yusuke1997/dblp-id-title huggingface dataset:
P-TransUNet: an improved parallel network for medical image segmentation
BART: bioinformatics array research tool
An exploration of the 3D chemical space has highlighted a specific shape profile for the compounds intended to inhibit protein-protein interactions
Predicting protein-ATP binding sites from primary sequence through fusing bi-profile sampling of multi-view features
NeuroTerrain - a client-server system for browsing 3D biomedical image data sets
Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach
Finding a suitable library size to call variants in RNA-Seq
Optimizing substitution matrix choice and gap parameters for sequence alignment
A new network representation of the metabolism to detect chemical transformation modules
MuTrack: a genome analysis system for large-scale mutagenesis in the mouse
Correction: CoNVEX: copy number variation estimation in exome sequencing data using HMM
Parallelized short read assembly of large genomes using de Bruijn graphs
Identification of hot regions in protein-protein interactions by sequential pattern mining
Multiple structure alignment and consensus identification for proteins
ZPS: visualization of recent adaptive evolution of proteins
ParPEST: a pipeline for EST data analysis based on parallel computing
StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy
Exon level integration of proteomics and microarray data
LigandRFs: random forest ensemble to identify ligand-binding residues from sequence information alone
Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data
Explainable deep drug-target representations for binding affinity prediction
The contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities
A format for databasing and comparison of AFLP fingerprint profiles
meth-SemiCancer: a cancer subtype classification framework via semi-supervised learning utilizing DNA methylation profiles
IPD 2.0: To derive insights from an evolving SARS-CoV-2 genome
Mendel, MD: a user-friendly online program for clinical exome analysis
The utility of MAS5 expression summary and detection call algorithms
Integrating experimental and computational approaches for the proteogenomic characterizations of microbial communities
CisOrtho: A program pipeline for genome-wide identification of transcription factor target genes using phylogenetic footprinting
Sparse clusterability: testing for cluster structure in high dimensions
Joint use of over- and under-sampling techniques and cross-validation for the development and assessment of prediction models
On the Choice and Number of Microarrays for Transcriptional Regulatory Network Inference
Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies
A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments
An integrated enhancement and reconstruction strategy for the quantitative extraction of actin stress fibers from fluorescence micrographs
NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly
A novel hybrid model to predict concomitant diseases for Hashimoto's thyroiditis
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology
Detecting temporal protein complexes from dynamic protein-protein interaction networks
Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites
Mining for Genotype-Phenotype Relations in Saccharomyces using Partial Least Squares
Swellix: a computational tool to explore RNA conformational space
Learning curves for drug response prediction in cancer cell lines
DROPA: DRIP-seq optimized peak annotator
Noise cancellation using total variation for copy number variation detection
Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance
recoup: flexible and versatile signal visualization from next generation sequencing
search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information
Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins
Convergence of genetic influences in comorbidity
CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing
Combining specificity determining and conserved residues improves functional site prediction
Differential C3NET reveals disease networks of direct physical interactions
Machine learning based DNA melt curve profiling enables automated novel genotype detection
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation
Comparative performances of DNA barcoding across insect orders
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing
The Use of Edge-Betweenness Clustering to Investigate Biological Function in Protein Interaction Networks
BITS 2017: the annual meeting of the Italian Society of Bioinformatics
GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants
Interrogating domain-domain interactions with parsimony based approaches
Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
s-dePooler: determination of polymorphism carriers from overlapping DNA pools
Novel implementation of conditional co-regulation by graph theory to derive co-expressed genes from microarray data
Biomedical articles share annotations with their citation neighbors
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia
Regulation of cell proliferation and apoptosis by growth hormone during zebrafish auditory hair cell regeneration
Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism
MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
Identification of consensus RNA secondary structures using suffix arrays
The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function
Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes
SCMPSP: Prediction and characterization of photosynthetic proteins based on a scoring card method
Extracting biomedical events from pairs of text entities
GPX - An Integrative Environment for the Storage and Retrieval of Raw and Processed Microarray Data
galaxieEST: addressing EST identity through automated phylogenetic analysis
Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network
Alignment of protein structures in the presence of domain motions
Proteome discovery pipeline for mass spectrometry-based proteomics
The PowerAtlas : a power and sample size atlas for microarray experimental design and research
PuFFIN - a parameter-free method to build nucleosome maps from paired-end reads
GOPET: A tool for automated predictions of Gene Ontology terms
A two-step site and mRNA-level model for predicting microRNA targets
Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes
OmniMapFree: A unified tool to visualise and explore sequenced genomes
DNAAlignEditor: DNA alignment editor tool
ParsEval: parallel comparison and analysis of gene structure annotations
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data
DiCleave: a deep learning model for predicting human Dicer cleavage sites
A comparative study of the svm and k-nn machine learning algorithms for the diagnosis of respiratory pathologies using pulmonary acoustic signals
Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?
Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model
Efficient computation of stochastic cell-size transient dynamics
Characterization of the emergent properties of a synthetic quasi-cellular system
PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments
Misty Mountain clustering: application to fast unsupervised flow cytometry gating
Hybrid cloud and cluster computing paradigms for life science applications
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data
Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach
A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction
eHive: An Artificial Intelligence workflow system for genomic analysis
A Bayesian nonparametric method for prediction in EST analysis
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models
A new real-time PCR method to overcome significant quantitative inaccuracy due to slight amplification inhibition
Revealing parasite influence in metabolic pathways in Apicomplexa infected patients
Stability of building gene regulatory networks with sparse autoregressive models
Reverse engineering gene regulatory network based on complex-valued ordinary differential equation model
MetSizeR: selecting the optimal sample size for metabolomic studies using an analysis based approach
Whole genome SNP genotype piecemeal imputation
The exceptional genomic word symmetry along DNA sequences
Mutations and CpG islands among hepatitis B virus genotypes in Europe
ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)
An automated resource for enhanced differential analysis
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens
MD-SVM: a novel SVM-based algorithm for the motif discovery of transcription factor binding sites
A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure
Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data
VisRseq: R-based visual framework for analysis of sequencing data
Triangle network motifs predict complexes by complementing high-error interactomes with structural information
Heterogeneous computing architecture for fast detection of SNP-SNP interactions
Large-scale integration of cancer microarray data identifies a robust common cancer signature
ModuleOrganizer: detecting modules in families of transposable elements
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization
Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements
Rapid evaluation and quality control of next generation sequencing data with FaQCs
Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes
An AUC-based permutation variable importance measure for random forests
Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks
Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity
Prediction models for drug-induced hepatotoxicity by using weighted molecular fingerprints
Dendroscope: An interactive viewer for large phylogenetic trees
An efficient method for mining cross-timepoint gene regulation sequential patterns from time course gene expression datasets
Detection of cell markers from single cell RNA-seq with sc2marker
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
MetaGenyo: a web tool for meta-analysis of genetic association studies
OrthoRefine: automated enhancement of prior ortholog identification via synteny
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida
Ensemble attribute profile clustering: discovering and characterizing groups of genes with similar patterns of biological features
VIRGO: visualization of A-to-I RNA editing sites in genomic sequences
Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation
Endoplasmic reticulum stress-related gene model predicts prognosis and guides therapies in lung adenocarcinoma
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations
Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution
Seven bacterial response-related genes are biomarkers for colon cancer
A literature-based similarity metric for biological processes
Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study
Distributed gene expression modelling for exploring variability in epigenetic function
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Reanalyze unassigned reads in Sanger based metagenomic data using conserved gene adjacency
mRNA: guanine- N 7 cap methyltransferases: identification of novel members of the family, evolutionary analysis, homology modeling, and analysis of sequence-structure-function relationships
Protein embedding based alignment
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research
caBIG TM VISDA: Modeling, visualization, and discovery for cluster analysis of genomic data
Association between ALS and retroviruses: evidence from bioinformatics analysis
Correction: Benchmarking tools for the alignment of functional noncodingDNA
PepDist: A New Framework for Protein-Peptide Binding Prediction based on Learning Peptide Distance Functions
Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation
A novel measure and significance testing in data analysis of cell image segmentation
Prediction and prioritization of autism-associated long non-coding RNAs using gene expression and sequence features
Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r
IgTM: An algorithm to predict transmembrane domains and topology in proteins
Insights into mechanism kinematics for protein motion simulation
Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks
Building blocks for automated elucidation of metabolites: Machine learning methods for NMR prediction
Detecting differentially methylated loci for multiple treatments based on high-throughput methylation data
Predicting adverse drug reactions through interpretable deep learning framework
A strategy to select suitable physicochemical attributes of amino acids for protein fold recognition
Towards the integration, annotation and association of historical microarray experiments with RNA-seq
Modeling the role of p53 pulses in DNA damage- induced cell death decision
NullHap - a versatile application to estimate haplotype frequencies from unphased genotypes in the presence of null alleles
DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data
In silico discovery of human natural antisense transcripts
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data
Identifying promoter features of co-regulated genes with similar network motifs
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering
Alternative splicing detection workflow needs a careful combination of sample prep and bioinformatics analysis
Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, Pf CelTOS, and human interleukin 2 as adjuvant
Three-dimensional protein model similarity analysis based on salient shape index
Identifying homogeneous subgroups of patients and important features: a topological machine learning approach
Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer
Denoising PCR-amplified metagenome data
The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites
A comparison of four clustering methods for brain expression microarray data
Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
Randomized boosting with multivariable base-learners for high-dimensional variable selection and prediction
Protein interface classification by evolutionary analysis
A comparison of probe-level and probeset models for small-sample gene expression data
CAGER: classification analysis of gene expression regulation using multiple information sources
GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm
A protein network refinement method based on module discovery and biological information
Empirical assessment of competitive hybridization and noise in ultra high density canine tiling arrays
A knowledge graph approach to predict and interpret disease-causing gene interactions
DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
Building the process-drug-side effect network to discover the relationship between biological Processes and side effects
PuMA: PubMed gene/cell type-relation Atlas
The alpha-Hemolysin nanopore transduction detector - single-molecule binding studies and immunological screening of antibodies and aptamers
Automatic block-wise genotype-phenotype association detection based on hidden Markov model
A vascular image registration method based on network structure and circuit simulation
Predicting lncRNA-protein interactions through deep learning framework employing multiple features and random forest algorithm
Delineating markers of disease-disease interaction: a systematic methodology and its application to multiple diabetes-helminth cohorts
CGHpower: exploring sample size calculations for chromosomal copy number experiments
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis
Instance-level semantic segmentation of nuclei based on multimodal structure encoding
Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data
MBECS: Microbiome Batch Effects Correction Suite
LooplessFluxSampler: an efficient toolbox for sampling the loopless flux solution space of metabolic models
A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns
Directional Darwinian Selection in proteins
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data
Bayesian meta-analysis models for microarray data: a comparative study
Effect of the number of removed lymph nodes on prostate cancer recurrence and survival: evidence from an observational study
Joint deep learning for batch effect removal and classification toward MALDI MS based metabolomics
Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology
MetaSel: a metaphase selection tool using a Gaussian-based classification technique
Effects of normalization on quantitative traits in association test
Streamlining differential exon and 3′ UTR usage with diffUTR
Standardized high-throughput evaluation of cell-based compound screens
RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays
Risk stratification and pathway analysis based on graph neural network and interpretable algorithm
DVA: predicting the functional impact of single nucleotide missense variants
In silico fragmentation for computer assisted identification of metabolite mass spectra
VPMBench: a test bench for variant prioritization methods
OLS Dialog: An open-source front end to the Ontology Lookup Service
Interactive exploration of ligand transportation through protein tunnels
Normalization method for metabolomics data using optimal selection of multiple internal standards
Fusing graph transformer with multi-aggregate GCN for enhanced drug-disease associations prediction
Computing H/D-Exchange rates of single residues from data of proteolytic fragments
CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets
Gene bi-targeting by viral and human miRNAs
Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso
The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
Extensions of ℓ 1 regularization increase detection specificity for cell-type specific parameters in dynamic models
HH-suite3 for fast remote homology detection and deep protein annotation
DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
Tools for T-RFLP data analysis using Excel
Prototyping a precision oncology 3.0 rapid learning platform
NBLAST: a cluster variant of BLAST for NxN comparisons
Identification of multimodal brain imaging association via a parameter decomposition based sparse multi-view canonical correlation analysis method
SVM-based prediction of caspase substrate cleavage sites
Comparative study of gene set enrichment methods
Prioritizing disease genes with an improved dual label propagation framework
oposSOM-Browser: an interactive tool to explore omics data landscapes in health science
Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein-ligand affinity prediction
BFL: a node and edge betweenness based fast layout algorithm for large scale networks
A method for estimating coherence of molecular mechanisms in major human disease and traits
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
Genomic analysis of gene regulation complexity
A method for analyzing censored survival phenotype with gene expression data
Accurate human genome analysis with element avidity sequencing
An automated framework for understanding structural variations in the binding grooves of MHC class II molecules
Using machine learning algorithms to identify genes essential for cell survival