yusuke1997/dblp-id-title huggingface dataset:
A network model predicts the intensity of residue-protein thermal coupling
Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs
Feature-weighted ordinal classification for predicting drug response in multiple myeloma
XdomView: protein domain and exon position visualization
A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images
A computer program for the design of optimal synthetic oligonucleotide probes for protein coding genes
PrecursorFinder: a customized biosynthetic precursor explorer
biotextgraph : graphical summarization of functional similarities from textual information
Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry
2020 Outstanding contributions to ISCB award: Judith Blake
Continuous-index hidden Markov modelling of array CGH copy number data
An algorithm for comparing multiple RNA secondary structures
MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes
bGWAS: an R package to perform Bayesian genome wide association studies
Semi-automated ontology generation within OBO-Edit
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information
jClust: a clustering and visualization toolbox
ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq data
SPNConverter: a new link between static and dynamic complex network analysis
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy
Modeling the adaptive immune system: predictions and simulations
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data
cloneRate: fast estimation of single-cell clonal dynamics using coalescent theory
ORT: a workflow linking genome-scale metabolic models with reactive transport codes
CRAFT: Compact genome Representation toward large-scale Alignment-Free daTabase
BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets
CluMSID: an R package for similarity-based clustering of tandem mass spectra to aid feature annotation in metabolomics
In silico read normalization using set multi-cover optimization
CytoCtrlAnalyser: a Cytoscape app for biomolecular network controllability analysis
DeepChargePredictor : a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms
Predicting synergistic anticancer drug combination based on low-rank global attention mechanism and bilinear predictor
Path: a tool to facilitate pathway-based genetic association analysis
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs
Combining dependent P- values with an empirical adaptation of Brown's method
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies
EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA
Comparative study on ChIP-seq data: normalization and binding pattern characterization
Functional protein biomarkers based on distributions of expression levels in single-cell imaging data
Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies
Classification of bacterial species from proteomic data using combinatorial approaches incorporating artificial neural networks, cluster analysis and principal components analysis
Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR
FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing
Application of network smoothing to glycan LC-MS profiling
Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties
MGIDI: toward an effective multivariate selection in biological experiments
Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES
Mining biological networks for unknown pathways
Techniques to cope with missing data in host-pathogen protein interaction prediction
invertFREGENE: software for simulating inversions in population genetic data
PPO: Predictor for Prokaryotic Operons
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra
Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences
Hierarchical tree snipping: clustering guided by prior knowledge
methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models
SPOT: a web-tool enabling swift profiling of transcriptomes
Mapping gene ontology to proteins based on protein-protein interaction data
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
Positive and negative forms of replicability in gene network analysis
Data bank homology search algorithm with linear computation complexity
genomation: a toolkit to summarize, annotate and visualize genomic intervals
Chemical substructures that enrich for biological activity
admixturegraph: an R package for admixture graph manipulation and fitting
A bibliography on computational algorithms in molecular biology and genetics
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
Detecting protein dissimilarities in multiple alignments using Bayesian variable selection
MASV - Multiple (BLAST) Annotation System Viewer
Alignment of molecular networks by integer quadratic programming
PATH: a task for the inference of phylogenies
A genotype calling algorithm for affymetrix SNP arrays
CONSORF: a consensus prediction system for prokaryotic coding sequences
DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis
Pathway studio - the analysis and navigation of molecular networks
Methodological aspects of the genetic dissection of gene expression
Mapper: an intelligent restriction mapping tool
The Naked Mole Rat Genome Resource: facilitating analyses of cancer and longevity-related adaptations
DrawGlycan-SNFG and gpAnnotate: rendering glycans and annotating glycopeptide mass spectra
MRMAssayDB: an integrated resource for validated targeted proteomics assays
Interpretable factor models of single-cell RNA-seq via variational autoencoders
LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs
PyCoMo: a python package for community metabolic model creation and analysis
Bayesian inference of protein-protein interactions from biological literature
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
GdClean: removal of Gadolinium contamination in mass cytometry data
AUGUR: a program to predict, display and analyze the tertiary structure of B-DNA
drexplorer: A tool to explore dose-response relationships and drug-drug interactions
Coherent coupling of feedback loops: a design principle of cell signaling networks
Improvement of the GenTHREADER Method for Genomic Fold Recognition
Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria
MODIG: integrating multi-omics and multi-dimensional gene network for cancer driver gene identification based on graph attention network model
PyDESeq2: a python package for bulk RNA-seq differential expression analysis
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort
A new algorithm for predicting splice site sequence based on an improvement of categorical discriminant analysis
A high-performance deep-learning-based pipeline for whole-brain vasculature segmentation at the capillary resolution
An effective structure learning method for constructing gene networks
SVPV: a structural variant prediction viewer for paired-end sequencing datasets
Use of extreme patient samples for outcome prediction from gene expression data
polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids
CNValidator: validating somatic copy-number inference
Predicting microbiomes through a deep latent space
Automatic improvement of deep learning-based cell segmentation in time-lapse microscopy by neural architecture search
ARGprofiler - a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
Modeling splice sites with Bayes networks
LipidGO: database for lipid-related GO terms and applications
Protein structure comparison by probability-based matching of secondary structure elements
XSI - a genotype compression tool for compressive genomics in large biobanks
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs
Generalized Born radii computation using linear models and neural networks
Quantifying functional impact of non-coding variants with multi-task Bayesian neural network
GMAP: a genomic mapping and alignment program for mRNA and EST sequence
Improved gene tree error correction in the presence of horizontal gene transfer
Multiomics-integrated deep language model enables in silico genome-wide detection of transcription factor binding site in unexplored biosamples
LoRDEC: accurate and efficient long read error correction
inGAP: an integrated next-generation genome analysis pipeline
pyNVR: investigating factors affecting feature selection from scRNA-seq data for lineage reconstruction
PSAR-Align: improving multiple sequence alignment using probabilistic sampling
Beware of mis-assembled genomes
Statistical framework to determine indel-length distribution
Approximately independent linkage disequilibrium blocks in human populations
MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction
PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics
Gene relevance based on multiple evidences in complex networks
Cpipe: a comprehensive computational platform for sequence and structure-based analyses of Cysteine residues
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
Enriching targeted sequencing experiments for rare disease alleles
Sparse multitask regression for identifying common mechanism of response to therapeutic targets
LibSBML: an API Library for SBML
Correction to: CITEdb: a manually curated database of cell-cell interactions in human
PROSTATA: a framework for protein stability assessment using transformers
YOABS: yet other aligner of biological sequences - an efficient linearly scaling nucleotide aligner
snpAD: an ancient DNA genotype caller
DARTpaths, an in silico platform to investigate molecular mechanisms of compounds
Co-sparse reduced-rank regression for association analysis between imaging phenotypes and genetic variants
Correction to: wpLogicNet: logic gate and structure inference in gene regulatory networks
Combining tree-based and dynamical systems for the inference of gene regulatory networks
The correlation error and finite-size correction in an ungapped sequence alignment
Markovian domain fingerprinting: statistical segmentation of protein sequences
Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis
Stochastic simulation GUI for biochemical networks
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities
Estimation of P-values for global alignments of protein sequences
The qualitative and time-dependent character of spatial relations in biomedical ontologies
Probabilistic representation of gene regulatory networks
Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection
TagDust - a program to eliminate artifacts from next generation sequencing data
Combining artificial intelligence: deep learning with Hi-C data to predict the functional effects of non-coding variants
A comparison of some neural and non-neural methods for identification of phytoplankton from flow cytometry data
The Network Library: a framework to rapidly integrate network biology resources
pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge
Accurate prediction of deleterious protein kinase polymorphisms
Bluues server: electrostatic properties of wild-type and mutated protein structures
The elucidation of protein function from its amino acid sequence
Modeling circRNA expression pattern with integrated sequence and epigenetic features demonstrates the potential involvement of H3K79me2 in circRNA expression
An application for assessing quality of RNA hybridized to Affymetrix GeneChips
ANTHEPROT: IBM PC and Apple Macintosh versions
SigMod: an exact and efficient method to identify a strongly interconnected disease-associated module in a gene network
Discovering research articles containing evolutionary timetrees by machine learning
Ordino: a visual cancer analysis tool for ranking and exploring genes, cell lines and tissue samples
regNet: an R package for network-based propagation of gene expression alterations
iDoComp: a compression scheme for assembled genomes
Mutational signature learning with supervised negative binomial non-negative matrix factorization
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
In silico identification of archaeal DNA-binding proteins
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
Literature mining discerns latent disease-gene relationships
BadiRate: estimating family turnover rates by likelihood-based methods
PEWO: a collection of workflows to benchmark phylogenetic placement
MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces
XtalPred: a web server for prediction of protein crystallizability
Robust gene coexpression networks using signed distance correlation
A sub-pathway-based approach for identifying drug response principal network
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile
PROCAIN server for remote protein sequence similarity search
ICT : isotope correction toolbox
Protein complex prediction via cost-based clustering
Metagenomics reveals our incomplete knowledge of global diversity
Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments
Correction to: Clustering spatial transcriptomics data
Identification of phylogenetically conserved microRNA cis -regulatory elements across 12 Drosophila species
Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty
Large-scale analysis of human gene expression variability associates highly variable drug targets with lower drug effectiveness and safety
Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes
Unified tests for fine-scale mapping and identifying sparse high-dimensional sequence associations
Gene and translation initiation site prediction in metagenomic sequences
On non-detects in qPCR data
Expression-based monitoring of transcription factor activity: the TELiS database
An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching
Genetic modification of flux for flux prediction of mutants
Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance
Co-registration and analysis of multiple imaging mass spectrometry datasets targeting different analytes
CPPpred: prediction of cell penetrating peptides
RetroSeq: transposable element discovery from next-generation sequencing data
snpEnrichR: analyzing co-localization of SNPs and their proxies in genomic regions
GeneE: Gene and protein query expansion with disambiguation
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation
Hybrid analysis of gene dynamics predicts context-specific expression and offers regulatory insights
PROLONG: penalized regression for outcome guided longitudinal omics analysis with network and group constraints
A profile for molecular biology databases and information resources
Selection of amino acid parameters for Fourier transform-based analysis of proteins
The Small-world Dynamics of Tree Networks and Data Mining in Phyloinformatics
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics
Mapping networks of light-dark transition in LOV photoreceptors
A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data
In silico structural modeling of multiple epigenetic marks on DNA
The Human Transcript Database: a catalogue of full length cDNA inserts
The Cytoscape BioGateway App: explorative network building from an RDF store
Addressing false discoveries in network inference
Inter-species pathway perturbation prediction via data-driven detection of functional homology
Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads
PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins
A parallelized strategy for epistasis analysis based on Empirical Bayesian Elastic Net models
Principal component analysis for clustering gene expression data
A semisupervised model to predict regulatory effects of genetic variants at single nucleotide resolution using massively parallel reporter assays
Ligand identification in CryoEM and X-ray maps using deep learning
Inference of microbial covariation networks using copula models with mixture margins
DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
CNVVdb: a database of copy number variations across vertebrate genomes
Ulla: a program for calculating environment-specific amino acid substitution tables
SCORE: Smart Consensus Of RNA Expression - a consensus tool for detecting differentially expressed genes in bacteria
Pisces: an accurate and versatile variant caller for somatic and germline next-generation sequencing data
Genomic sweeping for hypermethylated genes
Local correlation of expression profiles with gene annotations-proof of concept for a general conciliatory method
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space
FIRMA: a method for detection of alternative splicing from exon array data
BarleyExpress: a web-based submission tool for enriched microarray database annotations
Wordom: a program for efficient analysis of molecular dynamics simulations
Pathway hunting by random survival forests
Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue
Higher-order Markov models for metagenomic sequence classification
A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers
A heuristic managing errors for DNA sequencing
Superiority of network motifs over optimal networks and an application to the revelation of gene network evolution
Compounds In Literature (CIL): screening for compounds and relatives in PubMed
Harnessing networked workstations as a powerful parallel computer: a general paradigm illustrated using three programs for genetic linkage analysis
An automated benchmarking platform for MHC class II binding prediction methods
Prediction of missing sequences and branch lengths in phylogenomic data
AFS: identification and quantification of species composition by metagenomic sequencing
The Sequence Alerting Server - a new WEB server
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge
Guest Editor Preface: Plant & Animal Genome (PAG) Meeting Bioinformatics Session Paper Competition
The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression
BioThesaurus: a web-based thesaurus of protein and gene names
An examination of the conservation of surface patch polarity for proteins
RNA-eXpress annotates novel transcript features in RNA-seq data
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction
Neural network schemes for detecting rare events in human genomic DNA
COPE: an accurate k -mer-based pair-end reads connection tool to facilitate genome assembly
Modelling time course gene expression data with finite mixtures of linear additive models
TopHat: discovering splice junctions with RNA-Seq
scShaper: an ensemble method for fast and accurate linear trajectory inference from single-cell RNA-seq data
The Genomedata format for storing large-scale functional genomics data
Fast parsers for Entrez Gene
eMolTox: prediction of molecular toxicity with confidence
Integrating different data types by regularized unsupervised multiple kernel learning with application to cancer subtype discovery
A neuro-evolution approach to infer a Boolean network from time-series gene expressions
Systematic characterization and prediction of post-translational modification cross-talk between proteins
Adaptive space search-based molecular evolution optimization algorithm
Model-based deconvolution of genome-wide DNA binding
URL decay in MEDLINE - a 4-year follow-up study
Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic
CGHcall: calling aberrations for array CGH tumor profiles
A framework for scalable parameter estimation of gene circuit models using structural information
InterPreTS: protein Interaction Prediction through Tertiary Structure
A simple statistical method for discriminating outer membrane proteins with better accuracy
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies
appreci8: a pipeline for precise variant calling integrating 8 tools
PLIO: an ontology for formal description of protein-ligand interactions
3FunMap: full-sib family functional mapping of dynamic traits
Making automated multiple alignments of very large numbers of protein sequences
PK/DB: database for pharmacokinetic properties and predictive in silico ADME models
ANCHOR: web server for predicting protein binding regions in disordered proteins
PennDiff: detecting differential alternative splicing and transcription by RNA sequencing
OptiType: precision HLA typing from next-generation sequencing data
Computational modeling of cellular structures using conditional deep generative networks
Rebuttal to the Letter to the Editor in response to the paper: proper evaluation of alignment-free network comparison methods
Can transcriptome size be estimated from SAGE catalogs?
An alternative model of amino acid replacement
VCF-Explorer: filtering and analysing whole genome VCF files
Differential rhythmicity: detecting altered rhythmicity in biological data
GABAagent: a system for integrating data on GABA receptors