yusuke1997/dblp-id-title huggingface dataset:
DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding
Cyclone: java-based querying and computing with Pathway/Genome databases
LALNVIEW: a graphical viewer for pairwise sequence alignments
Sungear: interactive visualization and functional analysis of genomic datasets
Cluster Locator, online analysis and visualization of gene clustering
GIS: a biomedical text-mining system for gene information discovery
Inferring pairwise regulatory relationships from multiple time series datasets
Characterization of 1 H NMR spectroscopic data and the generation of synthetic validation sets
The COMER web server for protein analysis by homology
A software tool for the analysis of mass spectrometric disulfide mapping experiments
Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph
THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Supervised capacity preserving mapping: a clustering guided visualization method for scRNA-seq data
Boltzmann probability of RNA structural neighbors and riboswitch detection
Visualization for genomics: the Microbial Genome Viewer
Globally optimal stitching of tiled 3D microscopic image acquisitions
Platform-integrated mRNA isoform quantification
The 2025 ISCB Innovator Award - Dr Fabian Theis
queryMed: Semantic Web functions for linking pharmacological and medical knowledge to data
GoArrays: highly dynamic and efficient microarray probe design
RCNPRED: prediction of the residue co-ordination numbers in proteins
Structural variant analysis for linked-read sequencing data with gemtools
SIGNAL SCAN 4.0: additional databases and sequence formats
QuickJoin - fast neighbour-joining tree reconstruction
Non-parametric individual treatment effect estimation for survival data with random forests
Kmer-SSR: a fast and exhaustive SSR search algorithm
A UIMA wrapper for the NCBO annotator
TreeQTL: hierarchical error control for eQTL findings
The frequency of oligonucleotides in mammalian genic regions
MolClustPy: a Python package to characterize multivalent biomolecular clusters
Conformational sampling and structure prediction of multiple interacting loops in soluble and β -barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method
CellML2SBML: conversion of CellML into SBML
Isoform function prediction by Gene Ontology embedding
Model-based clustering of microarray expression data via latent Gaussian mixture models
FGDP: functional genomics data pipeline for automated, multiple microarray data analyses
Biological applications of the SAS system: an overview
ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy
Causal network perturbations for instance-specific analysis of single cell and disease samples
CEDIT: a C interface and macro facility for protein sequence alignment editing in colour with Microsoft Word 5.0 for PCs
CopyMap: localization and calling of copy number variation by joint analysis of hybridization data from multiple individuals
An ensemble correlation-based gene selection algorithm for cancer classification with gene expression data
Selecting signature oligonucleotides to identify organisms using DNA arrays
A fast data-driven method for genotype imputation, phasing and local ancestry inference: MendelImpute.jl
Impact of lossy compression of nanopore raw signal data on basecalling and consensus accuracy
SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
Modeling sample variables with an Experimental Factor Ontology
SignalViewer: analyzing microarray images
Partition-distance via the assignment problem
Omics AnalySIs System for PRecision Oncology (OASISPRO): a web-based omics analysis tool for clinical phenotype prediction
ArrayNorm: comprehensive normalization and analysis of microarray data
Efficient clustering of identity-by-descent between multiple individuals
New scoring schemes for protein fold recognition based on Voronoi contacts
HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins
Structure-based variable selection for survival data
MVSF-AB: accurate antibody-antigen binding affinity prediction via multi-view sequence feature learning
Local structural disorder imparts plasticity on linear motifs
scSGL: kernelized signed graph learning for single-cell gene regulatory network inference
Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities
An application of a relational database system for high-throughput prediction of elemental compositions from accurate mass values
aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data
A simple and efficient algorithm for gene selection using sparse logistic regression
IRiS: Construction of ARG networks at genomic scales
Boosting automatic event extraction from the literature using domain adaptation and coreference resolution
NavMol 3.0: enabling the representation of metabolic reactions by blind users
A strategy for assembling the maize (Zea mays L.) genome
SpliceTrap: a method to quantify alternative splicing under single cellular conditions
Sequence tagging for biomedical extractive question answering
DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins
scEpath: energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data
NGScloud: RNA-seq analysis of non-model species using cloud computing
MAGIC: access portal to a cross-platform gene expression compendium for maize
A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes
Shu: visualization of high-dimensional biological pathways
Identifying periodically expressed transcripts in microarray time series data
Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines
2023 ISCB Overton Prize: Jingyi Jessica Li
Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces
eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments
ClusterMap: compare multiple single cell RNA-Seq datasets across different experimental conditions
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments
Effective design and inference for cell sorting and sequencing based massively parallel reporter assays
DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data
Protein-protein interaction specificity is captured by contact preferences and interface composition
eSBMTools 1.0: enhanced native structure-based modeling tools
A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations
MiSearch adaptive pubMed search tool
A fast algorithm for counting the arrangements for packing identical items on a one-dimensional grid with application in DNA-protein and similar interactions
The Poisson Index: a new probabilistic model for protein-ligand binding site similarity
ClaNC: point-and-click software for classifying microarrays to nearest centroids
AMIGOS III: pseudo-torsion angle visualization and motif-based structure comparison of nucleic acids
Virtifier: a deep learning-based identifier for viral sequences from metagenomes
A novel signal processing approach for the detection of copy number variations in the human genome
Dual Attention and Patient Similarity Network for drug recommendation
GPseudoRank: a permutation sampler for single cell orderings
Planform: an application and database of graph-encoded planarian regenerative experiments
VitaPad: visualization tools for the analysis of pathway data
Simultaneous search for multiple QTL using the global optimization algorithm DIRECT
Hidden conformations in protein structures
MorphoTools2: an R package for multivariate morphometric analysis
Block HSIC Lasso: model-free biomarker detection for ultra-high dimensional data
Quantification of spatial tumor heterogeneity in immunohistochemistry staining images
ChromoWheel: a new spin on eukaryotic chromosome visualization
PASS: prediction of activity spectra for biologically active substances
TRFBA: an algorithm to integrate genome-scale metabolic and transcriptional regulatory networks with incorporation of expression data
Evaluating and improving cDNA sequence quality with cQC
Reference-independent comparative metagenomics using cross-assembly: crAss
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis
DELIMINATE - a fast and efficient method for loss-less compression of genomic sequences: Sequence analysis
MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification
COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer
ALEA: a toolbox for allele-specific epigenomics analysis
PoPMuSiC, rationally designing point mutations in protein structures
SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides
swissPIT: a novel approach for pipelined analysis of mass spectrometry data
lncFunTK: a toolkit for functional annotation of long noncoding RNAs
COPASI - a COmplex PAthway SImulator
Adaptive boosting-based computational model for predicting potential miRNA-disease associations
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery
Predicting small ligand binding sites in proteins using backbone structure
Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
Using coalitional games on biological networks to measure centrality and power of genes
A simple procedure for estimating the false discovery rate
Priors for genotyping polyploids
The code structure of the p53 DNA-binding domain and the prognosis of breast cancer patients
CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes
RepeatFS: a file system providing reproducibility through provenance and automation
Data Safe Havens in health research and healthcare
AutoDC: an automatic machine learning framework for disease classification
SVIM: structural variant identification using mapped long reads
The Z curve database: a graphic representation of genome sequences
PPTPP: a novel therapeutic peptide prediction method using physicochemical property encoding and adaptive feature representation learning
Efficient construction of an assembly string graph using the FM-index
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
BayesPeak - an R package for analysing ChIP-seq data
Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies
SMSSVD: SubMatrix Selection Singular Value Decomposition
Interactive gene networks with KNIT
Rule-based system for the fast identification of species of Indian Anopheline mosquitoes
iMapper : a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes
SIRAH tools: mapping, backmapping and visualization of coarse-grained models
Adjusting for gene-specific covariates to improve RNA-seq analysis
NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis
Haplotype reconstruction from genotype data using Imperfect Phylogeny
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum
Guiding discovery of protein sequence-structure-function modeling
VSDocker: a tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters
A new rule-based algorithm for identifying metabolic markers in prostate cancer using tandem mass spectrometry
CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing
The NCTU BioInfo Archive of biological data sets for bioinformatics research and experimentation
Automatic extraction of angiogenesis bioprocess from text
Greedily building protein networks with confidence
A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays
A comprehensive computational model of facilitated diffusion in prokaryotes
GandrKB--ontological microarray annotation and visualization
Consensus alignment for reliable framework prediction in homology modeling
Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics
Multiple instance learning of Calmodulin binding sites
switchBox: an R package for k-Top Scoring Pairs classifier development
Tree-guided Bayesian inference of population structures
GLIDE: combining local methods and diffusion state embeddings to predict missing interactions in biological networks
SATORI: a system for ontology-guided visual exploration of biomedical data repositories
Exploring the predictive power of polygenic scores derived from genome-wide association studies: a study of 10 complex traits
Overcoming selection bias in synthetic lethality prediction
Methods for combining peptide intensities to estimate relative protein abundance
GeneNoteBook, a collaborative notebook for comparative genomics
A fast and exhaustive method for heterogeneity and epistasis analysis based on multi-objective optimization
SHREC: a short-read error correction method
GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies
MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow
IMAGEne I: clustering and ranking of I.M.A.G.E. cDNA clones corresponding to known genes
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
RNA-Seq analysis in MeV
Adaptive algorithm of automated annotation
Biomartr: genomic data retrieval with R
Homology modeling, model and software evaluation: three related resources
Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE
FASTPAT: a fast and efficient algorithm for string searching in DNA sequences
Information theoretical probe selection for hybridisation experiments
Guided interactive image segmentation using machine learning and color-based image set clustering
Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome
Corrigendum to: NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
PhosD: inferring kinase-substrate interactions based on protein domains
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity
Recombinational DSBs-intersected genes converge on specific disease- and adaptability-related pathways
geck: trio-based comparative benchmarking of variant calls
PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization
Functional embedding for the classification of gene expression profiles
SiNoPsis: Single Nucleotide Polymorphisms selection and promoter profiling
Motif-based searching in TOPS protein topology databases
Prestige centrality-based functional outlier detection in gene expression analysis
TopPred II: an improved software for membrane protein structure predictions
Impact of ontology evolution on functional analyses
Weighted pooling - practical and cost-effective techniques for pooled high-throughput sequencing
A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
runibic: a Bioconductor package for parallel row-based biclustering of gene expression data
microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization
LASER server: ancestry tracing with genotypes or sequence reads
Icarus: visualizer for de novo assembly evaluation
Interpolated markov chains for eukaryotic promoter recognition
powsimR: power analysis for bulk and single cell RNA-seq experiments
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data
QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays
INPS: predicting the impact of non-synonymous variations on protein stability from sequence
Déjà vu - A study of duplicate citations in Medline
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification
COMPAM : visualization of combining pairwise alignments for multiple genomes
On the application of integer arithmetic in nucleotide sequence analysis
HiCNorm: removing biases in Hi-C data via Poisson regression
PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
SoFIA: a data integration framework for annotating high-throughput datasets
A fractional programming approach to efficient DNA melting temperature calculation
DISOPRED3: precise disordered region predictions with annotated protein-binding activity
Bayesian network feature finder (BANFF): an R package for gene network feature selection
Improved indel detection in DNA and RNA via realignment with ABRA2
P-SEA: a new efficient assignment of secondary structure from C alpha trace of proteins
Simulating psoriasis by altering transit amplifying cells
RNA secondary structure diagrams for very large molecules: RNAfdl
CaGE: Cardiac gene expression knowledgebase
Marker controlled superpixel nuclei segmentation and automatic counting on immunohistochemistry staining images
Design and implementation of a mosquito database through an entomological ontology
A general computational model of mitochondrial metabolism in a whole organelle scale
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices
Fast detection of differential chromatin domains with SCIDDO
3DRobot: automated generation of diverse and well-packed protein structure decoys
REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data
DCARS: differential correlation across ranked samples
Technical comment to "Database verification studies of SWISS-PROT and GenBank" by Karp et al
Visual and statistical comparison of metagenomes
ADGO: analysis of differentially expressed gene sets using composite GO annotation
T-Gene: improved target gene prediction
High-accuracy prediction of transmembrane inter-helix contacts and application to GPCR 3D structure modeling
Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer
SNPsFinder - a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes
A penalized regression approach to haplotype reconstruction of viral populations arising in early HIV/SIV infection
AStrap: identification of alternative splicing from transcript sequences without a reference genome
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision
Bayesian inference of fitness landscapes via tree-structured branching processes
Calculating the SNP-effective sample size from an alignment
Robust parameter estimation for dynamical systems from outlier-corrupted data
Predicting RNA H-type pseudoknots with the massively parallel genetic algorithm
From Sequence to Biology: The Impact on Bioinformatics
PanTools: representation, storage and exploration of pan-genomic data
Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python
Optimal contact map alignment of protein-protein interfaces
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs
Incorporating spatial-anatomical similarity into the VGWAS framework for AD biomarker detection
Wrapping SRS with CORBA: from textual data to distributed objects
Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing
PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions
Effector-GAN: prediction of fungal effector proteins based on pretrained deep representation learning methods and generative adversarial networks
SAGE2: parallel human genome assembly
An accessible database for mouse and human whole transcriptome qPCR primers
iGRLDTI: an improved graph representation learning method for predicting drug-target interactions over heterogeneous biological information network
Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming
SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms
scAMACE: model-based approach to the joint analysis of single-cell data on chromatin accessibility, gene expression and methylation
Advancing PICO element detection in biomedical text via deep neural networks
Biologistics - Diffusion coefficients for complete proteome of Escherichia coli
qsubsec: a lightweight template system for defining sun grid engine workflows
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation
NACHO: an R package for quality control of NanoString nCounter data
EWAS: epigenome-wide association study software 2.0
Dynamically weighted clustering with noise set
EMPReSS: European Mouse Phenotyping Resource for Standardized Screens
Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points
Detection of orthologous exons and isoforms using EGIO
Lung cancer subtype diagnosis using weakly-paired multi-omics data
Correction of sequence-based artifacts in serial analysis of gene expression
Limitations of Augustinsson plots
AggreRATE-Pred: a mathematical model for the prediction of change in aggregation rate upon point mutation
Classification using partial least squares with penalized logistic regression
DNA assembly with gaps (Dawg): simulating sequence evolution
MHCBN: a comprehensive database of MHC binding and non-binding peptides
Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers
MICC: an R package for identifying chromatin interactions from ChIA-PET data
SurreyFBA: a command line tool and graphics user interface for constraint-based modeling of genome-scale metabolic reaction networks
lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes
Non-linear tests for identifying differentially expressed genes or genetic networks
Phantom: investigating heterogeneous gene sets in time-course data
Fast identification of differential distributions in single-cell RNA-sequencing data with waddR