Topic 162

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120 items. Top items listed below.

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

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

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

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

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

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

CHEER: hierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning 162 13 4

Predicting candidate genes from phenotypes, functions, and anatomical site of expression 162 105 13 4

Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections 162 13 4

PickPocket : Pocket binding prediction for specific ligands family using neural networks. 162 105 13 4

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

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

DELPHI: accurate deep ensemble model for protein interaction sites prediction 105 13 4

TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding 162 105 13 4

RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis 162 13 4

A fully open-source framework for deep learning protein real-valued distances 162 13 4

Phylogenetic correlations have limited effect on coevolution-based contact prediction in proteins 162 105 13 4

GraphDTA: Predicting drug-target binding affinity with graph neural networks 162 105 13 4

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches 162 13 4

DeepMicro: deep representation learning for disease prediction based on microbiome data 162 13 4

Improving COVID-19 Testing Efficiency using Guided Agglomerative Sampling 162 13 4

Alignment-free identification of COI DNA barcode data with the Python package Alfie 162 13 4

Broccoli: combining phylogenetic and network analyses for orthology assignment 13 4

Exploring the quality of protein structural models from a Bayesian perspective 162 13 4

Anti-cancer Drug Synergy Prediction in Understudied Tissues using Transfer Learning 162 105 13 4

ToxVec: Deep Language Model-Based Representation Learning for Venom Peptide Classification 162 105 26 13 4

Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model 13 4

Prediction of specific TCR-peptide binding from large dictionaries of TCR-peptide pairs 162 13 4

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

Prediction of protein subcellular localization using deep learning and data augmentation 162 105 13 4

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

Predicting drug-target interactions using multi-label learning with community detection method (DTI-MLCD) 162 105 13 4

SCAPP: An algorithm for improved plasmid assembly in metagenomes 162 13 4

VIDHOP, viral host prediction with Deep Learning 162 105 13 4

SODA: Multi-locus species delimitation using quartet frequencies 162 13 4

T4SE-XGB: interpretable sequence-based prediction of type IV secreted effectors using eXtreme gradient boosting algorithm 105 13 4

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

Liftoff: an accurate gene annotation mapping tool 13 4

A Novel Riboswitch Classification based on Imbalanced Sequences achieved by Machine Learning 162 105 26 13 4

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function 105 26 13 4

SubFeat: Feature Subspacing Ensemble Classifier for Function Prediction of DNA, RNA and Protein Sequences 13 4

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning 105 13 4

FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models 162 13 4

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

Improving Metagenomic Classification using Discriminative k-mers from Sequencing Data 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

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

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

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

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

Learning a latent representation of human genomics using Avocado 13 4

DeepTE: a computational method for de novo classification of transposons with convolu-tional neural network 162 13 4

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

pDriver: A novel method for unravelling personalised coding and miRNA cancer drivers 13 4

rearrvisr: an R package to detect, classify, and visualize genome rearrangements 13 4

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine 162 13 4

Modern Hopfield Networks and Attention for Immune Repertoire Classification 162 26 13 4

Automating parameter selection to avoid implausible biological pathway models 162 13 4

PICRUSt2: An improved and customizable approach for metagenome inference 162 13 4

miTAR: a hybrid deep learning-based approach for predicting miRNA targets 105 26 13 4

miRinGO: Prediction of biological processes indirectly targeted by human microRNAs 13 4

Machine Learning and Deep Learning challenges for building 2'O site prediction 105 13 4

GeneRax: A tool for species tree-aware maximum likelihood based gene tree inference under gene duplication, transfer, and loss. 162 83 13 4

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

Primary case inference in viral outbreaks through analysis of intra-host variant population 162 13 4

Automated quality control of next generation sequencing data using machine learning 13 4

TranSynergy: Mechanism-Driven Interpretable Deep Neural Network for the Synergistic Prediction and Pathway Deconvolution of Drug Combinations 105 13 4

Struct2Graph: A graph attention network for structure based predictions of protein-protein interactions 105 26 13 4

DOMINO: a novel algorithm for network-based identification of active modules withreduced rate of false calls 162 13 4

Learning, Visualizing and Exploring 16S rRNA Structure Using an Attention-based Deep Neural Network 105 26 13 4

S-conLSH: Alignment-free gapped mapping of noisy long reads 13 4

StackRAM: a cross-species method for identifying RNA N6-methyladenosine sites based on stacked ensemble 105 13 4

Comparing orthology methods and their performance by recapitulating patterns of eukaryotic genome evolution. 162 13 4

HieRFIT: Hierarchical Random Forest for Information Transfer 147 13 4

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

Graph convolutional networks for drug response prediction 105 26 13 4

Metalign: Efficient alignment-based metagenomic profiling via containment min hash 13 4

Identification of Conserved Evolutionary Trajectories in Tumors 13 4

Machine learning with biomedical ontologies 162 13 4

HiTaC: Hierarchical Taxonomic Classification of Fungal ITS Sequences 162 13 4

JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation 147 13 4

Consensus Features Nested Cross-Validation 162 13 4

Coupled Co-clustering-based Unsupervised Transfer Learning for the Integrative Analysis of Single-Cell Genomic Data 147 43 13 4

AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data 13 4

iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC 162 13 4

scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data 13 4

Exploration of Chemical Space with Partial Labeled Noisy Student Self-Training for Improving Deep Learning: Application to Drug Metabolism 105 26 13 4

Post-prediction inference 13 4

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

A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis 13 4

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench 147 13 4

Combining Information from Crosslinks and Monolinks in the Modelling of Protein Structures 162 13 4

RootDigger: a root placement program for phylogenetic trees 162 13 4

Classifying protein structures into folds by convolutional neural networks, distance maps, and persistent homology 105 26 13 4

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics 165 13 4

Hierarchical progressive learning of cell identities in single-cell data 147 13 4

NECo: A node embedding algorithm for multiplex heterogeneous networks 13 4

Protein structure search to support the development of protein structure prediction methods 162 105 13 4

Consensus clustering applied to multi-omic disease subtyping 162 13 4

A novel algorithm to accurately classify metagenomic sequences 162 13 4