yusuke1997/dblp-id-title huggingface dataset:
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad
Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data
The sufficient minimal set of miRNA seed types
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data
Progressive approach for SNP calling and haplotype assembly using single molecular sequencing data
MIA: non-targeted mass isotopolome analysis
CSMD: a computational subtraction-based microbiome discovery pipeline for species-level characterization of clinical metagenomic samples
Lineage EM algorithm for inferring latent states from cellular lineage trees
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains
Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
Copy number variation has little impact on bead-array-based measures of DNA methylation
Detection of significant protein coevolution
Human protein-protein interaction prediction by a novel sequence-based co-evolution method: co-evolutionary divergence
6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project
GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution
Predicting giant transmembrane β-barrel architecture
Network-based prediction of drug-target interactions using an arbitrary-order proximity embedded deep forest
CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis
UAMRL: multi-granularity uncertainty-aware multimodal representation learning for drug-target affinity prediction
System estimation from metabolic time-series data
A distance-based test of association between paired heterogeneous genomic data
BigWig and BigBed: enabling browsing of large distributed datasets
HiCRep.py: fast comparison of Hi-C contact matrices in Python
German Conference on Bioinformatics 2003 (GCB'03)
ChIPWig: a random access-enabling lossless and lossy compression method for ChIP-seq data
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields
MOViDA: multiomics visible drug activity prediction with a biologically informed neural network model
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
ProPred1: Prediction of Promiscuous MHC Class-I Binding Sites
Spreadsheet statistics
A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes
M&Ms: a versatile software for building microbial mock communities
PETAL: a Python tool for deep analysis of biological pathways
DIALIGN: finding local similarities by multiple sequence alignment
GIL: a python package for designing custom indexing primers
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data
Statistical confidence measures for genome maps: application to the validation of genome assemblies
OSA: a fast and accurate alignment tool for RNA-Seq
DIEGO: detection of differential alternative splicing using Aitchison's geometry
Reiterative RNA folding and occupancy rate analysis for mRNA modelling
Precise score for the prediction of peptides cleaved by the proteasome
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction
nala: text mining natural language mutation mentions
HIITE: HIV-1 incidence and infection time estimator
Accounting for tumor purity improves cancer subtype classification from DNA methylation data
Estimating IBD tracts from low coverage NGS data
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
Converter: a program to convert crystallographic coordinates among different molecular graphics standards on PC-IBM platforms
Meta-IDBA: a de Novo assembler for metagenomic data
adverSCarial: assessing the vulnerability of single-cell RNA-sequencing classifiers to adversarial attacks
Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression
TSignal: a transformer model for signal peptide prediction
MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks
The estimation of relative site variability among aligned homologous protein sequences
ChemmineR: a compound mining framework for R
TPepRet: a deep learning model for characterizing T-cell receptors-antigen binding patterns
Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression
iNGNN-DTI: prediction of drug-target interaction with interpretable nested graph neural network and pretrained molecule models
SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision
Conditional canonical correlation estimation based on covariates with random forests
ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry
Four spreadsheet templates for the laboratory
Three-dimensional computation of atom depth in complex molecular structures
WiGID: wireless genome information database
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data
Building online genomics applications using BioPyramid
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information
A machine-readable specification for genomics assays
Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data
BatchQC: interactive software for evaluating sample and batch effects in genomic data
A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments
The spike-and-slab lasso Cox model for survival prediction and associated genes detection
Quartet Fiduccia-Mattheyses revisited for larger phylogenetic studies
CytoGPS: a web-enabled karyotype analysis tool for cytogenetics
MOM: maximum oligonucleotide mapping
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields
Novel overlapping subgraph clustering for the detection of antigen epitopes
breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data
CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures
GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks
A Ruby API to query the Ensembl database for genomic features
A temporal switch model for estimating transcriptional activity in gene expression
BicOverlapper: A tool for bicluster visualization
Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models
Enabling interspecies epigenomic comparison with CEpBrowser
The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
GeneFEAST: the pivotal, gene-centric step in functional enrichment analysis interpretation
Efficient combination of multiple word models for improved sequence comparison
DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol
Genome-wide detection of somatic mosaicism at short tandem repeats
Small, fuzzy and interpretable gene expression based classifiers
A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae
Inferring signaling pathways with probabilistic programming
Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities
Within-host evolution of CD8 + -TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus
Performance reproducibility index for classification
Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks
DEEPre: sequence-based enzyme EC number prediction by deep learning
Context-specific transcriptional regulatory network inference from global gene expression maps using double two-way t -tests
GRIMP: a web- and grid-based tool for high-speed analysis of large-scale genome-wide association using imputed data
SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads
Bayesian ensemble methods for survival prediction in gene expression data
Pseudotime estimation: deconfounding single cell time series
Divide-and-conquer approach for the exemplar breakpoint distance
CoSMeD: a user-friendly web server to estimate 5-year survival probability of left-sided and right-sided colorectal cancer patients using molecular data
A C library for retrieving specific reactions from the BioModels database
Bayesian network-response regression
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data
Mapping genome-genome epistasis: a high-dimensional model
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
rMFilter: acceleration of long read-based structure variation calling by chimeric read filtering
DNA Chisel, a versatile sequence optimizer
A general framework for association analysis of microbial communities on a taxonomic tree
Endowing protein language models with structural knowledge
LncRNA/DNA binding analysis reveals losses and gains and lineage specificity of genomic imprinting in mammals
A simple method to predict protein-binding from aligned sequences - application to MHC superfamily and ß2-microglobulin
deepNF: deep network fusion for protein function prediction
CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
Mapdiff: determining differences between two genomic maps
Identifying emerging phenomenon in long temporal phenotyping experiments
A method for delineating structurally homogeneous regions in protein sequences
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
Efficient 3D kernels for molecular property prediction
ntCard: a streaming algorithm for cardinality estimation in genomics data
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data
UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures
Strategy for improved characterization of human metabolic phenotypes using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS)
The effect of statistical normalization on network propagation scores
Mian: interactive web-based microbiome data table visualization and machine learning platform
Bayesian infinite mixture model based clustering of gene expression profiles
CIS: compound importance sampling method for protein-DNA binding site p-value estimation
SPIM workflow manager for HPC
PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory
Bali-Phy version 3: model-based co-estimation of alignment and phylogeny
GENLIB: new function to simulate haplotype transmission in large complex genealogies
qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets
Phylowood: interactive web-based animations of biogeographic and phylogeographic histories
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Scaling up single-cell RNA-seq data analysis with CellBridge workflow
Finding pathogenicity islands and gene transfer events in genome data
RCytoGPS: an R package for reading and visualizing cytogenetics data
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
FPLS-DC: functional partial least squares through distance covariance for imaging genetics
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning
Parallel computation and FASTA: confronting the problem of parallel database search for a fast sequence comparison algorithm
ndexr - an R package to interface with the network data exchange
Determining the evolutionary history of gene families
BULLET: a computer simulation of shotgun DNA sequencing
CWDPRNP: a tool for cervid prion sequence analysis in program R
Molecules to maps: tools for visualization and interaction in support of computational biology
KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models
Mapping personal functional data to personal genomes
Identification of differentially methylated loci using wavelet-based functional mixed models
Ontology quality assurance through analysis of term transformations
ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise
Haplotype reconstruction from SNP fragments by minimum error correction
PDBest: a user-friendly platform for manipulating and enhancing protein structures
ONIX: an interactive PC program for the examination of protein 3D structure from PDB
Mireval: a web tool for simple microRNA prediction in genome sequences
BindingSiteDTI: differential-scale binding site modelling for drug-target interaction prediction
Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients
Reducing the effect of the data order in algorithms for constructing phylogenetic trees
GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms
Shotgun: getting more from sequence similarity searches
Architecture of basic building blocks in protein and domain structural interaction networks
L2, 1-norm regularized multivariate regression model with applications to genomic prediction
Association rule mining to identify transcription factor interactions in genomic regions
Evaluating statistical approaches to leverage large clinical datasets for uncovering therapeutic and adverse medication effects
Strategies for the development of a peptide computer
PLIDflow: an open-source workflow for the online analysis of protein-ligand docking using galaxy
GATB: Genome Assembly & Analysis Tool Box
Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
GeneCruiser: a web service for the annotation of microarray data
Inverse perturbation for optimal intervention in gene regulatory networks
Bayesian consensus clustering
A self-updating road map of The Cancer Genome Atlas
Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization
Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)
PDB-wide collection of binding data: current status of the PDBbind database
eResponseNet: a package prioritizing candidate disease genes through cellular pathways
Finding regions of significance in SELDI measurements for identifying protein biomarkers
3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures
ProteoMill: efficient network-based functional analysis portal for proteomics data
EigenTHREADER: analogous protein fold recognition by efficient contact map threading
PRINCIPLE: a tool for associating genes with diseases via network propagation
Statistical agglomeration: peak summarization for direct infusion lipidomics
KMgene: a unified R package for gene-based association analysis for complex traits
Bringing numerous methods for expression and promoter analysis to a public cloud computing service
Sequence complexity profiles of prokaryotic genomic sequences: A fast algorithm for calculating linguistic complexity
Using drug descriptions and molecular structures for drug-drug interaction extraction from literature
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web
Tightly integrated multiomics-based deep tensor survival model for time-to-event prediction
Gene name ambiguity of eukaryotic nomenclatures
CytoSeg 2.0: automated extraction of actin filaments
Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm
On the discovery of hospital admission patterns - a clarification
A framework to decipher the genetic architecture of combinations of complex diseases: applications in cardiovascular medicine
Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
PgRC2: engineering the compression of sequencing reads
Alignment of 3D structures of macromolecular assemblies
SEQuel: improving the accuracy of genome assemblies
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
SlideSort: all pairs similarity search for short reads
Mutual enrichment in aggregated ranked lists with applications to gene expression regulation
A powerful and efficient set test for genetic markers that handles confounders
Kinpute: using identity by descent to improve genotype imputation
Identifying cell-specific microRNA transcriptional start sites
Gene selection for oligonucleotide array: an approach using PM probe level data
Structure-based calculation of drug efficiency indices
PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool
MALIGNED: a multiple sequence alignment editor
Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands
Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction
Kalign 3: multiple sequence alignment of large datasets
Mass spectrometry data processing using zero-crossing lines in multi-scale of Gaussian derivative wavelet
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites
Identification of associations between genotypes and longitudinal phenotypes via temporally-constrained group sparse canonical correlation analysis
Structural drift: a possible path to protein fold change
Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips®
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis
Scoring clustering solutions by their biological relevance
Predicting regulatory variants with composite statistic
Predicting rules on organization of cis-regulatory elements, taking the order of elements into account
SnapperDB: a database solution for routine sequencing analysis of bacterial isolates
A statistical framework for Illumina DNA methylation arrays
CIBRA identifies genomic alterations with a system-wide impact on tumor biology
Linc2GO: a human LincRNA function annotation resource based on ceRNA hypothesis
Optimization models for cancer classification: extracting gene interaction information from microarray expression data
Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features
QMEANDisCo - distance constraints applied on model quality estimation
Discriminative local subspaces in gene expression data for effective gene function prediction
LSMM: a statistical approach to integrating functional annotations with genome-wide association studies
Gene structure prediction using information on homologous protein sequence
Mixture models for protein structure ensembles
An event-driven approach for studying gene block evolution in bacteria
A representation model for biological entities by fusing structured axioms with unstructured texts
samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files
PrimAlign: PageRank-inspired Markovian alignment for large biological networks
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning
iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
MOCAT2: a metagenomic assembly, annotation and profiling framework
Statistical significance of variables driving systematic variation in high-dimensional data
HOMELETTE: a unified interface to homology modelling software
Error control variability in pathway-based microarray analysis
SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures
TOPAS: network-based structural alignment of RNA sequences
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks
CABEAN: a software for the control of asynchronous Boolean networks
HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs
Evaluation of ontology development tools for bioinformatics
GMD@CSB.DB: the Golm Metabolome Database
LocusZoom: regional visualization of genome-wide association scan results
SolupHred: a server to predict the pH-dependent aggregation of intrinsically disordered proteins
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
DeOri: a database of eukaryotic DNA replication origins
SPHINX - an algorithm for taxonomic binning of metagenomic sequences
SeqExpress: desktop analysis and visualization tool for gene expression experiments
ArchTEx: accurate extraction and visualization of next-generation sequence data
Determining epitope specificity of T-cell receptors with transformers
NIAPU: network-informed adaptive positive-unlabeled learning for disease gene identification
scrm: efficiently simulating long sequences using the approximated coalescent with recombination
SCOTCH: subtype A coreceptor tropism classification in HIV-1
3D flow field estimation and assessment for live cell fluorescence microscopy
DiNAMIC.Duo: detecting somatic DNA copy number differences without a normal reference
iPHACE: integrative navigation in pharmacological space
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors
SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings
Improving the performance of minimizers and winnowing schemes
Bayesian modelling of shared gene function
ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems
RiboTools: a Galaxy toolbox for qualitative ribosome profiling analysis
TiMEx: a waiting time model for mutually exclusive cancer alterations
miRNACancerMAP: an integrative web server inferring miRNA regulation network for cancer
Vfold-Pipeline: a web server for RNA 3D structure prediction from sequences
XGDAG: explainable gene-disease associations via graph neural networks
Estimating DNA coverage and abundance in metagenomes using a gamma approximation
OrderedList - a bioconductor package for detecting similarity in ordered gene lists
displayHTS: a R package for displaying data and results from high-throughput screening experiments
GeneScissors: a comprehensive approach to detecting and correcting spurious transcriptome inference owing to RNA-seq reads misalignment