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Computational Mass Spectrometry-Based Proteomics
Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides
Ten simple rules for maximizing the recommendations of the NIH data management and sharing plan
Conventional measures of intrinsic excitability are poor estimators of neuronal activity under realistic synaptic inputs
A model of tuberculosis clustering in low incidence countries reveals more transmission in the United Kingdom than the Netherlands between 2010 and 2015
AprioriGWAS , a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects
Identifying the DNA methylation preference of transcription factors using ProtBERT and SVM
Shape-preserving elastic solid models of macromolecules
Discovery of hierarchical representations for efficient planning
Self-organization of a doubly asynchronous irregular network state for spikes and bursts
Steps in the Bacterial Flagellar Motor
Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics
Emergence of Slow-Switching Assemblies in Structured Neuronal Networks
Understanding the Degradation of Hominid Gene Control
Global dynamics of neural mass models
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints
Automatic wound detection and size estimation using deep learning algorithms
Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
Seven Years; It's Time for a Change
Signal-to-signal neural networks for improved spike estimation from calcium imaging data
Efficient Algorithms for Probing the RNA Mutation Landscape
On the evolution and development of morphological complexity: A view from gene regulatory networks
Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood
Dog as an Outgroup to Human and Mouse
Robust information propagation through noisy neural circuits
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Canonical Cortical Circuit Model Explains Rivalry, Intermittent Rivalry, and Rivalry Memory
Attentional selection and communication through coherence: Scope and limitations
Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis
Cooperation is Fleeting in the World of Transposable Elements
Bursting in cerebellar stellate cells induced by pharmacological agents: Non-sequential spike adding
The Coda of the Transient Response in a Sensitive Cochlea: A Computational Modeling Study
Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models
Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins
The Roots of Bioinformatics in Protein Evolution
Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls
Pavlovian-Instrumental Interaction in 'Observing Behavior'
Explainable deep transfer learning model for disease risk prediction using high-dimensional genomic data
Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins
Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models
A causal framework for the drivers of animal social network structure
Blurring of High-Resolution Data Shows that the Effect of Intrinsic Nucleosome Occupancy on Transcription Factor Binding is Mostly Regional, Not Local
Preparing to move: Setting initial conditions to simplify interactions with complex objects
A computational model of induced pluripotent stem-cell derived cardiomyocytes for high throughput risk stratification of KCNQ1 genetic variants
The Emergence and Early Evolution of Biological Carbon-Fixation
Transient boosting of action potential backpropagation for few-shot temporal pattern learning
Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country
An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator
Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes
OutbreakFlow: Model-based Bayesian inference of disease outbreak dynamics with invertible neural networks and its application to the COVID-19 pandemics in Germany
Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways
Stoichiometric balance of protein copy numbers is measurable and functionally significant in a protein-protein interaction network for yeast endocytosis
Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor
A Mathematical Framework for the Selection of an Optimal Set of Peptides for Epitope-Based Vaccines
Specific excitatory connectivity for feature integration in mouse primary visual cortex
Environmental motion presented ahead of self-motion modulates heading direction estimation
Predicting change: Approximate inference under explicit representation of temporal structure in changing environments
Non-zero mean alpha oscillations revealed with computational model and empirical data
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
The neurocognitive role of working memory load when Pavlovian motivational control affects instrumental learning
Identification of the governing equation of stimulus-response data for run-and-tumble dynamics
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing
Predicting lymphatic filariasis elimination in data-limited settings: A reconstructive computational framework for combining data generation and model discovery
The nonlinear dynamics and fluctuations of mRNA levels in cell cycle coupled transcription
Assessing an effective undergraduate module teaching applied bioinformatics to biology students
Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons
Estimating the extrinsic incubation period of malaria using a mechanistic model of sporogony
Gain modulation and odor concentration invariance in early olfactory networks
Tumor vascular status controls oxygen delivery facilitated by infused polymerized hemoglobins with varying oxygen affinity
Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models
Correction: The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro , with Negative Feedback through PPM1A Upregulation
Mechanisms of mistrust: A Bayesian account of misinformation learning
Generalizing clusters of similar species as a signature of coexistence under competition
Bet-hedging strategies in expanding populations
Sequence representation as an early step in the evolution of language
Computational models to improve surveillance for cassava brown streak disease and minimize yield loss
Deep convolutional models improve predictions of macaque V1 responses to natural images
FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi
Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms
A Mapping of Drug Space from the Viewpoint of Small Molecule Metabolism
MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells
Intrinsic Valuation of Information in Decision Making under Uncertainty
A unitary model of auditory frequency change perception
The impact of DNA methylation on the cancer proteome
Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data
Accelerating Bayesian inference of dependency between mixed-type biological traits
Biased belief priors versus biased belief updating: Differential correlates of depression and anxiety
How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
Optimal Recall from Bounded Metaplastic Synapses: Predicting Functional Adaptations in Hippocampal Area CA3
Identifying Transmission Cycles at the Human-Animal Interface: The Role of Animal Reservoirs in Maintaining Gambiense Human African Trypanosomiasis
Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion
Co-Regulation of Metabolic Genes Is Better Explained by Flux Coupling Than by Network Distance
Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks
Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations
Continuous evaluation of cost-to-go for flexible reaching control and online decisions
The shapes of elongating gastruloids are consistent with convergent extension driven by a combination of active cell crawling and differential adhesion
Ten simple rules for successfully carrying out funded research projects
'Glocal' Robustness Analysis and Model Discrimination for Circadian Oscillators
Spatiotemporal dynamics of tumor-CAR T-cell interaction following local administration in solid cancers
Detection of genes with differential expression dispersion unravels the role of autophagy in cancer progression
Virus and CTL dynamics in the extrafollicular and follicular tissue compartments in SIV-infected macaques
A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression
How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility
Amplifying the redistribution of somato-dendritic inhibition by the interplay of three interneuron types
Constrained Allocation Flux Balance Analysis
A transcriptional cycling model recapitulates chromatin-dependent features of noisy inducible transcription
Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy
System identification of signaling dependent gene expression with different time-scale data
Mathematical modelling of mechanotransduction via RhoA signalling pathways
Modeling the progression of Type 2 diabetes with underlying obesity
Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices
CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach
How swarming bats can use the collective soundscape for obstacle avoidance
Landscape quantifies the intermediate state and transition dynamics in ecological networks
Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly
Building blocks and blueprints for bacterial autolysins
Structure and variability of delay activity in premotor cortex
Oscillations via Spike-Timing Dependent Plasticity in a Feed-Forward Model
Mechanical positioning of multiple nuclei in muscle cells
Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa
Evolution of phenotypic fluctuation under host-parasite interactions
Tumor hepatitis B virus RNA identifies a clinically and molecularly distinct subset of hepatocellular carcinoma
A multiscale model of complex endothelial cell dynamics in early angiogenesis
Differential receptive field organizations give rise to nearly identical neural correlations across three parallel sensory maps in weakly electric fish
A framework to assess the quality and impact of bioinformatics training across ELIXIR
How synaptic strength, short-term plasticity, and input synchrony contribute to neuronal spike output
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks
Opponent learning with different representations in the cortico-basal ganglia pathways can develop obsession-compulsion cycle
Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems
Modelling the synergistic effect of bacteriophage and antibiotics on bacteria: Killers and drivers of resistance evolution
Towards Prediction of Metabolic Products of Polyketide Synthases: An In Silico Analysis
Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load
The structured 'low temperature' phase of the retinal population code
Rational Mutational Analysis of a Multidrug MFS Transporter CaMdr1p of Candida albicans by Employing a Membrane Environment Based Computational Approach
Ten simple rules for implementing open and reproducible research practices after attending a training course
Spatial heterogeneity enhance robustness of large multi-species ecosystems
The Energy Landscapes of Repeat-Containing Proteins: Topology, Cooperativity, and the Folding Funnels of One-Dimensional Architectures
Combinatorial Gene Regulation Using Auto-Regulation
Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?
Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets
A framework for deriving analytic steady states of biochemical reaction networks
Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
Temporal progression along discrete coding states during decision-making in the mouse gustatory cortex
Learning with filopodia and spines: Complementary strong and weak competition lead to specialized, graded, and protected receptive fields
Protein Connectivity in Chemotaxis Receptor Complexes
The Dynamic Shift Detector: An algorithm to identify changes in parameter values governing populations
Incorporating human mobility to enhance epidemic response and estimate real-time reproduction numbers
Correction: An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway
SavvyCNV: Genome-wide CNV calling from off-target reads
Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework
Insights into adenosine A2A receptor activation through cooperative modulation of agonist and allosteric lipid interactions
Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers
Ten simple rules for effectively assessing lab environments
No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag
A digital DNA system favours the superiority of unidirectional inheritance over 'Lamarckian' inheritance
Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants
A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design
Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data
Excitable neuronal assemblies with adaptation as a building block of brain circuits for velocity-controlled signal propagation
A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT
Online analysis of microendoscopic 1-photon calcium imaging data streams
Chapter 7: Pharmacogenomics
Connectivity, Cycles, and Persistence Thresholds in Metapopulation Networks
Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane
Injury-related cell death and proteoglycan loss in articular cartilage: Numerical model combining necrosis, reactive oxygen species, and inflammatory cytokines
Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans
Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering
CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data
Computational Eurotransplant kidney allocation simulations demonstrate the feasibility and benefit of T-cell epitope matching
Deep attention networks reveal the rules of collective motion in zebrafish
Functional Connectivity and Tuning Curves in Populations of Simultaneously Recorded Neurons
SPOROS: A pipeline to analyze DISE/6mer seed toxicity
NIH Roadmap Interdisciplinary Research Initiatives
Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons
On Modeling HIV and T Cells In Vivo: Assessing Causal Estimators in Vaccine Trials
Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach
Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot
Learning the Structure of Biomedical Relationships from Unstructured Text
A computational framework for the investigation of phosphoinositide regulation
CHOIRBM: An R package for exploratory data analysis and interactive visualization of pain patient body map data
Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
Fine-scale family structure shapes influenza transmission risk in households: Insights from primary schools in Matsumoto city, 2014/15
Environmental uncertainty and the advantage of impulsive choice strategies
Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector
Detecting distant-homology protein structures by aligning deep neural-network based contact maps
Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis
If You Can't Measure It, You Can't Manage It
Ten quick tips for sharing open genomic data
The quality and complexity of pairwise maximum entropy models for large cortical populations
Nonlinearity of Mechanochemical Motions in Motor Proteins
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction
How immunity shapes the long-term dynamics of influenza H3N2
Ten simple rules for building an antiracist lab
Ten simple rules for implementing electronic lab notebooks (ELNs)
Enhanced viral infectivity and reduced interferon production are associated with high pathogenicity for influenza viruses
Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark
Complementary phase responses via functional differentiation of dual negative feedback loops
Modeling the temporal network dynamics of neuronal cultures
Towards optogenetic vision restoration with high resolution
Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets
Reflecting on 20 years of breast cancer modeling in CISNET: Recommendations for future cancer systems modeling efforts
Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling
The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau
On the role of transcription in positioning nucleosomes
Robust and efficient coding with grid cells
An Atlas of the Thioredoxin Fold Class Reveals the Complexity of Function-Enabling Adaptations
Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway
Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin
Targeted pandemic containment through identifying local contact network bottlenecks
A Review of 2011 for PLoS Computational Biology
Effective population size for culturally evolving traits
Loss of Genetic Redundancy in Reductive Genome Evolution
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study
Using pose estimation to identify regions and points on natural history specimens
The Voice of Bats: How Greater Mouse-eared Bats Recognize Individuals Based on Their Echolocation Calls
The Role of Additive Neurogenesis and Synaptic Plasticity in a Hippocampal Memory Model with Grid-Cell Like Input
Correction: Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load
Improving probabilistic infectious disease forecasting through coherence
Using Molecular Mechanics to Predict Bulk Material Properties of Fibronectin Fibers
On the impact of re-mating and residual fertility on the Sterile Insect Technique efficacy: Case study with the medfly, Ceratitis capitata
Ten Simple Rules for Protecting Research Integrity
Single nucleotide polymorphisms affect RNA-protein interactions at a distance through modulation of RNA secondary structures
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors
Adaptive dynamics of memory-one strategies in the repeated donation game
Modelling of the cancer cell cycle as a tool for rational drug development: A systems pharmacology approach to cyclotherapy
Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized
Between-tumor and within-tumor heterogeneity in invasive potential
Optimal Timing and Duration of Induction Therapy for HIV-1 Infection
Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
Ten simple rules to create a serious game, illustrated with examples from structural biology
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach
Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD: KRas protein-protein interface
Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor
Emergence of cooperation promoted by higher-order strategy updates
Implicit model to capture electrostatic features of membrane environment
Programming cell growth into different cluster shapes using diffusible signals
A phylogenetic approach to inferring the order in which mutations arise during cancer progression
Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation
The Role of Compensatory Mutations in the Emergence of Drug Resistance
Harnessing formal concepts of biological mechanism to analyze human disease
HELP: A computational framework for labelling and predicting human common and context-specific essential genes
The role of learned song in the evolution and speciation of Eastern and Spotted towhees
Model-Based Reasoning in Humans Becomes Automatic with Training
Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models
Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics
Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment