yusuke1997/dblp-id-title huggingface dataset:
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
npInv: accurate detection and genotyping of inversions using long read sub-alignment
Extracting cancer concepts from clinical notes using natural language processing: a systematic review
High-Throughput parallel blind Virtual Screening using BINDSURF
MultiVis.js: a software tool for the visualization of multiway chromatin interactions and SPRITE data
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information
BIN1 rs744373 variant shows different association with Alzheimer's disease in Caucasian and Asian populations
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks
ScreenMill: A freely available software suite for growth measurement, analysis and visualization of high-throughput screen data
Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Modeling the competition between lung metastases and the immune system using agents
miRMaid: a unified programming interface for microRNA data resources
Robust clustering in high dimensional data using statistical depths
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction
Eigen-Epistasis for detecting gene-gene interactions
πBUSS: a parallel BEAST/BEAGLE utility for sequence simulation under complex evolutionary scenarios
CASSIOPE: An expert system for conserved regions searches
KAOS: a new automated computational method for the identification of overexpressed genes
Improvement of peptide identification with considering the abundance of mRNA and peptide
Robust optimization of convolutional neural networks with a uniform experiment design method: a case of phonocardiogram testing in patients with heart diseases
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities
A rank-based marker selection method for high throughput scRNA-seq data
Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies
Towards large-scale sample annotation in gene expression repositories
Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes
Identifying regulatory elements and gene boundaries with comparative genomic sequence analysis
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks
SpotitPy: a semi-automated tool for object-based co-localization of fluorescent labels in microscopy images
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data
Robust differential expression analysis by learning discriminant boundary in multi-dimensional space of statistical attributes
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Correction: PathEx: A novel multi factors based datasets selector web tool
easyExon - A Java-based GUI tool for processing and visualization of Affymetrix exon array data
Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images
Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines
caGrid Workflow Toolkit: A Taverna based workflow tool for cancer Grid
CSN: unsupervised approach for inferring biological networks based on the genome alone
Analysis of networks of host proteins in the early time points following HIV transduction
Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences
wFleaBase: the Daphnia genome database
A new unsupervised gene clustering algorithm based on the integration of biological knowledge into expression data
DBNorm: normalizing high-density oligonucleotide microarray data based on distributions
Haplotype allelic classes for detecting ongoing positive selection
Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays
CLU: A new algorithm for EST clustering
SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data
Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
Distinguishing word identity and sequence context in DNA language models
Objective identification of residue ranges for the superposition of protein structures
Optimising oligonucleotide array design for ChIP-on-chip
Bayesian compositional regression with microbiome features via variational inference
The BioPrompt-box: an ontology-based clustering tool for searching in biological databases
Antimicrobial peptide similarity and classification through rough set theory using physicochemical boundaries
Comparative analysis and visualization of multiple collinear genomes
Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma
Computational analysis of genetic network involved in pancreatic cancer in human
Winnow-KAN: single-cell RNA-seq location recovery with small-gene-set spatial transcriptomics
FoCo: a simple and robust quantification algorithm of nuclear foci
Domain similarity based orthology detection
nGASP - the nematode genome annotation assessment project
Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data
Modeling lymphocyte homing and encounters in lymph nodes
A dropout-regularized classifier development approach optimized for precision medicine test discovery from omics data
Gene/protein name recognition based on support vector machine using dictionary as features
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets
A systems approach for analysis of high content screening assay data with topic modeling
MiMiR - an integrated platform for microarray data sharing, mining and analysis
Comparative analysis of long DNA sequences by per element information content using different contexts
Biological sequences as pictures - a generic two dimensional solution for iterated maps
Fast tree aggregation for consensus hierarchical clustering
Microarray meta-analysis database (M 2 DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Deciphering the role of RNA structure in translation efficiency
PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data
Fast max-margin clustering for unsupervised word sense disambiguation in biomedical texts
Biomedical named entity recognition using deep neural networks with contextual information
InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification
LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes
Detecting disease-associated genotype patterns
UTR extension and alternate polyadenylation in neuroplasticity: an emerging paradigm?
iPNHOT: a knowledge-based approach for identifying protein-nucleic acid interaction hot spots
Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis
optRF: Optimising random forest stability by determining the optimal number of trees
A random-permutations-based approach to fast read alignment
Drug-target interaction prediction via multiple classification strategies
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
JEDi: java essential dynamics inspector - a molecular trajectory analysis toolkit
An adaptive landscape for training in the essentials of next gen sequencing data acquisition and bioinformatic analysis
Joint Analysis of Transcriptional and post- Transcriptional Data: Searching Emergent Properties in Brain Tumor Samples
Sources of variation in Affymetrix microarray experiments
Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops
Time course transcriptome data analysis for in vitro modeling of dilated cardiomyopathy using patient-derived induced pluripotent stem cells
Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification
Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples
Selected proceedings of the 2010 Summit on Translational Bioinformatics
Primal-dual for classification with rejection (PD-CR): a novel method for classification and feature selection - an application in metabolomics studies
A comparison of the functional modules identified from time course and static PPI network data
An Automated Method for Rapid Identification of Putative Gene Family Members in Plants
riboviz: analysis and visualization of ribosome profiling datasets
A network-based pathway-expanding approach for pathway analysis
A two-layer integration framework for protein complex detection
FiNGS: high quality somatic mutations using filters for next generation sequencing
Fast index based algorithms and software for matching position specific scoring matrices
Challenges for automatically extracting molecular interactions from full-text articles
Towards validating the hypothesis of phylogenetic profiling
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling
Service-based analysis of biological pathways
Data-based RNA-seq simulations by binomial thinning
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Methods for comparative metagenomics
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime
SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping
Computational expression deconvolution in a complex mammalian organ
Candidate gene prioritization by network analysis of differential expression using machine learning approaches
ICC-CLASS: isotopically-coded cleavable crosslinking analysis software suite
Identification of putative pathogenic SNPs implied in schizophrenia-associated miRNAs
Integrative set enrichment testing for multiple omics platforms
GCRNN: graph convolutional recurrent neural network for compound-protein interaction prediction
Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches
pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data
BioVR: a platform for virtual reality assisted biological data integration and visualization
Sequence information gain based motif analysis
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples
Deep convolutional neural networks for annotating gene expression patterns in the mouse brain
Towards reliable isoform quantification using RNA-SEQ data
Empowering individual trait prediction using interactions for precision medicine
Neural sentence embedding models for semantic similarity estimation in the biomedical domain
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network
Variant Ranker: a web-tool to rank genomic data according to functional significance
A predictive model for secondary RNA structure using graph theory and a neural network
ORdensity: user-friendly R package to identify differentially expressed genes
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i)
Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs
Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach
Modeling binding specificities of transcription factor pairs with random forests
Evaluation of two methods for computational HLA haplotypes inference using a real dataset
Inference of miRNA targets using evolutionary conservation and pathway analysis
Using partially ordered sets to represent and predict true patterns of gene response to treatments
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores
Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study
A graph neural network approach for hierarchical mapping of breast cancer protein communities
Heterogeneous multiple kernel learning for breast cancer outcome evaluation
Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms
Fast parallel construction of variable-length Markov chains
Denoising self-supervised learning for disease-gene association prediction
A voting mechanism-based linear epitope prediction system for the host-specific Iridoviridae family
MetaboLab - advanced NMR data processing and analysis for metabolomics
Erratum to: A novel procedure on next generation sequencing data analysis using text mining algorithm
Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data
SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations
Using set theory to reduce redundancy in pathway sets
mLoc-mRNA: predicting multiple sub-cellular localization of mRNAs using random forest algorithm coupled with feature selection via elastic net
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts
Comparison of protein interaction networks reveals species conservation and divergence
Re-visiting protein-centric two-tier classification of existing DNA-protein complexes
Which gene did you mean?
Conditional random pattern model for copy number aberration detection
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data
Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics
Stability analysis of mixtures of mutagenetic trees
Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries
Classification of viral zoonosis through receptor pattern analysis
Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data
Performance of a blockwise approach in variable selection using linkage disequilibrium information
Prediction of peptides binding to MHC class I and II alleles by temporal motif mining
A hybrid short read mapping accelerator
A fast algorithm for genome-wide haplotype pattern mining
Analyzing a co-occurrence gene-interaction network to identify disease-gene association
Detecting Small Plant Peptides Using SPADA (Small Peptide Alignment Discovery Application)
TOPSAN: a collaborative annotation environment for structural genomics
A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions
caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts
Detecting protein complexes in protein interaction networks using a ranking algorithm with a refined merging procedure
Knowledge-based variable selection for learning rules from proteomic data
Mixed logistic regression in genome-wide association studies
c-REDUCE: Incorporating sequence conservation to detect motifs that correlate with expression
BioByGANS: biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework
A procedure to decompose high resolution mass spectra
bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data
Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities
Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling
A method of precise mRNA/DNA homology-based gene structure prediction
Improved cytokine-receptor interaction prediction by exploiting the negative sample space
Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis
PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery
A method for predicting protein complex in dynamic PPI networks
Few amino acid positions in rpoB are associated with most of the rifampin resistance in Mycobacterium tuberculosis
CATCHing putative causative variants in consanguineous families
Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories
Survival time prediction by integrating cox proportional hazards network and distribution function network
BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data
MetAssimulo: Simulation of Realistic NMR Metabolic Profiles
Better prediction of protein contact number using a support vector regression analysis of amino acid sequence
High-throughput sequence alignment using Graphics Processing Units
Improving duplicated nodes position in vertebrate gene trees
DASP3: identification of protein sequences belonging to functionally relevant groups
Using sensitivity analyses to understand bistable system behavior
A factor analysis model for functional genomics
A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation
CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU
Gene set analysis for longitudinal gene expression data
Rigidity analysis of protein biological assemblies and periodic crystal structures
Nonlinear Data Mining of Microarray Data Using Michaelis Menten Functions
AUCTSP: an improved biomarker gene pair class predictor
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein
Predicting biological system objectives de novo from internal state measurements
Priors, population sizes, and power in genome-wide hypothesis tests
Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells
2DDB - a bioinformatics solution for analysis of quantitative proteomics data
dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files
A multimodal graph neural network framework for cancer molecular subtype classification
Identification and characterization of subfamily-specific signatures in a large protein superfamily by a hidden Markov model approach
AtRTPrimer: database for Arabidopsis genome-wide homogeneous and specific RT-PCR primer-pairs
MethylSeqLogo: DNA methylation smart sequence logos
Variant effect predictions capture some aspects of deep mutational scanning experiments
A framework for protein structure classification and identification of novel protein structures
PRS-on-Spark (PRSoS): a novel, efficient and flexible approach for generating polygenic risk scores
The coming era of artificial intelligence in biological data science
Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach
Path-level interpretation of Gaussian graphical models using the pair-path subscore
Prediction of activity and specificity of CRISPR-Cpf1 using convolutional deep learning neural networks
The statistics of identifying differentially expressed genes in Expresso and TM4: a comparison
How repetitive are genomes?
STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data
GSV: A Web-based Genome Synteny Viewer for Customized Data
Biomedical semantic indexing by deep neural network with multi-task learning
Gene expression signature in adipose tissue of acromegaly patients
Micro-Mar: a database for dynamic representation of marine microbial biodiversity
Power and sample size of two-stage extreme phenotype sequencing design for next generation sequencing studies
Reference-guided de novo assembly approach improves genome reconstruction for related species
A novel investigation of the effect of iterations in sliding semi-landmarks for 3D human facial images
Modelling Lipid Metabolism to Improve Healthy Ageing
Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
A high-level 3D visualization API for Java and ImageJ
Evaluation and improvements of clustering algorithms for detecting remote homologous protein families
PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes
Sequence-structure relations of pseudoknot RNA
DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing
CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data
TE-Tracker: systematic identification of transposition events through whole-genome resequencing
Using random forest for reliable classification and cost-sensitive learning for medical diagnosis
Next-gen sequencing of multi-drug resistant Acinetobacter baumanii at Nashville General Hospital at Meharry
Barcodes for genomes and applications
A graph neural network framework for mapping histological topology in oral mucosal tissue
Infection status outcome, machine learning method and virus type interact to affect the optimised prediction of hepatitis virus immunoassay results from routine pathology laboratory assays in unbalanced data
Improving the prediction of disease-related variants using protein three-dimensional structure
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data
SimArray: a user-friendly and user-configurable microarray design tool
CerealsDB 3.0: expansion of resources and data integration
NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq
Computational modeling with forward and reverse engineering links signaling network and genomic regulatory responses: NF-kappaB signaling-induced gene expression responses in inflammation
CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
ISAAC - InterSpecies Analysing Application using Containers
AUTALASSO: an automatic adaptive LASSO for genome-wide prediction
Identification of fish species through tRNA-based primer design
Fast lossless compression via cascading Bloom filters
Leveraging TCGA gene expression data to build predictive models for cancer drug response
Exploiting and integrating rich features for biological literature classification
A stack LSTM structure for decoding continuous force from local field potential signal of primary motor cortex (M1)
Insertion and deletion correcting DNA barcodes based on watermarks
An integrative method to normalize RNA-Seq data