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Table of Contents

July 2022

Alzheimer's Disease (AD) causes changes of gene expression and regulation within the brain cells. Understanding how these changes at the cell-type level is critical to identifying genetic biomarkers and potential drug targets. The work by Gupta et al. predicted the gene regulatory networks along with cooperative circuits of transcription factors for major neuronal and glial cell types in the human brain, and analyzed their changes in AD. Using these cell-type networks, this work repurposed FDA approved drugs and identified novel genes likely involved in AD pathology at cellular resolution, aiming to move network biology forward to single-cell network medicine.

Image Credit: Dr. Chirag Gupta and Dr. Daifeng Wang, University of Wisconsin - Madison

Editorial

Ten simple rules to host an inclusive conference

Rocío Joo, Andrea Sánchez-Tapia, Sara Mortara, Yanina Bellini Saibene, Heather Turner, Dorothea Hug Peter, Natalia Soledad Morandeira, Matt Bannert, Batool Almazrouq, Elizabeth Hare, Laura Ación, Juan Pablo Narváez-Gómez, Marcela Alfaro Córdoba, Federico Marini, Rita Giordano, Silvia Canelón, Anicet Ebou, Adithi R. Upadhya, Joselyn Chávez, Janani Ravi

Education

Ten simple rules for designing and running a computing minor for bio/chem students

Rochelle-Jan Reyes, Nina Hosmane, Shasta Ihorn, Milo Johnson, Anagha Kulkarni, Jennifer Nelson, Michael Savvides, Duc Ta, Ilmi Yoon, Pleuni S. Pennings

Perspectives

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses

Wendi Bacon, Alexandra Holinski, Marina Pujol, Meredith Wilmott, Sarah L Morgan, on behalf of the European Molecular Biology Laboratory—European Bioinformatics Institute Training Team

Inferring the nature of linguistic computations in the brain

Sanne Ten Oever, Karthikeya Kaushik, Andrea E. Martin

Research Articles

nAdder: A scale-space approach for the 3D analysis of neuronal traces

Minh Son Phan, Katherine Matho, Emmanuel Beaurepaire, Jean Livet, Anatole Chessel

Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions

Saleh Fayaz, Mohammad Amin Fakharian, Ali Ghazizadeh

ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients

Bodhayan Prasad, Cathy McGeough, Amanda Eakin, Tan Ahmed, Dawn Small, Philip Gardiner, Adrian Pendleton, Gary Wright, Anthony J. Bjourson, David S. Gibson, Priyank Shukla

A Bayesian method for identifying associations between response variables and bacterial community composition

Adrian Verster, Nicholas Petronella, Judy Green, Fernando Matias, Stephen P. J. Brooks

Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour

Felix Molter, Armin W. Thomas, Scott A. Huettel, Hauke R. Heekeren, Peter N. C. Mohr

Trial-by-trial predictions of subjective time from human brain activity

Maxine T. Sherman, Zafeirios Fountas, Anil K. Seth, Warrick Roseboom

Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators

Vivian B. Brandenburg, Franz Narberhaus, Axel Mosig

Model-based translation of DNA damage signaling dynamics across cell types

Muriel M. Heldring, Lukas S. Wijaya, Marije Niemeijer, Huan Yang, Talel Lakhal, Sylvia E. Le Dévédec, Bob van de Water, Joost B. Beltman

Non-zero mean alpha oscillations revealed with computational model and empirical data

Alina A. Studenova, Arno Villringer, Vadim V. Nikulin

Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study

Joseph Chadi Lemaitre, Damiano Pasetto, Mario Zanon, Enrico Bertuzzo, Lorenzo Mari, Stefano Miccoli, Renato Casagrandi, Marino Gatto, Andrea Rinaldo

Role of actin filaments and cis binding in cadherin clustering and patterning

Qilin Yu, Taeyoon Kim, Vijay Rajagopal

Thalamic deep brain stimulation paradigm to reduce consciousness: Cortico-striatal dynamics implicated in mechanisms of consciousness

Michelle J. Redinbaugh, Mohsen Afrasiabi, Jessica M. Phillips, Niranjan A. Kambi, Sounak Mohanta, Aeyal Raz, Yuri B. Saalmann

Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort

Hyojung Paik, Jimin Kim, Sangjae Seo

Local and collective transitions in sparsely-interacting ecological communities

Stav Marcus, Ari M. Turner, Guy Bunin

The accuracy of absolute differential abundance analysis from relative count data

Kimberly E. Roche, Sayan Mukherjee

RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites

Hongli Ma, Han Wen, Zhiyuan Xue, Guojun Li, Zhaolei Zhang

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis

Yu Wang, Fengzhu Sun, Wei Lin, Shuqin Zhang

What are housekeeping genes?

Chintan J. Joshi, Wenfan Ke, Anna Drangowska-Way, Eyleen J. O’Rourke, Nathan E. Lewis

Modelling livestock infectious disease control policy under differing social perspectives on vaccination behaviour

Edward M. Hill, Naomi S. Prosser, Eamonn Ferguson, Jasmeet Kaler, Martin J. Green, Matt J. Keeling, Michael J. Tildesley

Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data

Long Liu, Qingyu Meng, Cherry Weng, Qing Lu, Tong Wang, Yalu Wen

Dimensionality reduction of longitudinal ’omics data using modern tensor factorizations

Uria Mor, Yotam Cohen, Rafael Valdés-Mas, Denise Kviatcovsky, Eran Elinav, Haim Avron

Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease

Chirag Gupta, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, Daifeng Wang

Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design

Jennifer Brennan, Lalit Jain, Sofia Garman, Ann E. Donnelly, Erik Scott Wright, Kevin Jamieson

Network resonance can be generated independently at distinct levels of neuronal organization

Eran Stark, Amir Levi, Horacio G. Rotstein

Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2

Jose M. Jimenez-Guardeño, Ana Maria Ortega-Prieto, Borja Menendez Moreno, Thomas J. A. Maguire, Adam Richardson, Juan Ignacio Diaz-Hernandez, Javier Diez Perez, Mark Zuckerman, Albert Mercadal Playa, Carlos Cordero Deline, Michael H. Malim, Rocio Teresa Martinez-Nunez

Modulation transfer functions for audiovisual speech

Nicolai F. Pedersen, Torsten Dau, Lars Kai Hansen, Jens Hjortkjær

Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence

Tahra L. Eissa, Joshua I. Gold, Krešimir Josić, Zachary P. Kilpatrick

Modeling scenarios for mitigating outbreaks in congregate settings

Seth Blumberg, Phoebe Lu, Ada T. Kwan, Christopher M. Hoover, James O. Lloyd-Smith, David Sears, Stefano M. Bertozzi, Lee Worden

To what extent naringenin binding and membrane depolarization shape mitoBK channel gating—A machine learning approach

Monika Richter-Laskowska, Paulina Trybek, Piotr Bednarczyk, Agata Wawrzkiewicz-Jałowiecka

Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway

Madeline Galbraith, Federico Bocci, José N. Onuchic

Haisu: Hierarchically supervised nonlinear dimensionality reduction

Kevin Christopher VanHorn, Murat Can Çobanoğlu

Modelling the modulation of cortical Up-Down state switching by astrocytes

Lisa Blum Moyse, Hugues Berry

Pooling strategies in V1 can account for the functional and structural diversity across species

Victor Boutin, Angelo Franciosini, Frédéric Chavane, Laurent U. Perrinet

Helix 8 in chemotactic receptors of the complement system

Szymon Wisniewski, Paulina Dragan, Anna Makal, Dorota Latek

Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model

Alvaro Ruiz-Martinez, Chang Gong, Hanwen Wang, Richard J. Sové, Haoyang Mi, Holly Kimko, Aleksander S. Popel

Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection

Hélène Cecilia, Roosmarie Vriens, Paul J. Wichgers Schreur, Mariken M. de Wit, Raphaëlle Métras, Pauline Ezanno, Quirine A. ten Bosch

Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning

Changyoung Yuhn, Marie Oshima, Yan Chen, Motoharu Hayakawa, Shigeki Yamada

A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness

Erin Angelini, Yue Wang, Joseph Xu Zhou, Hong Qian, Sui Huang

Examining the impact of ICU population interaction structure on modeled colonization dynamics of Staphylococcus aureus

Matthew S. Mietchen, Christopher T. Short, Matthew Samore, Eric T. Lofgren, CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare)

The computational relationship between reinforcement learning, social inference, and paranoia

Joseph M. Barnby, Mitul A. Mehta, Michael Moutoussis

The dopamine circuit as a reward-taxis navigation system

Omer Karin, Uri Alon

Graphia: A platform for the graph-based visualisation and analysis of high dimensional data

Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee, Tim Regan, Barbara B. Shih, James Prendergast, David A. Hume, Tim Angus

Chemophoresis engine: A general mechanism of ATPase-driven cargo transport

Takeshi Sugawara, Kunihiko Kaneko

Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems

Hélène Chabas, Viktor Müller, Sebastian Bonhoeffer, Roland R. Regoes

Suprathreshold perceptual decisions constrain models of confidence

Shannon M. Locke, Michael S. Landy, Pascal Mamassian

Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer

Alexander Kier Christensen, Matthew D. Piggott, Erik van Sebille, Maarten van Reeuwijk, Samraat Pawar

Cheater suppression and stochastic clearance through quorum sensing

Alexander S. Moffett, Peter J. Thomas, Michael Hinczewski, Andrew W. Eckford

Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs

Jiaye Tao, Heping Wang, Wenjian Wang, Na Mi, Wei Zhang, Qiujia Wen, Jiajing Ouyang, Xinyun Liang, Min Chen, Wentao Guo, Guoming Li, Jun Liu, Hanning Zhao, Xin Wang, Xuemeng Li, Shengjun Feng, Xinguang Liu, Zhiwei He, Zuguo Zhao