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
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010164
Education
Ten simple rules for designing and running a computing minor for bio/chem students
PLOS Computational Biology: published July 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010202
Perspectives
Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses
PLOS Computational Biology: published July 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010220
Inferring the nature of linguistic computations in the brain
PLOS Computational Biology: published July 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010269
Research Articles
A structured model and likelihood approach to estimate yeast prion propagon replication rates and their asymmetric transmission
PLOS Computational Biology: published July 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010107
nAdder: A scale-space approach for the 3D analysis of neuronal traces
PLOS Computational Biology: published July 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010211
Stimulus presentation can enhance spiking irregularity across subcortical and cortical regions
PLOS Computational Biology: published July 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010256
ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients
PLOS Computational Biology: published July 5, 2022 | https://doi.org/10.1371/journal.pcbi.1010204
A Bayesian method for identifying associations between response variables and bacterial community composition
PLOS Computational Biology: published July 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010108
Gaze-dependent evidence accumulation predicts multi-alternative risky choice behaviour
PLOS Computational Biology: published July 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010283
Trial-by-trial predictions of subjective time from human brain activity
PLOS Computational Biology: published July 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010223
Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators
PLOS Computational Biology: published July 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010240
Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing
PLOS Computational Biology: published July 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010261
Model-based translation of DNA damage signaling dynamics across cell types
PLOS Computational Biology: published July 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010264
Non-zero mean alpha oscillations revealed with computational model and empirical data
PLOS Computational Biology: published July 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010272
Optimal control of the spatial allocation of COVID-19 vaccines: Italy as a case study
PLOS Computational Biology: published July 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010237
Role of actin filaments and cis binding in cadherin clustering and patterning
PLOS Computational Biology: published July 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010257
Thalamic deep brain stimulation paradigm to reduce consciousness: Cortico-striatal dynamics implicated in mechanisms of consciousness
PLOS Computational Biology: published July 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010294
Analysis of the docking property of host variants of hACE2 for SARS-CoV-2 in a large cohort
PLOS Computational Biology: published July 11, 2022 | https://doi.org/10.1371/journal.pcbi.1009834
Local and collective transitions in sparsely-interacting ecological communities
PLOS Computational Biology: published July 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010274
The accuracy of absolute differential abundance analysis from relative count data
PLOS Computational Biology: published July 11, 2022 | https://doi.org/10.1371/journal.pcbi.1010284
RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites
PLOS Computational Biology: published July 12, 2022 | https://doi.org/10.1371/journal.pcbi.1010293
AC-PCoA: Adjustment for confounding factors using principal coordinate analysis
PLOS Computational Biology: published July 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010184
Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models
PLOS Computational Biology: published July 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010322
What are housekeeping genes?
PLOS Computational Biology: published July 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010295
Modelling livestock infectious disease control policy under differing social perspectives on vaccination behaviour
PLOS Computational Biology: published July 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010235
If you don’t let it in, you don’t have to get it out: Thought preemption as a method to control unwanted thoughts
PLOS Computational Biology: published July 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010285
NucleoMap: A computational tool for identifying nucleosomes in ultra-high resolution contact maps
PLOS Computational Biology: published July 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010265
Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data
PLOS Computational Biology: published July 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010328
Leveraging a physiologically-based quantitative translational modeling platform for designing B cell maturation antigen-targeting bispecific T cell engagers for treatment of multiple myeloma
PLOS Computational Biology: published July 15, 2022 | https://doi.org/10.1371/journal.pcbi.1009715
Dimensionality reduction of longitudinal ’omics data using modern tensor factorizations
PLOS Computational Biology: published July 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010212
Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease
PLOS Computational Biology: published July 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010287
Sample-efficient identification of high-dimensional antibiotic synergy with a normalized diagonal sampling design
PLOS Computational Biology: published July 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010311
Network resonance can be generated independently at distinct levels of neuronal organization
PLOS Computational Biology: published July 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010364
Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2
PLOS Computational Biology: published July 18, 2022 | https://doi.org/10.1371/journal.pcbi.1010330
Modulation transfer functions for audiovisual speech
PLOS Computational Biology: published July 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010273
Suboptimal human inference can invert the bias-variance trade-off for decisions with asymmetric evidence
PLOS Computational Biology: published July 19, 2022 | https://doi.org/10.1371/journal.pcbi.1010323
Modeling scenarios for mitigating outbreaks in congregate settings
PLOS Computational Biology: published July 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010308
To what extent naringenin binding and membrane depolarization shape mitoBK channel gating—A machine learning approach
PLOS Computational Biology: published July 20, 2022 | https://doi.org/10.1371/journal.pcbi.1010315
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010306
Haisu: Hierarchically supervised nonlinear dimensionality reduction
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010351
Asymmetric and adaptive reward coding via normalized reinforcement learning
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010350
Modelling the modulation of cortical Up-Down state switching by astrocytes
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010296
The spectrum of covariance matrices of randomly connected recurrent neuronal networks with linear dynamics
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010327
Pooling strategies in V1 can account for the functional and structural diversity across species
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010270
Helix 8 in chemotactic receptors of the complement system
PLOS Computational Biology: published July 21, 2022 | https://doi.org/10.1371/journal.pcbi.1009994
Simulations of tumor growth and response to immunotherapy by coupling a spatial agent-based model with a whole-patient quantitative systems pharmacology model
PLOS Computational Biology: published July 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010254
Heterogeneity of Rift Valley fever virus transmission potential across livestock hosts, quantified through a model-based analysis of host viral load and vector infection
PLOS Computational Biology: published July 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010314
Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning
PLOS Computational Biology: published July 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009996
A model for the intrinsic limit of cancer therapy: Duality of treatment-induced cell death and treatment-induced stemness
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010319
Examining the impact of ICU population interaction structure on modeled colonization dynamics of Staphylococcus aureus
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010352
The computational relationship between reinforcement learning, social inference, and paranoia
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010326
The dopamine circuit as a reward-taxis navigation system
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010340
Graphia: A platform for the graph-based visualisation and analysis of high dimensional data
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010310
Chemophoresis engine: A general mechanism of ATPase-driven cargo transport
PLOS Computational Biology: published July 25, 2022 | https://doi.org/10.1371/journal.pcbi.1010324
Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems
PLOS Computational Biology: published July 26, 2022 | https://doi.org/10.1371/journal.pcbi.1010329
Suprathreshold perceptual decisions constrain models of confidence
PLOS Computational Biology: published July 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010318
Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer
PLOS Computational Biology: published July 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010291
Cheater suppression and stochastic clearance through quorum sensing
PLOS Computational Biology: published July 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010292
Physiological characterization of electrodermal activity enables scalable near real-time autonomic nervous system activation inference
PLOS Computational Biology: published July 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010275
Binding mechanism of oseltamivir and influenza neuraminidase suggests perspectives for the design of new anti-influenza drugs
PLOS Computational Biology: published July 28, 2022 | https://doi.org/10.1371/journal.pcbi.1010343