yusuke1997/dblp-id-title huggingface dataset:
BALCONY: an R package for MSA and functional compartments of protein variability analysis
Flipping NextGen: using biological systems to characterize NextGen sequencing technologies
Bayesian refinement of protein functional site matching
DepthTools: an R package for a robust analysis of gene expression data
Hydropathicity-based prediction of pain-causing NaV1.7 variants
Relation extraction between bacteria and biotopes from biomedical texts with attention mechanisms and domain-specific contextual representations
Heterodimeric protein complex identification by naïve Bayes classifiers
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein
DIPSBC - data integration platform for systems biology collaborations
Ioncopy: an R Shiny app to call copy number alterations in targeted NGS data
An efficient ensemble method for missing value imputation in microarray gene expression data
Employing phylogenetic tree shape statistics to resolve the underlying host population structure
BACA: bubble chArt to compare annotations
Using Kinect to classify Parkinson's disease stages related to severity of gait impairment
DeepQA: improving the estimation of single protein model quality with deep belief networks
On the rank-distance median of 3 permutations
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
Methodology and software to detect viral integration site hot-spots
Amplification of the Gene Ontology annotation of Affymetrix probe sets
Assessment and optimisation of normalisation methods for dual-colour antibody microarrays
Domain motions of Argonaute, the catalytic engine of RNA interference
Pathway activity inference for multiclass disease classification through a mathematical programming optimisation framework
Comparative analysis of five protein-protein interaction corpora
Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
A restraint molecular dynamics and simulated annealing approach for protein homology modeling utilizing mean angles
ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context
Discriminative motif discovery in DNA and protein sequences using the DEME algorithm
Stochastic models for the in silico simulation of synaptic processes
Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance
Ontology-guided data preparation for discovering genotype-phenotype relationships
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes
Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction
Effects of dependence in high-dimensional multiple testing problems
SamQL: a structured query language and filtering tool for the SAM/BAM file format
MedSurv: a software application for creating, conducting and managing medical surveys and questionnaires
Distance correlation application to gene co-expression network analysis
Compositional zero-inflated network estimation for microbiome data
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome
CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology
A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
Web-based design and analysis tools for CRISPR base editing
Computationally efficient flux variability analysis
Impact of gene annotation choice on the quantification of RNA-seq data
Oasis 2: improved online analysis of small RNA-seq data
DecoFungi: a web application for automatic characterisation of dye decolorisation in fungal strains
neoDL: a novel neoantigen intrinsic feature-based deep learning model identifies IDH wild-type glioblastomas with the longest survival
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms
Structure prediction for the helical skeletons detected from the low resolution protein density map
A framework for generalized subspace pattern mining in high-dimensional datasets
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis
TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing
Novel group-based QSAR and combinatorial design of CK-1δ inhibitors as neuroprotective agents
Comparative evaluation of set-level techniques in predictive classification of gene expression samples
Integrative network-based Bayesian analysis of diverse genomics data
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis
Detecting selection in low-coverage high-throughput sequencing data using principal component analysis
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays
IOAT: an interactive tool for statistical analysis of omics data and clinical data
stam - a Bioconductor compliant R package for structured analysis of microarray data
Ensemble learning for prediction of the bioactivity capacity of herbal medicines from chromatographic fingerprints
PALMER: improving pathway annotation based on the biomedical literature mining with a constrained latent block model
A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data
Detection of Lineage-Specific Evolutionary Changes among Primate Species
An algorithm for the determination and quantification of components of nucleic acid mixtures based on single sequencing reactions
A computational method for detecting copy number variations using scale-space filtering
Optimizing biomedical information retrieval with a keyword frequency-driven prompt enhancement strategy
IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods
Extracting causal relations on HIV drug resistance from literature
Imaging findings and clinical relevance of 68 Ga-Pentixafor PET in atherosclerosis: a systematic review
HEROIC: a platform for remote collection of electroencephalographic data using consumer-grade brain wearables
MFSynDCP: multi-source feature collaborative interactive learning for drug combination synergy prediction
Correction: Detecting protein complexes with multiple properties by an adaptive harmony search algorithm
Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information
Readjoiner: a fast and memory efficient string graph-based sequence assembler
Genome-wide tracts of homozygosity and exome analyses reveal repetitive elements with Barrets esophagus/esophageal adenocarcinoma risk
Exploratory and inferential analysis of gene cluster neighborhood graphs
Information assessment on predicting protein-protein interactions
Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data
MaxAlign: maximizing usable data in an alignment
Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model
A new fruit fly optimization algorithm enhanced support vector machine for diagnosis of breast cancer based on high-level features
Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
ReadDB Provides Efficient Storage for Mapped Short Reads
CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology
NERI: network-medicine based integrative approach for disease gene prioritization by relative importance
GeCoNet-Tool: a software package for gene co-expression network construction and analysis
Bio: : NEXUS: a Perl API for the NEXUS format for comparative biological data
On Sackin's original proposal: the variance of the leaves' depths as a phylogenetic balance index
Molecular dynamics simulation and bioinformatics study on chloroplast stromal ridge complex from rice ( Oryza sativa L.)
Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data
NemoProfile as an efficient approach to network motif analysis with instance collection
Evaluation of clustering algorithms for protein-protein interaction networks
Biological representation of chemicals using latent target interaction profile
Entourage: all-in-one sequence analysis software for genome assembly, virus detection, virus discovery, and intrasample variation profiling
A gene regulatory network inference model based on pseudo-siamese network
Clustering protein environments for function prediction: finding PROSITE motifs in 3D
Short clones or long clones? A simulation study on the use of paired reads in metagenomics
Spectral embedding finds meaningful (relevant) structure in image and microarray data
Multiple-testing correction in metabolome-wide association studies
Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
An integrative network-based approach to identify novel disease genes and pathways: a case study in the context of inflammatory bowel disease
Constructing and analysing dynamic models with modelbase v1.2.3: a software update
Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest
An iterative workflow for creating biomedical visualizations using Inkscape and D3.js
A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments
Genovar: a detection and visualization tool for genomic variants
A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions
RDML-Ninja and RDMLdb for standardized exchange of qPCR data
FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis
GeneRank: Using search engine technology for the analysis of microarray experiments
CGH-Profiler: Data mining based on genomic aberration profiles
A new massively parallel nanoball sequencing platform for whole exome research
Advances in the REDCAT software package
Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes
PoPMuSiC 2.1 : a web server for the estimation of protein stability changes upon mutation and sequence optimality
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
A hierarchical Naïve Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays
Representing and comparing protein structures as paths in three-dimensional space
miRge 2.0 for comprehensive analysis of microRNA sequencing data
Practical aliquoting of flowering plant genomes
Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis
Predicting functional upstream open reading frames in Saccharomyces cerevisiae
dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
Computing the family-free DCJ similarity
Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements
Effective type label-based synergistic representation learning for biomedical event trigger detection
Most parsimonious haplotype allele sharing determination
Identification of genes and pathways involved in kidney renal clear cell carcinoma
VGAEDTI: drug-target interaction prediction based on variational inference and graph autoencoder
Boosting forward-time population genetic simulators through genotype compression
Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree
SAFER: sub-hypergraph attention-based neural network for predicting effective responses to dose combinations
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data
DNA methylation arrays as surrogate measures of cell mixture distribution
Semi-Automatic Segmentation of Multiple Mouse Embryos in MR Images
Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data
SING: Subgraph search In Non-homogeneous Graphs
Sequence-based bacterial small RNAs prediction using ensemble learning strategies
The data paper: a mechanism to incentivize data publishing in biodiversity science
Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
The accuracy of several multiple sequence alignment programs for proteins
Development of sparse Bayesian multinomial generalized linear model for multi-class prediction
A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks
The computational prediction of drug-disease interactions using the dual-network L2,1-CMF method
Multiobjective grammar-based genetic programming applied to the study of asthma and allergy epidemiology
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens
Exploiting dependencies of pairwise comparison outcomes to predict patterns of gene response
HIDEN: Hierarchical decomposition of regulatory networks
HIHISIV: a database of gene expression in HIV and SIV host immune response
MonaGO: a novel gene ontology enrichment analysis visualisation system
Evaluating a linear k-mer model for protein-DNA interactions using high-throughput SELEX data
Evaluating the accuracy of amplicon-based microbiome computational pipelines on simulated human gut microbial communities
DRaW: prediction of COVID-19 antivirals by deep learning - an objection on using matrix factorization
Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution
CircuitsDB: a database of mixed microRNA/transcription factor feed-forward regulatory circuits in human and mouse
Amino acid empirical contact energy definitions for fold recognition in the space of contact maps
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data
SomatoSim: precision simulation of somatic single nucleotide variants
Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data
Pathogen detection in RNA-seq data with Pathonoia
Jetset: selecting the optimal microarray probe set to represent a gene
DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data
A high-throughput pipeline for designing microarray-based pathogen diagnostic assays
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing
Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers
Pathway-based drug repositioning using causal inference
13 C labeling experiments at metabolic nonstationary conditions: An exploratory study
MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects
GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing
A parallel method for enumerating amino acid compositions and masses of all theoretical peptides
metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences
Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study
Fitting Gaussian mixture models on incomplete data
Multi-scale structural community organisation of the human genome
A multiscale mathematical model of cell dynamics during neurogenesis in the mouse cerebral cortex
Dotplotic: a lightweight visualization tool for BLAST + alignments and genomic annotations
Statistically principled feature selection for single cell transcriptomics
GlyStruct: glycation prediction using structural properties of amino acid residues
Divergence of protein-coding capacity and regulation in the Bacillus cereus sensu lato group
Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins
RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins
Optimal combination of feature selection and classification via local hyperplane based learning strategy
Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data
Accurately estimating the length distributions of genomic micro-satellites by tumor purity deconvolution
Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias
GAGE: generally applicable gene set enrichment for pathway analysis
Assessing the impact of human genome annotation choice on RNA-seq expression estimates
BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data
Efficient identification of multiple pathways: RNA-Seq analysis of livers from 56Fe ion irradiated mice
Prediction of the functional class of metal-binding proteins from sequence derived physicochemical properties by support vector machine approach
A novel noise handling method to improve clustering of gene expression patterns
ClonoCalc and ClonoPlot: immune repertoire analysis from raw files to publication figures with graphical user interface
VOLARE: visual analysis of disease-associated microbiome-immune system interplay
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
A novel computational method for automatic segmentation, quantification and comparative analysis of immunohistochemically labeled tissue sections
Quantifying the relationship between sequence and three-dimensional structure conservation in RNA
Separate-channel analysis of two-channel microarrays: recovering inter-spot information
Identifying genes associated with brain volumetric differences through tissue specific transcriptomic inference from GWAS summary data
The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network
DGCPPISP: a PPI site prediction model based on dynamic graph convolutional network and two-stage transfer learning
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability
CARE 2.0: reducing false-positive sequencing error corrections using machine learning
ANMDA: anti-noise based computational model for predicting potential miRNA-disease associations
Physically-based in silico light sheet microscopy for visualizing fluorescent brain models
The topology of metabolic isotope labeling networks
A new dynamical layout algorithm for complex biochemical reaction networks
A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data
InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation
MLGO: phylogeny reconstruction and ancestral inference from gene-order data
Integrating random walk and binary regression to identify novel miRNA-disease association
Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA
PlncRNA-HDeep: plant long noncoding RNA prediction using hybrid deep learning based on two encoding styles
FPGA accelerator for protein secondary structure prediction based on the GOR algorithm
Identifying indispensable proteins of the type III secretion systems of Salmonella enterica serovar Typhimurium strain LT2
The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database
GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly
Correntropy induced loss based sparse robust graph regularized extreme learning machine for cancer classification
BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes
Transcriptome profile of OVCAR3 cisplatin-resistant ovarian cancer cell line
phenosim - A software to simulate phenotypes for testing in genome-wide association studies
An empirical Bayes approach to normalization and differential abundance testing for microbiome data
SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes
BMC Bioinformatics comes of age
Quick, "Imputation-free" meta-analysis with proxy-SNPs
Unsupervised gene set testing based on random matrix theory
Randomized quantile residuals for diagnosing zero-inflated generalized linear mixed models with applications to microbiome count data
Comparing de novo transcriptome assembly tools in di- and autotetraploid non-model plant species
MCL-DTI: using drug multimodal information and bi-directional cross-attention learning method for predicting drug-target interaction
BioCause: Annotating and analysing causality in the biomedical domain
Conditional variable importance for random forests
Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts
MTAP: The Motif Tool Assessment Platform
Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies
Learning transcriptional regulatory networks from high throughput gene expression data using continuous three-way mutual information
Integrative approach for detecting membrane proteins
Identification of single nucleotide polymorphisms from the transcriptome of an organism with a whole genome duplication
Predicting mostly disordered proteins by using structure-unknown protein data
Natural product-likeness score revisited: an open-source, open-data implementation
Bayesian approach for predicting responses to therapy from high-dimensional time-course gene expression profiles
Genome SEGE: A database for 'intronless' genes in eukaryotic genomes
A motif-independent metric for DNA sequence specificity
isma: an R package for the integrative analysis of mutations detected by multiple pipelines
Refining electronic medical records representation in manifold subspace
PCA via joint graph Laplacian and sparse constraint: Identification of differentially expressed genes and sample clustering on gene expression data
Repetitive DNA profile of the amphibian mitogenome
Integrative prescreening in analysis of multiple cancer genomic studies
McTwo: a two-step feature selection algorithm based on maximal information coefficient