yusuke1997/dblp-id-title huggingface dataset:
DNA barcode analysis: a comparison of phylogenetic and statistical classification methods
Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry
A framework for significance analysis of gene expression data using dimension reduction methods
BioBuilder as a database development and functional annotation platform for proteins
A tool for design of primers for microRNA-specific quantitative RT-qPCR
Clustering proteins from interaction networks for the prediction of cellular functions
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images
MCKAT: a multi-dimensional copy number variant kernel association test
Compromise or optimize? The breakpoint anti-median
Analysis of concordance of different haplotype block partitioning algorithms
SNP haplotype tagging from DNA pools of two individuals
Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies
Machine learning for genomic prediction of growth traits in aquaculture: a case study of the Australasian snapper (Chrysophrys auratus)
Protein complex detection based on partially shared multi-view clustering
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees
Enhancing predictions of antimicrobial resistance of pathogens by expanding the potential resistance gene repertoire using a pan-genome-based feature selection approach
Towards a HPC-oriented parallel implementation of a learning algorithm for bioinformatics applications
Improving the power of gene set enrichment analyses
GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes
Predicting antifreeze proteins with weighted generalized dipeptide composition and multi-regression feature selection ensemble
Constructing multilayer PPI networks based on homologous proteins and integrating multiple PageRank to identify essential proteins
Amino acid sequence associated with bacteriophage recombination site helps to reveal genes potentially acquired through horizontal gene transfer
IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data
Enhanced peptide quantification using spectral count clustering and cluster abundance
Drug-target interaction prediction by integrating heterogeneous information with mutual attention network
PeTTSy: a computational tool for perturbation analysis of complex systems biology models
Use of Attribute Driven Incremental Discretization and Logic Learning Machine to build a prognostic classifier for neuroblastoma patients
Artificial neural network classifier predicts neuroblastoma patients' outcome
Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries
MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge
Revision history aware repositories of computational models of biological systems
An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome
SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
Comparison of ARIMA and Random Forest time series models for prediction of avian influenza H5N1 outbreaks
High-order dynamic Bayesian Network learning with hidden common causes for causal gene regulatory network
TableButler - A tool for combining, handling and processing of huge data tables
A neural network-based method for polypharmacy side effects prediction
ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing
Context-sensitive use of bioinformatics tools with complementary functionalities for generation of relevant hypothesis
Local edge-enhanced active contour for accurate skin lesion border detection
PhenUMA: a tool for integrating the biomedical relationships among genes and diseases
Analyzing magnetic bead QuantiGene® Plex 2.0 gene expression data in high throughput mode using QGprofiler
Computational prediction of type III secreted proteins from gram-negative bacteria
OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations
Cellular quantitative analysis of neuroblastoma tumor and splitting overlapping cells
Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow
A neural strategy for the inference of SH3 domain-peptide interaction specificity
Cogito: automated and generic comparison of annotated genomic intervals
A purely bioinformatic pipeline for the prediction of mammalian odorant receptor gene enhancers
Classifying microscopic images as acute lymphoblastic leukemia by Resnet ensemble model and Taguchi method
An Active Learning Based Classification Strategy for the Minority Class Problem: Application to Histopathology Annotation
Exploring the dynamics and interplay of human papillomavirus and cervical tumorigenesis by integrating biological data into a mathematical model
Comparing functional annotation analyses with Catmap
Efficient path-based computations on pedigree graphs with compact encodings
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet
CL-ACP: a parallel combination of CNN and LSTM anticancer peptide recognition model
ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
MANTIS: an R package that simulates multilocus models of pathogen evolution
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model
A diabetes prediction model based on Boruta feature selection and ensemble learning
Scenario driven data modelling: a method for integrating diverse sources of data and data streams
Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization
A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy
CAISC: A software to integrate copy number variations and single nucleotide mutations for genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
MSA: reproducible mutational signature attribution with confidence based on simulations
A Platform for Processing Expression of Short Time Series (PESTS)
Hierarchical classification strategy for Phenotype extraction from epidermal growth factor receptor endocytosis screening
Discovering causal interactions using Bayesian network scoring and information gain
HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues
Improved benchmarks for computational motif discovery
primetv: a viewer for reconciled trees
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II
Extending the BEAGLE library to a multi-FPGA platform
mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code
Automating dChip: toward reproducible sharing of microarray data analysis
IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model
Flexible docking-based molecular dynamics simulation of natural product compounds and Ebola virus Nucleocapsid (EBOV NP): a computational approach to discover new drug for combating Ebola
Optimizationof neural network architecture using genetic programming improvesdetection and modeling of gene-gene interactions in studies of humandiseases
Robust identification of molecular phenotypes using semi-supervised learning
Semi-supervised discovery of differential genes
Super-sparse principal component analyses for high-throughput genomic data
Content-rich biological network constructed by mining PubMed abstracts
User centered and ontology based information retrieval system for life sciences
Efficient design of synthetic gene circuits under cell-to-cell variability
CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge
DNA microarray data and contextual analysis of correlation graphs
Comparative proteomics: assessment of biological variability and dataset comparability
Biological event composition
ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs
A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype
Adaptable data management for systems biology investigations
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation
Retrieval with gene queries
Algorithm-driven Artifacts in median polish summarization of Microarray data
MeInfoText: associated gene methylation and cancer information from text mining
POINeT: protein interactome with sub-network analysis and hub prioritization
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development
Identifying functional relationships among human genes by systematic analysis of biological literature
PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways
Making sense of EST sequences by CLOBBing them
CirPred, the first structure modeling and linker design system for circularly permuted proteins
Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks
Empirical estimation of sequencing error rates using smoothing splines
A computer simulation model of Wolbachia invasion for disease vector population modification
AStruct: detection of allele-specific RNA secondary structure in structuromic probing data
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins
PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides
LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)
GMMchi: gene expression clustering using Gaussian mixture modeling
Minimum redundancy maximum relevance feature selection approach for temporal gene expression data
CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction
An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information
From microarray to biology: an integrated experimental, statistical and in silico analysis of how the extracellular matrix modulates the phenotype of cancer cells
GMOseek: a user friendly tool for optimized GMO testing
Enhancing biomedical named entity recognition with parallel boundary detection and category classification
Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions
Accessing the SEED genome databases via Web services API: tools for programmers
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry
A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls
Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES)
A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework
Molecular dissection of cardiac hypertrophy induced by interleukin-18
Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009
Asynchronous adaptive time step in quantitative cellular automata modeling
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
The Average Mutual Information Profile as a Genomic Signature
Comparison of protein structures by growing neighborhood alignments
NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads
Deep learning and multi-omics approach to predict drug responses in cancer
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
Unsupervised modeling of mutational landscapes of adeno-associated viruses viability
A Bayesian method and its variational approximation for prediction of genomic breeding values in multiple traits
Implementing a genomic data management system using iRODS in Wellcome Trust Sanger Institute
Estimation of protein function using template-based alignment of enzyme active sites
Feature selection of gene expression data for Cancer classification using double RBF-kernels
SAQC: SNP array quality control
AceTree: a major update and case study in the long term maintenance of open-source scientific software
LogicNet: probabilistic continuous logics in reconstructing gene regulatory networks
Evolutionary Pareto-optimization of stably folding peptides
Querying the public databases for sequences using complex keywords contained in the feature lines
Scalable high-throughput identification of genetic targets by network filtering
TipMT: Identification of PCR-based taxon-specific markers
LEAping to conclusions: A computational reanalysis of late embryogenesis abundant proteins and their possible roles
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
BICOSS: Bayesian iterative conditional stochastic search for GWAS
Comparison of pathway analysis and constraint-based methods for cell factory design
IntEREst: intron-exon retention estimator
Large-scale prediction of protein-protein interactions from structures
Identifying gene and protein mentions in text using conditional random fields
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
Candidate genes within known QTL of type 1 diabetes from mouse models
Quantifying and filtering knowledge generated by literature based discovery
A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures
Visualization-based discovery and analysis of genomic aberrations in microarray data
MetWAMer: eukaryotic translation initiation site prediction
A deep adversarial variational autoencoder model for dimensionality reduction in single-cell RNA sequencing analysis
WebArray: an online platform for microarray data analysis
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App
Delivering informatics for clinical research in developing countries
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
Identifying protein-protein interface via a novel multi-scale local sequence and structural representation
Semi-supervised machine learning for automated species identification by collagen peptide mass fingerprinting
High expression of cuproptosis-related SLC31A1 gene in relation to unfavorable outcome and deregulated immune cell infiltration in breast cancer: an analysis based on public databases
In silico modelling of hormone response elements
Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining
ExonMiner: Web service for analysis of GeneChip Exon array data
MCRWR: a new method to measure the similarity of documents based on semantic network
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study
LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation
Selected proceedings of Machine Learning in Systems Biology: MLSB 2016
Browsing repeats in genomes: Pygram and an application to non-coding region analysis
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
The LO-BaFL method and ALS microarray expression analysis
Clique-based data mining for related genes in a biomedical database
CLEP-GAN: an innovative approach to subject-independent ECG reconstruction from PPG signals
M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species
Epimetheus - a multi-profile normalizer for epigenomic sequencing data
An evolutionary method for learning HMM structure: prediction of protein secondary structure
Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA
Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes
Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data
A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
MGMR: leveraging RNA-Seq population data to optimize expression estimation
Prototype Semantic Infrastructure for Automated Small Molecule Classification and Annotation in Lipidomics
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
IKKβ inhibitor identification: a multi-filter driven novel scaffold
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes
Systematic noise degrades gene co-expression signals but can be corrected
MethylNet: an automated and modular deep learning approach for DNA methylation analysis
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes
SSF-DDI: a deep learning method utilizing drug sequence and substructure features for drug-drug interaction prediction
Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments
Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index
Maximum common subgraph: some upper bound and lower bound results
Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression
Functionally specified protein signatures distinctive for each of the different blue copper proteins
sdef: an R package to synthesize lists of significant features in related experiments
SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data
A novel method for drug-target interaction prediction based on graph transformers model
ARCA: the interactive database for arbovirus reported cases in the Americas
ncRNAclassifier: a tool for detection and classification of transposable element sequences in RNA hairpins
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements
AMON: annotation of metabolite origins via networks to integrate microbiome and metabolome data
A comparative study of cell classifiers for image-based high-throughput screening
Microarray-based Cancer Prediction Using Single Genes
PopMLvis: a tool for analysis and visualization of population structure using genotype data from genome-wide association studies
Identification and validation of tumor-infiltrating lymphocyte-related prognosis signature for predicting prognosis and immunotherapeutic response in bladder cancer
Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4
Bison: bisulfite alignment on nodes of a cluster
Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
Model based analysis of real-time PCR data from DNA binding dye protocols
PACVr: plastome assembly coverage visualization in R
Secondary structural entropy in RNA switch (Riboswitch) identification
Core stemness mechanisms revealed through homology
Identifying restrictions in the order of accumulation of mutations during tumor progression: effects of passengers, evolutionary models, and sampling
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression
Extracting semantically enriched events from biomedical literature
Geminivirus data warehouse: a database enriched with machine learning approaches
lncEvo: automated identification and conservation study of long noncoding RNAs
Deep learning-based classification model for GPR151 activator activity prediction
Structure-informed clustering for population stratification in association studies
Mathematical model for empirically optimizing large scale production of soluble protein domains
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
Segmentor: a tool for manual refinement of 3D microscopy annotations
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data
Taxonomic colouring of phylogenetic trees of protein sequences
Protein translational control and its contribution to oncogenesis revealed by computational methods
Statistical ensemble of gene regulatory networks of macrophage differentiation
Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches
Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints
Bioinformatic pipelines in Python with leaf
Periodicity and dosage optimization of an RNAi model in eukaryotes cells
Improving the accuracy of protein secondary structure prediction using structural alignment
RecMotif: a novel fast algorithm for weak motif discovery
QTLs for bone mineral density of femurs and tibias in recombinant inbred strains derived from C57BL/6J and DBA/2J inbred strains
Structure prediction of polyglutamine disease proteins: comparison of methods
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks
FLARE: a fast and flexible workflow for identifying RNA editing foci
Ab Initio prediction of mycobacteriophages protein structure and function
Array2BIO: from microarray expression data to functional annotation of co-regulated genes
Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data
A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining
MILANO - custom annotation of microarray results using automatic literature searches
Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method
Assessing microscope image focus quality with deep learning
Negated bio-events: analysis and identification
Towards a lightweight generic computational grid framework for biological research
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
Maximum independent sets of commuting and noninterfering inversions
Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost