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HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data 62 4 2

Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure 89 19 9 4

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies 107 52 12 9 5 4

Machine learning-based investigation of the cancer protein secretory pathway 112 14 9 4

The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes 31 20 9 5

A novel single-cell based method for breast cancer prognosis 43 26 4

Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications 185 21 5

Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression 31 9

Integrated metabolic modeling, culturing and transcriptomics explains enhanced virulence of V. cholerae during co-infection with ETEC 114 12

The landscape of metabolic pathway dependencies in cancer cell lines 186 9 3

Development of an objective index, neural activity score (NAS), reveals neural network ontogeny and treatment effects on microelectrode arrays 4 2

Global computational alignment of tumor and cell line transcriptional profiles 43 14 9 4

Multi-omics approach highlights differences between functional RLP classes in Arabidopsis thaliana 134 9 5

Denoising large-scale biological data using network filters 26 4

Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments 158 112 4

Co-expression networks from gene expression variability between genetically identical seedlings can reveal novel regulatory relationships 134 9 5 4

Functional and structural basis of extreme non-coding conservation in vertebrate mRNAs 134 49 31 9 3

Complementary effects of adaptation and gain control on sound encoding in primary auditory cortex 23 2

Co-expression signatures of combinatorial gene regulation 134 31 9 3

Bidirectional regulation of cognitive and anxiety-like behaviors by dentate gyrus mossy cells in male and female mice 56 11 2

Probabilistic Approach to Understand Errors in Sequencing and its based Applications 145 4

Raman spectroscopy-based measurements of single-cell phenotypic diversity in microbial communities 158 38 18 17 5

Adaptation supports short-term memory in a visual change detection task 100 23 2

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis 43 9 4

Pathway-based and phylogenetically adjusted quantification of metabolic interaction between microbial species 143 29 4

Imputing missing RNA-seq data from DNA methylation by using transfer learning based-deep neural network 105 26 4

The functional relevance of task-state functional connectivity 22 2

Noncanonical targeting contributes significantly to miRNA-mediated regulation. 7

Controlling for Human Population Stratification in Rare Variant Association Studies 145 123 19 4

Detection of complex genetic architecture using two-locus population differentiation: modeling epistasis 19 9 4

Individual-subject functional localization increases univariate activation but not multivariate pattern discriminability in the 'multiple-demand' frontoparietal network 22 2

Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators and co-option of cellular pathways 112 1

In-silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs 37 1

Predicting global dynamics of spatial microbial communities from local interaction rules 158 99 38 17 5

Heterogeneity in human hippocampal CaMKII transcripts reveals allosteric hub-dependent regulation 51 8 3

A novel role for the C-terminal domain of the influenza A virus host shutoff endoribonuclease PA-X in mediating rapid turnover of the PA-X protein 41 3

Uncovering modeling features of viral replication dynamics from high-throughput single-cell virology experiments 38 21 4

A comparative study of supervised machine learning algorithms for the prediction of long-range chromatin interactions 105 26 4

Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection? 76 1

Towards an evolutionarily appropriate null model: jointly inferring demography and purifying selection 83 21 5 4

Same, Same, but Different: Molecular Analyses of Streptococcus pneumoniae Immune Evasion Proteins Identifies new Domains and Reveals Structural Differences between PspC and Hic Variants 121 114 12 9 8

Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins 24 1

Genome-wide predictions of genetic redundancy in Arabidopsis thaliana 134 16 9 5

Model-based analysis of polymorphisms in an enhancer reveals cis-regulatory mechanisms 134 112 4

Epigenome-based Splicing Prediction using a Recurrent Neural Network 31 9 4

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq 41

A new synuclein-transgenic mouse model for early Parkinson's reveals molecular features of preclinical disease 54 11 9 3

Collateral fitness effects of mutations 21 5 3

Characterizing microRNA-mediated modulation of gene expression noise and its effect on synthetic gene circuits 74 38 9

Polygenic risk score based on weight gain trajectories is a strong predictor of childhood obesity 19 4

A Genome-based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates 26 4

Exploring the Sequence Fitness Landscape of a Bridge Between Protein Folds 149 91 38 8 4

Lagging strand encoding promotes adaptive evolution 21 5

A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data 38 8

Uncertainty-driven regulation of learning and exploration in adolescents: A computational account 58 23 2

Seminal fluid protein divergence among populations exhibiting postmating prezygotic reproductive isolation 132 21 5

Leveraging functional annotation to identify genes associated with complex diseases 19 9 4

Emergence of Non-Linear Mixed Selectivity in Prefrontal Cortex after Training 100 23 2

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens 37 1

Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice 9 3

Pathway Analysis within Multiple Human Ancestries Reveals Novel Signals for Epistasis in Complex Traits 19 4

Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology 31 8

Studying models of balancing selection usingphase-type theory 21 5 4

Allele-specific alternative splicing in human tissues 19 9 4

Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach 37 1

A Multiscale and Comparative Model for Receptor Binding of 2019 Novel Coronavirus and the Implication of its Life Cycle in Host Cells 36 1

Neural mechanisms underlying distractor inhibition on the basis of feature and/or spatial expectations. 23 2

Transcription factor binding dynamics shape noise across biological processes 134 31 9 3

Enrichment of genomic variation in pathways linked to autism 9 4

Identification and functional analysis of long non-coding RNAs in autism spectrum disorders 9

Gene expression in the cardiovascular system of the domestic sheep (Ovis aries); a new tool to advance our understanding of cardiovascular disease. 120 9

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods 81 40 31 21 9 5

Simulating bout-and-pause patterns with reinforcement learning 7 2

Transcription factor-target relationships complicated by knockout analysis 134 9 3

Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns 134 9 5

cFIT: Integration and transfer learning of single cell transcriptomes, illustrated by fetal brain cell development 43 4

Hierarchical Markov Random Field model captures spatial dependency in gene expression, demonstrating regulation via the 3D genome 89 31 4

Mapping the Role of AcrAB-TolC Efflux Pumps in the Evolution of Antibiotic Resistance Reveals Near-MIC Treatments Facilitate Resistance Acquisition 52 12 5

Cyclooxgenase-2 is induced by SARS-CoV-2 infection but does not affect viral entry or replication 36 1

Impact of cell-type and context-dependent regulatory variants on human immune traits 19 9

Behavioural relevance of spontaneous, transient brain network interactions in fMRI 22 2

A minimal yet flexible likelihood framework to assess correlated evolution 83 21 4

Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities 17 5

miRNA activity inferred from single cell mRNA expression 43 4

Molecular Evolution of the Sex Peptide Network in Drosophila 56 21 5

The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells 97 9 4

Novel functional insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies 60 9

Terminitor: Cleavage Site Prediction Using Deep Learning Models 105 26 4

Common postzygotic mutational signature in multiple healthy adult tissues related to embryonic hypoxia 9 3

Comparative study of transcriptomics-based scoring metrics for the epithelial-hybrid-mesenchymal spectrum 98 14 9 4

Towards understanding the regulation of histone H1 somatic subtypes with OMICs. 31 9 3

Power analysis of transcriptome-wide association study: implications for practical protocol choice 145 123 19 4

Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy 14 10 9

Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers 112 38 26 4

Dynamics of chromosomal target search by a membrane-integrated one-component receptor 127 8 3

A Phylogenetic Approach to Inferring the Order in Which Mutations Arise during Cancer Progression 83 14 4