yusuke1997/dblp-id-title huggingface dataset:
CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing
MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data
A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
LCQS: an efficient lossless compression tool of quality scores with random access functionality
Research on predicting 2D-HP protein folding using reinforcement learning with full state space
Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons
Advanced analysis and visualization of gene copy number and expression data
A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi
Ranked retrieval of Computational Biology models
ENVirT: inference of ecological characteristics of viruses from metagenomic data
An assessment of catalytic residue 3D ensembles for the prediction of enzyme function
Reactome pathway analysis: a high-performance in-memory approach
Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14: 89
Modeling mis-folded lysozyme aggregates
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics
PRISE2: Software for designing sequence-selective PCR primers and probes
Metrics for GO based protein semantic similarity: a systematic evaluation
Classification of drug molecules considering their IC 50 values using mixed-integer linear programming based hyper-boxes method
A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes
A robust method for estimating gene expression states using Affymetrix microarray probe level data
Domain architecture conservation in orthologs
Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases
Beyond microarrays: Finding key transcription factors controlling signal transduction pathways
Feature extraction method for proteins based on Markov tripeptide by compressive sensing
Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer
Classification of protein quaternary structure by functional domain composition
Identification of recurrent regions of copy-number variants across multiple individuals
Comparison study of microarray meta-analysis methods
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning
Development of models for predicting Torsade de Pointes cardiac arrhythmias using perceptron neural networks
A combined approach to data mining of textual and structured data to identify cancer-related targets
HPG-DHunter: an ultrafast, friendly tool for DMR detection and visualization
Not proper ROC curves as new tool for the analysis of differentially expressed genes in microarray experiments
Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement
WEBnm@ v2.0: Web server and services for comparing protein flexibility
Simple and flexible classification of gene expression microarrays via Swirls and Ripples
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis
GCORE-sib: An efficient gene-gene interaction tool for genome-wide association studies based on discordant sib pairs
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology
RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets
Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks
KEGG orthology prediction of bacterial proteins using natural language processing
ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process
An improved string composition method for sequence comparison
Exploiting structural and topological information to improve prediction of RNA-protein binding sites
Peak picking NMR spectral data using non-negative matrix factorization
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification
MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
Transcript mapping based on dRNA-seq data
Multiple alignment and structure prediction of non-coding RNA sequences
Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops
Gene ontology based transfer learning for protein subcellular localization
Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images
Diagnostic and prognostic values of pyroptosis-related genes for the hepatocellular carcinoma
Indexing a protein-protein interaction network expedites network alignment
A cross-species alignment tool ( CAT )
OmicsVis: an interactive tool for visually analyzing metabolomics data
Browsing Isolated Population Data
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
Transcriptional network classifiers
ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries
OMWare: a tool for efficient assembly of genome-wide physical maps
A user-friendly web portal for T-Coffee on supercomputers
The EDKB: an established knowledge base for endocrine disrupting chemicals
A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation
Evaluating tools for transcription factor binding site prediction
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review
A NMF based approach for integrating multiple data sources to predict HIV-1-human PPIs
Does multi-way, long-range chromatin contact data advance 3D genome reconstruction?
Hellinger distance-based stable sparse feature selection for high-dimensional class-imbalanced data
Erratum to: 'Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images'
Correction to: Enhancing SVM for survival data using local invariances and weighting
Automatic pathway building in biological association networks
Primates and mouse NumtS in the UCSC Genome Browser
FGMP: assessing fungal genome completeness
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities
Conceiving an application ontology to model patient human papillomavirus vaccine counseling for dialogue management
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement
Avoiding background knowledge: literature based discovery from important information
Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function
BS-Seeker3: ultrafast pipeline for bisulfite sequencing
Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data
Correction to: The Kendrick modelling platform: language abstractions and tools for epidemiology
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes
NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference
SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency
New in silico approach to assessing RNA secondary structures with non-canonical base pairs
ISOL@: an Italian SOLAnaceae genomics resource
Protein Ranking by Semi-Supervised Network Propagation
Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder
Detecting epigenetic motifs in low coverage and metagenomics settings
Feature selection and nearest centroid classification for protein mass spectrometry
Data reduction for spectral clustering to analyze high throughput flow cytometry data
Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers
Guest editors' introduction to the Proceedings of the 9 th International Symposium on Biomedical Research and Applications
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
Efficient alignment-free DNA barcode analytics
Bidirectional best hit r -window gene clusters
Improved results in proteomics by use of local and peptide-class specific false discovery rates
CAraCAl: CAMML with the integration of chromatin accessibility
Reads2Type: a web application for rapid microbial taxonomy identification
S3QL: A distributed domain specific language for controlled semantic integration of life sciences data
A cell-level quality control workflow for high-throughput image analysis
Inferring transcript phylogenies
TFinDit: transcription factor-DNA interaction data depository
CircularLogo: A lightweight web application to visualize intra-motif dependencies
Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software)
Inferring clonal evolution of tumors from single nucleotide somatic mutations
The projection score - an evaluation criterion for variable subset selection in PCA visualization
robustica: customizable robust independent component analysis
The HHMI National Genomics Research Initiative at Western Kentucky University
Framework for a Protein Ontology
SplitTester : software to identify domains responsible for functional divergence in protein family
vivaGen - a survival data set generator for software testing
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks
Normalization for triple-target microarray experiments
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
KaBOB: ontology-based semantic integration of biomedical databases
MR-GGI: accurate inference of gene-gene interactions using Mendelian randomization
Hierarchical structural component modeling of microRNA-mRNA integration analysis
Hybridization thermodynamics of NimbleGen Microarrays
Mapping proteins to disease terminologies: from UniProt to MeSH
NestedMICA as an ab initio protein motif discovery tool
MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm
Incorporating gene co-expression network in identification of cancer prognosis markers
Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model
Deciphering transcriptional regulations coordinating the response to environmental changes
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach
HoughFeature, a novel method for assessing drug effects in three-color cDNA microarray experiments
PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies
Computational approaches for isoform detection and estimation: good and bad news
An efficient scRNA-seq dropout imputation method using graph attention network
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms
Moara: a Java library for extracting and normalizing gene and protein mentions
Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs
Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
Protein contact order prediction from primary sequences
CircPrimer: a software for annotating circRNAs and determining the specificity of circRNA primers
Unsupervised Bayesian linear unmixing of gene expression microarrays
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
A hierarchical opportunistic screening model for osteoporosis using machine learning applied to clinical data and CT images
Automatically transferring supervised targets method for segmenting lung lesion regions with CT imaging
A multimodal deep learning model to infer cell-type-specific functional gene networks
DiseaseNet: a transfer learning approach to noncommunicable disease classification
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
OncomiRdbB: a comprehensive database of microRNAs and their targets in breast cancer
Biodiversity Informatics: the emergence of a field
Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images
SAMPI: Protein Identification with Mass Spectra Alignments
CDK-Taverna: an open workflow environment for cheminformatics
Evaluation of sample size effect on the identification of haplotype blocks
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
3-Dimensional facial expression recognition in human using multi-points warping
ImiRP: a computational approach to microRNA target site mutation
NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors
NetworkPainter: dynamic intracellular pathway animation in Cytobank
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction
On deducing causality in metabolic networks
An in silico platform for the design of heterologous pathways in nonnative metabolite production
Morphometic analysis of TCGA glioblastoma multiforme
Accurate classification of white blood cells by coupling pre-trained ResNet and DenseNet with SCAM mechanism
The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases
A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
A theorem proving approach for automatically synthesizing visualizations of flow cytometry data
Integrated web service for improving alignment quality based on segments comparison
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data
Leveraging Bayesian networks and information theory to learn risk factors for breast cancer metastasis
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach
Recovering rearranged cancer chromosomes from karyotype graphs
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation
MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells
Two molecular measures of relatedness based on haplotype sharing
Direct construction of sparse suffix arrays with Libsais
Coding Prony's method in MATLAB and applying it to biomedical signal filtering
Automated peptide mapping and protein-topographical annotation of proteomics data
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
WATERS: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences
Gene selection for classification of microarray data based on the Bayes error
Image-based classification of plant genus and family for trained and untrained plant species
TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes
Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
PathBinder - text empirics and automatic extraction of biomolecular interactions
On pairwise distances and median score of three genomes under DCJ
catmap: Case-control And TDT Meta-Analysis Package
Exposure time independent summary statistics for assessment of drug dependent cell line growth inhibition
Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation
A flood-based information flow analysis and network minimization method for gene regulatory networks
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells
Multi-task learning for cross-platform siRNA efficacy prediction: an in-silico study
Pairwise ratio transformation of gene expression data leads to improved checkpoint response prediction in lung cancer patients
A fisheye viewer for microarray-based gene expression data
Comprehensive anticancer drug response prediction based on a simple cell line-drug complex network model
Spatial normalization of array-CGH data
Genoviz Software Development Kit: Java tool kit for building genomics visualization applications
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe
m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network
Deep clustering of protein folding simulations
Information-based methods for predicting gene function from systematic gene knock-downs
Bayesian model-based inference of transcription factor activity
A reverse-engineering approach to dissect post-translational modulators of transcription factor's activity from transcriptional data
A Dynamic Noise Level Algorithm for Spectral Screening of Peptide MS/MS Spectra
Bioinformatic analysis of gene regulation in Geobacter sulfurreducens
Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0
From genes to functional classes in the study of biological systems
microclass: an R-package for 16S taxonomy classification
G-Bean: an ontology-graph based web tool for biomedical literature retrieval
Feature-specific quantile normalization and feature-specific mean-variance normalization deliver robust bi-directional classification and feature selection performance between microarray and RNAseq data
Multi-domain semantic similarity in biomedical research
Calculating the most likely intron splicing orders in S. pombe, fruit fly, Arabidopsis thaliana, and humans
Erratum to: Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction
SimCAL: a flexible tool to compute biochemical reaction similarity
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT ® standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences
Integrated analysis of DNA copy number and gene expression microarray data using gene sets
JunctionViewer: customizable annotation software for repeat-rich genomic regions
Enumeration method for tree-like chemical compounds with benzene rings and naphthalene rings by breadth-first search order
Towards realistic benchmarks for multiple alignments of non-coding sequences
Mendelian randomisation analysis of clustered causal effects of body mass on cardiometabolic biomarkers
NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences
Erratum to: Improving protein order-disorder classification using charge-hydropathy plots
Multichromosomal median and halving problems under different genomic distances
A methodology to assess the intrinsic discriminative ability of a distance function and its interplay with clustering algorithms for microarray data analysis
Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty
Heterozygous genome assembly via binary classification of homologous sequence
Using genomic signatures for HIV-1 sub-typing
GrAPFI: predicting enzymatic function of proteins from domain similarity graphs
Biomedical event extraction based on GRU integrating attention mechanism
Indicators for the Data Usage Index (DUI): an incentive for publishing primary biodiversity data through global information infrastructure
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition
Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38
XcisClique: analysis of regulatory bicliques
FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities
Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone
A new regularized least squares support vector regression for gene selection
Hypoxia classifier for transcriptome datasets
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction
Microarray analysis and quantitative real-time PCR validation of gene expression during auditory hair cell regeneration in zebrafish ( Danio rerio )
Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis
Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology
Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information
Hybrid attentional memory network for computational drug repositioning
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine
RUBic: rapid unsupervised biclustering
An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients
GenPhyloData: realistic simulation of gene family evolution
Predicting viral proteins that evade the innate immune system: a machine learning-based immunoinformatics tool
Integrative analysis workflow for the structural and functional classification of C-type lectins
A signature of immune-related genes correlating with clinical prognosis and immune microenvironment in sepsis
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS
STELLAR: fast and exact local alignments
vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
Direct calibration of PICKY-designed microarrays
An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma 66 promoters
Recommendations for performance optimizations when using GATK3.8 and GATK4
SubMDTA: drug target affinity prediction based on substructure extraction and multi-scale features
Integration of the Gene Ontology into an object-oriented architecture
Mining FDA drug labels using an unsupervised learning technique - topic modeling
Comparison of lists of genes based on functional profiles