting presynaptic NMDA receptor-mediated second messenger cascades.

Image Credit: Marja-Leena Linne, Ausra Saudargiene, Tiina Manninen, Noora Pihlajarinne

Editorials

Ten simple rules for writing Dockerfiles for reproducible data science

Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen J. Eglen, Tim Head, Tony Hirst, Benjamin D. Evans

Ten simple rules for writing a paper about scientific software

Joseph D. Romano, Jason H. Moore

Ten simple rules for starting research in your late teens

Cameron Mura, Mike Chalupa, Abigail M. Newbury, Jack Chalupa, Philip E. Bourne

Education

Twelve quick steps for genome assembly and annotation in the classroom

Hyungtaek Jung, Tomer Ventura, J. Sook Chung, Woo-Jin Kim, Bo-Hye Nam, Hee Jeong Kong, Young-Ok Kim, Min-Seung Jeon, Seong-il Eyun

Perspective

Ten simple rules for increased lab resilience

Matthias C. Rillig, Milos Bielcik, V. Bala Chaudhary, Leonie Grünfeld, Stefanie Maaß, India Mansour, Masahiro Ryo, Stavros D. Veresoglou

Review

Transforming the study of organisms: Phenomic data models and knowledge bases

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel

Research Articles

Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex

Tiina Manninen, Ausra Saudargiene, Marja-Leena Linne

Deep learning predicts short non-coding RNA functions from only raw sequence data

Teresa Maria Rosaria Noviello, Francesco Ceccarelli, Michele Ceccarelli, Luigi Cerulo

Machine learning assisted intraoperative assessment of brain tumor margins using HRMAS NMR spectroscopy

Doruk Cakmakci, Emin Onur Karakaslar, Elisa Ruhland, Marie-Pierre Chenard, Francois Proust, Martial Piotto, Izzie Jacques Namer, A. Ercument Cicek

Using B cell receptor lineage structures to predict affinity

Duncan K. Ralph, Frederick A. Matsen IV

Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms

Ran Li, Liangyong Yu, Bo Zhou, Xiangrui Zeng, Zhenyu Wang, Xiaoyan Yang, Jing Zhang, Xin Gao, Rui Jiang, Min Xu

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines

Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Skrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz

Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins

Amir Bitran, William M. Jacobs, Eugene Shakhnovich

Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus

Jingwei Ma, Myan Do, Mark A. Le Gros, Charles S. Peskin, Carolyn A. Larabell, Yoichiro Mori, Samuel A. Isaacson

Systems biology informed deep learning for inferring parameters and hidden dynamics

Alireza Yazdani, Lu Lu, Maziar Raissi, George Em Karniadakis

Evolution of multicellular life cycles under costly fragmentation

Yuriy Pichugin, Arne Traulsen

Modeling HIV-1 infection in the brain

Colin T. Barker, Naveen K. Vaidya

EventEpi—A natural language processing framework for event-based surveillance

Auss Abbood, Alexander Ullrich, Rüdiger Busche, Stéphane Ghozzi

Poisson balanced spiking networks

Camille E. Rullán Buxó, Jonathan W. Pillow

Within-host mechanisms of immune regulation explain the contrasting dynamics of two helminth species in both single and dual infections

Chiara Vanalli, Lorenzo Mari, Lorenzo Righetto, Renato Casagrandi, Marino Gatto, Isabella M. Cattadori

Integrative analysis of structural variations using short-reads and linked-reads yields highly specific and sensitive predictions

Riccha Sethi, Julia Becker, Jos de Graaf, Martin Löwer, Martin Suchan, Ugur Sahin, David Weber

Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach

Howard Bowman, Joseph L. Brooks, Omid Hajilou, Alexia Zoumpoulaki, Vladimir Litvak

In silico prediction of ARB resistance: A first step in creating personalized ARB therapy

Shane D. Anderson, Asna Tabassum, Jae Kyung Yeon, Garima Sharma, Priscilla Santos, Tik Hang Soong, Yin Win Thu, Isaac Nies, Tomomi Kurita, Andrew Chandler, Abdelaziz Alsamarah, Rhye-Samuel Kanassatega, Yun L. Luo, Wesley M. Botello-Smith, Bradley T. Andresen

Phenotypes to remember: Evolutionary developmental memory capacity and robustness

András Szilágyi, Péter Szabó, Mauro Santos, Eörs Szathmáry

Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits

Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu, Binghuang Cai, Nicholas Cain, Atle E. Rimehaug, Alexander J. Stasik, Gaute T. Einevoll, Stefan Mihalas, Christof Koch, Anton Arkhipov

Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

Magdalena San Roman, Andreas Wagner

Deconvolution of heterogeneous tumor samples using partial reference signals

Yufang Qin, Weiwei Zhang, Xiaoqiang Sun, Siwei Nan, Nana Wei, Hua-Jun Wu, Xiaoqi Zheng

Dopamine release, diffusion and uptake: A computational model for synaptic and volume transmission

Kathleen Wiencke, Annette Horstmann, David Mathar, Arno Villringer, Jane Neumann

Inferring a network from dynamical signals at its nodes

Corey Weistuch, Luca Agozzino, Lilianne R. Mujica-Parodi, Ken A. Dill

Inference of mutability landscapes of tumors from single cell sequencing data

Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums

Identifying longevity associated genes by integrating gene expression and curated annotations

F. William Townes, Kareem Carr, Jeffrey W. Miller

The role of sensory uncertainty in simple contour integration

Yanli Zhou, Luigi Acerbi, Wei Ji Ma

Remote homology search with hidden Potts models

Grey W. Wilburn, Sean R. Eddy

Biological network growth in complex environments: A computational framework

Torsten Johann Paul, Philip Kollmannsberger

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells

Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka

An exact method for quantifying the reliability of end-of-epidemic declarations in real time

Kris V. Parag, Christl A. Donnelly, Rahul Jha, Robin N. Thompson

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein

Model-based decoupling of evoked and spontaneous neural activity in calcium imaging data

Marcus A. Triplett, Zac Pujic, Biao Sun, Lilach Avitan, Geoffrey J. Goodhill

Modelling pathogen spread in a healthcare network: Indirect patient movements

Monika J. Piotrowska, Konrad Sakowski, André Karch, Hannan Tahir, Johannes Horn, Mirjam E. Kretzschmar, Rafael T. Mikolajczyk