yusuke1997/dblp-id-title huggingface dataset:
FunDMDeep-m6A: identification and prioritization of functional differential m6A methylation genes
Cross-dependent graph neural networks for molecular property prediction
Voronto: mapper for expression data to ontologies
JavaShade: multiple sequence alignment box-and-shading on the World Wide Web
VirusPredictor: XGBoost-based software to predict virus-related sequences in human data
Gene set analysis in the cloud
DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research
iLSGRN: inference of large-scale gene regulatory networks based on multi-model fusion
IsoFrog: a reversible jump Markov Chain Monte Carlo feature selection-based method for predicting isoform functions
Identifying functional modules in interaction networks through overlapping Markov clustering
Constructing linkage maps in the genomics era with MapDisto 2.0
An alignment-free model for comparison of regulatory sequences
Xtalk: a path-based approach for identifying crosstalk between signaling pathways
Bio-Mirror project for public bio-data distribution
Prognostic transcriptional association networks: a new supervised approach based on regression trees
ADEPT: a computer program for prediction of protein antigenic determinants
OREMPRO web server: orientation and assessment of atomistic and coarse-grained structures of membrane proteins
MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing
Prediction of HLA-DQ3.2ß Ligands: evidence of multiple registers in class II binding peptides
Robust reconstruction of single-cell RNA-seq data with iterative gene weight updates
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data
Network clustering: probing biological heterogeneity by sparse graphical models
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships
Inference and visualization of DNA damage patterns using a grade of membership model
AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow
Novel SARS-CoV-2 encoded small RNAs in the passage to humans
Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data
DeepSite: protein-binding site predictor using 3D-convolutional neural networks
ProViz: protein interaction visualization and exploration
caspo: a toolbox for automated reasoning on the response of logical signaling networks families
Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields
A global network of biomedical relationships derived from text
Accurate large-scale phylogeny-aware alignment using BAli-Phy
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation
CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures
Gaussian mixture copulas for high-dimensional clustering and dependency-based subtyping
OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents
Aligning gene expression time series with time warping algorithms
RainbowSTORM: an open-source ImageJ plug-in for spectroscopic single-molecule localization microscopy (sSMLM) data analysis and image reconstruction
Annotation of biologically relevant ligands in UniProtKB using ChEBI
Spial: analysis of subtype-specific features in multiple sequence alignments of proteins
Probabilistic framework for integration of mass spectrum and retention time information in small molecule identification
The Sequence Alignment/Map format and SAMtools
A new dynamic tool to perform assembly of expressed sequence tags (ESTs)
An ensemble biclustering approach for querying gene expression compendia with experimental lists
MeSHProbeNet: a self-attentive probe net for MeSH indexing
piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
ModuleAlign: module-based global alignment of protein-protein interaction networks
Progenetix.net: an online repository for molecular cytogenetic aberration data
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation
Porter: a new, accurate server for protein secondary structure prediction
LoFtool: a gene intolerance score based on loss-of-function variants in 60 706 individuals
FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes
More challenges for machine-learning protein interactions
StochHMM: a flexible hidden Markov model tool and C++ library
miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data
medpie: an information extraction package for medical message board posts
Gsmodutils: a python based framework for test-driven genome scale metabolic model development
BioBERT: a pre-trained biomedical language representation model for biomedical text mining
Connection topology of proteins
AliSim-HPC: parallel sequence simulator for phylogenetics
An evolution strategy approach for the balanced minimum evolution problem
MEScan: a powerful statistical framework for genome-scale mutual exclusivity analysis of cancer mutations
Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures
CGH-Explorer: a program for analysis of array-CGH data
DACTAL: divide-and-conquer trees (almost) without alignments
MetaPOAP: presence or absence of metabolic pathways in metagenome-assembled genomes
BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing
Nozzle: a report generation toolkit for data analysis pipelines
A compression mechanism for sequence databases to improve the efficiency of conventional tools
Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
Genome annotation in the presence of insertional RNA editing
Detecting cryptically simple protein sequences using the SIMPLE algorithm
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
Boolean dynamics of genetic regulatory networks inferred from microarray time series data
BioQ: tracing experimental origins in public genomic databases using a novel data provenance model
PyBamView: a browser-based application for viewing short read alignments
LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences
A computer program for construction of circular restriction maps
Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence
ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Network-based multi-task learning models for biomarker selection and cancer outcome prediction
History of the enzyme nomenclature system
Predicting gene function through systematic analysis and quality assessment of high-throughput data
Optimal structural inference of signaling pathways from unordered and overlapping gene sets
Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome analysis
Closing the computational biology 'knowledge gap': Spanish Wikipedia as a case study
NetPhosYeast: prediction of protein phosphorylation sites in yeast
Mass spectrometry-based protein identification with accurate statistical significance assignment
MoMo: discovery of statistically significant post-translational modification motifs
Literature mining of host-pathogen interactions: comparing feature-based supervised learning and language-based approaches
CSAR: a contig scaffolding tool using algebraic rearrangements
GeneBuilder: interactive in silico prediction of gene structure
KELLER: estimating time-varying interactions between genes
Maximum likelihood estimates of allele frequencies and error rates from samples of related individuals by gene counting
m2ST: dual multi-scale graph clustering for spatially resolved transcriptomics
IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data
mirPub: a database for searching microRNA publications
Bayesian inference on biopolymer models
FORRepeats: detects repeats on entire chromosomes and between genomes
Matrix correlations for high-dimensional data: the modified RV-coefficient
Bag of Peaks: interpretation of NMR spectrometry
Making sense of microarray data distributions
A practical and robust sequence search strategy for structural genomics target selection
Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST
A comprehensive quality control workflow for paired tumor-normal NGS experiments
Estimation of steady-state flux rates in metabolic systems by computer simulations of radioactive tracer experiments
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles
Missense variants pathogenicity annotation from homologous proteins
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
mGPfusion: predicting protein stability changes with Gaussian process kernel learning and data fusion
Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition
Eigen- R 2 for dissecting variation in high-dimensional studies
SNPbox: a modular software package for large-scale primer design
Electronically subtracting expression patterns from a mixed cell population
Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms
An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function
GCHap: fast MLEs for haplotype frequencies by gene counting
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes
Prediction of mRNA polyadenylation sites by support vector machine
Plant photosynthesis phenomics data quality control
SORTALLER: predicting allergens using substantially optimized algorithm on allergen family featured peptides
T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
A novel constrained reconstruction model towards high-resolution subtomogram averaging
Differential transcript usage analysis of bulk and single-cell RNA-seq data with DTUrtle
Parallel BLAST on split databases
grenedalf: population genetic statistics for the next generation of pool sequencing
A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data
NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
SynMap2 and SynMap3D: web-based whole-genome synteny browsers
Paloverde : an OpenGL 3D phylogeny browser
Accurate prediction of toxicity peptide and its function using multi-view tensor learning and latent semantic learning framework
selscan 2.0: scanning for sweeps in unphased data
PBIT: Pipeline Builder for Identification of drug Targets for infectious diseases
CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations
Robustifying genomic classifiers to batch effects via ensemble learning
PheWAS analysis on large-scale biobank data with PheTK
Identifying cancer driver genes in tumor genome sequencing studies
Automatic registration of microarray images. I. Rectangular grid
GCevobase: an evolution-based database for GC content in eukaryotic genomes
JAX-RNAfold: scalable differentiable folding
Selenzyme: enzyme selection tool for pathway design
A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees
PathCase: pathways database system
Modeling disease progression using dynamics of pathway connectivity
CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases
Non-parametric, hypothesis-based analysis of microarrays for comparison of several phenotypes
K-RET: knowledgeable biomedical relation extraction system
Minimum message length inference of secondary structure from protein coordinate data
Approximating facial expression effects on diagnostic accuracy via generative AI in medical genetics
Quantitative characterization of antigens using monoclonal antibody reactivities
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support
Inter-residue interactions in alpha-helical transmembrane proteins
Using imperfect secondary structure predictions to improve molecular structure computations
Principal network analysis: identification of subnetworks representing major dynamics using gene expression data
tqDist: a library for computing the quartet and triplet distances between binary or general trees
HMI-PRED 2.0: a biologist-oriented web application for prediction of host-microbe protein-protein interaction by interface mimicry
AlzCode: a platform for multiview analysis of genes related to Alzheimer's disease
Using hidden Markov models and observed evolution to annotate viral genomes
3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
MMG: a probabilistic tool to identify submodules of metabolic pathways
A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences
MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction
3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis
PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants
GLOBIC: a very fast microcomputer program for fingerprinting, characterization and comparison of long nucleotide sequences
Improving genome annotations using phylogenetic profile anomaly detection
QCEWAS: automated quality control of results of epigenome-wide association studies
An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier
PAR: a PARallel and distributed job crusher
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery
Pkgndep : a tool for analyzing dependency heaviness of R packages
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads
Identifying B-cell epitopes using AlphaFold2 predicted structures and pretrained language model
Simulating Epstein-Barr virus infection with C-ImmSim
A mixture model for estimating the local false discovery rate in DNA microarray analysis
JenPep: a database of quantitative functional peptide data for immunology
Many-core algorithms for high-dimensional gradients on phylogenetic trees
Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper
Efficient estimation of emission probabilities in profile hidden Markov models
CASMAP: detection of statistically significant combinations of SNPs in association mapping
P-SAMS: a web site for plant artificial microRNA and synthetic trans -acting small interfering RNA design
Alignment-free protein interaction network comparison
invMap: a sensitive mapping tool for long noisy reads with inversion structural variants
Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage
Identification of transcription factor binding sites with variable-order Bayesian networks
ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data
CAFE: a computational tool for the study of gene family evolution
Transcription-associated protein families are primarily taxon-specific
Discovering homotypic binding events at high spatial resolution
Predictor correlation impacts machine learning algorithms: implications for genomic studies
PartsGenie: an integrated tool for optimizing and sharing synthetic biology parts
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia
Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool
Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction
A comparative analysis of algorithms for somatic SNV detection in cancer
Pelican: pedigree editor for linkage computer analysis
Compression of nucleotide databases for fast searching
Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA
anota : analysis of differential translation in genome-wide studies
A note about computing all local alignments
Metal reduction kinetics in Shewanella
PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits
Historian: accurate reconstruction of ancestral sequences and evolutionary rates
Tally-2.0: upgraded validator of tandem repeat detection in protein sequences
Distance-based clustering of CGH data
Prior information-assisted integrative analysis of multiple datasets
Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs
Modified RNAs and predictions with the ViennaRNA Package
GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database
bnstruct: an R package for Bayesian Network structure learning in the presence of missing data
Genomic mutation consequence calculator
GPCRRD: G protein-coupled receptor spatial restraint database for 3D structure modeling and function annotation
MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data
ISMB 2016 Proceedings
Inferring disease-associated long non-coding RNAs using genome-wide tissue expression profiles
Cross-modality and self-supervised protein embedding for compound-protein affinity and contact prediction
Insights on the alteration of functionality of a tyrosine kinase 2 variant: a molecular dynamics study
ChAsE: chromatin analysis and exploration tool
InterPep2: global peptide-protein docking using interaction surface templates
RecGraph: recombination-aware alignment of sequences to variation graphs
IWTomics: testing high-resolution sequence-based 'Omics' data at multiple locations and scales
Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces
Cleavage-stage embryo segmentation using SAM-based dual branch pipeline: development and evaluation with the CleavageEmbryo dataset
Multivariate Welch t -test on distances
SEEDS: data driven inference of structural model errors and unknown inputs for dynamic systems biology
A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data
Statistical methods of background correction for Illumina BeadArray data
SamCluster: An Integrated Scheme for Automatic Discovery of Sample Classes Using Gene Expression Profile
ASGART: fast and parallel genome scale segmental duplications mapping
An extension of the graph theoretical approach to predict the secondary structure of large RNAs: the complex of 16S and 23S rRNAs from E. coli as a case study
Naïve Bayes for microRNA target predictions - machine learning for microRNA targets
shinyÉPICo: a graphical pipeline to analyze Illumina DNA methylation arrays
AMICI: high-performance sensitivity analysis for large ordinary differential equation models
Improved methods for multi-trait fine mapping of pleiotropic risk loci
meta-PPISP: a meta web server for protein-protein interaction site prediction
M2IA: a web server for microbiome and metabolome integrative analysis
Predicting site-specific human selective pressure using evolutionary signatures
ISMB/ECCB 2017 proceedings
StAmP-DB: a platform for structures of polymorphic amyloid fibril cores
An approximate Bayesian approach for mapping paired-end DNA reads to a reference genome
SIST: stress-induced structural transitions in superhelical DNA
A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors
Profile sequence analysis and database searches on a transputer machine connected to a Macintosh computer
pymzML v2.0: introducing a highly compressed and seekable gzip format
PreDNA: accurate prediction of DNA-binding sites in proteins by integrating sequence and geometric structure information
Family Rank: a graphical domain knowledge informed feature ranking algorithm
A new statistic for efficient detection of repetitive sequences
Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations
expam - high-resolution analysis of metagenomes using distance trees
Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data
Issues of Z-factor and an approach to avoid them for quality control in high-throughput screening studies
JAMIE: joint analysis of multiple ChIP-chip experiments
MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data
An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics
Automated cell type discovery and classification through knowledge transfer
Linearity of network proximity measures: implications for set-based queries and significance testing
BTS: a scalable Bayesian Tissue Score for prioritizing GWAS variants and their functional contexts across >1000s of omics datasets
Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector
The fobitools framework: the first steps towards food enrichment analysis
Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins
HBexplore - a new tool for identifying and analysing hydrogen bonding patterns in biological macromolecules
Recognizing names in biomedical texts: a machine learning approach
MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data
Discriminating precursors of common fragments for large-scale metabolite profiling by triple quadrupole mass spectrometry
TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis
Openness weighted association studies: leveraging personal genome information to prioritize non-coding variants
Genome-wide selection of tag SNPs using multiple-marker correlation
clustermq enables efficient parallelization of genomic analyses
MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences
BRAT: bisulfite-treated reads analysis tool
Reference point insensitive molecular data analysis
MINS2: Revisiting the molecular code for transmembrane-helix recognition by the Sec61 translocon
SAFE-clustering: Single-cell Aggregated (from Ensemble) clustering for single-cell RNA-seq data
PedMerge : merging pedigrees to facilitate family-based genetic statistical analyses
PopDrowser: the Population Drosophila Browser
DriverGroup : a novel method for identifying driver gene groups
SwS: a solvation web service for nucleic acids
Defining and providing robust controls for microRNA prediction