yusuke1997/dblp-id-title huggingface dataset:
De novo identification of in vivo binding sites from ChIP-chip data
RSAP-Net: joint optic disc and cup segmentation with a residual spatial attention path module and MSRCR-PT pre-processing algorithm
Iterative sub-network component analysis enables reconstruction of large scale genetic networks
RNAalifold: improved consensus structure prediction for RNA alignments
Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens
FRAGS: estimation of coding sequence substitution rates from fragmentary data
SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups
Prediction of a common structural scaffold for proteasome lid, COP9-signalosome and eIF3 complexes
Orthogonal multimodality integration and clustering in single-cell data
Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
Grammar-based compression approach to extraction of common rules among multiple trees of glycans and RNAs
Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique
Predicting drug combination side effects based on a metapath-based heterogeneous graph neural network
MGSEA - a multivariate Gene set enrichment analysis
Drug-target interaction prediction using semi-bipartite graph model and deep learning
DRPnet: automated particle picking in cryo-electron micrographs using deep regression
A binning tool to reconstruct viral haplotypes from assembled contigs
Arena-Idb: a platform to build human non-coding RNA interaction networks
Evaluation of microarray data normalization procedures using spike-in experiments
Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate
DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples
Disulfide by design 2.0: a web-based tool for disulfide engineering in proteins
The scoring of poses in protein-protein docking: current capabilities and future directions
Relationship between insertion/deletion (indel) frequency of proteins and essentiality
Iam hiQ - a novel pair of accuracy indices for imputed genotypes
Direct coupling analysis and the attention mechanism
A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium
Spliceator: multi-species splice site prediction using convolutional neural networks
SeqRate: sequence-based protein folding type classification and rates prediction
A semi-nonparametric mixture model for selecting functionally consistent proteins
Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information
Multiple consensus trees: a method to separate divergent genes
Tree Pruner: An efficient tool for selecting data from a biased genetic database
Prioritising positively selected variants in whole-genome sequencing data using FineMAV
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data
Mathematical design of prokaryotic clone-based microarrays
PPLook: an automated data mining tool for protein-protein interaction
Speeding up tandem mass spectrometry-based database searching by longest common prefix
Convex hulls in hamming space enable efficient search for similarity and clustering of genomic sequences
Aligning the unalignable: bacteriophage whole genome alignments
H2r : Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments
Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case
An improved algorithm for flux variability analysis
MIMAS 3.0 is a Multiomics Information Management and Annotation System
SVM Classifier - a comprehensive java interface for support vector machine classification of microarray data
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Model annotation and discovery with the Physiome Model Repository
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis -regulatory elements and transcription factors
HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements
eQTL Viewer: visualizing how sequence variation affects genome-wide transcription
T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
UNCLES: method for the identification of genes differentially consistently co-expressed in a specific subset of datasets
Preprocessing of gene expression data by optimally robust estimators
Protein docking prediction using predicted protein-protein interface
A detailed map of coupled circadian clock and cell cycle with qualitative dynamics validation
Pitfalls in applying text mining to scientific literature
Detecting pore-lining regions in transmembrane protein sequences
Drug repositioning for non-small cell lung cancer by using machine learning algorithms and topological graph theory
SIS: a program to generate draft genome sequence scaffolds for prokaryotes
Combinatorial identification of DNA methylation patterns over age in the human brain
D3PM: a comprehensive database for protein motions ranging from residue to domain
Assumptions on decision making and environment can yield multiple steady states in microbial community models
Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions
ViVaMBC: estimating viral sequence variation in complex populations from illumina deep-sequencing data using model-based clustering
Determinants of Antigenicity and Specificity in immune response for Protein Sequences
Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization
dbVOR: a database system for importing pedigree, phenotype and genotype data and exporting selected subsets
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Web services and workflow management for biological resources
A Bayesian approach to efficient differential allocation for resampling-based significance testing
Relations as patterns: bridging the gap between OBO and OWL
EC: an efficient error correction algorithm for short reads
Examination of blood samples using deep learning and mobile microscopy
Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL)
Prediction of TF target sites based on atomistic models of protein-DNA complexes
vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding
CLINE: a web-tool for the comparison of biological dendrogram structures
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics
Class-balanced negative training sets for improving classifier model predictions of enhancer-promoter interactions
Using caching and optimization techniques to improve performance of the Ensembl website
eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model
VAMPS: a website for visualization and analysis of microbial population structures
Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis
K-SPMM: a database of murine spermatogenic promoters modules & motifs
MMinte: an application for predicting metabolic interactions among the microbial species in a community
Reduction, alignment and visualisation of large diverse sequence families
multiplierz: an extensible API based desktop environment for proteomics data analysis
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
Unveiling molecular moieties through hierarchical Grad-CAM graph explainability
CLAST: CUDA implemented large-scale alignment search tool
Single-cell gene expression analysis reveals β-cell dysfunction and deficit mechanisms in type 2 diabetes
CamurWeb: a classification software and a large knowledge base for gene expression data of cancer
SADI, SHARE, and the in silico scientific method
SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes
HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs
MethylPCA: a toolkit to control for confounders in methylome-wide association studies
Automated classification of protein expression levels in immunohistochemistry images to improve the detection of cancer biomarkers
Predicting links between tumor samples and genes using 2-Layered graph based diffusion approach
Introduction: advanced intelligent computing theories and their applications in bioinformatics
Gene flow analysis method, the D-statistic, is robust in a wide parameter space
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy
A single-model quality assessment method for poor quality protein structure
Comparison of different cell type correction methods for genome-scale epigenetics studies
De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
Cache-Oblivious parallel SIMD Viterbi decoding for sequence search in HMMER
GWAS on your notebook: fast semi-parallel linear and logistic regression for genome-wide association studies
Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data
Asymmetric bagging and feature selection for activities prediction of drug molecules
Leveraging pre-trained language models for mining microbiome-disease relationships
GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism
Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework
Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach
Argudas: lessons for argumentation in biology based on a gene expression use case
Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling
SPODOBASE : an EST database for the lepidopteran crop pest Spodoptera
tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities
ASMPKS: an analysis system for modular polyketide synthases
Identification of multiplicatively acting modulatory mutational signatures in cancer
Probabilistic prioritization of candidate pathway association with pathway score
NEAT: an efficient network enrichment analysis test
Supervised multivariate analysis of sequence groups to identify specificity determining residues
Linear space string correction algorithm using the Damerau-Levenshtein distance
SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides
Incorporating background frequency improves entropy-based residue conservation measures
CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome
Identifying significant temporal variation in time course microarray data without replicates
Power analysis for RNA-Seq differential expression studies using generalized linear mixed effects models
Multitask learning for biomedical named entity recognition with cross-sharing structure
Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes
Watchdog - a workflow management system for the distributed analysis of large-scale experimental data
Machine-learning algorithms based on personalized pathways for a novel predictive model for the diagnosis of hepatocellular carcinoma
timeClip: pathway analysis for time course data without replicates
A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection
Correction: Completing a genomic characterisation of microscopic tumour samples with copy number
VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data
Normalizing biomedical terms by minimizing ambiguity and variability
Trends in modeling Biomedical Complex Systems
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
MetaVelvet-DL: a MetaVelvet deep learning extension for de novo metagenome assembly
How oligoclonal are germinal centers? A new method for estimating clonal diversity from immunohistological sections
SNPEVG: a graphical tool for GWAS graphing with mouse clicks
Robust flux balance analysis of multiscale biochemical reaction networks
Accurate peak list extraction from proteomic mass spectra for identification and profiling studies
Web-based interrogation of gene expression signatures using EXALT
Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity
IMSE: interaction information attention and molecular structure based drug drug interaction extraction
Correlation of geographical distribution of mycobacteriophages with genomic clusters and genome distance
Refining discordant gene trees
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information
Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors
MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis
Automated parameter estimation for biological models using Bayesian statistical model checking
Development, evaluation and application of 3D QSAR Pharmacophore model in the discovery of potential human renin inhibitors
Efficient inference of homologs in large eukaryotic pan-proteomes
Bioinformatic analyses of mammalian 5'-UTR sequence properties of mRNAs predicts alternative translation initiation sites
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins
"PolyMin" : software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation
Comparison of module detection algorithms in protein networks and investigation of the biological meaning of predicted modules
SEARCHPATTOOL: a new method for mining the most specific frequent patterns for binding sites with application to prokaryotic DNA sequences
Exploring the transcriptome of non-model oleaginous microalga Dunaliella tertiolecta through high-throughput sequencing and high performance computing
A hybrid gene selection method based on gene scoring strategy and improved particle swarm optimization
DeepSEA: an alignment-free explainable approach to annotate antimicrobial resistance proteins
SNPPicker: High quality tag SNP selection across multiple populations
G-bic: generating synthetic benchmarks for biclustering
Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties
Inferring the role of transcription factors in regulatory networks
L2-norm multiple kernel learning and its application to biomedical data fusion
Identification of transcription factor contexts in literature using machine learning approaches
A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes
rMotifGen: random motif generator for DNA and protein sequences
ADaM: augmenting existing approximate fast matching algorithms with efficient and exact range queries
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction
MCLCBA: multi-view contrastive learning network for RNA methylation site prediction
SNAD: Sequence Name Annotation-based Designer
Origin and evolution of gene families in Bacteria and Archaea
Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets
BAMarray TM : Java software for Bayesian analysis of variance for microarray data
Fangorn Forest (F2): a machine learning approach to classify genes and genera in the family Geminiviridae
LS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
Erratum to: Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server
Multiple genome comparison based on overlap regions of pairwise local alignments
HiCMC: High-Efficiency Contact Matrix Compressor
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
LDkit: a parallel computing toolkit for linkage disequilibrium analysis
Rprot-Vec: a deep learning approach for fast protein structure similarity calculation
Completing sparse and disconnected protein-protein network by deep learning
Correction to: GASAL2: a GPU accelerated sequence alignment library for high-throughput NGS data
Hierarchical modularity of nested bow-ties in metabolic networks
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data
Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction
Independent component analysis reveals new and biologically significant structures in micro array data
MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads
BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods
Modeling biochemical transformation processes and information processing with Narrator
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments
A DSSM network for inferring and prioritizing cell-type-specific regulons using single-cell RNA-seq data
LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system
An interpretable DIC risk prediction model based on convolutional neural networks with time series data
ICoVax 2013: The 3 rd ISV Pre-conference Computational Vaccinology Workshop
Learning by aggregating experts and filtering novices: a solution to crowdsourcing problems in bioinformatics
MoAIMS: efficient software for detection of enriched regions of MeRIP-Seq
A statistical framework for differential network analysis from microarray data
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis
Relation extraction for biological pathway construction using node2vec
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
Robust discovery of periodically expressed genes using the laplace periodogram
Copy-number-variation and copy-number-alteration region detection by cumulative plots
Influence of degree correlations on network structure and stability in protein-protein interaction networks
A support vector machine based test for incongruence between sets of trees in tree space
Recursive Cluster Elimination (RCE) for classification and feature selection from gene expression data
ClustalXeed : a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment
An algorithm for mapping positively selected members of quasispecies-type viruses
VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments
Inferring 3D chromatin structure using a multiscale approach based on quaternions
Diagnostic prediction of complex diseases using phase-only correlation based on virtual sample template
Structural studies on molecular mechanisms of Nelfinavir resistance caused by non-active site mutation V77I in HIV-1 protease
An eQTL biological data visualization challenge and approaches from the visualization community
DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs
Binding affinity prediction for protein-ligand complex using deep attention mechanism based on intermolecular interactions
A preliminary PET radiomics study of brain metastases using a fully automatic segmentation method
Evaluating the impact of topological protein features on the negative examples selection
On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
A computational framework for modeling and studying pertussis epidemiology and vaccination
MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis
Fast randomized approximate string matching with succinct hash data structures
CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization
JCBIE: a joint continual learning neural network for biomedical information extraction
SCATrans: semantic cross-attention transformer for drug-drug interaction predication through multimodal biomedical data
Classification of bioinformatics workflows using weighted versions of partitioning and hierarchical clustering algorithms
Conifer: clonal tree inference for tumor heterogeneity with single-cell and bulk sequencing data
An integrated approach for SNP calling based on population of genomes
ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay
fLPS: Fast discovery of compositional biases for the protein universe
Parallel tiled Nussinov RNA folding loop nest generated using both dependence graph transitive closure and loop skewing
A transformer model for cause-specific hazard prediction
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
Integrated QSAR study for inhibitors of hedgehog signal pathway against multiple cell lines: a collaborative filtering method
A model-independent approach to infer hierarchical codon substitution dynamics
The comprehensive updated regulatory network of Escherichia coli K-12
A combinational feature selection and ensemble neural network method for classification of gene expression data
Transcript quantification with RNA-Seq data
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data
The dynamics of alternative pathways to compensatory substitution
EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks
STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes