yusuke1997/dblp-id-title huggingface dataset:
DRfit: a Java tool for the analysis of discrete data from multi-well plate assays
Sparse canonical methods for biological data integration: application to a cross-platform study
A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality
Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting
An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment
An adaptive bin framework search method for a beta-sheet protein homopolymer model
ACG: rapid inference of population history from recombining nucleotide sequences
(PS) 2 -v2: template-based protein structure prediction server
Compression of next-generation sequencing quality scores using memetic algorithm
Ab initio and homology based prediction of protein domains by recursive neural networks
Cytokit: a single-cell analysis toolkit for high dimensional fluorescent microscopy imaging
Graph-based iterative Group Analysis enhances microarray interpretation
Analyzing the simplicial decomposition of spatial protein structures
MINE: Module Identification in NEtworks
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
PVT: an efficient computational procedure to speed up next-generation sequence analysis
Automated recognition of malignancy mentions in biomedical literature
VARUS: sampling complementary RNA reads from the sequence read archive
Nestor3D: multiple alignment of protein structures based on ligand or prosthetic group position
DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity
Identification of QTLs controlling gene expression networks defined a priori
TESTLoc: protein subcellular localization prediction from EST data
Development of electronic medical records for clinical and research purposes: the breast cancer module using an implementation framework in a middle income country- Malaysia
Dynamic covariation between gene expression and proteome characteristics
Prediction of plant secondary metabolic pathways using deep transfer learning
Identification of DNA-binding proteins using multi-features fusion and binary firefly optimization algorithm
Considering scores between unrelated proteins in the search database improves profile comparison
Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites
A framework for predictive modeling of microbiome multi-omics data: latent interacting variable-effects (LIVE) modeling
Interactive visual exploration of overlapping similar structures for three-dimensional microscope images
JISTIC: Identification of Significant Targets in Cancer
Alvis: a tool for contig and read ALignment VISualisation and chimera detection
PhyteByte: identification of foods containing compounds with specific pharmacological properties
A Regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data
HPG pore: an efficient and scalable framework for nanopore sequencing data
A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling
Assessing the impact of exact reads on reducing the error rate of read mapping
GECO: gene expression clustering optimization app for non-linear data visualization of patterns
Galaxy CloudMan: delivering cloud compute clusters
From the desktop to the grid: scalable bioinformatics via workflow conversion
Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab
puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis
Using a logical model to predict the growth of yeast
Automatic extraction of reliable regions from multiple sequence alignments
Application of a correlation correction factor in a microarray cross-platform reproducibility study
Combining spatial and chemical information for clustering pharmacophores
BATVI: Fast, sensitive and accurate detection of virus integrations
Detection of internal exon deletion with exon Del
Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training
A note on generalized Genome Scan Meta-Analysis statistics
DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences
A computational and analysis tool for proteomics research
MOST: most-similar ligand based approach to target prediction
VANTED: A system for advanced data analysis and visualization in the context of biological networks
Caryoscope: An Open Source Java application for viewing microarray data in a genomic context
GO-based Functional Dissimilarity of Gene Sets
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis
In silico method for systematic analysis of feature importance in microRNA-mRNA interactions
Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast
G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
HMMvar-func: a new method for predicting the functional outcome of genetic variants
PaPI: pseudo amino acid composition to score human protein-coding variants
BaPreS: a software tool for predicting bacteriocins using an optimal set of features
Principal component tests: applied to temporal gene expression data
A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
Cancer characterization and feature set extraction by discriminative margin clustering
CNVDeep: deep association of copy number variants with neurocognitive disorders
LongStitch: high-quality genome assembly correction and scaffolding using long reads
Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence
Value of gadoxetic acid-enhanced MRI for microvascular invasion of small hepatocellular carcinoma: a retrospective study
EPMLR: Sequence-based linear B-cell epitope prediction method using multiple linear regression
DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination
RSEARCH: Finding homologs of single structured RNA sequences
Review of medical image recognition technologies to detect melanomas using neural networks
3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction
Overview of BioCreAtIvE task 1B: normalized gene lists
A novel min-cost flow method for estimating transcript expression with RNA-Seq
Transmembrane helix prediction using amino acid property features and latent semantic analysis
K i DoQ: using docking based energy scores to develop ligand based model for predicting antibacterials
FastQTLmapping: an ultra-fast and memory efficient package for mQTL-like analysis
HPIDB - a unified resource for host-pathogen interactions
A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees
Real-time interactive data mining for chemical imaging information: application to automated histopathology
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis
A novel parametric approach to mine gene regulatory relationship from microarray datasets
B.E.A.R. GeneInfo: A tool for identifying gene-related biomedical publications through user modifiable queries
CCL-DTI: contributing the contrastive loss in drug-target interaction prediction
Parametric and non-parametric gradient matching for network inference: a comparison
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking
LM-Merger: a workflow for merging logical models with an application to gene regulatory network models
HeMoQuest: a webserver for qualitative prediction of transient heme binding to protein motifs
A decision theory paradigm for evaluating identifier mapping and filtering methods using data integration
Eliciting candidate anatomical routes for protein interactions: a scenario from endocrine physiology
An algorithm for chemical genomic profiling that minimizes batch effects: Bucket evaluations
Response projected clustering for direct association with physiological and clinical response data
The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes
Willows: a memory efficient tree and forest construction package
Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents
Predicting drug-disease associations by using similarity constrained matrix factorization
A transversal approach to predict gene product networks from ontology-based similarity
The influence of sample biases on estimations of marine microbial diversity
Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
DynGO: a tool for visualizing and mining of Gene Ontology and its associations
Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers
BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment
Crossfit analysis: a novel method to characterize the dynamics of induced plant responses
Robust imputation method for missing values in microarray data
Boolean implication analysis unveils candidate universal relationships in microbiome data
Base calling for high-throughput short-read sequencing: dynamic programming solutions
Pairwise alignment of nucleotide sequences using maximal exact matches
Identification of highly synchronized subnetworks from gene expression data
DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms
Model of visual attention for video sequences
Identifying tandem Ankyrin repeats in protein structures
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data
Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable
Exploring the functional composition of the human microbiome using a hand-curated microbial trait database
Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data
A machine learning approach for viral genome classification
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
Utilizing RNA-seq data in monotone iterative generalized linear model to elevate prior knowledge quality of the circRNA-miRNA-mRNA regulatory axis
Efficient test for nonlinear dependence of two continuous variables
Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data
Predicting the protein-protein interactions using primary structures with predicted protein surface
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
ABC: software for interactive browsing of genomic multiple sequence alignment data
PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies
A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis
Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells
DrugQuest - a text mining workflow for drug association discovery
Intelligent fluorescence image analysis of giant unilamellar vesicles using convolutional neural network
TAFFEL: Independent Enrichment Analysis of gene sets
FluxCTTX: A LIMS-based tool for management and analysis of cytotoxicity assays data
Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images
Near-optimal assembly for shotgun sequencing with noisy reads
LDpop: an interactive online tool to calculate and visualize geographic LD patterns
Link prediction in drug-target interactions network using similarity indices
Identification of concepts bridging diverse biomedical domains
miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
Genome dedoubling by DCJ and reversal
In-silico discovery of cancer-specific peptide-HLA complexes for targeted therapy
Difference-based clustering of short time-course microarray data with replicates
GC/MS Based Metabolomics: Development of a Data Mining System for Metabolite Identification by using Soft Independent Modeling of Class Analogy (SIMCA)
Prediction and interpretation of miRNA-disease associations based on miRNA target genes using canonical correlation analysis
Collective prediction of protein functions from protein-protein interaction networks
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation
Raman2imzML converts Raman imaging data into the standard mass spectrometry imaging format
Cross-population analysis for functional characterization of type II diabetes variants
Applying dynamic Bayesian networks to perturbed gene expression data
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
Deep learning approach for early prediction of COVID-19 mortality using chest X-ray and electronic health records
A pan-cancer somatic mutation embedding using autoencoders
RRCRank: a fusion method using rank strategy for residue-residue contact prediction
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry
Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology
Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR
Estimating genealogies from linked marker data: a Bayesian approach
Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes
A method to incorporate prior information into score test for genetic association studies
Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach
An effective approach to detecting both small and large complexes from protein-protein interaction networks
Efficient automatic 3D segmentation of cell nuclei for high-content screening
Characterization of phylogenetic networks with NetTest
Partitioning of functional gene expression data using principal points
Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS
Analysis of biomedical data with multilevel glyphs
A simulation study investigating power estimates in phenome-wide association studies
ScaPD: a database for human scaffold proteins
Semantically linking molecular entities in literature through entity relationships
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences
Improving the organization and interactivity of metabolic pathfinding with precomputed pathways
Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data
iGC - an integrated analysis package of gene expression and copy number alteration
Answering medical questions in Chinese using automatically mined knowledge and deep neural networks: an end-to-end solution
A laminar augmented cascading flexible neural forest model for classification of cancer subtypes based on gene expression data
Publishing perishing? Towards tomorrow's information architecture
A method for named entity normalization in biomedical articles: application to diseases and plants
Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM
Refine gene functional similarity network based on interaction networks
Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma
Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library
Application of network link prediction in drug discovery
Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles
Cache and energy efficient algorithms for Nussinov's RNA Folding
An analysis of single amino acid repeats as use case for application specific background models
Modelling the interaction of steroid receptors with endocrine disrupting chemicals
Accelerating pairwise statistical significance estimation for local alignment by harvesting GPU's power
Fast and accurate protein substructure searching with simulated annealing and GPUs
Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays
Predicting condensate formation of protein and RNA under various environmental conditions
Deep learning algorithm reveals two prognostic subtypes in patients with gliomas
Empirical array quality weights in the analysis of microarray data
Kernel based methods for accelerated failure time model with ultra-high dimensional data
SAE-Impute: imputation for single-cell data via subspace regression and auto-encoders
String correction using the Damerau-Levenshtein distance
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700 TM /Panther TM probe-to-gene annotations
PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping
Exploring subdomain variation in biomedical language
VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens
Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization
gsGator: an integrated web platform for cross-species gene set analysis
On consensus biomarker selection
Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
Treelink: data integration, clustering and visualization of phylogenetic trees
Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota
The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)
Semi-automated quantitative Drosophila wings measurements
Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites
Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions
QSRA - a quality-value guided de novo short read assembler
FunSpec: a web-based cluster interpreter for yeast
H2rs: Deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments
SCC: an accurate imputation method for scRNA-seq dropouts based on a mixture model
Haplin power analysis: a software module for power and sample size calculations in genetic association analyses of family triads and unrelated controls
Correction: Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE
Synima: a Synteny imaging tool for annotated genome assemblies
Bioinformatics in phylogeography: analitical methods and applications
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis
Constructing xenobiotic maps of metabolism to predict enzymes catalyzing metabolites capable of binding to DNA
TransST: transfer learning embedded spatial factor modeling of spatial transcriptomics data
GVCBLUP: a computer package for genomic prediction and variance component estimation of additive and dominance effects
Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data
MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions
Magicmol: a light-weighted pipeline for drug-like molecule evolution and quick chemical space exploration
Improving variant calling using population data and deep learning
A high performance prediction of HPV genotypes by Chaos game representation and singular value decomposition
Gene differential coexpression analysis based on biweight correlation and maximum clique
Third international conference "Bioinformatics: from Algorithms to Applications" (BiATA 2019) - Saint Petersburg, Russia. 20-22 June 2019
shinyBN: an online application for interactive Bayesian network inference and visualization
Microscopy cell nuclei segmentation with enhanced U-Net
Recursive gene selection based on maximum margin criterion: a comparison with SVM-RFE
Partitioning of copy-number genotypes in pedigrees
alleHap: an efficient algorithm to reconstruct zero-recombinant haplotypes from parent-offspring pedigrees
Quantiprot - a Python package for quantitative analysis of protein sequences
An integrated Bayesian analysis of LOH and copy number data
Improving accuracy for cancer classification with a new algorithm for genes selection
Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2
Reconstructing ancestral gene orders with duplications guided by synteny level genome reconstruction
Identification of miRNA biomarkers for stomach adenocarcinoma
Correction: Inference of miRNA targets using evolutionary conservation and pathway analysis
Reporting and connecting cell type names and gating definitions through ontologies
ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains
RNA 3D structure prediction guided by independent folding of homologous sequences
A fast algorithm for determining the best combination of local alignments to a query sequence
RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences
The MEPS server for identifying protein conformational epitopes
Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups
Instance-based concept learning from multiclass DNA microarray data