yusuke1997/dblp-id-title huggingface dataset:
ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells
Large-scale exploration and analysis of drug combinations
polyDFEv2.0: testing for invariance of the distribution of fitness effects within and across species
Family specific rates of protein evolution
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations
Patika web : a Web interface for analyzing biological pathways through advanced querying and visualization
Dealing with sparse data in predicting outcomes of HIV combination therapies
accuMUlate: a mutation caller designed for mutation accumulation experiments
SSuMMo: rapid analysis, comparison and visualization of microbial communities
A novel web server predicts amino acid residue protection against hydrogen-deuterium exchange
Phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories revealed by AI-MiXeR
REMORA: a pilot in the ocean of BioMoby web-services
Growth in Bioinformatics
The use of structure information to increase alignment accuracy does not aid homologue detection with profile HMMs
Bi-correlation clustering algorithm for determining a set of co-regulated genes
Identifying differentially methylated sites in samples with varying tumor purity
The MIPS mammalian protein?Cprotein interaction database
massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation
HyDRA: gene prioritization via hybrid distance-score rank aggregation
PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences
C3D: a tool to predict 3D genomic interactions between cis-regulatory elements
A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens
Enumeration of condition-dependent dense modules in protein interaction networks
SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error
GAzer: gene set analyzer
GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity
Determining the minimum number of types necessary to represent the sizes of protein atoms
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization
Bioinformatics challenges for personalized medicine
Succinct colored de Bruijn graphs
Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes
Protein homology detection by HMM?CHMM comparison
SensSB: a software toolbox for the development and sensitivity analysis of systems biology models
A coalescent-based method for population tree inference with haplotypes
BSeQC: quality control of bisulfite sequencing experiments
Integrating multi-attribute similarity networks for robust representation of the protein space
Integrating genomic correlation structure improves copy number variations detection
Mixture models for analysis of the taxonomic composition of metagenomes
Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana
Drug repositioning through integration of prior knowledge and projections of drugs and diseases
Particle Gibbs sampling for Bayesian phylogenetic inference
scCross: efficient search for rare subpopulations across multiple single-cell samples
Persistent voids: a new structural metric for membrane fusion
Epiviz File Server: Query, transform and interactively explore data from indexed genomic files
MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing
Protein homology reveals new targets for bioactive small molecules
circDeep: deep learning approach for circular RNA classification from other long non-coding RNA
Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships
E-Pedigrees: a large-scale automatic family pedigree prediction application
A method for subtype analysis with somatic mutations
Exploration of conformational transition pathways from coarse-grained simulations
MeQA: a pipeline for MeDIP-seq data quality assessment and analysis
StatQuant: a post-quantification analysis toolbox for improving quantitative mass spectrometry
FastEpistasis: a high performance computing solution for quantitative trait epistasis
scHiCPTR: unsupervised pseudotime inference through dual graph refinement for single-cell Hi-C data
Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays
The 2025 Outstanding Contributions to ISCB Award - Dr Lucia Peixoto
PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem
An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems
A compressive seeding algorithm in conjunction with reordering-based compression
Conditional out-of-distribution generation for unpaired data using transfer VAE
Choosing BLAST options for better detection of orthologs as reciprocal best hits
Make Interactive Complex Heatmaps in R
A web server for inferring the human N -acetyltransferase-2 (NAT2) enzymatic phenotype from NAT2 genotype
Financing a future for public biological data
Matched Forest: supervised learning for high-dimensional matched case-control studies
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
PamgeneAnalyzeR: open and reproducible pipeline for kinase profiling
Predicting DNA recognition by Cys 2 His 2 zinc finger proteins
AnaGram: protein function assignment
BEESEM: estimation of binding energy models using HT-SELEX data
Comparing bioassay response and similarity ensemble approaches to probing protein pharmacology
Prediction of potential disease-associated microRNAs based on random walk
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments
Sausage: protein threading with flexible force fields
AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison
DEEPrior: a deep learning tool for the prioritization of gene fusions
DeepMHCI: an anchor position-aware deep interaction model for accurate MHC-I peptide binding affinity prediction
Rabifier2: an improved bioinformatic classifier of Rab GTPases
Discriminative modelling of context-specific amino acid substitution probabilities
Benefits of dimension reduction in penalized regression methods for high-dimensional grouped data: a case study in low sample size
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
statgenMPP : an R package implementing an IBD-based mixed model approach for QTL mapping in a wide range of multi-parent populations
MultiNEP: a multi-omics network enhancement framework for prioritizing disease genes and metabolites simultaneously
MACE: mutation-oriented profiling of chemical response and gene expression in cancers
RNA interaction format: a general data format for RNA interactions
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements
UniGene Tabulator: a full parser for the UniGene format
scFeatures: multi-view representations of single-cell and spatial data for disease outcome prediction
Improving biomedical named entity recognition by dynamic caching inter-sentence information
DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins
PhaGAA: an integrated web server platform for phage genome annotation and analysis
ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities
AMPer: a database and an automated discovery tool for antimicrobial peptides
VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing
TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions
Identifying related journals through log analysis
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation
PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model
A feed-forward loop guarantees robust behavior in Escherichia coli carbohydrate uptake
Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus
Information-incorporated gene network construction with FDR control
Bayesian metabolic flux analysis reveals intracellular flux couplings
Functionally guided alignment of protein interaction networks for module detection
POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix
Seqalert - a daily sequence alertness server for the EMBL and SWISSPROT databases
MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit
FILTREST3D: discrimination of structural models using restraints from experimental data
Sharing and executing linked data queries in a collaborative environment
Modeling multi-scale data via a network of networks
SCATTER: a program to correct UV spectra recorded with an LKB Ultrospec interfaced to an Apple IIe for light scattering by particles or aggregates
Learning structural motif representations for efficient protein structure search
Web-based GeneChip analysis system for large-scale collaborative projects
Variomes: a high recall search engine to support the curation of genomic variants
Supersplat - spliced RNA-seq alignment
Maximum likelihood estimation of quantitative trait loci parameters with the aid of genetic markers using a standard statistical package
STOCHSIM: modelling of stochastic biomolecular processes
PRIMEGEN, a tool for designing primers from multiple alignments
Co-evolutionary distance predictions contain flexibility information
Inferring subgroup-specific driver genes from heterogeneous cancer samples via subspace learning with subgroup indication
A novel strategy for dynamic modeling of genome-scale interaction networks
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes
PM - protein music
Exploring the structure and function of temporal networks with dynamic graphlets
Bayesian networks for mass spectrometric metabolite identification via molecular fingerprints
CROP: correlation-based reduction of feature multiplicities in untargeted metabolomic data
Continuous chromatin state feature annotation of the human epigenome
FoldX force field revisited, an improved version
pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments
Support vector machine classification on the web
Evaluation of iterative alignment algorithms for multiple alignment
GENECOUNTING: haplotype analysis with missing genotypes
DROP: an SVM domain linker predictor trained with optimal features selected by random forest
Modeling nonlinearity in dilution design microarray data
quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes
Inferring gene targets of drugs and chemical compounds from gene expression profiles
Geometric potentials from deep learning improve prediction of CDR H3 loop structures
REALGAR: a web app of integrated respiratory omics data
PhyLAT: a phylogenetic local alignment tool
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies
A reference database for circular dichroism spectroscopy covering fold and secondary structure space
Discover regulatory DNA elements using chromatin signatures and artificial neural network
A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
A system-level analysis of patient disease trajectories based on clinical, phenotypic and molecular similarities
Atlas: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages
Unsupervised feature selection under perturbations: meeting the challenges of biological data
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
Inference of the human polyadenylation code
Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes
Enriched random forests
BLAST Search Updater: a notification system for new database matches
PHi-C2: interpreting Hi-C data as the dynamic 3D genome state
PVAAS: identify variants associated with aberrant splicing from RNA-seq
SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal
Comparative ab initio prediction of gene structures using pair HMMs
SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra
LDmat: efficiently queryable compression of linkage disequilibrium matrices
ConSpeciFix: classifying prokaryotic species based on gene flow
CaMelia: imputation in single-cell methylomes based on local similarities between cells
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs
PDQ Wizard: automated prioritization and characterization of gene and protein lists using biomedical literature
GSDS 2.0: an upgraded gene feature visualization server
When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants
Straightening Caenorhabditis elegans images
Papers on normalization, variable selection, classification or clustering of microarray data
A BASIC program on heterokaryosis and survival in Phycomyces
Comparison of various algorithms for recognizing short coding sequences of human genes
KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure
Succinct data structures for assembling large genomes
Enhancing the prediction of disease-gene associations with multimodal deep learning
Sequanix: a dynamic graphical interface for Snakemake workflows
Genetic algorithm-based optimization of hydrophobicity tables
The role of miRNAs in complex formation and control
Correction to: Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions
HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature
IsoTools: a flexible workflow for long-read transcriptome sequencing analysis
Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets
Silent DNA: speaking RNA language?
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments
Mechanotransduction map: simulation model, molecular pathway, gene set
AIONER: all-in-one scheme-based biomedical named entity recognition using deep learning
The Burkholderia Genome Database: facilitating flexible queries and comparative analyses
A consensus procedure for predicting the location of alpha-helical transmembrane segments in proteins
Detection of de novo copy number deletions from targeted sequencing of trios
Combo: a whole genome comparative browser
Struo: a pipeline for building custom databases for common metagenome profilers
CoPE: a collaborative pedigree drawing environment
PIPENN: protein interface prediction from sequence with an ensemble of neural nets
SNPicker: a graphical tool for primer picking in designing mutagenic endonuclease restriction assays
Snoopy - a unifying Petri net framework to investigate biomolecular networks
Efficient exact inference for dynamical systems with noisy measurements using sequential approximate Bayesian computation
BioPAX-Parser: parsing and enrichment analysis of BioPAX pathways
Inference attacks against differentially private query results from genomic datasets including dependent tuples
CnnPOGTP: a novel CNN-based predictor for identifying the optimal growth temperatures of prokaryotes using only genomic k -mers distribution
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects
A multiobjective memetic algorithm for PPI network alignment
Transcription regulatory region analysis using signal detection and fuzzy clustering
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data
Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models
Network inference using steady-state data and Goldbeter-Koshland kinetics
Multiple testing on the directed acyclic graph of gene ontology
Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier
BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network
Enhancing Hi-C contact matrices for loop detection with Capricorn: a multiview diffusion model
Inference of gene regulatory networks from genome-wide knockout fitness data
Representation of amino acids as five-bit or three-bit patterns for filtering protein databases
SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting
Algorithms for optimal protein structure alignment
Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
Correction to: Prediction of gene co-expression from chromatin contacts with graph attention network
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks
scHLAcount: allele-specific HLA expression from single-cell gene expression data
GWAR: robust analysis and meta-analysis of genome-wide association studies
A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection
Construction of co-complex score matrix for protein complex prediction from AP-MS data
Protein pocket detection via convex hull surface evolution and associated Reeb graph
Inferring gene regulatory networks from multiple microarray datasets
PS-Net: human perception-guided segmentation network for EM cell membrane
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization
A Bayesian model for single cell transcript expression analysis on MERFISH data
Sipros/ProRata: a versatile informatics system for quantitative community proteomics
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF)
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure
Negative correlation between compositional symmetries and local recombination rates
cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats
A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
TissueEnrich: Tissue-specific gene enrichment analysis
HPODNets: deep graph convolutional networks for predicting human protein-phenotype associations
A novel means of using gene clusters in a two-step empirical Bayes method for predicting classes of samples
Taverna: a tool for the composition and enactment of bioinformatics workflows
Graph contextualized attention network for predicting synthetic lethality in human cancers
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
CYBERTRACK2.0: zero-inflated model-based cell clustering and population tracking method for longitudinal mass cytometry data
keeSeek: searching distant non-existing words in genomes for PCR-based applications
Modeling cell proliferation in human acute myeloid leukemia xenografts
ArchSchema: a tool for interactive graphing of related Pfam domain architectures
Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics
Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences
MGV: a generic graph viewer for comparative omics data
Fun&Co: identification of key functional differences in transcriptomes
TAXOKEY: a universal taxonomic key program using DOS text files and graphics
Sawfish: improving long-read structural variant discovery and genotyping with local haplotype modeling
Classification with correlated features: unreliability of feature ranking and solutions
MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation
Crumble: reference free lossy compression of sequence quality values
SATINN: an automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants
Assessment of phylogenomic and orthology approaches for phylogenetic inference
PERMOL: restraint-based protein homology modeling using DYANA or CNS
rehh : an R package to detect footprints of selection in genome-wide SNP data from haplotype structure
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy
Genetic fine-mapping from summary data using a nonlocal prior improves the detection of multiple causal variants
Harnessing virtual machines to simplify next-generation DNA sequencing analysis
CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
BreakPoint Surveyor: a pipeline for structural variant visualization
The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis
Benchmarking table recognition performance on biomedical literature on neurological disorders
PrimeArray: genome-scale primer design for DNA-microarray construction
HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification
eCAMI: simultaneous classification and motif identification for enzyme annotation
A microcomputer network for biochemistry
siDRM : an effective and generally applicable online siRNA design tool
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions
Target prediction and a statistical sampling algorithm for RNA-RNA interaction
Estimation of speciation times under the multispecies coalescent
A cross-comparison of a large dataset of genes
ImmunoTar - integrative prioritization of cell surface targets for cancer immunotherapy
fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences
Gathering insights on disease etiology from gene expression profiles of healthy tissues
Literome: PubMed-scale genomic knowledge base in the cloud
DICHROWEB: an interactive website for the analysis of protein secondary structure from circular dichroism spectra
A biclustering algorithm for extracting bit-patterns from binary datasets
KGBassembler: a karyotype-based genome assembler for Brassicaceae species