yusuke1997/dblp-id-title huggingface dataset:
VPF-Class: taxonomic assignment and host prediction of uncultivated viruses based on viral protein families
METASIM: object-oriented modelling of cell regulation
OBIYagns: a grid-based biochemical simulator with a parameter estimator
WebArrayDB: cross-platform microarray data analysis and public data repository
Interactome-transcriptome integration for predicting distant metastasis in breast cancer
A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data
Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony
DiffScreen: the merging of image subtraction and molecular genetics for the rapid analysis of differentially screened cDNA libraries
rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output
Neuro-symbolic representation learning on biological knowledge graphs
Accurate continuous geographic assignment from low- to high-density SNP data
OpTiles: an R package for adaptive tiling and methylation variability profiling
Scalable metagenomic taxonomy classification using a reference genome database
PilZ domain is part of the bacterial c-di-GMP binding protein
A study of the efficiency of pooling in haplotype estimation
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors
Extending protein interaction networks using proteoforms and small molecules
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens
struct: an R/Bioconductor-based framework for standardized metabolomics data analysis and beyond
Efficient comparison of sets of intervals with NC-lists
mcaGUI: microbial community analysis R-Graphical User Interface (GUI)
ChemHub: a knowledgebase of functional chemicals for synthetic biology studies
An empirical Bayesian ranking method, with applications to high throughput biology
Multiple DNA and protein sequence alignment on a workstation and a supercomputer
MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR metabolomics data
Identification of amyloid fibril-forming segments based on structure and residue-based statistical potential
Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin
MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data
SORTEZ: a relational translator for NCBI's ASN.1 database
Regional imaging genetic enrichment analysis
Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler
NET-GE: a web-server for NETwork-based human gene enrichment
SeDuS: segmental duplication simulator
Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis
CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data
Domain identification by clustering sequence alignments
Cancer subtype identification by consensus guided graph autoencoders
SPLASH: structural pattern localization analysis by sequential histograms
PRISM: methylation pattern-based, reference-free inference of subclonal makeup
Integrated gene set analysis for microRNA studies
Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules
The new Virgil database: a service of rich links
FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines
DeepSimulator: a deep simulator for Nanopore sequencing
LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
Relating drug-protein interaction network with drug side effects
A scale-independent signal processing method for sequence analysis
IndepthPathway: an integrated tool for in-depth pathway enrichment analysis based on single-cell sequencing data
VisGenome: visualization of single and comparative genome representations
CASPR, an analysis pipeline for single and paired guide RNA CRISPR screens, reveals optimal target selection for long non-coding RNAs
A greedier approach for finding tag SNPs
EpimiRBase: a comprehensive database of microRNA-epilepsy associations
psygenet2r: a R/Bioconductor package for the analysis of psychiatric disease genes
New algorithms for multi-class cancer diagnosis using tumor gene expression signatures
Identification of topological features in renal tumor microenvironment associated with patient survival
Associating quantitative behavioral traits with gene expression in the brain: searching for diamonds in the hay
Query Chem: a Google-powered web search combining text and chemical structures
The SMARTCyp cytochrome P450 metabolism prediction server
Network structures and algorithms in Bioconductor
SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing
Linking the growth inhibition response from the National Cancer Institute's anticancer screen to gene expression levels and other molecular target data
Ligand-binding site prediction using ligand-interacting and binding site-enriched protein triangles
An improved rhythmicity analysis method using Gaussian Processes detects cell-density dependent circadian oscillations in stem cells
Genetic algorithms for simultaneous variable and sample selection in metabonomics
Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data
The chemical organization of signaling interactions
OmicsViz: Cytoscape plug-in for visualizing omics data across species
SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution
HFBD: a biomarker knowledge database for heart failure heterogeneity and personalized applications
PhasiHunter: a robust phased siRNA regulatory cascade mining tool based on multiple reference sequences
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier
Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries
CellMeSH: probabilistic cell-type identification using indexed literature
Statistical search on the Semantic Web
SMARTCyp 3.0: enhanced cytochrome P450 site-of-metabolism prediction server
GPGPS: a robust prognostic gene pair signature of glioma ensembling IDH mutation and 1p/19q co-deletion
miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants
Pipit: visualizing functional impacts of structural variations
PathwayVote: an R package for robust pathway enrichment analysis for DNA methylation data using a consensus-based voting framework
Dynamite extended: two new services to simplify protein dynamic analysis
R/qtl: QTL Mapping in Experimental Crosses
ChiBE: interactive visualization and manipulation of BioPAX pathway models
QuimP: analyzing transmembrane signalling in highly deformable cells
SRMA: an R package for resequencing array data analysis
AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data
Sequence analysis by electronic mail: a tool for accessing Internet e- mail servers
RICOPILI: Rapid Imputation for COnsortias PIpeLIne
Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm
T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life
BNFinder: exact and efficient method for learning Bayesian networks
SureTypeSC - a Random Forest and Gaussian mixture predictor of high confidence genotypes in single-cell data
PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads
Big data and other challenges in the quest for orthologs
DigestiFlow: from BCL to FASTQ with ease
A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa
FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases
A System for Automated Bacterial (genome) Integrated Annotation - SABIA
Efficient privacy-preserving string search and an application in genomics
PIRA PCR designer for restriction analysis of single nucleotide polymorphisms
Identity-by-descent filtering of exome sequence data for disease-gene identification in autosomal recessive disorders
DAnTE: a statistical tool for quantitative analysis of -omics data
Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates
TAGster: efficient selection of LD tag SNPs in single or multiple populations
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data
DISSCO: direct imputation of summary statistics allowing covariates
Graph-based Word Sense Disambiguation of biomedical documents
Cumulative logit modelling for ordinal response variables: applications to biomedical research
XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking
LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures
FastContact: rapid estimate of contact and binding free energies
Visualizing plant metabolomic correlation networks using clique-metabolite matrices
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model
Rapid classification of a protein fold family using a statistical analysis of dipolar couplings
A personalized committee classification approach to improving prediction of breast cancer metastasis
Simple topological properties predict functional misannotations in a metabolic network
Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
Optimization of signal-to-noise ratio for efficient microarray probe design
A model diagram layout extension for SBML
A personal computer program for large-scale comparisons of related nucleotide sequences
MotifNet: a web-server for network motif analysis
RBR: library-less repeat detection for ESTs
DOCKGROUND resource for studying protein-protein interfaces
M 3 D: a kernel-based test for spatially correlated changes in methylation profiles
SONiCS: PCR stutter noise correction in genome-scale microsatellites
Visualization of genomic aberrations using Affymetrix SNP arrays
Improved BLAST searches using longer words for protein seeding
MuSiC: a tool for multiple sequence alignment with constraints
Conditional generative modeling for de novo protein design with hierarchical functions
Chordomics: a visualization tool for linking function to phylogeny in microbiomes
Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes
Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster
An Excel spreadsheet computer program combining algorithms for prediction of protein structural characteristics
metaGraphite-a new layer of pathway annotation to get metabolite networks
M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
A phylogenetic mixture model for the identification of functionally divergent protein residues
Aliro: an automated machine learning tool leveraging large language models
AKT: ancestry and kinship toolkit
Pattern matching of biological sequences with limited storage
A deep neural network approach for learning intrinsic protein-RNA binding preferences
Exodus: sequencing-based pipeline for quantification of pooled variants
Understanding protein dispensability through machine-learning analysis of high-throughput data
Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc
Probabilistic partitioning methods to find significant patterns in ChIP-Seq data
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
Bayesian analysis of signaling networks governing embryonic stem cell fate decisions
Time accelerated Monte Carlo simulations of biological networks using the binomial r-leap method
Static network structure can be used to model the phenotypic effects of perturbations in regulatory networks
A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas
ReadBouncer: precise and scalable adaptive sampling for nanopore sequencing
HMM-Kalign: a tool for generating sub-optimal HMM alignments
MetaFusion: a high-confidence metacaller for filtering and prioritizing RNA-seq gene fusion candidates
The role of long-range interactions in defining the secondary structure of proteins is overestimated
BioPlat: a software for human cancer biomarker discovery
Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)
A novel sensitive method for the detection of user-defined compositional bias in biological sequences
GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records
CellH5: a format for data exchange in high-content screening
Integrated convolution and self-attention for improving peptide toxicity prediction
Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework
forgeNet: a graph deep neural network model using tree-based ensemble classifiers for feature graph construction
Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding
PEA: an integrated R toolkit for plant epitranscriptome analysis
PyMod 2.0: improvements in protein sequence-structure analysis and homology modeling within PyMOL
PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013
Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions
Data mining techniques to study the disulfide-bonding state in proteins: signal peptide is a strong descriptor
HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network
Cobweb: a Java applet for network exploration and visualisation
Reference alignment of SNP microarray signals for copy number analysis of tumors
Flexible data integration and curation using a graph-based approach
BioTextQuest + : a knowledge integration platform for literature mining and concept discovery
Biomarker identification by interpretable maximum mean discrepancy
A set-theoretic approach to database searching and clustering
E-MAGMA: an eQTL-informed method to identify risk genes using genome-wide association study summary statistics
'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces
Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures
Predicting pathway membership via domain signatures
DeepOM: single-molecule optical genome mapping via deep learning
MeSH: a window into full text for document summarization
tHapMix: simulating tumour samples through haplotype mixtures
Apparently low reproducibility of true differential expression discoveries in microarray studies
A k -mer scheme to predict piRNAs and characterize locust piRNAs
ASURAT: functional annotation-driven unsupervised clustering of single-cell transcriptomes
HitWalker2: visual analytics for precision medicine and beyond
STEM: species tree estimation using maximum likelihood for gene trees under coalescence
A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data
The use of microcomputers for the quantitation of light intensity patterns using digitized video signals
Translation initiation start prediction in human cDNAs with high accuracy
A statistical framework for biomarker discovery in metabolomic time course data
TurboKnot: rapid prediction of conserved RNA secondary structures including pseudoknots
The hydrophobic cores of proteins predicted by wavelet analysis
RNAsnoop : efficient target prediction for H/ACA snoRNAs
Robust classification of single-cell transcriptome data by nonnegative matrix factorization
Local RNA base pairing probabilities in large sequences
MRLR: unraveling high-resolution meiotic recombination by linked reads
A rapid method for computationally inferring transcriptome coverage and microarray sensitivity
ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files
Statistical analysis in dBASE-compatible databases
Comparative study of RNA-seq- and Microarray-derived coexpression networks in Arabidopsis thaliana
Erratum to: BAli-Phy version 3: model-based co-estimation of alignment and phylogeny
JASSA: a comprehensive tool for prediction of SUMOylation sites and SIMs
Metrics for regulated biochemical pathway systems
Phylogenetic inference under recombination using Bayesian stochastic topology selection
Utilizing image and caption information for biomedical document classification
GeneCards: a novel functional genomics compendium with automated data mining and query reformulation support
Comparison of Affymetrix GeneChip expression measures
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection
VOLTA: adVanced mOLecular neTwork Analysis
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data
NucleoFinder: a statistical approach for the detection of nucleosome positions
ARROGANT: an application to manipulate large gene collections
Tedna: a transposable element de novo assembler
'Multifrequency' location and clustering of sequence patterns from proteins
Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing
MobiDB: a comprehensive database of intrinsic protein disorder annotations
Software for genome mapping by fingerprinting techniques
ThetaMater: Bayesian estimation of population size parameter θ from genomic data
A fast and automated solution for accurately resolving protein domain architectures
R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R
Maligner: a fast ordered restriction map aligner
What we do not know about sequence analysis and sequence databases
SPEARS: Standard Performance Evaluation of Ancestral haplotype Reconstruction through Simulation
ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models
ampir: an R package for fast genome-wide prediction of antimicrobial peptides
XPXP: improving polygenic prediction by cross-population and cross-phenotype analysis
Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure
PGAGENE: integrating quantitative gene-specific results from the NHLBI Programs for Genomic Applications
Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging
Assessing identity, redundancy and confounds in Gene Ontology annotations over time
VIRTLAB: a virtual molecular biology laboratory
Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA
A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications
Algorithms for identifying local molecular sequence features
QSLiMFinder: improved short linear motif prediction using specific query protein data
Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searching
Privacy-preserving federated genome-wide association studies via dynamic sampling
Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web
Computational protein profile similarity screening for quantitative mass spectrometry experiments
TreeMerge: a new method for improving the scalability of species tree estimation methods
PathScan: a tool for discerning mutational significance in groups of putative cancer genes
GlycanAnalysis Plug-in: a database search tool for N -glycan structures using mass spectrometry
ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data
PhyloWidget: web-based visualizations for the tree of life
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data
Peakr: simulating solid-state NMR spectra of proteins
Effective drug-target interaction prediction with mutual interaction neural network
Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity
Neuron segmentation using 3D wavelet integrated encoder-decoder network
A general species delimitation method with applications to phylogenetic placements
Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection
MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data
Bathometer: lightning fast depth-of-reads query
Targeted retrieval of gene expression measurements using regulatory models
Structural bioinformatics enhances mechanistic interpretation of genomic variation, demonstrated through the analyses of 935 distinct RAS family mutations
Efficient short read mapping to a pangenome that is represented by a graph of ED strings
The Sleipnir library for computational functional genomics
Statistical analysis and graphical display of multivariate data on the Macintosh
A conditional denoising VAE-based framework for antimicrobial peptides generation with preserving desirable properties
CART - a chemical annotation retrieval toolkit
ZOOM! Zillions of oligos mapped
A new approach to testing mediation of the microbiome at both the community and individual taxon levels
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
Quick calculation for sample size while controlling false discovery rate with application to microarray analysis
MaxLink: network-based prioritization of genes tightly linked to a disease seed set
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments
Correcting systematic bias and instrument measurement drift with mzRefinery
Decomposing mosaic tandem repeats accurately from long reads
Polypharmacy side-effect prediction with enhanced interpretability based on graph feature attention network
DiffTool: building, visualizing and querying protein clusters
MeRP: a high-throughput pipeline for Mendelian randomization analysis
A novel methodology on distributed representations of proteins using their interacting ligands
Application of canonical correlation analysis for identifying viral integration preferences
MODEVO: exploring modularity and evolution of protein interaction networks
THETA: a new genotypic approach for predicting HIV-1 CRF02-AG coreceptor usage
metaModules identifies key functional subnetworks in microbiome-related disease