yusuke1997/dblp-id-title huggingface dataset:
OffsampleAI: artificial intelligence approach to recognize off-sample mass spectrometry images
MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Lineage grammars: describing, simulating and analyzing population dynamics
CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation
A deep learning method for lincRNA detection using auto-encoder algorithm
Predicting RNA secondary structure via adaptive deep recurrent neural networks with energy-based filter
Class prediction for high-dimensional class-imbalanced data
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
A mapping-free natural language processing-based technique for sequence search in nanopore long-reads
KNIME-CDK: Workflow-driven Cheminformatics
A voting approach to identify a small number of highly predictive genes using multiple classifiers
Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods
SNP-based pathway enrichment analysis for genome-wide association studies
Correction to: Deep user identification model with multiple biometric data
Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation
Biomedical named entity recognition with the combined feature attention and fully-shared multi-task learning
A multistep bioinformatic approach detects putative regulatory elements in gene promoters
BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data
TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins
Field phenotyping of grapevine growth using dense stereo reconstruction
SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data
Small molecule modulation of microbiota: a systems pharmacology perspective
Exact reconstruction of gene regulatory networks using compressive sensing
A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers
SIGNATURE: A workbench for gene expression signature analysis
SaeGraphDTI: drug-target interaction prediction based on sequence attribute extraction and graph neural network
PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models
METROID: an automated method for robust quantification of subcellular fluorescence events at low SNR
BioPhysConnectoR: Connecting Sequence Information and Biophysical Models
CONSTAX: a tool for improved taxonomic resolution of environmental fungal ITS sequences
Buffered codons in human transcriptional units
Integration of open access literature into the RCSB Protein Data Bank using BioLit
Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures
Software for selecting the most informative sets of genomic loci for multi-target microbial typing
PoGO: Prediction of Gene Ontology terms for fungal proteins
PCVR: a pre-trained contextualized visual representation for DNA sequence classification
Correction: Using empirical biological knowledge to infer regulatory networks from multi-omics data
G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
PocketMatch: A new algorithm to compare binding sites in protein structures
Representativeness of variation benchmark datasets
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation
ContextMap 2: fast and accurate context-based RNA-seq mapping
Querying large read collections in main memory: a versatile data structure
DOTcvpSB, a software toolbox for dynamic optimization in systems biology
Identifying cross-category relations in gene ontology and constructing genome-specific term association networks
Quasi-cellular systems: stochastic simulation analysis at nanoscale range
A better sequence-read simulator program for metagenomics
GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness
Phylo-rs: an extensible phylogenetic analysis library in rust
ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs
Comparison of metaheuristics to measure gene effects on phylogenetic supports and topologies
Duration learning for analysis of nanopore ionic current blockades
Binary image representation of a ligand binding site: its application to efficient sampling of a conformational ensemble
REDfold: accurate RNA secondary structure prediction using residual encoder-decoder network
Structural fragment clustering reveals novel structural and functional motifs in alpha -helical transmembrane proteins
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite
Metaprotein expression modeling for label-free quantitative proteomics
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars
Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool
A biosegmentation benchmark for evaluation of bioimage analysis methods
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
A Fully Automatic Gridding Method for cDNA Microarray Images
IDPM: an online database for ion distribution in protein molecules
GRAPE: a pathway template method to characterize tissue-specific functionality from gene expression profiles
Identification of differentially expressed subnetworks based on multivariate ANOVA
Nonlinear physics opens a new paradigm for accurate transcription start site prediction
A density-based clustering approach for identifying overlapping protein complexes with functional preferences
Fingerprint restoration using cubic Bezier curve
Prediction of B-cell epitopes using evolutionary information and propensity scales
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma
The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires
CeModule: an integrative framework for discovering regulatory patterns from genomic data in cancer
An improved method for identifying functionally linked proteins using phylogenetic profiles
chngpt: threshold regression model estimation and inference
Bacterial syntenies: an exact approach with gene quorum
G-Tric: generating three-way synthetic datasets with triclustering solutions
Coordination characterization of zinc metalloproteins
CyTRANSFINDER: a Cytoscape 3.3 plugin for three-component (TF, gene, miRNA) signal transduction pathway construction
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
Hypercluster: a flexible tool for parallelized unsupervised clustering optimization
Next generation genome annotation with mGene.ngs
Flora Capture: a citizen science application for collecting structured plant observations
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins
Enhancer prediction in the human genome by probabilistic modelling of the chromatin feature patterns
Interactive visual exploration and refinement of cluster assignments
Parameter advising for multiple sequence alignment
A model to predict the function of hypothetical proteins through a nine-point classification scoring schema
RRW: repeated random walks on genome-scale protein networks for local cluster discovery
Machine learning prediction of oncology drug targets based on protein and network properties
Enhancing ontology-driven diagnostic reasoning with a symptom-dependency-aware Naïve Bayes classifier
CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction
Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome
LC-MSsim - a simulation software for liquid chromatography mass spectrometry data
AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations
Discrete profile comparison using information bottleneck
SimBA: simulation algorithm to fit extant-population distributions
Stochastic Petri Nets in Systems Biology
Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
Validating subcellular localization prediction tools with mycobacterial proteins
Discrimination of cell cycle phases in PCNA-immunolabeled cells
EDGAR: A software framework for the comparative analysis of prokaryotic genomes
Protein sequences classification by means of feature extraction with substitution matrices
Statistical Analysis of Dendritic Spine Distributions in Rat Hippocampal Cultures
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease
dbMDEGA: a database for meta-analysis of differentially expressed genes in autism spectrum disorder
Use Of Neural Networks To Predict And Analyse Membrane Proteins In The Proteome
Fast and accurate branch lengths estimation for phylogenomic trees
Identifying miRNA sponge modules using biclustering and regulatory scores
Correction to: Identifying miRNA synergism using multiple-intervention causal inference
Identification of essential proteins based on edge features and the fusion of multiple-source biological information
LONMF: a non-negative matrix factorization model based on graph Laplacian and optimal transmission for paired single-cell multi-omics data integration
A new permutation strategy of pathway-based approach for genome-wide association study
Erratum to: General continuous-time Markov model of sequence evolution via insertions/deletions: are alignment probabilities factorable?
Broadwick: a framework for computational epidemiology
A white-box approach to microarray probe response characterization: the BaFL pipeline
Protein kinases associated with the yeast phosphoproteome
ToTem: a tool for variant calling pipeline optimization
Local search for the generalized tree alignment
On the statistical assessment of classifiers using DNA microarray data
Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP
Compo: composite motif discovery using discrete models
Comparison of methods for estimating the nucleotide substitution matrix
An internet-based bioinformatics toolkit for plant biosecurity diagnosis and surveillance of viruses and viroids
Temporal and spatial relationship of gene expression in the infarcted rat heart
Correlated mutations via regularized multinomial regression
Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters - the case of phage λ
Learning to classify species with barcodes
Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations
simplePHENOTYPES: SIMulation of pleiotropic, linked and epistatic phenotypes
scFTAT: a novel cell annotation method integrating FFT and transformer
Grammar-based distance in progressive multiple sequence alignment
FITBAR: a web tool for the robust prediction of prokaryotic regulons
ACID: annotation of cassette and integron data
Gene classification for microarray data with multiple time measurements
Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila
Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data
Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data
Identification of novel alternative splicing biomarkers for breast cancer with LC/MS/MS and RNA-Seq
Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania
Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures
Gene prediction in metagenomic fragments: A large scale machine learning approach
MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences
Incorporating pathway information into boosting estimation of high-dimensional risk prediction models
A proximal LAVA method for genome-wide association and prediction of traits with mixed inheritance patterns
Biomedical named entity recognition using improved green anaconda-assisted Bi-GRU-based hierarchical ResNet model
A stochastic model of size control in the budding yeast cell cycle
Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator
Improving biomedical named entity recognition with syntactic information
Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases
BpWrapper: BioPerl-based sequence and tree utilities for rapid prototyping of bioinformatics pipelines
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites
BioWord: a sequence manipulation suite for Microsoft Word
antiCODE: a natural sense-antisense transcripts database
Designing and development of multi-epitope chimeric vaccine against Helicobacter pylori by exploring its entire immunogenic epitopes: an immunoinformatic approach
pROC: an open-source package for R and S+ to analyze and compare ROC curves
Communication and re-use of chemical information in bioscience
RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information
DeepECA: an end-to-end learning framework for protein contact prediction from a multiple sequence alignment
MultiDomainBenchmark: a multi-domain query and subject database suite
Gene set enrichment analysis for non-monotone association and multiple experimental categories
coMET: visualisation of regional epigenome-wide association scan results and DNA co-methylation patterns
Comparing the performance of selected variant callers using synthetic data and genome segmentation
Boosting scRNA-seq data clustering by cluster-aware feature weighting
Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping
Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method
BIMMER: a novel algorithm for detecting differential DNA methylation regions from MBDCap-seq data
Fast and sensitive multiple alignment of large genomic sequences
RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement
Generalization of the normal-exponential model: exploration of a more accurate parametrisation for the signal distribution on Illumina BeadArrays
Automatic echocardiographic anomalies interpretation using a stacked residual-dense network model
Predicting enhancers in mammalian genomes using supervised hidden Markov models
preAssemble: a tool for automatic sequencer trace data processing
Estimation of allele frequency and association mapping using next-generation sequencing data
Optimizations for the EcoPod field identification tool
Applications of proteochemometrics - from species extrapolation to cell line sensitivity modelling
Robust and accurate prediction of self-interacting proteins from protein sequence information by exploiting weighted sparse representation based classifier
BioLegato: a programmable, object-oriented graphic user interface
EGenBio : A Data Management System for Evolutionary Genomics and Biodiversity
TEMPROT: protein function annotation using transformers embeddings and homology search
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
Surprising results on phylogenetic tree building methods based on molecular sequences
PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome
Analyzing postprandial metabolomics data using multiway models: a simulation study
Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators
Highlights of the BioTM 2010 workshop on advances in bio text mining
imputeqc: an R package for assessing imputation quality of genotypes and optimizing imputation parameters
enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets
Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature
Diabetes classification model based on boosting algorithms
A novel subnetwork alignment approach predicts new components of the cell cycle regulatory apparatus in Plasmodium falciparum
Prediction of virus-host infectious association by supervised learning methods
PyClone-VI: scalable inference of clonal population structures using whole genome data
Context based mixture model for cell phase identification in automated fluorescence microscopy
SEAseq: a portable and cloud-based chromatin occupancy analysis suite
Effect of various normalization methods on Applied Biosystems expression array system data
Towards a career in bioinformatics
Predicting viral exposure response from modeling the changes of co-expression networks using time series gene expression data
Quantitative analysis of numerical solvers for oscillatory biomolecular system models
Automated classifiers for early detection and diagnosis of retinopathy in diabetic eyes
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments
Mining contextually meaningful subgraphs from a vertex-attributed graph
MSLP: mRNA subcellular localization predictor based on machine learning techniques
Bayesian optimal discovery procedure for simultaneous significance testing
Impact of image segmentation on high-content screening data quality for SK-BR-3 cells
Efficient motif finding algorithms for large-alphabet inputs
Robust pathway sampling in phenotype prediction. Application to triple negative breast cancer
Biomedical event extraction from abstracts and full papers using search-based structured prediction
ShrinkCRISPR: a flexible method for differential fitness analysis of CRISPR-Cas9 screen data
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs
Evaluation of open search methods based on theoretical mass spectra comparison
Homology modeling of a voltage-gated potassium channel (human K v 7.1)
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments
Repliscan: a tool for classifying replication timing regions
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15 N-NOESY
A comparison of internal validation techniques for multifactor dimensionality reduction
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips
Phylogeny-guided interaction mapping in seven eukaryotes
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of Trinity
PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm
RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads
CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination
Fast and robust imputation for miRNA expression data using constrained least squares
Prediction of uridine modifications in tRNA sequences
A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data
A new measure for functional similarity of gene products based on Gene Ontology
Fast design of arbitrary length loops in proteins using InteractiveRosetta
Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering
Using single cell sequencing data to model the evolutionary history of a tumor
Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data
Improved statistical model checking methods for pathway analysis
A fast weak motif-finding algorithm based on community detection in graphs
Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem
Event inference in multidomain families with phylogenetic reconciliation
Genomic prediction of tuberculosis drug-resistance: benchmarking existing databases and prediction algorithms
The Gene Set Builder: collation, curation, and distribution of sets of genes
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
MetNet Online: a novel integrated resource for plant systems biology
WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network
Maximizing Kolmogorov Complexity for accurate and robust bright field cell segmentation
Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family
Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences
Bioinformatics analysis of disordered proteins in prokaryotes
Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data
New statistical potential for quality assessment of protein models and a survey of energy functions
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network
Detecting Succinylation sites from protein sequences using ensemble support vector machine
PHY*FI: fast and easy online creation and manipulation of phylogeny color figures
Beware to ignore the rare: how imputing zero-values can improve the quality of 16S rRNA gene studies results
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells
In silico re-identification of properties of drug target proteins
From event-labeled gene trees to species trees
Feature selection for splice site prediction: A new method using EDA-based feature ranking
AFFECT: an R package for accelerated functional failure time model with error-contaminated survival times and applications to gene expression data
Tools for integrated sequence-structure analysis with UCSF Chimera
Imaging analysis of 13 rare cases of renal collecting (Bellini) duct carcinoma in northern China: a case series and literature review
COZOID: contact zone identifier for visual analysis of protein-protein interactions
SGCP: a spectral self-learning method for clustering genes in co-expression networks