yusuke1997/dblp-id-title huggingface dataset:
Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors
UCHIME improves sensitivity and speed of chimera detection
A note on difficult structure alignment problems
RENT+: an improved method for inferring local genealogical trees from haplotypes with recombination
CAPLA: improved prediction of protein-ligand binding affinity by a deep learning approach based on a cross-attention mechanism
A fast and robust statistical test based on likelihood ratio with Bartlett correction to identify Granger causality between gene sets
Designing a general method for predicting the regulatory relationships between long noncoding RNAs and protein-coding genes based on multi-omics characteristics
MaxBench: evaluation of sequence and structure comparison methods
UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples
Ultra-fast scalable estimation of single-cell differentiation potency from scRNA-Seq data
BALL-SNPgp - from genetic variants toward computational diagnostics
A boosting approach to structure learning of graphs with and without prior knowledge
Implementation of a gene expression index calculation method based on the PDNN model
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites
Threshold Average Precision (TAP- k ): a measure of retrieval designed for bioinformatics
A comparison of cluster analysis methods using DNA methylation data
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data
Estimating the activity of transcription factors by the effect on their target genes
scAce: an adaptive embedding and clustering method for single-cell gene expression data
Ontology development for biological systems: immunology
Modified signal-to-noise: a new simple and practical gene filtering approach based on the concept of projective adaptive resonance theory (PART) filtering method
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
Formalizing concepts of species, sex and developmental stage in anatomical ontologies
A bioimage informatics approach to automatically extract complex fungal networks
Tiki, at the head of a new superfamily of enzymes
Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions
DNABarcodes: an R package for the systematic construction of DNA sample tags
CX, an algorithm that identifies protruding atoms in proteins
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
Correction to: Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization
MOCCASIN: converting MATLAB ODE models to SBML
Multiobjective multifactor dimensionality reduction to detect SNP-SNP interactions
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein-protein complexes upon mutation
Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation
Modeling stochasticity and robustness in gene regulatory networks
An automatic method for CASP9 free modeling structure prediction assessment
Improved prediction of protein-Cprotein binding sites using a support vector machines approach
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
Accounting for pairwise distance restraints in FFT-based protein-protein docking
Comparison of methods for phylogenetic B-cell lineage inference using time-resolved antibody repertoire simulations (AbSim)
A system-level approach for deciphering the transcriptional response to prion infection
The Bioinformatics Template Library-generic components for biocomputing
A combinatorial approach to graphlet counting
Genome-wide detection of intervals of genetic heterogeneity associated with complex traits
MetaSMC: a coalescent-based shotgun sequence simulator for evolving microbial populations
Census 2: isobaric labeling data analysis
Gating mass cytometry data by deep learning
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
Extending the method of mathematically controlled comparison to include numerical comparisons
Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction
ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences
Multiscale reaction-diffusion simulations with Smoldyn
Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification
Powerful and efficient SNP-set association tests across multiple phenotypes using GWAS summary data
Thalia: semantic search engine for biomedical abstracts
Identifying differentially expressed proteins in two-dimensional electrophoresis experiments: inputs from transcriptomics statistical tools
A Novel method for similarity analysis and protein sub-cellular localization prediction
3dRPC: a web server for 3D RNA-protein structure prediction
PEMT: a patent enrichment tool for drug discovery
Genome-wide search of nucleosome patterns using visual analytics
TranScout: prediction of gene expression regulatory proteins from their sequences
interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots
GetBonNie for building, analyzing and sharing rule-based models
Long-term context-dependent genetic adaptation of the viral genetic cloud
GC3-biased gene domains in mammalian genomes
HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen-Deuterium Exchange Mass-Spectrometry datasets of different protein states
Statistical alignment based on fragment insertion and deletion models
Implicit motif distribution based hybrid computational kernel for sequence classification
fastp: an ultra-fast all-in-one FASTQ preprocessor
TSSub: eukaryotic protein subcellular localization by extracting features from profiles
Canvas: versatile and scalable detection of copy number variants
BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals
Curation and annotation of planarian gene expression patterns with segmented reference morphologies
Reduced space sequence alignment
Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data
A rapid computer technique for analysing molecular interactions
GRACKLE: an interpretable matrix factorization approach for biomedical representation learning
Accelerating Bayesian inference for evolutionary biology models
MEGA-V: detection of variant gene sets in patient cohorts
sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies
Design of a DNA chip for detection of unknown genetically modified organisms (GMOs)
Positional integratomic approach in identification of genomic candidate regions for Parkinson's disease
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data
Automatic assignment of reaction operators to enzymatic reactions
RegaDB: community-driven data management and analysis for infectious diseases
Molecular generation strategy and optimization based on A2C reinforcement learning in de novo drug design
High-throughput prediction of protein antigenicity using protein microarray data
Mediation analysis for survival data with high-dimensional mediators
A program for template matching of protein sequences
Detecting two-locus associations allowing for interactions in genome-wide association studies
MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly
CGARS: cancer genome analysis by rank sums
Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm
FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences
STAMP: statistical analysis of taxonomic and functional profiles
SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes
eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE)
BiTrinA - multiscale binarization and trinarization with quality analysis
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data
DiffPaSS - high-performance differentiable pairing of protein sequences using soft scores
aRrayLasso: a network-based approach to microarray interconversion
On the relation between input and output distributions of scRNA-seq experiments
SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology
MetExtract: a new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals in metabolomics research
ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy
Discriminative pattern discovery for the characterization of different network populations
BamSnap: a lightweight viewer for sequencing reads in BAM files
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter
IntSide: a web server for the chemical and biological examination of drug side effects
Methods for comparing a DNA sequence with a protein sequence
maTE: discovering expressed interactions between microRNAs and their targets
SequenceLDhot: detecting recombination hotspots
Significant sequence similarities in promoters and precursors of Arabidopsis thaliana non-conserved microRNAs
Weighting hidden Markov models for maximum discrimination
VARiD: A variation detection framework for color-space and letter-space platforms
A network-based zoning for parallel whole-cell simulation
HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data
Recoverable one-dimensional encoding of three-dimensional protein structures
Assessing protein coding region integrity in cDNA sequencing projects
easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations
Efficient parameterization of large-scale dynamic models based on relative measurements
An in silico model of LINE-1-mediated neoplastic evolution
Predicted dynamical couplings of protein residues characterize catalysis, transport and allostery
SAMStat 2: quality control for next generation sequencing data
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists
TRITON: a graphical tool for ligand-binding protein engineering
MedBlast: searching articles related to a biological sequence
How to optimally sample a sequence for rapid analysis
MDSubSampler: a posteriori sampling of important protein conformations from biomolecular simulations
IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach
Methods for calculating the probabilities of finding patterns in sequences
MS1FA: Shiny app for the annotation of redundant features in untargeted metabolomics datasets
DiagnoProt: a tool for discovery of new molecules by mass spectrometry
ProteoStats - a library for estimating false discovery rates in proteomics pipelines
GeneCluster 2.0: an advanced toolset for bioarray analysis
Robust relative compression of genomes with random access
VIZ-GRAIL: visualizing functional connections across disease loci
Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage
AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification
Molecular genetics and computer analyses
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences
Genetic network inference: from co-expression clustering to reverse engineering
ISMB/ECCB 2025 Proceedings
SoluProt: prediction of soluble protein expression in Escherichia coli
NCS: incorporating positioning data to quantify nucleosome stability in yeast
Attentive Variational Information Bottleneck for TCR-peptide interaction prediction
The 'shortmer' approach to nucleic acid sequence analysis. I: Computer simulation of sequencing projects to find economical primer sets
AlphaFold at CASP13
Identification of cancer driver genes in focal genomic aberrations from whole-exome sequencing data
REStLESS: automated translation of glycan sequences from residue-based notation to SMILES and atomic coordinates
PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping
GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
LinkinPath: from sequence to interconnected pathway
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method
Lnetwork: an efficient and effective method for constructing phylogenetic networks
FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution
Semblans: automated assembly and processing of RNA-seq data
SICOP : identifying significant co-interaction patterns
Efficient penalized generalized linear mixed models for variable selection and genetic risk prediction in high-dimensional data
Sensitive and fast mapping of di-base encoded reads
Reconstruction of genealogical relationships with applications to Phase III of HapMap
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data
enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways
A sequence comparison and gene expression data integration add-on for the Pathway Tools software
Dual multiple change-point model leads to more accurate recombination detection
EXPERFARM: a new package in BASIC for teaching genetics
Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization
PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes
An online database for the detection of novel archaeal sequences in human ESTs
DIPLOMO: the tool for a new type of evolutionary analysis
LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics
DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins
An iterative refinement algorithm for consistency based multiple structural alignment methods
Electrostatic potentials of proteins in water: a structured continuum approach
The LabelHash Server and Tools for substructure-based functional annotation
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis
rGREAT : an R/bioconductor package for functional enrichment on genomic regions
A deterministic motif finding algorithm with application to the human genome
Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers
Data-dependent bucketing improves reference-free compression of sequencing reads
Evaluation and optimization of clustering in gene expression data analysis
Clustering cDNA sequences
Compressed filesystem for managing large genome collections
Topological approximate Bayesian computation for parameter inference of an angiogenesis model
Computer-assisted restriction mapping: an integrated approach to handling experimental uncertainty
DIBS: a repository of disordered binding sites mediating interactions with ordered proteins
A knowledge-based scoring function to assess quaternary associations of proteins
DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways
SEAN: SNP prediction and display program utilizing EST sequence clusters
Accurate identification of orthologous segments among multiple genomes
monaLisa: an R/Bioconductor package for identifying regulatory motifs
RTFBSDB: an integrated framework for transcription factor binding site analysis
Methyl-Analyzer - whole genome DNA methylation profiling
Valid and invalid implementations of GOR secondary structure predictions
A review of feature selection techniques in bioinformatics
Cytoscape.js 2023 update: a graph theory library for visualization and analysis
Condition specific transcription factor binding site characterization in Saccharomyces cerevisiae
Methyl side-chain dynamics prediction based on protein structure
Multi-way relation-enhanced hypergraph representation learning for anti-cancer drug synergy prediction
Omics Pipe: a community-based framework for reproducible multi-omics data analysis
PyLasso: a PyMOL plugin to identify lassos
RRDB: a comprehensive and non-redundant benchmark for RNA-RNA docking and scoring
Statistical analysis of glycosylation profiles to compare tissue type and inflammatory disease state
Modeling sequence-sequence interactions for drug response
SIMFIT: a microcomputer software-toolkit for modelistic studies in biochemistry
ABC random forests for Bayesian parameter inference
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning
The emerging paradigm and open problems in comparative genomics
Quality classification of tandem mass spectrometry data
scKINETICS: inference of regulatory velocity with single-cell transcriptomics data
XRRpred: accurate predictor of crystal structure quality from protein sequence
DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug-target interactions
PRODECOMPv3: decompositions of NMR projections for protein backbone and side-chain assignments and structural studies
DNACompress: fast and effective DNA sequence compression
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads
LocusZoom.js: interactive and embeddable visualization of genetic association study results
From viral evolution to spatial contagion: a biologically modulated Hawkes model
DRUMMER - rapid detection of RNA modifications through comparative nanopore sequencing
OMEN: network-based driver gene identification using mutual exclusivity
A deeper look into transcription regulatory code by preferred pair distance templates for transcription factor binding sites
Mining and evaluation of molecular relationships in literature
Allergen Atlas: a comprehensive knowledge center and analysis resource for allergen information
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering
Graph-based consensus clustering for class discovery from gene expression data
Correction to: BIODICA: a computational environment for Independent Component Analysis of omics data
Genes related to differentiation are correlated with the gene regulatory network structure
Boolean network sketches: a unifying framework for logical model inference
CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm
Pooled variable scaling for cluster analysis
Automated image analysis for array hybridization experiments
Distribution of words with a predefined range of mismatches to a DNA probe in bacterial genomes
Rtpca: an R package for differential thermal proximity coaggregation analysis
Xwalk: computing and visualizing distances in cross-linking experiments
Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)
BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing
RTExtract: time-series NMR spectra quantification based on 3D surface ridge tracking
ScalaBLAST 2.0: rapid and robust BLAST calculations on multiprocessor systems
switchde: inference of switch-like differential expression along single-cell trajectories
Identifying and ranking potential driver genes of Alzheimer's disease using multiview evidence aggregation
Predicting GPCR-G-protein coupling using hidden Markov models
HangOut: generating clean PSI-BLAST profiles for domains with long insertions
scMAE: a masked autoencoder for single-cell RNA-seq clustering
IMSEQ - a fast and error aware approach to immunogenetic sequence analysis
Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING)
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis
Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows
JUMP: replicability analysis of high-throughput experiments with applications to spatial transcriptomic studies
Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities
Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review
Microarray data assembler
CASPAR: a hierarchical Bayesian approach to predict survival times in cancer from gene expression data
simurg: simulate bacterial pangenomes in R
Digitally predicting protein localization and manipulating protein activity in fluorescence images using 4D reslicing GAN
Functional integration of a metabolic network model and expression data without arbitrary thresholding
GeneNet: a gene network database and its automated visualization
Importing ArrayExpress datasets into R/Bioconductor
TCRpair: prediction of functional pairing between HLA-A*02: 01-restricted T-cell receptor α and β chains
Composition and abstraction of logical regulatory modules: application to multicellular systems
Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure
Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context
Sequoya: multiobjective multiple sequence alignment in Python
GenABEL: an R library for genome-wide association analysis
Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching
wiSDOM: a visual and statistical analytics for interrogating microbiome
PrISM: precision for integrative structural models
Inference of 3D genome architecture by modeling overdispersion of Hi-C data
DSEARCH: sensitive database searching using distributed computing
SEAL: a distributed short read mapping and duplicate removal tool
vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines
FRANz: reconstruction of wild multi-generation pedigrees
RxnBLAST: molecular scaffold and reactive chemical environment feature extractor for biochemical reactions
Sorad: a systems biology approach to predict and modulate dynamic signaling pathway response from phosphoproteome time-course measurements
Measuring covariation in RNA alignments: physical realism improves information measures
An ontology for biological function based on molecular interactions
PhyloMAd: efficient assessment of phylogenomic model adequacy