yusuke1997/dblp-id-title huggingface dataset:
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features
Research Electronic Data Capture (REDCap) - planning, collecting and managing data for clinical and translational research
A network model for angiogenesis in ovarian cancer
Correction to: Detailed prediction of protein sub-nuclear localization
Machine learning methods for metabolic pathway prediction
Multiple sequence alignments of partially coding nucleic acid sequences
Advantages of using graph databases to explore chromatin conformation capture experiments
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics
Combining techniques for screening and evaluating interaction terms on high-dimensional time-to-event data
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships
Using optimal control to understand complex metabolic pathways
polyClustR: defining communities of reconciled cancer subtypes with biological and prognostic significance
A Perl procedure for protein identification by Peptide Mass Fingerprinting
ProTrack3D: a comprehensive tool for segmentation and tracking of proteins with split and fusion
Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features
CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data
Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks
Automatic delineation of malignancy in histopathological head and neck slides
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function
A systematic strategy for the discovery of candidate genes responsible for phenotypic variation
Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment
geneHapR: an R package for gene haplotypic statistics and visualization
Calibur: a tool for clustering large numbers of protein decoys
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets
CNN-DDI: a learning-based method for predicting drug-drug interactions using convolution neural networks
Calling SNPs without a reference sequence
ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research
Classification of microarrays; synergistic effects between normalization, gene selection and machine learning
Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats
The Biodiversity Informatics Potential Index
eXamine: Exploring annotated modules in networks
Spatial rank-based multifactor dimensionality reduction to detect gene-gene interactions for multivariate phenotypes
An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH
Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
Investigating skewness to understand gene expression heterogeneity in large patient cohorts
Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships
BSXplorer: analytical framework for exploratory analysis of BS-seq data
iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website
Motivated Proteins: A web application for studying small three-dimensional protein motifs
Analysis of energy-based algorithms for RNA secondary structure prediction
GPCRs from fusarium graminearum detection, modeling and virtual screening - the search for new routes to control head blight disease
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining
Collectively encoding protein properties enriches protein language models
Predicting protein subcellular locations using hierarchical ensemble of Bayesian classifiers based on Markov chains
V-MitoSNP: visualization of human mitochondrial SNPs
Putative markers for the detection of early-stage bladder cancer selected by urine metabolomics
SeqAn An efficient, generic C++ library for sequence analysis
CANTARE: finding and visualizing network-based multi-omic predictive models
EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast
tRigon: an R package and Shiny App for integrative (path-)omics data analysis
Statistical modeling of STR capillary electrophoresis signal
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network
Gene Fusion Markup Language: a prototype for exchanging gene fusion data
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas
Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS)
Covariance regression with random forests
A semi-automated technique for labeling and counting of apoptosing retinal cells
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG
Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers
Evolution of 3'UTR-associated RNAs
Mining protein loops using a structural alphabet and statistical exceptionality
Rational selection of experimental readout and intervention sites for reducing uncertainties in computational model predictions
BLProt: Prediction of bioluminescent proteins based on Support Vector Machine and ReliefF feature selection
Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets
FAVR (Filtering and Annotation of Variants that are Rare): methods to facilitate the analysis of rare germline genetic variants from massively parallel sequencing datasets
Predicting blood pressure from physiological index data using the SVR algorithm
A website to identify shared genes in Saccharomyces cerevisiae homozygous deletion library screens
The 2006 Automated Function Prediction Meeting
Adaptive filtering of microarray gene expression data based on Gaussian mixture decomposition
Heuristics for the inversion median problem
Predictive modelling using pathway scores: robustness and significance of pathway collections
Correction to: Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
Using coevolution to improve protein subfamily classification
Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms
EXACT2: the semantics of biomedical protocols
phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics
HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2
False occurrences of functional motifs in protein sequences highlight evolutionary constraints
Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis
On the persistence of supplementary resources in biomedical publications
Prodigy protein: Python package for zero-shot protein engineering using protein language models
Strategies for measuring evolutionary conservation of RNA secondary structures
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes
Efficient iterative Hi-C scaffolder based on N-best neighbors
Stochastic Lanczos estimation of genomic variance components for linear mixed-effects models
Mapping data elements to terminological resources for integrating biomedical data sources
Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways
An efficient exact algorithm for computing all pairwise distances between reconciliations in the duplication-transfer-loss model
Computationally efficient multi-sample flow cytometry data analysis using Gaussian mixture models
WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis
A new cross-platform architecture for epi-info software suite
RGmatch: matching genomic regions to proximal genes in omics data integration
Denoiseit: denoising gene expression data using rank based isolation trees
Evaluation of potential role of Atp5g3 in modulating alcohol preference and obesity
A Grid-based solution for management and analysis of microarrays in distributed experiments
MVDA: a multi-view genomic data integration methodology
CapsNet-SSP: multilane capsule network for predicting human saliva-secretory proteins
ProtPlat: an efficient pre-training platform for protein classification based on FastText
SPoRE: a mathematical model to predict double strand breaks and axis protein sites in meiosis
Context-specific functional module based drug efficacy prediction
Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation
A comparative study of conservation and variation scores
Toward PWAS: discovering pathways associated with human disorders
Polyphony: superposition independent methods for ensemble-based drug discovery
Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer
Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals
fagin: synteny-based phylostratigraphy and finer classification of young genes
Structural disorder of plasmid-encoded proteins in Bacteria and Archaea
Literature data-based de novo candidates for drug repurposing
Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma
Visualising very large phylogenetic trees in three dimensional hyperbolic space
PyGNA: a unified framework for geneset network analysis
Array-A-Lizer: A serial DNA microarray quality analyzer
GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach
Time-dependent ARMA modeling of genomic sequences
TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach
GEN3VA: aggregation and analysis of gene expression signatures from related studies
The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web
High-throughput identification of interacting protein-protein binding sites
Analysis and modelling of motility of cell populations with MotoCell
DI2: prior-free and multi-item discretization of biological data and its applications
Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis
Coronavirus 3CL pro proteinase cleavage sites: Possible relevance to SARS virus pathology
EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
PMS5: an efficient exact algorithm for the (l, d)-motif finding problem
PALSSE: A program to delineate linear secondary structural elements from protein structures
Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation
Motif Tool Manager: a web-based platform for motif discovery
An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data
Comparative genomics meets topology: a novel view on genome median and halving problems
ReCSAI: recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy
Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods
BEST: a web server for brain expression Spatio-temporal pattern analysis
Predicting DNA-binding sites of proteins from amino acid sequence
HiCcompare: an R-package for joint normalization and comparison of HI-C datasets
ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery
Analysis and prediction of human acetylation using a cascade classifier based on support vector machine
Automated seeding of specialised wiki knowledgebases with BioKb
Identification of putative domain linkers by a neural network - application to a large sequence database
Stability of gene contributions and identification of outliers in multivariate analysis of microarray data
Protein-protein interaction based on pairwise similarity
Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments
Sparse regression models for unraveling group and individual associations in eQTL mapping
GOTA: GO term annotation of biomedical literature
Performance improvement for a 2D convolutional neural network by using SSC encoding on protein-protein interaction tasks
Investigating heterogeneous protein annotations toward cross-corpora utilization
A protein interaction based model for schizophrenia study
Correction: G-bic: generating synthetic benchmarks for biclustering
Transforming L1000 profiles to RNA-seq-like profiles with deep learning
Base-pair ambiguity and the kinetics of RNA folding
Identification of coherent patterns in gene expression data using an efficient biclustering algorithm and parallel coordinate visualization
Efficient analysis and extraction of MS/MS result data from Mascot TM result files
Evaluation of the impact of Illumina error correction tools on de novo genome assembly
Novel domain expansion methods to improve the computational efficiency of the Chemical Master Equation solution for large biological networks
penalizedclr: an R package for penalized conditional logistic regression for integration of multiple omics layers
Erratum to: Integrating mean and variance heterogeneities to identify differentially expressed genes
DriverSub-SVM: a machine learning approach for cancer subtype classification by integrating patient-specific and global driver genes
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information
A structural analysis of in vitro catalytic activities of hammerhead ribozymes
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients
Protein language models uncover carbohydrate-active enzyme function in metagenomics
Classifying short genomic fragments from novel lineages using composition and homology
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction
Classifying kinase conformations using a machine learning approach
Robustness evaluations of pathway activity inference methods on gene expression data
Computational reconstruction of proteome-wide protein interaction networks between HTLV retroviruses and Homo sapiens
Rule-based spatial modeling with diffusing, geometrically constrained molecules
Motif-directed network component analysis for regulatory network inference
MOSBIE: a tool for comparison and analysis of rule-based biochemical models
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction
Protein structure similarity from principle component correlation analysis
Uncovering transcriptional interactions via an adaptive fuzzy logic approach
Efficient discovery of responses of proteins to compounds using active learning
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data
NoRCE: non-coding RNA sets cis enrichment tool
Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach
FELLA: an R package to enrich metabolomics data
PASTRY: achieving balanced power for detecting risk and protective minor alleles in meta-analysis of association studies with overlapping subjects
TopoFilter: a MATLAB package for mechanistic model identification in systems biology
GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis
Correction of scaling mismatches in oligonucleotide microarray data
A global optimization algorithm for protein surface alignment
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network
InCoB2012 Conference: from biological data to knowledge to technological breakthroughs
Comparative analyses of bidirectional promoters in vertebrates
A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies
scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis
Bioinformatics approach to predict target genes for dysregulated microRNAs in hepatocellular carcinoma: study on a chemically-induced HCC mouse model
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome
Random number generation for DNA-based security circuitry
Algorithmic tools for tripartite data analysis
ISU FLUture: a veterinary diagnostic laboratory web-based platform to monitor the temporal genetic patterns of Influenza A virus in swine
Deriving stratified effects from joint models investigating gene-environment interactions
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs
Single-character insertion-deletion model preserves long indels in ancestral sequence reconstruction
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations
MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets
Evolution of orthologous tandemly arrayed gene clusters
Chromhome: A rich internet application for accessing comparative chromosome homology maps
Improvements in viral gene annotation using large language models and soft alignments
A multivariate Poisson-log normal mixture model for clustering transcriptome sequencing data
SuperLigands - a database of ligand structures derived from the Protein Data Bank
Mathematical modeling of the immune system recognition to mammary carcinoma antigen
In silico experimental evolution: a tool to test evolutionary scenarios
GBParsy: A GenBank flatfile parser library with high speed
Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL
Spatial location and its relevance for terminological inferences in bio-ontologies
A protein domain interaction interface database: InterPare
Template-based C8-SCORPION: a protein 8-state secondary structure prediction method using structural information and context-based features
Sensitive detection of pathway perturbations in cancers
Inconsistencies over time in 5% of NetAffx probe-to-gene annotations
Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images
Major copy proportion analysis of tumor samples using SNP arrays
A phenome-guided drug repositioning through a latent variable model
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification
MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature
Regulation of metabolic networks by small molecule metabolites
2-D chemical structure image-based in silico model to predict agonist activity for androgen receptor
Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
Essentiality and centrality in protein interaction networks revisited
Prioritizing candidate diseases-related metabolites based on literature and functional similarity
Drug repositioning based on individual bi-random walks on a heterogeneous network
Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
DeepWalk based method to predict lncRNA-miRNA associations via lncRNA-miRNA-disease-protein-drug graph
MyClone: rapid and precise reconstruction of clonal population structures for tumors
Replication of epistatic DNA loci in two case-control GWAS studies using OPE algorithm
Deep self-supervised machine learning algorithms with a novel feature elimination and selection approaches for blood test-based multi-dimensional health risks classification
Comparison of phosphorylation patterns across eukaryotes by discriminative N-gram analysis
Accurate assembly of full-length consensus for viral quasispecies
Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis
RACS: rapid analysis of ChIP-Seq data for contig based genomes
Genome alignment with graph data structures: a comparison
Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease
HMCDA: a novel method based on the heterogeneous graph neural network and metapath for circRNA-disease associations prediction
ProbABEL package for genome-wide association analysis of imputed data
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
Domainoid: domain-oriented orthology inference
Between proteins and phenotypes: annotation and interpretation of mutations
New methods to measure residues coevolution in proteins
Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem
Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization
Screening of selective histone deacetylase inhibitors by proteochemometric modeling
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
Benchmarking and refining probability-based models for nucleosome-DNA interaction
MosaicIA: an ImageJ/Fiji plugin for spatial pattern and interaction analysis
Boosting for high-dimensional two-class prediction
Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays
DeeP4med: deep learning for P4 medicine to predict normal and cancer transcriptome in multiple human tissues
A powerful association for comorbidity analysis based on score based test
VAliBS: a visual aligner for bisulfite sequences
Data-driven discovery of seasonally linked diseases from an Electronic Health Records system
PDRLGB: precise DNA-binding residue prediction using a light gradient boosting machine
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer
Enriching a biomedical event corpus with meta-knowledge annotation
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning
Redundancy analysis allows improved detection of methylation changes in large genomic regions
Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration