yusuke1997/dblp-id-title huggingface dataset:
MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing
Adaptive digital tissue deconvolution
Improve homology search sensitivity of PacBio data by correcting frameshifts
Atomic-level evolutionary information improves protein-protein interface scoring
Super LeArner Prediction of NAb Panels (SLAPNAP): a containerized tool for predicting combination monoclonal broadly neutralizing antibody sensitivity
Wessim: a whole-exome sequencing simulator based on in silico exome capture
Efficient parsimony-based methods for phylogenetic network reconstruction
ChromothripsisDB: a curated database of chromothripsis
A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia
ProCaff: protein-carbohydrate complex binding affinity database
Top-down analysis of protein samples by de novo sequencing techniques
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data
Orthologue chemical space and its influence on target prediction
Aligning two sequences within a specified diagonal band
TFExplorer: integrated analysis database for predicted transcription regulatory elements
A Bayesian model integration for mutation calling through data partitioning
Mustguseal: a server for multiple structure-guided sequence alignment of protein families
Strand-seq enables reliable separation of long reads by chromosome via expectation maximization
A novel essential domain perspective for exploring gene essentiality
PyMod 3: a complete suite for structural bioinformatics in PyMOL
Updated site concordance factors minimize effects of homoplasy and taxon sampling
A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation
Trajectory-oriented Bayesian experiment design versus Fisher A-optimal design: an in depth comparison study
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences
RNAtive to recognize native-like structure in a set of RNA 3D models
Gene expression data analysis with a dynamically extended self-organized map that exploits class information
Genetic test bed for feature selection
Cladogramer: incorporating haplotype frequency into cladogram analysis
scGNN 2.0: a graph neural network tool for imputation and clustering of single-cell RNA-Seq data
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
Drug-target interaction prediction by learning from local information and neighbors
Voroprot: an interactive tool for the analysis and visualization of complex geometric features of protein structure
ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data
arrayMagic: two-colour cDNA microarray quality control, preprocessing
SERAPHIM: studying environmental rasters and phylogenetically informed movements
WALTZ-DB: a benchmark database of amyloidogenic hexapeptides
Inferring single-cell gene expression mechanisms using stochastic simulation
simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes
In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids
Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites
Intersession reproducibility of mass spectrometry profiles and its effect on accuracy of multivariate classification models
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures
Automatic recognition and annotation of gene expression patterns of fly embryos
metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data
Container-based bioinformatics with Pachyderm
timeOmics: an R package for longitudinal multi-omics data integration
The DIMA web resource - exploring the protein domain network
An extensible automated protein annotation tool: standardizing input and output using validated XML
DISPOT: a simple knowledge-based protein domain interaction statistical potential
Primaclade - a flexible tool to find conserved PCR primers across multiple species
A tool for aligning very similar DNA sequences
PedMine - a simulated annealing algorithm to identify maximally unrelated individuals in population isolates
The design of optimal therapeutic small interfering RNA molecules targeting diverse strains of influenza A virus
A hint to search for metalloproteins in gene banks
sORF finder: a program package to identify small open reading frames with high coding potential
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia
Domain size distributions can predict domain boundaries
Characterization of mismatch and high-signal intensity probes associated with Affymetrix genechips
easyRNASeq: a bioconductor package for processing RNA-Seq data
Alignment-free sequence comparison-a review
CellMontage: similar expression profile search server
A benchmark for comparing precision medicine methods in thyroid cancer diagnosis using tissue microarrays
iMap: a database-driven utility to integrate and access the genetic and physical maps of maize
CNet: a multi-omics approach to detecting clinically associated, combinatory genomic signatures
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs
SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap
A generic algorithm for finding restriction sites within DNA sequences
TIminer: NGS data mining pipeline for cancer immunology and immunotherapy
OpenSegSPIM: a user-friendly segmentation tool for SPIM data
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment
BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes
Efficient detection of differentially methylated regions using DiMmeR
SWOTein: a structure-based approach to predict stability Strengths and Weaknesses of prOTEINs
RNA-Seq Atlas - a reference database for gene expression profiling in normal tissue by next-generation sequencing
SeSAW : balancing sequence and structural information in protein functional mapping
Histogram-based DNA analysis for the visualization of chromosome, genome and species information
Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version
ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples
BAM-matcher: a tool for rapid NGS sample matching
TMCompare: transmembrane region sequence and structure
Accurate, scalable cohort variant calls using DeepVariant and GLnexus
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development
Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it
Novel domain combinations in proteins encoded by chimeric transcripts
New graphic representation of structural parameters of proteins
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows
Big Data Smart Socket (BDSS): a system that abstracts data transfer habits from end users
W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification
Computational functional genomics-based reduction of disease-related gene sets to their key components
Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT
Linear functional organization of the omic embedding space
The MI bundle: enabling network and structural biology in genome visualization tools
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae
DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning
Improving annotation propagation on molecular networks through random walks: introducing ChemWalker
HYPROSP II-A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments
FingerPRINTScan: intelligent searching of the PRINTS motif database
Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach
Gene regulatory networks by transcription factors and microRNAs in breast cancer
TreeView: an application to display phylogenetic trees on personal computers
Evaluation of methods for generative modeling of cell and nuclear shape
Concerning the accuracy of Fido and parameter choice
Bio-knowledge-based filters improve residue-residue contact prediction accuracy
An algorithm to analyse the hydrolysis pathway of peptides and proteins by sequence analyses of unfractionated digestion mixtures
Java-based application framework for visualization of gene regulatory region annotations
Enrichment of regulatory signals in conserved non-coding genomic sequence
Benchmarking and improving the performance of variant-calling pipelines with RecallME
Industrial methodology for process verification in research (IMPROVER): toward systems biology verification
BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data
PheGWAS: a new dimension to visualize GWAS across multiple phenotypes
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
A kinase sequence database: sequence alignments and family assignment
ASP-G: an ASP-based method for finding attractors in genetic regulatory networks
ProDy : Protein Dynamics Inferred from Theory and Experiments
Modelling interaction sites in protein domains with interaction profile hidden Markov models
LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants
Reconstruction of genetic association networks from microarray data: a partial least squares approach
Identification of cell types from single-cell transcriptomes using a novel clustering method
Identification of transcript regulatory patterns in cell differentiation
Metapaths : similarity search in heterogeneous knowledge graphs via meta-paths
Fast protein block searches
NOVA: a software to analyze complexome profiling data
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis
HSPIR: a manually annotated heat shock protein information resource
Methods and challenges in timing chromosomal abnormalities within cancer samples
Coriolis: enabling metagenomic classification on lightweight mobile devices
GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology
scCNC: a method based on capsule network for clustering scRNA-seq data
admetSAR 2.0: web-service for prediction and optimization of chemical ADMET properties
Identifying critical transitions of complex diseases based on a single sample
NIFAS: visual analysis of domain evolution in proteins
DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications
htSeqTools: high-throughput sequencing quality control, processing and visualization in R
Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species
A robust computational pipeline for model-based and data-driven phenotype clustering
Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression-based convolutional neural networks
Rethinking GWAS: how lessons from genetic screens and artificial intelligence could reveal biological mechanisms
Identifying distantly related protein sequences
Proteins associated with diseases show enhanced sequence correlation between charged residues
Improving genomics-based predictions for precision medicine through active elicitation of expert knowledge
ADViSELipidomics: a workflow for analyzing lipidomics data
GEIGER: investigating evolutionary radiations
Correction to: HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition
Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors
Embeddings of genomic region sets capture rich biological associations in lower dimensions
Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acid sequences
Selecting PCR designed mismatch primers to create diagnostic restriction sites
PsyGeNET: a knowledge platform on psychiatric disorders and their genes
m5c-iEnsem: 5-methylcytosine sites identification through ensemble models
CODOC: efficient access, analysis and compression of depth of coverage signals
VoroCNN: deep convolutional neural network built on 3D Voronoi tessellation of protein structures
PERMORY-MPI: a program for high-speed parallel permutation testing in genome-wide association studies
PubMed-EX: a web browser extension to enhance PubMed search with text mining features
Identification and visualization of cage-shaped proteins
Efficient Bayesian inference under the structured coalescent
Classification of microarrays to nearest centroids
Visualization-based cancer microarray data classification analysis
Unbiased curriculum learning enhanced global-local graph neural network for protein thermodynamic stability prediction
FractBias: a graphical tool for assessing fractionation bias following polyploidy
IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis
Identification and measurement of neighbor-dependent nucleotide substitution processes
SCIM: universal single-cell matching with unpaired feature sets
How sequence alignment scores correspond to probability models
FermiKit: assembly-based variant calling for Illumina resequencing data
Exploring gene content with pangene graphs
SimBoolNet - a Cytoscape plugin for dynamic simulation of signaling networks
GeneclusterViz: a tool for conserved gene cluster visualization, exploration and analysis
Transcription factor prediction using protein 3D secondary structures
EPS: an empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes
Pathway analysis in metabolic databases via differential metabolic display (DMD)
P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics
APE: Analyses of Phylogenetics and Evolution in R language
De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae
iPromoter-BnCNN: a novel branched CNN-based predictor for identifying and classifying sigma promoters
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
aPCoA: covariate adjusted principal coordinates analysis
GWAS Analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis
SeqWho: reliable, rapid determination of sequence file identity using k -mer frequencies in Random Forest classifiers
Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells
Data exploration tools for the Gene Ontology database
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome
FineStr: a web server for single-base-resolution nucleosome positioning
SonicParanoid: fast, accurate and easy orthology inference
Genome-wide synteny through highly sensitive sequence alignment: Satsuma
Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge
Impact of dimeric organization of enzyme on its function: the case of photosynthetic water splitting
The Naïve Bayes classifier++ for metagenomic taxonomic classification - query evaluation
Insights on protein thermal stability: a graph representation of molecular interactions
Semi-supervised peak calling with SPAN and JBR genome browser
GpABC: a Julia package for approximate Bayesian computation with Gaussian process emulation
CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction
An integrative approach to understanding the combinatorial histone code at functional elements
lrgpr: interactive linear mixed model analysis of genome-wide association studies with composite hypothesis testing and regression diagnostics in R
EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
GEAR: genomic enrichment analysis of regional DNA copy number changes
scConnect: a method for exploratory analysis of cell-cell communication based on single-cell RNA-sequencing data
VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern
MULTI: a program for multicomponent analysis of spectra
Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs
HMMoC - a compiler for hidden Markov models
Identification of population-level differentially expressed genes in one-phenotype data
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Multi-task deep latent spaces for cancer survival and drug sensitivity prediction
Inferring qualitative relations in genetic networks and metabolic pathways
Computational identification of putative programmed translational frameshift sites
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
FP2VEC: a new molecular featurizer for learning molecular properties
DPRml: distributed phylogeny reconstruction by maximum likelihood
SIGNORApp: a Cytoscape 3 application to access SIGNOR data
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins
Off-target predictions in CRISPR-Cas9 gene editing using deep learning
Methods for discovering novel motifs in nucleic acid sequences
BioNetGen 2.2: advances in rule-based modeling
Identifying differentially expressed transcripts from RNA-seq data with biological variation
A novel comprehensive wave-form MS data processing method
Pitfalls of supervised feature selection
DiversePathsJ: diverse shortest paths for bioimage analysis
LBERT: Lexically-aware Transformers based Bidirectional Encoder Representation model for learning Universal Bio-Entity Relations
Pathway identification by network pruning in the metabolic network of Escherichia coli
Bioimage informatics: a new area of engineering biology
Medusa: a simple tool for interaction graph analysis
FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners
Alignment-free detection of local similarity among viral and bacterial genomes
Gene- and pathway-based association tests for multiple traits with GWAS summary statistics
ADME-AP: a database of ADME associated proteins
Multiple sequence alignment using partial order graphs
SEGE: A database on 'intron less/single exonic' genes from eukaryotes
A vector-based method for drawing RNA secondary structure
Improving compound-protein interaction prediction by building up highly credible negative samples
CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
psupertime: supervised pseudotime analysis for time-series single-cell RNA-seq data
TOPD/FMTS: a new software to compare phylogenetic trees
A computer program for molecular weight determination of DNA fragments (HOWBIG)
Statistical considerations for digital approaches to non-invasive fetal genotyping
iMIRAGE: an R package to impute microRNA expression using protein-coding genes
Malin: maximum likelihood analysis of intron evolution in eukaryotes
Exploring the diversity of complex metabolic networks
Transposable element annotation of the rice genome
MIAH: automatic alignment of eukaryotic SSU rRNAs
An improved sequence handling package that runs on the Apple Macintosh
Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function
Statistical analysis of the cancer cell's molecular entropy using high-throughput data
dRFEtools: dynamic recursive feature elimination for omics
Increased power of microarray analysis by use of an algorithm based on a multivariate procedure
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning
Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells
Genome compression: a novel approach for large collections
RNA design via structure-aware multifrontier ensemble optimization
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project
Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model
A distance metric for a class of tree-sibling phylogenetic networks
A Web interface generator for molecular biology programs in Unix
Online Predicted Human Interaction Database
CoMut: visualizing integrated molecular information with comutation plots
PepC: proteomics software for identifying differentially expressed proteins based on spectral counting
PedNavigator: a pedigree drawing servlet for large and inbred populations
ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees
NRGC: a novel referential genome compression algorithm
Early cancer detection from genome-wide cell-free DNA fragmentation via shuffled frog leaping algorithm and support vector machine
DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures
AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria
Phosformer: an explainable transformer model for protein kinase-specific phosphorylation predictions
sismonr: simulation of in silico multi-omic networks with adjustable ploidy and post-transcriptional regulation in R
Accelerated enumeration of extreme rays through a positive-definite elementarity test
dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis
SAPIN: A framework for the structural analysis of protein interaction networks
Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction
Epigenomics coverage data extraction and aggregation in R with tidyCoverage
The Merck Gene Index browser: an extensible data integration system for gene finding, gene characterization and EST data mining
Overlap graph-based generation of haplotigs for diploids and polyploids
Nonparametric IPSS: fast, flexible feature selection with false discovery control
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool
COMPUCELL, a multi-model framework for simulation of morphogenesis
GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor
RAxML Grove: an empirical phylogenetic tree database
Comment on 'A congruence index for testing topological similarity between trees'
GeneSwitches: ordering gene expression and functional events in single-cell experiments
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach