yusuke1997/dblp-id-title huggingface dataset:
rNAV 2.0: a visualization tool for bacterial sRNA-mediated regulatory networks mining
AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing
A structured overview of simultaneous component based data integration
A novel data mining method to identify assay-specific signatures in functional genomic studies
De novo Nanopore read quality improvement using deep learning
ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons
Network analysis of genes regulated in renal diseases: implications for a molecular-based classification
Domain fusion analysis by applying relational algebra to protein sequence and domain databases
A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank
Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups
Iterative approach to model identification of biological networks
Ensemble-based prediction of RNA secondary structures
In-vitro diagnosis of single and poly microbial species targeted for diabetic foot infection using e-nose technology
A boosting approach for prediction of protein-RNA binding residues
P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps
SNP calling by sequencing pooled samples
Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures
PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation
R2R - software to speed the depiction of aesthetic consensus RNA secondary structures
FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy
Transcriptome analysis of breast cancer in African American women
Analysis of significant factors for dengue fever incidence prediction
Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data
Curation of complex, context-dependent immunological data
Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets
ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs
SVAT: Secure outsourcing of variant annotation and genotype aggregation
Using hexamers to predict cis-regulatory motifs in Drosophila
PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes
Analysis on relationship between extreme pathways and correlated reaction sets
ORFik: a comprehensive R toolkit for the analysis of translation
Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data
Enhanced CT combined with texture analysis for differential diagnosis of pleomorphic adenoma and adenolymphoma
Knowledge-augmented pre-trained language models for biomedical relation extraction
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder
ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology
Statistical significance of quantitative PCR
MolTalk - a programming library for protein structures and structure analysis
Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments
Competition between protein aggregation and protein complex formation
Identification and analysis of conserved pockets on protein surfaces
I-TASSER server for protein 3D structure prediction
Frequent contiguous pattern mining over biological sequences of protein misfolded diseases
CAT: computer aided triage improving upon the Bayes risk through ε-refusal triage rules
Gradient boosting with knockoff filters: a biostatistical approach to variable selection
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA-protein interaction identification
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community
SummonChimera infers integrated viral genomes with nucleotide precision from NGS data
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families
Discovering multi-level structures in bio-molecular data through the Bernstein inequality
Moonlighting protein prediction using physico-chemical and evolutional properties via machine learning methods
A first principles approach to differential expression in microarray data analysis
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation
A computational approach based on the colored Petri net formalism for studying multiple sclerosis
Reliable genomic strategies for species classification of plant genetic resources
NeuRank: learning to rank with neural networks for drug-target interaction prediction
Comparative optimism in models involving both classical clinical and gene expression information
A copula method for modeling directional dependence of genes
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model
APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools
Bayesian statistical modelling of human protein interaction network incorporating protein disorder information
Protein function prediction through multi-view multi-label latent tensor reconstruction
Computational method for reducing variance with Affymetrix microarrays
Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq
Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
Reconciliation-based detection of co-evolving gene families
ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data
IIMLP: integrated information-entropy-based method for LncRNA prediction
Using expected sequence features to improve basecalling accuracy of amplicon pyrosequencing data
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
MIWE: detecting the critical states of complex biological systems by the mutual information weighted entropy
Subsystems-based servers for rapid annotation of genomes and metagenomes
Correcting ligands, metabolites, and pathways
The impact of measurement errors in the identification of regulatory networks
Diagnosing Lassa virus infection by tracking the antiviral response
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions
A MATLAB-based app to improve LC-MS/MS data analysis for N-linked glycan peak identification
Visualization of protein interaction networks: problems and solutions
Non-Markovian effects on protein sequence evolution due to site dependent substitution rates
PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Calcium (Ca2+) waves data calibration and analysis using image processing techniques
Investigating perturbed pathway modules from gene expression data via structural equation models
Detection of gene pathways with predictive power for breast cancer prognosis
SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data
Estimation of mosaic loss of Y chromosome cell fraction with genotyping arrays lacking coverage in the pseudoautosomal region
CURE-SMOTE algorithm and hybrid algorithm for feature selection and parameter optimization based on random forests
ConSole: using modularity of contact maps to locate Solenoid domains in protein structures
Identifying dysregulated pathways in cancers from pathway interaction networks
Probabilistic topic modeling for the analysis and classification of genomic sequences
Incorporating time-delays in S-System model for reverse engineering genetic networks
Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy
An infrastructure for precision medicine through analysis of big data
Probabilistic estimation of microarray data reliability and underlying gene expression
A Markov blanket-based method for detecting causal SNPs in GWAS
Toward the automated generation of genome-scale metabolic networks in the SEED
AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU
Semi-supervised Learning for the BioNLP Gene Regulation Network
Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design
PFBNet: a priori-fused boosting method for gene regulatory network inference
MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution
Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning
Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences
Visualizing the knowledge structure and evolution of bioinformatics
Computational analyses of curcuminoid analogs against kinase domain of HER2
Pysim-sv: a package for simulating structural variation data with GC-biases
Multi-location gram-positive and gram-negative bacterial protein subcellular localization using gene ontology and multi-label classifier ensemble
Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files
SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants
Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability
Analysis of X-ray Structures of Matrix Metalloproteinases via Chaotic Map Clustering
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites
Leveraging domain information to restructure biological prediction
Googling DNA sequences on the World Wide Web
VTBuilder: a tool for the assembly of multi isoform transcriptomes
Squid - a simple bioinformatics grid
Structure alignment based on coding of local geometric measures
Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences
M-AMST: an automatic 3D neuron tracing method based on mean shift and adapted minimum spanning tree
Selective prediction of interaction sites in protein structures with THEMATICS
GVC: efficient random access compression for gene sequence variations
Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference
Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products
lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation
Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree
Lower bounds on multiple sequence alignment using exact 3-way alignment
A proximity-based graph clustering method for the identification and application of transcription factor clusters
MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing
Correlated fragile site expression allows the identification of candidate fragile genes involved in immunity and associated with carcinogenesis
Sparse logistic regression with a L1/2 penalty for gene selection in cancer classification
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms
Local data commons: the sleeping beauty in the community of data commons
ROBOT: A Tool for Automating Ontology Workflows
Generating confidence intervals on biological networks
Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes
Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage
Fast ancestral gene order reconstruction of genomes with unequal gene content
MAFcounter: an efficient tool for counting the occurrences of k-mers in MAF files
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines
Prediction of super-secondary structure in alpha-helical and beta-barrel transmembrane proteins
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues
Reverse engineering gene regulatory network from microarray data using linear time-variant model
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP
Raman spectroscopy-based prediction of ofloxacin concentration in solution using a novel loss function and an improved GA-CNN model
BAC-browser: the tool for synthetic biology
Successful classification of cocaine dependence using brain imaging: a generalizable machine learning approach
ParticleCall: A particle filter for base calling in next-generation sequencing systems
Bioinformatics recipes: creating, executing and distributing reproducible data analysis workflows
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana
Molecular cancer classification using a meta-sample-based regularized robust coding method
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment
Whole genome association mapping by incompatibilities and local perfect phylogenies
BioReader: a text mining tool for performing classification of biomedical literature
Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data
MAE-FMD: Multi-agent evolutionary method for functional module detection in protein-protein interaction networks
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction
Identifying mutation regions for closely related individuals without a known pedigree
Direct maximum parsimony phylogeny reconstruction from genotype data
Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes
Detecting long tandem duplications in genomic sequences
Adaptive diffusion kernel learning from biological networks for protein function prediction
SEMgsa: topology-based pathway enrichment analysis with structural equation models
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures
Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions
SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models
Large-scale reverse docking profiles and their applications
Roastgsa: a comparison of rotation-based scores for gene set enrichment analysis
DOVIS: an implementation for high-throughput virtual screening using AutoDock
Colonyzer: automated quantification of micro-organism growth characteristics on solid agar
Predicting RNA-Protein Interactions Using Only Sequence Information
Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines
HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features
pcrEfficiency: a Web tool for PCR amplification efficiency prediction
Using BERT to identify drug-target interactions from whole PubMed
Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins
Machine learning to reveal an astute risk predictive framework for Gynecologic Cancer and its impact on women psychology: Bangladeshi perspective
Methods for discovering genomic loci exhibiting complex patterns of differential methylation
Computational prediction of plasma protein binding of cyclic peptides from small molecule experimental data using sparse modeling techniques
Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering
Copy number variation genotyping using family information
Extractor for ESI quadrupole TOF tandem MS data enabled for high throughput batch processing
Inferring gene expression dynamics via functional regression analysis
A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data
Network-based functional enrichment
Clustering cancer gene expression data: a comparative study
A tutorial in displaying mass spectrometry-based proteomic data using heat maps
A novel statistical approach for identification of the master regulator transcription factor
Dynamic Probabilistic Threshold Networks to Infer Signaling Pathways from Time-Course Perturbation Data
DNLC: differential network local consistency analysis
Biologically relevant effects of mRNA amplification on gene expression profiles
ASPDock: protein-protein docking algorithm using atomic solvation parameters model
m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Intrinsic limitations in mainstream methods of identifying network motifs in biology
The Ninth Asia Pacific Bioinformatics Conference (APBC2011)
RAG: An Update to the RNA-As-Graphs Resource
Evaluation of copy number variation detection for a SNP array platform
MCL-CAw: a refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure
Multi-resBind: a residual network-based multi-label classifier for in vivo RNA binding prediction and preference visualization
NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories
Graph embeddings on gene ontology annotations for protein-protein interaction prediction
Individualized markers optimize class prediction of microarray data
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation
HerpesDRG: a comprehensive resource for human herpesvirus antiviral drug resistance genotyping
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset's complexity
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation
Molecular evolution of dihydrouridine synthases
Evaluation of time profile reconstruction from complex two-color microarray designs
Peptide ligand screening of alpha-synuclein aggregation modulators by in silico panning
Simultaneous identification of long similar substrings in large sets of sequences
An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917
An incremental approach to automated protein localisation
Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies
Entities, relations, events: representing biomolecular semantics
A proposed metric for assessing the measurement quality of individual microarrays
Reuse of terminological resources for efficient ontological engineering in Life Sciences
Building a knowledge base to assist clinical decision-making using the Pediatric Research Database (PRD) and machine learning: a case study on pediatric asthma patients
AlzPharm: integration of neurodegeneration data using RDF
Slim-Prim: an integrated data system for clinical and translational research
A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping
FACT - a framework for the functional interpretation of high-throughput experiments
flowVS: channel-specific variance stabilization in flow cytometry
A parametric survival model with bayesian structural equation based on multi-omics integration
Predicting PDZ domain mediated protein interactions from structure
Modeling heterocyst pattern formation in cyanobacteria
Reference-based genome compression using the longest matched substrings with parallelization consideration
Control procedures and estimators of the false discovery rate and their application in low-dimensional settings: an empirical investigation
Lower expression of genes near microRNA in C. elegans germline
STEM: a tool for the analysis of short time series gene expression data
A feature selection approach for identification of signature genes from SAGE data
SparkEC: speeding up alignment-based DNA error correction tools
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment
The modeled structure of the RNA dependent RNA polymerase of GBV-C Virus suggests a role for motif E in Flaviviridae RNA polymerases
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
FASTAFS: file system virtualisation of random access compressed FASTA files
SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics
Design of microarray probes for virus identification and detection of emerging viruses at the genus level
CFVisual: an interactive desktop platform for drawing gene structure and protein architecture
Learning to detect boundary information for brain image segmentation
mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing
A novel method for high accuracy sumoylation site prediction from protein sequences
F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks
Mining impactful discoveries from the biomedical literature
A practical comparison of two K-Means clustering algorithms
Themes in biomedical natural language processing: BioNLP08
The Kendrick modelling platform: language abstractions and tools for epidemiology
A novel application of motion analysis for detecting stress responses in embryos at different stages of development
Integrating genetic and gene expression data in network-based stratification analysis of cancers
Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays
Deconvolution of gene expression from cell populations across the C. elegans lineage
HybGFS: a hybrid method for genome-fingerprint scanning
Exact approaches for scaffolding
Efficient error correction for next-generation sequencing of viral amplicons
virtualArray: a R/bioconductor package to merge raw data from different microarray platforms
2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib
Booly: a new data integration platform
Edge detection in microscopy images using curvelets
Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations