yusuke1997/dblp-id-title huggingface dataset:
Comparative evaluation of word composition distances for the recognition of SCOP relationships
Constrained mixture estimation for analysis and robust classification of clinical time series
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology
GenoProfiler: batch processing of high-throughput capillary fingerprinting data
ntEdit: scalable genome sequence polishing
Inferring signalling dynamics by integrating interventional with observational data
ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats
Imagene: an integrated computer environment for sequence annotation and analysis
Phylogenetic distances are encoded in networks of interacting pathways
Efficient searching and annotation of metabolic networks using chemical similarity
A learning-based framework for miRNA-disease association identification using neural networks
Automated segmentation and recognition of C. elegans whole-body cells
SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles
Enabling reproducible real-time quantitative PCR research: the RDML package
A Mathematical Programming Approach for Gene Selection and Tissue Classification
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks
Metabomxtr: an R package for mixture-model analysis of non-targeted metabolomics data
SCLpred: protein subcellular localization prediction by N-to-1 neural networks
MEpurity: estimating tumor purity using DNA methylation data
A regression framework incorporating quantitative and negative interaction data improves quantitative prediction of PDZ domain-peptide interaction from primary sequence
Phylogeny-based classification of microbial communities
SAIL - a software system for sample and phenotype availability across biobanks and cohorts
Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra
Single assay-wide variance experimental (SAVE) design for high-throughput screening
MPBLAST : improved BLAST performance with multiplexed queries
Comparative visualization of genetic and physical maps with Strudel
Prediction of splice sites with dependency graphs and their expanded bayesian networks
Predicting protein-DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver
Highly accurate classification of chest radiographic reports using a deep learning natural language model pre-trained on 3.8 million text reports
A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images
Evolutionary HMMs: a Bayesian approach to multiple alignment
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design
Figure summarizer browser extensions for PubMed Central
SimSeq: a nonparametric approach to simulation of RNA-sequence datasets
Correcting for ascertainment bias in the inference of population structure
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping
ORCO: Ollivier-Ricci Curvature-Omics - an unsupervised method for analyzing robustness in biological systems
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
Making whole genome multiple alignments usable for biologists
stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics
Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies
GNorm2: an improved gene name recognition and normalization system
MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences
CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation
Zero is not absence: censoring-based differential abundance analysis for microbiome data
A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns
Soap-HT-BLAST: high throughput BLAST based on Web services
INCA: a computational platform for isotopically non-stationary metabolic flux analysis
XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data
CscoreTool: fast Hi-C compartment analysis at high resolution
DualAligner: a dual alignment-based strategy to align protein interaction networks
Sparse multi-view matrix factorization: a multivariate approach to multiple tissue comparisons
GE-mini: a mobile APP for large-scale gene expression visualization
Explicit formulation of different receptor-G-protein interactions and effector regulation
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices
SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis
Scaling tree-based automated machine learning to biomedical big data with a feature set selector
CruzDB: software for annotation of genomic intervals with UCSC genome-browser database
AiO, combining DNA/protein programs and oligo-management
The discovery of transcriptional modules by a two-stage matrix decomposition approach
An Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
Statistical significance based on length and position of the local score in a model of i.i.d. sequences
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
A new era in bioimage informatics
Estimation of Transformation Parameters for Microarray Data
PANAL: an integrated resource for Protein sequence ANALysis
ExpressionView - an interactive viewer for modules identified in gene expression data
EASY-an Expert Analysis SYstem for interpreting database search outputs
EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
SNP cherry picker: maximizing the chance of finding an association with a disease SNP
FoldIndex copyright: a simple tool to predict whether a given protein sequence is intrinsically unfolded
A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data
Accounting for probe-level noise in principal component analysis of microarray data
A Brownian dynamics model for the chromatin fiber
Identification of aberrant chromosomal regions from gene expression microarray studies applied to human breast cancer
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes
SpatialQC: automated quality control for spatial transcriptome data
AVIA 3.0: interactive portal for genomic variant and sample level analysis
seqgra: principled selection of neural network architectures for genomics prediction tasks
LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations
DrDimont: explainable drug response prediction from differential analysis of multi-omics networks
Predicting the multi-label protein subcellular localization through multi-information fusion and MLSI dimensionality reduction based on MLFE classifier
Biological pathway kinetic rate constants are scale-invariant
PACdb: PolyA Cleavage Site and 3'-UTR Database
Consed: a graphical editor for next-generation sequencing
HiPub: translating PubMed and PMC texts to networks for knowledge discovery
Prediction of the translocon-mediated membrane insertion free energies of protein sequences
Identification of distant family relationships
RAMPART: a workflow management system for de novo genome assembly
A reinforcement-learning-based approach to enhance exhaustive protein loop sampling
TreeSnatcher: coding trees from images
ADSP - a new package for computational sequence analysis
Allele-specific multi-sample copy number segmentation in ASCAT
ProtVirDB: a database of protozoan virulent proteins
PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance
DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms
pdm_utils: a SEA-PHAGES MySQL phage database management toolkit
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences
Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime
DeepFold-PLM: accelerating protein structure prediction via efficient homology search using protein language models
PNL : a software to build polygenic risk scores using a super learner approach based on PairNet, a Convolutional Neural Network
Exome-based analysis for RNA epigenome sequencing data
Clumppling : cluster matching and permutation program with integer linear programming
ISD: a software package for Bayesian NMR structure calculation
DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants
Telogator: a method for reporting chromosome-specific telomere lengths from long reads
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs
Coverage-preserving sparsification of overlap graphs for long-read assembly
BinDash, software for fast genome distance estimation on a typical personal laptop
TRANSWESD: inferring cellular networks with transitive reduction
NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction
CRISPR-DO for genome-wide CRISPR design and optimization
Epigenomic annotation-based interpretation of genomic data: from enrichment analysis to machine learning
ChemSpot: a hybrid system for chemical named entity recognition
Identification of biochemical networks by S-tree based genetic programming
Reconstructing transcription factor activities in hierarchical transcription network motifs
A data-acquisition system for the analysis of the isometric tension generated by an electrically stimulated skeletal muscle
scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data
An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics
Viral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs
Prediction of allosteric communication pathways in proteins
Predicting RNA-protein binding sites and motifs through combining local and global deep convolutional neural networks
ECCB2022: the 21st European Conference on Computational Biology
Combination of text-mining algorithms increases the performance
The ruggedness of protein-protein energy landscape and the cutoff for 1/ r n potentials
Simulation-based model selection for dynamical systems in systems and population biology
Alignment of BLAST High-scoring Segment Pairs Based on the Longest Increasing Subsequence Algorithm
EBIMed - text crunching to gather facts for proteins from Medline
Another look at matrix correlations
Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures
PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data
Constrained clusters of gene expression profiles with pathological features
SAGA: a subgraph matching tool for biological graphs
Evidence for human microRNA-offset RNAs in small RNA sequencing data
A dictionary to identify small molecules and drugs in free text
FCSlib: an open-source tool for fluorescence fluctuation spectroscopy analysis for mobility, number and molecular brightness in R
ProMode: a database of normal mode analyses on protein molecules with a full-atom model
Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65
Learning locality-sensitive bucketing functions
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification
Inferring the experimental design for accurate gene regulatory network inference
Correlation of amino acid preference and mammalian viral genome type
Finding hydrophobic microdomains using an object-oriented database
Efficient computation of the kinship coefficients
Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra
MIRMMR: binary classification of microsatellite instability using methylation and mutations
A non-linear regression method for estimation of gene-environment heritability
MALDIrppa: quality control and robust analysis for mass spectrometry data
pNovo 3: precise de novo peptide sequencing using a learning-to-rank framework
pyseer: a comprehensive tool for microbial pangenome-wide association studies
SPARSE: a sparse hypergraph neural network for learning multiple types of latent combinations to accurately predict drug-drug interactions
MINERVA API and plugins: opening molecular network analysis and visualization to the community
The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators
Integration of methylation QTL and enhancer-target gene maps with schizophrenia GWAS summary results identifies novel genes
shinyExprPortal: a configurable 'shiny' portal for sharing analysis of molecular expression data
Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape
SATurn: a modular bioinformatics framework for the design of robust maintainable web-based and standalone applications
SGI: automatic clinical subgroup identification in omics datasets
PedigreeNet: a web-based pedigree viewer for biological databases
PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes
A decomposition model to track gene expression signatures: preview on observer-independent classification of ovarian cancer
G-compass: a web-based comparative genome browser between human and other vertebrate genomes
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human
USNAP : fast unique dense region detection and its application to lung cancer
The misuse of terms in scientific literature
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts
signeR: an empirical Bayesian approach to mutational signature discovery
Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms
Detection of microRNAs in color space
stAIcalc: tRNA adaptation index calculator based on species-specific weights
A natural upper bound to the accuracy of predicting protein stability changes upon mutations
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction
Towards the knowledge-based design of universal influenza epitope ensemble vaccines
MSMExplorer: visualizing Markov state models for biomolecule folding simulations
MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins
INstruct: a database of high-quality 3D structurally resolved protein interactome networks
Application of the GA/KNN method to SELDI proteomics data
pHMM-tree: phylogeny of profile hidden Markov models
CiVi: circular genome visualization with unique features to analyze sequence elements
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling
FABSIM: a software for generating F ST distributions with various ascertainment biases
Random rotation for identifying differentially expressed genes with linear models following batch effect correction
The 2025 ISCB Accomplishments by a Senior Scientist Award - Dr Amos Bairoch
MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks
A Bayesian Network Approach to Operon Prediction
DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function
All hits all the time: parameter-free calculation of spaced seed sensitivity
Largenet2: an object-oriented programming library for simulating large adaptive networks
Sample size determination for the false discovery rate
SEQGEL: a versatile and comfortable DNA editor which supports a special keyboard and a speech synthesizer
SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis
Robust synthetic gene network design via library-based search method
Significance tests for analyzing gene expression data with small sample sizes
LAMSA: fast split read alignment with long approximate matches
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics
Tumor phylogeny inference using tree-constrained importance sampling
Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation
Accurate calling of homeoallelic genotypes of iSelect markers using inbred structured populations
Discovering subnetworks in SBML models
A quality control algorithm for filtering SNPs in genome-wide association studies
Supporting the SBML layout extension
HExpoChem: a systems biology resource to explore human exposure to chemicals
Tracing weak neuron fibers
A novel randomized iterative strategy for aligning multiple protein sequences
Discovering protein drug targets using knowledge graph embeddings
Efficient gradient boosting for prognostic biomarker discovery
Clustering microarray gene expression data using weighted Chinese restaurant process
Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
ARMBIS: accurate and robust matching of brain image sequences from multiple modal imaging techniques
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
An improved residual network using deep fusion for identifying RNA 5-methylcytosine sites
Combining signals from spotted cDNA microarrays obtained at different scanning intensities
Statistically rigorous automated protein annotation
Bibliometric analysis of neuroscience publications quantifies the impact of data sharing
Feature selection and classification of noisy proteomics mass spectrometry data based on one-bit perturbed compressed sensing
Automated radioligand receptor binding analysis with templates for Lotus
Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations
HomologMiner: looking for homologous genomic groups in whole genomes
Exploring spatial patterns of gene expression from Fruit Fly embryogenesis on the iPhone
Gene finding with a hidden Markov model of genome structure and evolution
Distribution of information in biomedical abstracts and full-text publications
VCNet: vector-based gene co-expression network construction and its application to RNA-seq data
Evolutionary design of multiple genes encoding the same protein
SCide: Identification of Stabilization Centers in Proteins
Cost-effective and accurate method of measuring fetal fraction using SNP imputation
Fast motif matching revisited: high-order PWMs, SNPs and indels
LMdist: Local Manifold distance accurately measures beta diversity in ecological gradients
SCAN: SNP and copy number annotation
gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations
MAVIS: merging, annotation, validation, and illustration of structural variants
PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
dbNEI2.0: building multilayer network for drug-NEI-disease
MaveQuest: a web resource for planning experimental tests of human variant effects
genozip: a fast and efficient compression tool for VCF files
A toolkit for capturing and sharing FuGE experiments
Streamlining the construction of large-scale dynamic models using generic kinetic equations
SIMA: Simultaneous Multiple Alignment of LC/MS Peak Lists
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification
Stochastic reaction-diffusion simulation with MesoRD
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
proovread : large-scale high-accuracy PacBio correction through iterative short read consensus
ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning
FACETS: multi-faceted functional decomposition of protein interaction networks
Identifying driver genes for individual patients through inductive matrix completion
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
ATID: a web-oriented database for collection of publicly available alternative translational initiation events
Enlight: web-based integration of GWAS results with biological annotations
ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity
SDMinP: a program to control the family wise error rate using step-down minP adjusted P -values
Identification of genes involved in the same pathways using a Hidden Markov Model-based approach
Power enhancement via multivariate outlier testing with gene expression arrays
Anomaly detection in mixed high-dimensional molecular data
Tabix: fast retrieval of sequence features from generic TAB-delimited files
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome
Effect of separate sampling on classification accuracy
The Kappa platform for rule-based modeling
SMuRF: portable and accurate ensemble prediction of somatic mutations
GAME: detecting cis -regulatory elements using a genetic algorithm
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins
Non-redundant compendium of human ncRNA genes in GeneCards
S-SPatt: simple statistics for patterns on Markov chains
MutaFrame - an interpretative visualization framework for deleteriousness prediction of missense variants in the human exome
DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier
tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation
Search the Human cDNA Database at TIGR
RAbHIT: R Antibody Haplotype Inference Tool
DiffCircaPipeline: a framework for multifaceted characterization of differential rhythmicity
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data
CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline
Characterization of structural variants with single molecule and hybrid sequencing approaches
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap
Site of metabolism prediction for six biotransformations mediated by cytochromes P450
CoDNaS-RNA: a database of conformational diversity in the native state of RNA
Object-oriented parsing of biological databases with Python