yusuke1997/dblp-id-title huggingface dataset:
SIR: a simple indexing and retrieval system for biological flat file databases
CHIT: an allele-specific method for testing the association between molecular quantitative traits and phenotype-genotype interaction
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
Software for the development and evaluation of probabilistic identification matrices
InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias
Extrema-weighted feature extraction for functional data
Network principal component analysis: a versatile tool for the investigation of multigroup and multiblock datasets
Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach
VizStruct for visualization of genome-wide SNP analyses
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation
The systematic analysis of ultraconserved genomic regions in the budding yeast
NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols
AdaTiSS: a novel data-Adaptive robust method for identifying Tissue Specificity Scores
Some features on RNA folding structures of cytochrome c oxidase subunit II and cytochrome P450
FIT: statistical modeling tool for transcriptome dynamics under fluctuating field conditions
PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution
A memory-efficient algorithm for multiple sequence alignment with constraints
Hopper: software for automating data tracking and flow in DNA sequencing
Quantifying optimal accuracy of local primary sequence bioinformatics methods
Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis
ALOHOMORA: a tool for linkage analysis using 10K SNP array data
MUFold-SSW: a new web server for predicting protein secondary structures, torsion angles and turns
Large scale analysis of signal reachability
TimeTree: a public knowledge-base of divergence times among organisms
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
Host-parasite relations of bacteria and phages can be unveiled by Oligostickiness , a measure of relaxed sequence similarity
IDDkin: network-based influence deep diffusion model for enhancing prediction of kinase inhibitors
PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data
Triplet repeats in human genome: distribution and their association with genes and other genomic regions
Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data
AURA: Atlas of UTR Regulatory Activity
Base-pair probability profiles of RNA secondary structures
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences
DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages
Differential gene expression detection and sample classification using penalized linear regression models
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data
FELLS: fast estimator of latent local structure
A functional analysis of omic network embedding spaces reveals key altered functions in cancer
scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling
Evaluation of bottom-up and top-down mass spectrum identifications with different customized protein sequences databases
Topological entropy of DNA sequences
Sequence type analysis and recombinational tests (START)
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads
PolyRound: polytope rounding for random sampling in metabolic networks
Discovering regulatory motifs in the Plasmodium genome using comparative genomics
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
DeepUMQA: ultrafast shape recognition-based protein model quality assessment using deep learning
TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts
YeastSpotter: accurate and parameter-free web segmentation for microscopy images of yeast cells
Regularized adversarial learning for normalization of multi-batch untargeted metabolomics data
Correcting for link loss in causal network inference caused by regulator interference
ploidyNGS: visually exploring ploidy with Next Generation Sequencing data
Faster cyclic loess: normalizing RNA arrays via linear models
A statistical framework for recovering pseudo-dynamic networks from static data
Disease gene identification based on generic and disease-specific genome networks
A generalization of the PST algorithm: modeling the sparse nature of protein sequences
NCOurd: modelling length distributions of NCO events and gene conversion tracts
MATICCE: mapping transitions in continuous character evolution
Finding cis -regulatory modules in Drosophila using phylogenetic hidden Markov models
3Cnet: pathogenicity prediction of human variants using multitask learning with evolutionary constraints
reconCNV: interactive visualization of copy number data from high-throughput sequencing
Automated inference of molecular mechanisms of disease from amino acid substitutions
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?
DAFGA: diversity analysis of functional gene amplicons
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos
The early introduction of dynamic programming into computational biology
A compositional mediation model for a binary outcome: Application to microbiome studies
xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery
Chainy: an universal tool for standardized relative quantification in real-time PCR
Response to "Comments on 'Bayesian variable selection for disease classification using gene expression data'"
Exploring drivers of gene expression in the Cancer Genome Atlas
Complex networks approach to gene expression driven phenotype imaging
Generating precise mechanical stimuli and recording chordotonal organ discharge patterns using a microcomputer
Improved dropClust R package with integrative analysis support for scRNA-seq data
TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
VarSelLCM: an R/C++ package for variable selection in model-based clustering of mixed-data with missing values
Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
Prediction of nuclear export signals using weighted regular expressions (Wregex)
Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions
Functional and structural genomics using PEDANT
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis
MetaMutationalSigs: comparison of mutational signature refitting results made easy
Seevolution: visualizing chromosome evolution
Conformational analysis of molecular chains using nano-kinematics
ViPTree: the viral proteomic tree server
Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases
Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation
Response: an empirical comparison of several recent epistatic interaction detection methods
Multimodal representation learning for predicting molecule-disease relations
Galgo: a bi-objective evolutionary meta-heuristic identifies robust transcriptomic classifiers associated with patient outcome across multiple cancer types
SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone
Fragment-free approach to protein folding using conditional neural fields
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles
PoseFilter: a PyMOL plugin for filtering and analyzing small molecule docking in symmetric binding sites
High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features
Meta-analytic framework for liquid association
Identification of active transcription factor and miRNA regulatory pathways in Alzheimer's disease
Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts
Discontinuous epitope prediction based on mimotope analysis
GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search
Pre-calculated protein structure alignments at the RCSB PDB website
MS-Decipher: a user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides
CellularPotts.jl: simulating multiscale cellular models in Julia
Predicting protein localization in budding Yeast
Single cell clustering based on cell-pair differentiability correlation and variance analysis
Gene network inference by fusing data from diverse distributions
IBIS integrated biological imaging system: electron micrograph image-processing software running on Unix workstations
CABS-dock standalone: a toolbox for flexible protein-peptide docking
Detection of stoichiometric inconsistencies in biomolecular models
Pclust: protein network visualization highlighting experimental data
Using population data for assessing next-generation sequencing performance
Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment
funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types
MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets
Performance of an iterated T-HMM for homology detection
Janus - a comprehensive tool investigating the two faces of transcription
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data
BOSS: a novel scaffolding algorithm based on an optimized scaffold graph
Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics
A microcomputer FORTRAN program for rapid determination of lethal concentrations of biocides in mosquito control
Predicting subcellular localization of proteins using machine-learned classifiers
CisGenome Browser: a flexible tool for genomic data visualization
penalizedSVM: a R-package for feature selection SVM classification
PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees
A fast and flexible approach to oligonucleotide probe design for genomes and gene families
scACCorDiON: a clustering approach for explainable patient level cell-cell communication graph analysis
GP3: GenePix post-processing program for automated analysis of raw microarray data
emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry
Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion
ChemMapper: a versatile web server for exploring pharmacology and chemical structure association based on molecular 3D similarity method
LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins
The impact of function perturbations in Boolean networks
Complexity measures of the mature miRNA for improving pre-miRNAs prediction
Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules
BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs
Complementary feature selection from alternative splicing events and gene expression for phenotype prediction
UniMaP: finding unique mass and peptide signatures in the human proteome
DaMiRseq - an R/Bioconductor package for data mining of RNA-Seq data: normalization, feature selection and classification
scGCL: an imputation method for scRNA-seq data based on graph contrastive learning
MAnGO: an interactive R-based tool for two-colour microarray analysis
Knowledge-guided inference of domain-domain interactions from incomplete protein-protein interaction networks
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models
DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation
Single cell network analysis with a mixture of Nested Effects Models
OverProt: secondary structure consensus for protein families
Hypergraph-based logistic matrix factorization for metabolite-disease interaction prediction
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models
A new algorithm for cluster analysis of genomic methylation: the Helicobacter pylori case
geoCancerPrognosticDatasetsRetriever: a bioinformatics tool to easily identify cancer prognostic datasets on Gene Expression Omnibus (GEO)
Selective mutation accumulation: a computational model of the paternal age effect
CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications
TimeClust: a clustering tool for gene expression time series
GCLink: a graph contrastive link prediction framework for gene regulatory network inference
TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction
MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation
CORNA: testing gene lists for regulation by microRNAs
READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
Outlier detection at the transcriptome-proteome interface
LS-GKM: a new gkm-SVM for large-scale datasets
Predicting folding free energy changes upon single point mutations
Data-driven speciation tree prior for better species divergence times in calibration-poor molecular phylogenies
UProC: tools for ultra-fast protein domain classification
MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins
GeneFIND web server for protein family identification and information retrieval
An algorithm for the detection of surface-active alpha helices with the potential to anchor proteins at the membrane interface
Hopper: a mathematically optimal algorithm for sketching biological data
NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy
The 'subsequent artificial neural network' (SANN) approach might bring more classificatory power to ANN-based DNA microarray analyses
RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies
Services for prediction of drug susceptibility for HIV proteases and reverse transcriptases at the HIV drug research centre
CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity
Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts
The SwissLipids knowledgebase for lipid biology
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization
RADER: a RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening
jSquid: a Java applet for graphical on-line network exploration
Markovian negentropies in bioinformatics. 1. A picture of footprints after the interaction of the HIV-1 -RNA packaging region with drugs
MacP12: a protein property multi-profile plot program for the Apple Macintosh
AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins
Correcting population stratification in genetic association studies using a phylogenetic approach
PAML: a program package for phylogenetic analysis by maximum likelihood
Functional profiling of microarray experiments using text-mining derived bioentities
A strategy for finding regions of similarity in complete genome sequences
MacMatch: a tool for pattern-based protein secondary structure prediction
Turtle: Identifying frequent k -mers with cache-efficient algorithms
FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model
MLR-tagging: informative SNP selection for unphased genotypes based on multiple linear regression
The high-level similarity of some disparate gene expression measures
SPDE: a multi-functional software for sequence processing and data extraction
scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets
Acquire: an open-source comprehensive cancer biobanking system
Transfer learning across ontologies for phenome-genome association prediction
A regression model for estimating DNA copy number applied to capture sequencing data
Ensemble classifier for protein fold pattern recognition
Isolated ZP-N domains constitute the N-terminal extensions of Zona Pellucida proteins
Parameter balancing: consistent parameter sets for kinetic metabolic models
Bios2cor: an R package integrating dynamic and evolutionary correlations to identify functionally important residues in proteins
Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns
TRamWAy: mapping physical properties of individual biomolecule random motion in large-scale single-particle tracking experiments
An in silico proteomics screen to predict and prioritize protein-protein interactions dependent on post-translationally modified motifs
Granular clustering of de novo protein models
pLoc-mAnimal: predict subcellular localization of animal proteins with both single and multiple sites
The EBI RDF platform: linked open data for the life sciences
Preferred in vivo ubiquitination sites
Analyzing microarray data using CLANS
Predicting cross-tissue hormone-gene relations using balanced word embeddings
Gag-protease coevolution shapes the outcome of lopinavir-inclusive treatment regimens in chronically infected HIV-1 subtype C patients
mORCA: sailing bioinformatics world with mobile devices
Meta-analysis of gene expression data: a predictor-based approach
Evolutionary algorithms for finding optimal gene sets in microarray prediction
LOESS correction for length variation in gene set-based genomic sequence analysis
Speeding up tandem mass spectrometry database search: metric embeddings and fast near neighbor search
oggmap: a Python package to extract gene ages per orthogroup and link them with single-cell RNA data
arrayQCplot: software for checking the quality of microarray data
SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo
A Cytoscape app for motif enumeration with ISMAGS
WIlsON: Web-based Interactive Omics VisualizatioN
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
IBD-Groupon: an efficient method for detecting group-wise identity-by-descent regions simultaneously in multiple individuals based on pairwise IBD relationships
Learning from the ligand: using ligand-based features to improve binding affinity prediction
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA)
Inverse Potts model improves accuracy of phylogenetic profiling
Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: a case for the second derivative
GameRank: R package for feature selection and construction
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions
Model-based gene set analysis for Bioconductor
Knowledge discovery by automated identification and ranking of implicit relationships
EPGA: de novo assembly using the distributions of reads and insert size
EPIMHC: a curated database of MHC-binding peptides for customized computational vaccinology
Toward the assessment of predicted inter-residue distance
NSSRF: global network similarity search with subgraph signatures and its applications
EvAM-Tools: tools for evolutionary accumulation and cancer progression models
Performance optimization in DNA short-read alignment
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network
Pathway recognition and augmentation by computational analysis of microarray expression data
EuGène-maize: a web site for maize gene prediction
ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching
Large-scale computation of elementary flux modes with bit pattern trees
Ontologizing gene-expression microarray data: characterizing clusters with Gene Ontology
Evolutionary design principles of modules that control cellular differentiation: consequences for hysteresis and multistationarity
F2CS: FSSP to CATH and SCOP prediction server
Extracting gene pathway relations using a hybrid grammar: the Arizona Relation Parser
Tools for mapping high-throughput sequencing data
Protein-ligand interaction prediction: an improved chemogenomics approach
PathwayAccess: CellDesigner plugins for pathway databases
PheWAS-ME: a web-app for interactive exploration of multimorbidity patterns in PheWAS
Dynamic correlations: exact and approximate methods for mutual information
Improved sensitivity of biological sequence database searches
Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data
Temporal waves of coherent gene expression during Drosophila embryogenesis
Molecular mechanisms underlying COPD-muscle dysfunction unveiled through a systems medicine approach
Ensemble dependence model for classification and prediction of cancer and normal gene expression data
Generating samples under a Wright-Fisher neutral model of genetic variation
FARAO: the flexible all-round annotation organizer
OfftargetFinder: a web tool for species-specific RNAi design
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1
Prediction of protein-RNA binding sites by a random forest method with combined features
Drug repositioning based on bounded nuclear norm regularization
BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort
Back translation for molecule generation
On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
Generating Boolean networks with a prescribed attractor structure
RDP3: a flexible and fast computer program for analyzing recombination
Selective integration of multiple biological data for supervised network inference
Polynomial algebra of discrete models in systems biology
MADGE: scalable distributed data management software for cDNA microarrays
Automated Microarray Image Analysis Toolbox for MATLAB