yusuke1997/dblp-id-title huggingface dataset:
Integrative platform to translate gene sets to networks
Integrative classification and analysis of multiple arrayCGH datasets with probe alignment
CAST: an iterative algorithm for the complexity analysis of sequence tracts
STAR: an algorithm to Search for Tandem Approximate Repeats
Extracting patterns of database and software usage from the bioinformatics literature
PBSIM: PacBio reads simulator - toward accurate genome assembly
PICS2: next-generation fine mapping via probabilistic identification of causal SNPs
CCLasso: correlation inference for compositional data through Lasso
Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system
preciseTAD: a transfer learning framework for 3D domain boundary prediction at base-pair resolution
DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors
Comparing systemic properties of ensembles of biological networks by graphical and statistical methods
On-line tools for sequence retrieval and multivariate statistics in molecular biology
HideNseek, a post-genome approach to locate transgenes exemplified in Arabidopsis thaliana
Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters
Comparing complex variants in family trios
Predicting fine-grained cell types from histology images through cross-modal learning in spatial transcriptomics
Model selection for metabolomics: predicting diagnosis of coronary artery disease using automated machine learning
AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets
A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription
Functional geometry of protein interactomes
Alignment of metabolic pathways
Development of a two-dimensional agent-based model for chronic chagasic cardiomyopathy after stem cell transplantation
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study
Putting the Predictive Toxicology Challenge Into Perspective: Reflections on the Results
K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals
Biological network mapping and source signal deduction
TO-GO: a Java-based Gene Ontology navigation environment
Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates
DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis
HCNet: a database of heart and calcium functional network
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
Genotype-phenotype associations: substitution models to detect evolutionary associations between phenotypic variables and genotypic evolutionary rate
Large scale data mining approach for gene-specific standardization of microarray gene expression data
Exhaustive database searching for amino acid mutations in proteomes
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation
Simulating trees with millions of species
Development and application of an algorithm to compute weighted multiple glycan alignments
Reverse network diffusion to remove indirect noise for better inference of gene regulatory networks
Tightly integrated genomic and epigenomic data mining using tensor decomposition
RIscoper: a tool for RNA-RNA interaction extraction from the literature
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
Classification based upon gene expression data: bias and precision of error rates
DCI: learning causal differences between gene regulatory networks
Linking cells across single-cell modalities by synergistic matching of neighborhood structure
scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss
MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis
Transmembrane proteins in the Protein Data Bank: identification and classification
BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates
Phylogenetic trees based on gene content
Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution
FLOSS: flexible ordered subset analysis for linkage mapping of complex traits
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
Comment on 'Discovering hospital admission patterns using models learnt from electronic hospital records'. The importance of using the right codes
OmicsQ: a user-friendly platform for interactive quantitative omics data analysis
miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources
Developing a move-set for protein model refinement
A Bayesian framework for multiple trait colocalization from summary association statistics
FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees
A new framework for computational protein design through cost function network optimization
cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data
SciApps: a cloud-based platform for reproducible bioinformatics workflows
UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations
MICER: a pre-trained encoder-decoder architecture for molecular image captioning
VarSome: the human genomic variant search engine
An MCMC algorithm for detecting short adjacent repeats shared by multiple sequences
OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria
ShortCake: an integrated platform for efficient and reproducible single-cell analysis
HLA class I binding prediction via convolutional neural networks
Six Rossmannoid folds, including the Class I aminoacyl-tRNA synthetases, share a partial core with the anti-codon-binding domain of a Class II aminoacyl-tRNA synthetase
Improving deconvolution methods in biology through open innovation competitions: an application to the connectivity map
BinDNase: a discriminatory approach for transcription factor binding prediction using DNase I hypersensitivity data
Computational prediction of RNA editing sites
GenMap: ultra-fast computation of genome mappability
The position end-set tree: a small automaton for word recognition in biological sequences
Vernal: a tool for mining fuzzy network motifs in RNA
MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides
Representing metabolic pathway information: an object-oriented approach
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations
Piecewise linear approximation of protein structures using the principle of minimum message length
myChEMBL: a virtual machine implementation of open data and cheminformatics tools
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values
'Location, Location, Location': a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate
Inferring models of multiscale copy number evolution for single-tumor phylogenetics
Genome-wide genetic heterogeneity discovery with categorical covariates
Wavelets in bioinformatics and computational biology: state of art and perspectives
Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis
Alignment of the UMLS semantic network with BioTop: methodology and assessment
TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception
MaSTerClass: a case-based reasoning system for the classification of biomedical terms
VISA: Visual Sequence Analysis for the comparison of multiple amino acid sequences
Reconstruction of clonal trees and tumor composition from multi-sample sequencing data
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees
Cell membrane proteins with high N-glycosylation, high expression and multiple interaction partners are preferred by mammalian viruses as receptors
Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine
chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts
Modes and clustering for time-warped gene expression profile data
Autocycler: long-read consensus assembly for bacterial genomes
Assemble CRISPRs from metagenomic sequencing data
Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes
Empirical comparison of web-based antimicrobial peptide prediction tools
Gene Teller: an extensible Alexa Skill for gene-relevant databases
Models@Home: distributed computing in bioinformatics using a screensaver based approach
Jumping across biomedical contexts using compressive data fusion
Genome-wide association studies using a penalized moving-window regression
A Classifier-based approach to identify genetic similarities between diseases
Deep fusion of contextual and object-based representations for delineation of multiple nuclear phenotypes
Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS
A Bayesian regression approach to the inference of regulatory networks from gene expression data
Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
M@CBETH: a microarray classification benchmarking tool
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery
annonex2embl: automatic preparation of annotated DNA sequences for bulk submissions to ENA
Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
Hadoop-BAM: directly manipulating next generation sequencing data in the cloud
Convolutional neural networks for classification of alignments of non-coding RNA sequences
i6mA-Pred: identifying DNA N6-methyladenine sites in the rice genome
MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples
Learning protein-DNA interaction landscapes by integrating experimental data through computational models
Improved gap size estimation for scaffolding algorithms
Coolpup.py: versatile pile-up analysis of Hi-C data
A parallel graph decomposition algorithm for DNA sequencing with nanopores
SubLoc: a server/client suite for protein subcellular location based on SOAP
Predicting novel metabolic pathways through subgraph mining
Topology of small-world networks of protein?Cprotein complex structures
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier
RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens
INTERSNP: genome-wide interaction analysis guided by a priori information
mlf-core: a framework for deterministic machine learning
Targeted interrogation of copy number variation using SCIMMkit
ODS_BOOTSTRAP: assessing the statistical reliability of physical maps by bootstrap resampling
A probabilistic graphical model for system-wide analysis of gene regulatory networks
A meta-analysis of two-dimensional electrophoresis pattern of the Parkinson's disease-related protein DJ-1
HI: haplotype improver using paired-end short reads
Determining a unique defining DNA sequence for yeast species using hashing techniques
PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design
Correction to: kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue
COMA server for protein distant homology search
A gene-level methylome-wide association analysis identifies novel Alzheimer's disease genes
Bioclojure: a functional library for the manipulation of biological sequences
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
Personalized identification of altered pathways in cancer using accumulated normal tissue data
The SBML discrete stochastic models test suite
FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads
Computer vision-based automated peak picking applied to protein NMR spectra
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells
RNAglib: a python package for RNA 2.5 D graphs
Electrophoretic data classification for phylogenetics and biostatistics
MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis
GDSCTools for mining pharmacogenomic interactions in cancer
Synergizing CRISPR/Cas9 off-target predictions for ensemble insights and practical applications
DIAmeter: matching peptides to data-independent acquisition mass spectrometry data
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly
DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data
A word-oriented approach to alignment validation
Penalized mixtures of factor analyzers with application to clustering high-dimensional microarray data
Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers
MMpred: a distance-assisted multimodal conformation sampling for de novo protein structure prediction
Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome
Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes
Log-linear model-based multifactor dimensionality reduction method to detect gene-gene interactions
Modular model of TNFα cytotoxicity
HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins
GTShark: genotype compression in large projects
MethylAid: visual and interactive quality control of large Illumina 450k datasets
CLICK and EXPANDER: a system for clustering and visualizing gene expression data
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data
GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data
The DynaSig-ML Python package: automated learning of biomolecular dynamics-function relationships
MASS: meta-analysis of score statistics for sequencing studies
PhagesDB: the actinobacteriophage database
A fast, sensitive pattern-matching approach for protein sequences
DNAApp: a mobile application for sequencing data analysis
HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph
gcFront: a tool for determining a Pareto front of growth-coupled cell factory designs
Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency
Trying out a million genes to find the perfect pair with RTIST
Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning
Improving circRNA-disease association prediction by sequence and ontology representations with convolutional and recurrent neural networks
Integrating heterogeneous knowledge graphs into drug-drug interaction extraction from the literature
Highly specific prediction of phosphorylation sites in proteins
linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type
Exploring the potential of template-based modelling
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
Reducing the search space for causal genetic variants with VASP
A general purpose non-linear curve fitting program for the British Broadcasting Corporation Microcomputer
SOMP: web server for in silico prediction of sites of metabolism for drug-like compounds
Characteristic Substructures and Properties in Chemical Carcinogens Studied by the Cascade Model
SMotif: a server for structural motifs in proteins
Controlling large Boolean networks with single-step perturbations
A multiple network learning approach to capture system-wide condition-specific responses
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
AGScan: a pluggable microarray image quantification software based on the ImageJ library
capC-MAP: software for analysis of Capture-C data
Family classification without domain chaining
Improving protein disorder prediction by deep bidirectional long short-term memory recurrent neural networks
Discovering epistatic feature interactions from neural network models of regulatory DNA sequences
Euclidian space and grouping of biological objects
Transform-MinER: transforming molecules in enzyme reactions
Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer
A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing
Spectral clustering based on learning similarity matrix
SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements
PathFXweb: a web application for identifying drug safety and efficacy phenotypes
Microbiome Toolbox: methodological approaches to derive and visualize microbiome trajectories
GENESIS: genome evolution scenarios
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization
Longest Biased Interval and Longest Non-negative Sum Interval
Fast computation for genome-wide association studies using boosted one-step statistics
NeBcon: protein contact map prediction using neural network training coupled with naïve Bayes classifiers
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories
Roll: a new algorithm for the detection of protein pockets and cavities with a rolling probe sphere
The electronic spreadsheet as a general-purpose programming tool
Multiple alignment by sequence annealing
SLIDE - a web-based tool for interactive visualization of large-scale - omics data
Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks
Correction of sequencing errors in a mixed set of reads
Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
genBlastG: using BLAST searches to build homologous gene models
Partitioned learning of deep Boltzmann machines for SNP data
Deep learning-based multi-functional therapeutic peptides prediction with a multi-label focal dice loss function
JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation
TripLexicon: prediction and analysis of gene regulatory RNA-DNA interactions
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
geWorkbench: an open source platform for integrative genomics
A semi-supervised learning framework for quantitative structure-activity regression modelling
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
Lightweight comparison of RNAs based on exact sequence-structure matches
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
DockAFM: benchmarking protein structures by docking under AFM topographs
Pinetree: a step-wise gene expression simulator with codon-specific translation rates
Superior feature-set ranking for small samples using bolstered error estimation
BlastGraph: a comparative genomics tool based on BLAST and graph algorithms
Wavelet-based image fusion in multi-view three-dimensional microscopy
Sequence alignment using machine learning for accurate template-based protein structure prediction
A literature-based method for assessing the functional coherence of a gene group
Comment on 'On the inference of spatial structure from population genetics data'
HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data
MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome/exome sequence data
The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequence
Bioinformatics software for biologists in the genomics era
BAllC and BAllCools: efficient formatting and operating for single-cell DNA methylation data
BETRA: a helpful tool for Beckman Microgenie users
Automatic clustering of docking poses in virtual screening process using self-organizing map
Discovering hidden viral piracy
Multi-SNP mediation intersection-union test
The Xeno-glycomics database (XDB): a relational database of qualitative and quantitative pig glycome repertoire
PMAnalyzer: a new web interface for bacterial growth curve analysis
Treevolution: visual analysis of phylogenetic trees
DEFPARAM: a program package for aligning elliptical sections of biological objects containing an n-fold symmetry
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies
Click-words: learning to predict document keywords from a user perspective
Glimma: interactive graphics for gene expression analysis
A robust, high-sensitivity algorithm for automated detection of proteins in two-dimensional electrophoresis gels
Tfcancer: a manually curated database of transcription factors associated with human cancers
Increased sensitivity with automated validation of XL-MS cleavable peptide crosslinks
Accurate in silico prediction of species-specific methylation sites based on information gain feature optimization
The discordant method: a novel approach for differential correlation
A new sequence distance measure for phylogenetic tree construction
The genetic map comparator: a user-friendly application to display and compare genetic maps
A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins
High-quality, customizable heuristics for RNA 3D structure alignment
Building alternative consensus trees and supertrees using k -means and Robinson and Foulds distance
mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes
Efficient permutation-based genome-wide association studies for normal and skewed phenotypic distributions
SplicingFactory - splicing diversity analysis for transcriptome data
SPARQL-enabled identifier conversion with Identifiers.org
BQsupports: systematic assessment of the support and novelty of new biomedical associations
An automated workflow for parallel processing of large multiview SPIM recordings
Ranking of multidimensional drug profiling data by fractional-adjusted bi-partitional scores
MetFlow: an interactive and integrated workflow for metabolomics data cleaning and differential metabolite discovery