yusuke1997/dblp-id-title huggingface dataset:
Moiety modeling framework for deriving moiety abundances from mass spectrometry measured isotopologues
SamSelect: a sample sequence selection algorithm for quorum planted motif search on large DNA datasets
NPF: network propagation for protein function prediction
Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack
RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences
IP4M: an integrated platform for mass spectrometry-based metabolomics data mining
BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint
Analysis and remedy of negativity problem in hybrid stochastic simulation algorithm and its application
Prediction of protein structural classes by different feature expressions based on 2-D wavelet denoising and fusion
A machine learning approach for the identification of odorant binding proteins from sequence-derived properties
Selection of microbial biomarkers with genetic algorithm and principal component analysis
Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data
Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network
A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction
Bayesian kinetic modeling for tracer-based metabolomic data
Testing for association between RNA-Seq and high-dimensional data
An application of statistics to comparative metagenomics
IntelliGO: a new vector-based semantic similarity measure including annotation origin
A comparison study of succinct data structures for use in GWAS
Joint mapping of genes and conditions via multidimensional unfolding analysis
SNARER: new molecular descriptors for SNARE proteins classification
Phylogenetic tree construction using trinucleotide usage profile (TUP)
JCDSA: a joint covariate detection tool for survival analysis on tumor expression profiles
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data
PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis
Metabolomic database annotations viaquery of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm
Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks
scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data
Context-aware multi-token concept recognition of biological entities
Combining single-cell ATAC and RNA sequencing for supervised cell annotation
Non-parametric synergy modeling of chemical compounds with Gaussian processes
Protein complex detection using interaction reliability assessment and weighted clustering coefficient
GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs
Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling
Multi-proteins similarity-based sampling to select representative genomes from large databases
Predicting microRNA targets in time-series microarray experiments via functional data analysis
Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data
Mining a stroke knowledge graph from literature
Haplotype-based score test for linkage in nuclear families
Correction: Determination of the differentially expressed genes in microarray experiments using local FDR
A resource for benchmarking the usefulness of protein structure models
Classification of protein motifs based on subcellular localization uncovers evolutionary relationships at both sequence and functional levels
Analysis and prediction of antibacterial peptides
Application of kernel functions for accurate similarity search in large chemical databases
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
A deep learning method to more accurately recall known lysine acetylation sites
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains
TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
PGen: large-scale genomic variations analysis workflow and browser in SoyKB
JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles
Bagging survival tree procedure for variable selection and prediction in the presence of nonsusceptible patients
A detailed error analysis of 13 kernel methods for protein-protein interaction extraction
Functional enrichment analyses and construction of functional similarity networks with high confidence function prediction by PFP
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data
CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques
ChIPseqR: Analysis of ChIP-seq Experiments
The impact of sequence length and number of sequences on promoter prediction performance
Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease
Integrated metabolome and transcriptome analysis of the NCI60 dataset
APA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement
Super paramagnetic clustering of protein sequences
Accurate reconstruction of viral quasispecies spectra through improved estimation of strain richness
disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data
Phylogenetic analysis of modularity in protein interaction networks
nocoRNAc: Characterization of non-coding RNAs in prokaryotes
Gene set analysis using variance component tests
CellExcite: an efficient simulation environment for excitable cells
Reconstruction of a gene regulatory network of the induced systemic resistance defense response in Arabidopsis using boolean networks
JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture
Genealyzer: web application for the analysis and comparison of gene expression data
Lateral gene transfer, rearrangement, reconciliation
Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology
Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'
Kangaroo - A pattern-matching program for biological sequences
A joint model of regulatory and metabolic networks
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects
Biomarker correlation network in colorectal carcinoma by tumor anatomic location
MLM-based typographical error correction of unstructured medical texts for named entity recognition
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases
Retraction: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase
Intuitive representation of surface properties of biomolecules using BioBlender
Comprehensive analysis of correlation coefficients estimated from pooling heterogeneous microarray data
MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development
Metabolome searcher: a high throughput tool for metabolite identification and metabolic pathway mapping directly from mass spectrometry and using genome restriction
Learning a Markov Logic network for supervised gene regulatory network inference
DegreeCox - a network-based regularization method for survival analysis
A new approach for prediction of tumor sensitivity to targeted drugs based on functional data
Transcription regulation: a genomic network
4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing
PhenoFam-gene set enrichment analysis through protein structural information
Computational identification of biomarker genes for lung cancer considering treatment and non-treatment studies
Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies
Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs
Nuclei instance segmentation from histopathology images using Bayesian dropout based deep learning
Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis
Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
SPIKE - a database, visualization and analysis tool of cellular signaling pathways
Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016
Epitopemap: a web application for integrated whole proteome epitope prediction
Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process
Poly: a quantitative analysis tool for simple sequence repeat (SSR) tracts in DNA
MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials
Genetic weighted k-means algorithm for clustering large-scale gene expression data
Scalable deep text comprehension for Cancer surveillance on high-performance computing
Motif kernel generated by genetic programming improves remote homology and fold detection
readat: An R package for reading and working with SomaLogic ADAT files
NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads
Populous: a tool for building OWL ontologies from templates
A weighting approach for judging the effect of patient strata on high-dimensional risk prediction signatures
A novel method for prokaryotic promoter prediction based on DNA stability
SVNN: an efficient PacBio-specific pipeline for structural variations calling using neural networks
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
A survey of DNA motif finding algorithms
Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations
ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences
Compressed sensing improved iterative reconstruction-reprojection algorithm for electron tomography
Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Multivariate Hawkes process models of the occurrence of regulatory elements
Identifying conserved protein complexes between species by constructing interolog networks
Enhancing protein-vitamin binding residues prediction by multiple heterogeneous subspace SVMs ensemble
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Structator: fast index-based search for RNA sequence-structure patterns
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
Direct comparison shows that mRNA-based diagnostics incorporate information which cannot be learned directly from genomic mutations
Systematic error detection in experimental high-throughput screening
Computational protein biomarker prediction: a case study for prostate cancer
SHIVA - a web application for drug resistance and tropism testing in HIV
A comparison of topologically associating domain callers over mammals at high resolution
Predicting chemotherapy response using a variational autoencoder approach
Development of a prediction system for tail-anchored proteins
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon
An unsupervised classification scheme for improving predictions of prokaryotic TIS
Integration of bioinformatics tools in candidate gene prioritization of co-regulated gene sets in Saccharomyces cerevisiae
A method to identify differential expression profiles of time-course gene data with Fourier transformation
Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables
PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system
New threats to health data privacy
CMA - a comprehensive Bioconductor package for supervised classification with high dimensional data
Epitopia: a web-server for predicting B-cell epitopes
A census of α-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq
Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling
A random set scoring model for prioritization of disease candidate genes using protein complexes and data-mining of GeneRIF, OMIM and PubMed records
FACT: Functional annotation transfer between proteins with similar feature architectures
Computer simulations of the signalling network in FLT3 +-acute myeloid leukaemia - indications for an optimal dosage of inhibitors against FLT3 and CDK6
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform
Is EC class predictable from reaction mechanism?
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships
Sensitive detection of circular DNAs at single-nucleotide resolution using guided realignment of partially aligned reads
Accurate and fast mitotic detection using an anchor-free method based on full-scale connection with recurrent deep layer aggregation in 4D microscopy images
PeanutMap: an online genome database for comparative molecular maps of peanut
Application of text-mining for updating protein post-translational modification annotation in UniProtKB
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
A novel similarity-measure for the analysis of genetic data in complex phenotypes
Identification of a small optimal subset of CpG sites as bio-markers from high-throughput DNA methylation profiles
m5CPred-SVM: a novel method for predicting m5C sites of RNA
Cell Subset Prediction for Blood Genomic Studies
ConStruct: Improved construction of RNA consensus structures
Evaluation of gene expression in muscle in mouse model lacking of vitamin C synthesis
Smith-Waterman Peak Alignment for Comprehensive Two-dimensional Gas Chromatography Mass Spectrometry
Alignment of short reads to multiple genomes using hashing
Pathogen metadata platform: software for accessing and analyzing pathogen strain information
BibGlimpse: The case for a light-weight reprint manager in distributed literature research
JINet: easy and secure private data analysis for everyone
A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data
The prognostic value and immune landscaps of m6A/m5C-related lncRNAs signature in the low grade glioma
Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis
Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons
Exploring biological network structure with clustered random networks
Investigation of model stacking for drug sensitivity prediction
CellSim: a novel software to calculate cell similarity and identify their co-regulation networks
DDIGIP: predicting drug-drug interactions based on Gaussian interaction profile kernels
Mulcom: a multiple comparison statistical test for microarray data in Bioconductor
MPHASYS: a mouse phenotype analysis system
The reactive metabolite target protein database (TPDB) - a web-accessible resource
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM
Cis -motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves
Comparing segmentations by applying randomization techniques
HIMA2: high-dimensional mediation analysis and its application in epigenome-wide DNA methylation data
Signal reachability facilitates characterization of probabilistic signaling networks
CAFTAN: a tool for fast mapping, and quality assessment of cDNAs
Relating destabilizing regions to known functional sites in proteins
How accurately is ncRNA aligned within whole-genome multiple alignments?
A novel glaucomatous representation method based on Radon and wavelet transform
Highlights from the ISCB Student Council Symposium 2013
Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm
Examining the role of unmeasured confounding in mediation analysis with genetic and genomic applications
LTPConstraint: a transfer learning based end-to-end method for RNA secondary structure prediction
Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm
Towards the genome-scale discovery of bivariate monotonic classifiers
Improved analysis of bacterial CGH data beyond the log-ratio paradigm
A systematic comparison of human mitochondrial genome assembly tools
Analyzing the field of bioinformatics with the multi-faceted topic modeling technique
Cloud computing for comparative genomics
Particle simulation approach for subcellular dynamics and interactions of biological molecules
The simulation of meiosis in diploid and tetraploid organisms using various genetic models
A two-sample Bayesian t -test for microarray data
Genomics and Pathway Biology - a new post-genomics M.Sc. programme from Edinburgh University
Predicting anatomic therapeutic chemical classification codes using tiered learning
Holomics - a user-friendly R shiny application for multi-omics data integration and analysis
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs
Greedy de novo motif discovery to construct motif repositories for bacterial proteomes
cmFSM: a scalable CPU-MIC coordinated drug-finding tool by frequent subgraph mining
Adaptively capturing the heterogeneity of expression for cancer biomarker identification
Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes
Bioinformatics determination of ETEC signature genes as potential targets for molecular diagnosis and reverse vaccinology
GraphCruch 2: Software tool for network modeling, alignment and clustering
Hybrid deep learning approach to improve classification of low-volume high-dimensional data
Quartet decomposition server: a platform for analyzing phylogenetic trees
Phylogenetic network analysis as a parsimony optimization problem
Computational vaccinology and the ICoVax 2012 workshop
Popularity and performance of bioinformatics software: the case of gene set analysis
Factors affecting interactome-based prediction of human genes associated with clinical signs
Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE
PathSys: integrating molecular interaction graphs for systems biology
Multi-dimensional characterization of electrostatic surface potential computation on graphics processors
RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures
CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction
ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts
Ancestral sequence alignment under optimal conditions
Recrafting the neighbor-joining method
Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions
Finding consistent disease subnetworks across microarray datasets
proMAD: semiquantitative densitometric measurement of protein microarrays
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies
Predicting protein residue-residue contacts using random forests and deep networks
A double classification tree search algorithm for index SNP selection
A gene pattern mining algorithm using interchangeable gene sets for prokaryotes
SLR: a scaffolding algorithm based on long reads and contig classification
Soft graph clustering for single-cell RNA sequencing data
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads
Improving feature selection performance using pairwise pre-evaluation
Integration of multiple data sources to prioritize candidate genes using discounted rating system
Qxpak.5: Old mixed model solutions for new genomics problems
Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks
Associations of longitudinal D-Dimer and Factor II on early trauma survival risk
Predicting disease associations via biological network analysis
Protein-protein interaction prediction based on ordinal regression and recurrent convolutional neural networks
Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides
EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation
Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline
Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes
ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface
Normalizing alternate representations of large sequence variants across multiple bacterial genomes
A data management infrastructure for the integration of imaging and omics data in life sciences
Meta-All: a system for managing metabolic pathway information
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform
Discrimination of outer membrane proteins with improved performance
Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata
An introduction to new robust linear and monotonic correlation coefficients
PredGPI: a GPI-anchor predictor
Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration
A graph-search framework for associating gene identifiers with documents
CSmetaPred: a consensus method for prediction of catalytic residues
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes