Topic 4

bioinformatics methods method data available datasets https based com github accuracy approach tool learning developed accurate sequencing software algorithm tools can large analysis computational existing performance present information using machine approaches biological prediction introduce package sample framework deep dataset applied set algorithms used user statistical use genome single application samples throughput source models allows pipeline genomics applications identification quality scale sequence sets seq art classification high real detection challenging automated open enables simulated number genomic techniques predict problem new inference image reference technologies such reads code freely it accurately read sequences implemented uses improve be research standard researchers identifying images

5336 items. Top items listed below.

A deep learning framework for characterization of genotype data 26 4

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

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

A consensus-based ensemble approach to improve de novo transcriptome assembly 25 4

Boundary-Forest Clustering: Large-Scale Consensus Clustering of Biological Sequences 145 4

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

Variance-adjusted Mahalanobis (VAM): a fast and accurate method for cell-specific gene set scoring 43 4

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

Multi-tissue transcriptome-wide association studies 19 4

SCRAPP: A tool to assess the diversity of microbial samples from phylogenetic placements 162 13 4

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

Kmer2SNP: reference-free SNP calling from raw reads based on matching 13 4

Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative Models 43 4

graphsim: An R package for simulating gene expression data from graph structures of biological pathways 13 4

On the automatic annotation of gene functions using observational data and phylogenetic trees 162 13 4

MRLocus: identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity 19 13 4

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

Network-based imputation of dropouts in single-cell RNA sequencing data 147 43 13 4

Probabilistic gene expression signatures identify cell-types from single cell RNA-seq data 43 4

BATMAN: fast and accurate integration of single-cell RNA-Seq datasets via minimum-weight matching 147 43 13 4

Balrog: A universal protein model for prokaryotic gene prediction 162 13 4

Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer 112 13 4

DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning 105 26 13 4

Probabilistic index models for testing differential expression in single cell RNA sequencing data 43 4

A Deep Learning Framework for Predicting Human Essential Genes by Integrating Sequence and Functional data 105 26 4

On the discovery of population-specific state transitions from multi-sample multi-condition single-cell RNA sequencing data 43 4

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

mbkmeans: fast clustering for single cell data using mini-batch k-means 147 43 13 4

Detection of pre-microRNA with Convolutional Neural Networks 105 26 4

CoCoNet: Boosting RNA contact prediction by convolutional neural networks 105 26 13 4

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

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

Subpopulation identification for single-cell RNA-sequencing data using functional data analysis 43 4

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution 147 43 13 4

A Self-Attention Model for Inferring Cooperativity between Regulatory Features 13 4

Finding human gene-disease associations using a Network Enhanced Similarity Search (NESS) of multi-species heterogeneous functional genomics data 13 4

Efficient and Flexible Integration of Variant Characteristics in Rare Variant Association Studies Using Integrated Nested Laplace Approximation 145 13 4

Detection of differential RNA modifications from direct RNA sequencing of human cell lines 147 13 4

Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic experiment 83 4

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

Towards CNN Representations for Small Mass Spectrometry Data Classification: From Transfer Learning to Cumulative Learning 26 4

scLM: automatic detection of consensus gene clusters across multiple single-cell datasets 147 43 13 4

Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper 25 13 4

Denoising large-scale biological data using network filters 26 4

Identifying Genomic Islands with Deep Neural Networks 26 4

Design and power analysis for multi-sample single cell genomics experiments 43 4

Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics 19 4

Using Conditional Generative Adversarial Networks to Boost the Performance of Machine Learning in Microbiome Datasets 26 4

miRNA activity inferred from single cell mRNA expression 43 4

Using a supervised principal components analysis for variable selection in high-dimensional datasets reduces false discovery rates 123 83 4

A statistical nonparametric method for identifying consistently important features across samples 147 13 4

Single Individual Haplotype Reconstruction Using Fuzzy C-Means Clustering With Minimum Error Correction 145 4

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data 112 4

Annotating Gene Ontology terms for protein sequences with the Transformer model 105 26 4

A composite method to infer drug resistance with mixed genomic data 26 4

PAN: Personalized Annotation-based Networks for the Prediction of Breast Cancer Relapse 112 13 4

CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data 31 7 4

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement 43 26 4

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

Detecting genomic deletions from high-throughput sequence data with unsupervised learning 13 4

Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data 43 4

HELLO: A hybrid variant calling approach 25 4

ECMarker: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages 105 26 13 4

Cluster similarity spectrum integration of single-cell genomics data 147 43 4

Improving replicability in single-cell RNA-Seq cell type discovery with Dune 147 43 4

A genome-wide case-only test for the detection of digenic inheritance in human exomes 145 19 4

Partitioning gene-based variance of complex traits by gene score regression 19 13 4

Supervised Adversarial Alignment of scRNA-seq Data 147 43 26 4

Iterative point set registration for aligning scRNA-seq data 43 26 4

A Bayesian inference tool for identifying artifactual calls from differential transcript abundance analyses 83 4

Metabolic pathway inference using multi-label classification with rich pathway features 26 4

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data. 13 4

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

Choosing representative proteins based on splicing structure similarity improves the accuracy of gene tree reconstruction 162 13 4

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection 145 4

ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data 176 62 4

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

A rigorous method for integrating multiple heterogeneous databases in genetic studies 123 4

iMDA-BN: Identification of miRNA-Disease Associations based on the Biological Network and Graph Embedding Algorithm 105 26 4

DNA methylation changes with age as a complex system: a parenclitic network approach to a family-based cohort of patients with Down Syndrome 26 4

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

DeepPheno: Predicting single gene loss of function phenotypes 105 26 13 4

A deep learning framework for high-throughput mechanism-driven phenotype compound screening 26 4

Deep learning approaches predict non-coding RNA functions from only raw sequence data 162 105 13 4

Predicting Alignment Distances via Continuous Sequence Matching 140 26 4

AnnapuRNA: a scoring function for predicting RNA-small molecule interactions. 105 13 4

Learned SPARCOM: Unfolded Deep Super-Resolution Microscopy 184 70 26 18 4

Network reconstruction for trans acting genetic loci using multi-omics data and prior information 112 4

Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data 111 105 26 4

Using high-throughput phenotypes to enable genomic selection by inferring genotypes 145 53 19 4

The Gene Expression Deconvolution Interactive Tool (GEDIT): Accurate Cell Type Quantification from Gene Expression Data 13 4

Functional assessments of PTEN variants using machine-assisted phenotype scoring 26 4

ACE: A Probabilistic Model for Characterizing Gene-Level Essentiality in CRISPR Screens 139 43 4

Improving the coverage of credible sets in Bayesian genetic fine-mapping 19 4

XGSEA: CROSS-species Gene Set Enrichment Analysis via domain adaptation 13 4

Comparison of High-Throughput Single-Cell RNA Sequencing Data Processing Pipelines 43 4

Genome-wide co-expression distributions as a metric to prioritize genes of functional importance 43 4

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

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments 13 4

Post-prediction inference 13 4