yusuke1997/dblp-id-title huggingface dataset:
Two-stage designs applying methods differing in costs
MATCH-UP/MATRIX: a microcomputer program designed to search for protein primary structure homology
MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants
GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach
ePlatypus: an ecosystem for computational analysis of immunogenomics data
r8s: inferring absolute rates of molecular evolution, divergence times in the absence of a molecular clock
Compositional data network analysis via lasso penalized D-trace loss
MTG2: an efficient algorithm for multivariate linear mixed model analysis based on genomic information
ARIA2: Automated NOE assignment and data integration in NMR structure calculation
LIGSIFT: an open-source tool for ligand structural alignment and virtual screening
Chromosome aberrations produced by ionizing radiation: Monte Carlo simulations and chromosome painting data
Improvement of 3D protein models using multiple templates guided by single-template model quality assessment
RAPTR-SV: a hybrid method for the detection of structural variants
A set of Macintosh computer programs for the design and analysis of synthetic genes
Higher-order genetic interaction discovery with network-based biological priors
GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography
Gene expression data preprocessing
MAPS: a microarray project system for gene expression experiment information and data validation
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model
Gradient lasso for Cox proportional hazards model
Comorbidity4j: a tool for interactive analysis of disease comorbidities over large patient datasets
Errors between sites in restriction site mapping
A statistical framework for genomic data fusion
Identification of novel transcripts in annotated genomes using RNA-Seq
dsMTL: a computational framework for privacy-preserving, distributed multi-task machine learning
Robustness portraits of diverse biological networks conserved despite order-of-magnitude parameter uncertainty
Random sampling of elementary flux modes in large-scale metabolic networks
On biases of attention in scientific discovery
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data
Post hoc power estimation in large-scale multiple testing problems
IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning
Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape
The assembly of miRNA-mRNA-protein regulatory networks using high-throughput expression data
Gaussian process test for high-throughput sequencing time series: application to experimental evolution
Predicting pseudoknotted structures across two RNA sequences
An expression index for Affymetrix GeneChips based on the generalized logarithm
DisProt: a database of protein disorder
High precision protein functional site detection using 3D convolutional neural networks
Retention time alignment algorithms for LC/MS data must consider non-linear shifts
DATF: a database of Arabidopsis transcription factors
Matrix2png: a utility for visualizing matrix data
Simultaneous prediction of multiple outcomes using revised stacking algorithms
GeneDn: for high-level expression design of heterologous genes in a prokaryotic system
phippery : a software suite for PhIP-Seq data analysis
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
A knowledge-driven approach to cluster validity assessment
Differential dependency network analysis to identify condition-specific topological changes in biological networks
ISCB: past-present perspective for the International Society for Computational Biology
DROSOPOSON: a knowledge base on chromosomal localization of transposable element insertions in Drosophila
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
MSMS : a coalescent simulation program including recombination, demographic structure and selection at a single locus
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation
Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arrays
SALAI-Net: species-agnostic local ancestry inference network
Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets
Analysis of matched mRNA measurements from two different microarray technologies
Metabolomics spectral formatting, alignment and conversion tools (MSFACTs)
Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis
SW-Tandem: a highly efficient tool for large-scale peptide identification with parallel spectrum dot product on Sunway TaihuLight
Prediction of both conserved and nonconserved microRNA targets in animals
SAMFIRE: multi-locus variant calling for time-resolved sequence data
Finding stable local optimal RNA secondary structures
Anduril 2: upgraded large-scale data integration framework
Global network alignment using multiscale spectral signatures
miTRATA: a web-based tool for mi croRNA Tr uncation a nd T ailing A nalysis
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS
Deep statistical modelling of nanopore sequencing translocation times reveals latent non-B DNA structures
UNIREP: a microcomputer program to find unique and repetitive nucleotide sequences in genomes
An empirical Bayes mixture model for SNP detection in pooled sequencing data
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
Genomic data integration using guided clustering
ZeroGEN: leveraging language models for zero-shot ligand design from protein sequences
Metaxa2 Database Builder: enabling taxonomic identification from metagenomic or metabarcoding data using any genetic marker
zCall: a rare variant caller for array-based genotyping: Genetics and population analysis
SHEPHARD: a modular and extensible software architecture for analyzing and annotating large protein datasets
Polar labeling: silver standard algorithm for training disease classifiers
SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics
A novel parallel approach to the likelihood-based estimation of admixture in population genetics
Surface ID: a geometry-aware system for protein molecular surface comparison
Hi-Jack: a novel computational framework for pathway-based inference of host-pathogen interactions
Enhancing generalizability and performance in drug-target interaction identification by integrating pharmacophore and pre-trained models
Improving performances of suboptimal greedy iterative biclustering heuristics via localization
scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction
3D-SURFER: software for high-throughput protein surface comparison and analysis
Detection of eQTL modules mediated by activity levels of transcription factors
Efficiently quantifying DNA methylation for bulk- and single-cell bisulfite data
Identification of expression signatures for non-small-cell lung carcinoma subtype classification
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides
Cleaver: software for identifying taxon specific restriction endonuclease recognition sites
SpotCaliper: fast wavelet-based spot detection with accurate size estimation
ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data
Serial NetEvolve: a flexible utility for generating serially-sampled sequences along a tree or recombinant network
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
Probabilistic analysis of gene expression measurements from heterogeneous tissues
FASPR: an open-source tool for fast and accurate protein side-chain packing
Adaptive multi-agent architecture for functional sequence motifs recognition
A conditional density error model for the statistical analysis of microarray data
minoTour, real-time monitoring and analysis for nanopore sequencers
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network
Easyfig: a genome comparison visualizer
SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods
ChromoScan: a scan statistic application for identifying chromosomal regions in genomic studies
An enzyme mechanism language for the mathematical modeling of metabolic pathways
PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order
Log-odds sequence logos
Correcting errors in short reads by multiple alignments
Clustering of gene expression data using a local shape-based similarity measure
HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition
A criticality-based framework for task composition in multi-agent bioinformatics integration systems
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
Robust quantitative scratch assay
Fast and compact matching statistics analytics
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships
A novel missense-mutation-related feature extraction scheme for 'driver' mutation identification
FourCSeq: analysis of 4C sequencing data
PIANA: protein interactions and network analysis
Dr.seq: a quality control and analysis pipeline for droplet sequencing
<tt>Forseti</tt>: a mechanistic and predictive model of the splicing status of scRNA-seq reads
ksrates: positioning whole-genome duplications relative to speciation events in KS distributions
Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing
Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion
Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations
GNU MCSim: Bayesian statistical inference for SBML-coded systems biology models
AuthorReward: increasing community curation in biological knowledge wikis through automated authorship quantification
Reordering contigs of draft genomes using the Mauve Aligner
CoV-AbDab: the coronavirus antibody database
Multinomial modeling and an evaluation of common data-mining algorithms for identifying signals of disproportionate reporting in pharmacovigilance databases
Benchmarking substrate-based kinase activity inference using phosphoproteomic data
Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networks
Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning
A fast top-down method for constructing reliable radiation hybrid frameworks
GeneCardsTM 2002: towards a complete, object-oriented, human gene compendium
EnrichRBP: an automated and interpretable computational platform for predicting and analysing RNA-binding protein events
Integrating population-level and cell-based signatures for drug repositioning
CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets
GeneGenerator - a flexible algorithm for gene prediction and its application to maize sequences
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
Choice of species affects phylogenetic stability of deep nodes: an empirical example in Terrabacteria
MAGNAMWAR: an R package for genome-wide association studies of bacterial orthologs
A microcomputer program for the identification of tRNA genes
Interactional and functional centrality in transcriptional co-expression networks
decorate: differential epigenetic correlation test
On the stability of log-rank test under labeling errors
Bivartect: accurate and memory-saving breakpoint detection by direct read comparison
CyTOFmerge: integrating mass cytometry data across multiple panels
Estimating classification probabilities in high-dimensional diagnostic studies
ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations
BLESS 2: accurate, memory-efficient and fast error correction method
Development of simulation models for protein folding in a thermal annealing process - I: A simulation of BPTI folding by the pearl necklace model
Enhancing the drug discovery process: Bayesian inference for the analysis and comparison of dose-response experiments
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA)
SPARSim single cell: a count data simulator for scRNA-seq data
An investigation into the use of hypertext as a user interface to taxonomic keys
A framework for scientific data modeling and automated software development
FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes
STATSEARCH: a GCG-compatible program for assessing statistical significance during DNA and protein databank searches
The MEMPACK alpha-helical transmembrane protein structure prediction server
Fast and accurate long-read alignment with Burrows-Wheeler transform
MetaSanity: an integrated microbial genome evaluation and annotation pipeline
Comments on sequence normalization of tiling array expression
Direct mapping and alignment of protein sequences onto genomic sequence
A Grid-enabled web portal for NMR structure refinement with AMBER
Protein analyst - a distributed object environment for protein sequence and structure analysis
Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Mtreemix: a software package for learning and using mixture models of mutagenetic trees
Haplotype assembly of autotetraploid potato using integer linear programing
GOLD-Graphical Overview of Linkage Disequilibrium
NodMutDB: a database for genes and mutants involved in symbiosis
CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens
Information-incorporated sparse convex clustering for disease subtyping
Graph sharpening plus graph integration: a synergy that improves protein functional classification
A novel splicing outcome reveals more than 2000 new mammalian protein isoforms
Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations
CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes
Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development
Swan: a library for the analysis and visualization of long-read transcriptomes
ISQuest: finding insertion sequences in prokaryotic sequence fragment data
Trimmomatic: a flexible trimmer for Illumina sequence data
Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
PPIT: an R package for inferring microbial taxonomy from nifH sequences
markophylo: Markov chain analysis on phylogenetic trees
Optimal metabolic route search based on atom mappings
CloneIt: finding cloning strategies, in-frame deletions and frameshifts
Merging of multi-string BWTs with applications
Aggrescan3D standalone package for structure-based prediction of protein aggregation properties
htsget: a protocol for securely streaming genomic data
Fast accessibility-based prediction of RNA-RNA interactions
deBGR: an efficient and near-exact representation of the weighted de Bruijn graph
MAVEN: a tool for visualization and functional analysis of genome-wide association results
Evaluating the Drosophila Bicoid morphogen gradient system through dissecting the noise in transcriptional bursts
GelScape: a web-based server for interactively annotating, manipulating, comparing and archiving 1D and 2D gel images
Limited agreement among three global gene expression methods highlights the requirement for non-global validation
DSC: public domain protein secondary structure predication
LSAT: learning about alternative transcripts in MEDLINE
A deep learning architecture for metabolic pathway prediction
Two-dimensional segmentation for analyzing Hi-C data
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development
CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis
A neighborhood-regularization method leveraging multiview data for predicting the frequency of drug-side effects
BigBWA: approaching the Burrows-Wheeler aligner to Big Data technologies
Tagging SNP-set selection with maximum information based on linkage disequilibrium structure in genome-wide association studies
Detection of differentially expressed segments in tiling array data
NCL: a C++ class library for interpreting data files in NEXUS format
ECCB 2016: The 15th European Conference on Computational Biology
An RNA folding method capable of identifying pseudoknots and base triples
PltDB: a blood platelets-based gene expression database for disease investigation
Inferring the soybean ( Glycine max ) microRNA functional network based on target gene network
AmpliBASE MT TM : a Mycobacterium tuberculosis diversity knowledgebase
Bayesian negative binomial regression for differential expression with confounding factors
Pathogen-Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data
Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data
Detecting overlapping coding sequences with pairwise alignments
CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling
Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data
Determining conserved metabolic biomarkers from a million database queries
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments
BELHD: improving biomedical entity linking with homonym disambiguation
APP2: automatic tracing of 3D neuron morphology based on hierarchical pruning of a gray-weighted image distance-tree
Soft windowing application to improve analysis of high-throughput phenotyping data
k -link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA
Inferring progression models for CGH data
MultiBaC: an R package to remove batch effects in multi-omic experiments
cyNeo4j: connecting Neo4j and Cytoscape
iCFN: an efficient exact algorithm for multistate protein design
Conformal inference for reliable single cell RNA-seq annotation
pySolo: a complete suite for sleep analysis in Drosophila
MM-6mAPred: identifying DNA N6-methyladenine sites based on Markov model
Lost in translation: bioinformatic analysis of variations affecting the translation initiation codon in the human genome
De novo detection of copy number variation by co-assembly
Cloud4Psi: cloud computing for 3D protein structure similarity searching
Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis
Normality of oligonucleotide microarray data and implications for parametric statistical analyses
Computational Analysis of Stop Codon Readthrough in D.melanogaster
DeepCDR: a hybrid graph convolutional network for predicting cancer drug response
Kinase selectivity potential for inhibitors targeting the ATP binding site: a network analysis
Spectral identification of topological domains
Relational graph convolutional networks for predicting blood-brain barrier penetration of drug molecules
Comparing genomes with rearrangements and segmental duplications
Composition of seed sequence is a major determinant of microRNA targeting patterns
GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms
Detection of DNA copy number alterations using penalized least squares regression
RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data
Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases
MsPAC: a tool for haplotype-phased structural variant detection
Mosdepth: quick coverage calculation for genomes and exomes
VSEAMS: a pipeline for variant set enrichment analysis using summary GWAS data identifies IKZF3 , BATF and ESRRA as key transcription factors in type 1 diabetes
A variable selection approach for highly correlated predictors in high-dimensional genomic data
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs
Using association rule mining to determine promising secondary phenotyping hypotheses
Experimental design schemes for learning Boolean network models
Biomedical evidence engineering for data-driven discovery
Graphical Methods for Class Prediction Using Dimension Reduction Techniques on DNA Microarray Data
An access interface for the MS-DOS diskette format of GenBank(R), a gene sequence database
4DGenome: a comprehensive database of chromatin interactions
Predicting interactions in protein networks by completing defective cliques
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions
The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes
The antigenic index: a novel algorithm for predicting antigenic determinants
Sufficient statistics and expectation maximization algorithms in phylogenetic tree models
An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training
A mechanism for maintaining an up-to-date GenBank database via Usenet
Earliest pages of bioinformatics
OMWSA: detection of DNA repeats using moving window spectral analysis
Genome-wide association studies of brain imaging data via weighted distance correlation
Assembling the 20 Gb white spruce ( Picea glauca ) genome from whole-genome shotgun sequencing data
BeoBLAST: distributed BLAST and PSI-BLAST on a Beowulf cluster
TESE: generating specific protein structure test set ensembles
yacrd and fpa: upstream tools for long-read genome assembly