yusuke1997/dblp-id-title huggingface dataset:
MetumpX - a metabolomics support package for untargeted mass spectrometry
Ontologies for Behavior
Ligand-Info, Searching for Similar Small Compounds Using Index Profiles
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data
DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal
Recombination-filtered genomic datasets by information maximization
COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM
Exploring generative deep learning for omics data using log-linear models
NIBNA: a network-based node importance approach for identifying breast cancer drivers
BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
CTRD: a fast applet for computing signed translocation distance between genomes
Correlated evolution of transcription factors and their binding sites
Improved database searches for orthologous sequences by conditioning on outgroup sequences
THOR: targeted high-throughput ortholog reconstructor
GenomeRing: alignment visualization based on SuperGenome coordinates
Towards a reproducible interactome: semantic-based detection of redundancies to unify protein-protein interaction databases
GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form
Novel human lncRNA-disease association inference based on lncRNA expression profiles
Genomic sequences and RNA-binding proteins predict RNA splicing efficiency in various single-cell contexts
Causal relationship inference for a large-scale cellular network
Regulatory motif finding by logic regression
VizPrimer: a web server for visualized PCR primer design based on known gene structure
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
Hyperscape: visualization for complex biological networks
NMF-RI: blind spectral unmixing of highly mixed multispectral flow and image cytometry data
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data
CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
CoreDetector: a flexible and efficient program for core-genome alignment of evolutionary diverse genomes
PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes
Hierarchical deep learning for predicting GO annotations by integrating protein knowledge
PRSice: Polygenic Risk Score software
XEMBL: distributing EMBL data in XML format
Oligonucleotide microarray identification of Bacillus anthracis strains using support vector machines
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data
LION LBD: a literature-based discovery system for cancer biology
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins
Fijiyama: a registration tool for 3D multimodal time-lapse imaging
SEGMENT: identifying compositional domains in DNA sequences
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
Identification of the most significant amphipathic helix with application to HIV and MHV envelope proteins
hipFG: high-throughput harmonization and integration pipeline for functional genomics data
Physical protein-protein interactions predicted from microarrays
Quality control of single-cell RNA-seq by SinQC
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets
PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes
MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data
Nexplorer: phylogeny-based exploration of sequence family data
Clusterv: a tool for assessing the reliability of clusters discovered in DNA microarray data
ALTRE: workflow for defining ALTered regulatory elements using chromatin accessibility data
SIGNAL SCAN: a computer program that scans DNA sequences for eukaryotic transcriptional elements
Sequence tube maps: making graph genomes intuitive to commuters
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition
Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data
MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor
ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
First insight into the prediction of protein folding rate change upon point mutation
LOGICOIL - multi-state prediction of coiled-coil oligomeric state
Computer-assisted curation of a human regulatory core network from the biological literature
Finding metabolic pathways using atom tracking
Binary analysis and optimization-based normalization of gene expression data
TCVS: tree-guided compositional variable selection analysis of microbiome data
Design centering enables robustness screening of pattern formation models
BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis
Integration of gel-based proteome data with pProRep
BLight: efficient exact associative structure for k-mers
Fast genotyping of known SNPs through approximate k -mer matching
Local multiple sequence alignment using dead-end elimination
Local Structure Prediction with Local Structure-based Sequence Profiles
DisruPPI: structure-based computational redesign algorithm for protein binding disruption
seq++: analyzing biological sequences with a range of Markov-related models
GAPWM: a genetic algorithm method for optimizing a position weight matrix
PDV: an integrative proteomics data viewer
Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models
Letter to the editor: Testing on external independent datasets is necessary to corroborate machine learning model improvement
Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning
TargetSA: adaptive simulated annealing for target-specific drug design
Connecting mathematical models to genomes: joint estimation of model parameters and genome-wide marker effects on these parameters
SCIP: a single-cell image processor toolbox
Generation of patterns from gene expression data by assigning confidence to differentially expressed genes
Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics
GSATools: analysis of allosteric communication and functional local motions using a structural alphabet
Evaluation of tools for long read RNA-seq splice-aware alignment
Three minimal sequences found in Ebola virus genomes and absent from human DNA
A simple method to control over-alignment in the MAFFT multiple sequence alignment program
Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine
node.dating: dating ancestors in phylogenetic trees in R
Using clusters of computers for large QU-GENE simulation experiments
TICO: a tool for improving predictions of prokaryotic translation initiation sites
Single-cell regulome data analysis by SCRAT
NanoSplicer: accurate identification of splice junctions using Oxford Nanopore sequencing
Detection of generic spaced motifs using submotif pattern mining
Multidrug representation learning based on pretraining model and molecular graph for drug interaction and combination prediction
Interaction screening by Kendall's partial correlation for ultrahigh-dimensional data with survival trait
Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data
Tysserand - fast and accurate reconstruction of spatial networks from bioimages
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction
Two different approaches to computer-aided teaching of microbial genetics
DockStar: a novel ILP-based integrative method for structural modeling of multimolecular protein complexes
densityCut: an efficient and versatile topological approach for automatic clustering of biological data
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package
Re-identification of individuals in genomic data-sharing beacons via allele inference
MetaCache: context-aware classification of metagenomic reads using minhashing
The mRNA landscape at yeast translation initiation sites
AlphaMap: an open-source Python package for the visual annotation of proteomics data with sequence-specific knowledge
Drawing phylogenetic trees in LATEX and Microsoft Word
PADRE: a package for analyzing and displaying reticulate evolution
A non-linear regression program in BASIC for estimating Km and Vmax
Comparison of microarray designs for class comparison and class discovery
Eukaryotic transcription factor binding sites - modeling and integrative search methods
Fast, accurate, and reliable molecular docking with QuickVina 2
DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent
GenomicTools : a computational platform for developing high-throughput analytics in genomics
Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes
Differential coexpression in human tissues and the confounding effect of mean expression levels
mod_bio: Apache modules for Next-Generation sequencing data
MaConDa: a publicly accessible mass spectrometry contaminants database
Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level
Prediction of gene regulatory connections with joint single-cell foundation models and graph-based learning
Microbial genotype-phenotype mapping by class association rule mining
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data
miRseqViewer: multi-panel visualization of sequence, structure and expression for analysis of microRNA sequencing data
MELTING, computing the melting temperature of nucleic acid duplex
Hydra image processor: 5-D GPU image analysis library with MATLAB and python wrappers
AssociationDB: web-based exploration of genomic association
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures
Wigwams: identifying gene modules co-regulated across multiple biological conditions
An integrated family of amino acid sequence analysis programs
TRI_tool: a web-tool for prediction of protein-protein interactions in human transcriptional regulation
SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2-human mimicry and interactions
Deshrinking ridge regression for genome-wide association studies
MANSEK and SUNHCA. Two interactive programs for the hydrophobic cluster analysis of protein sequences
Optimization of HAART with genetic algorithms and agent-based models of HIV infection
Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
Bayesian reconstruction and differential testing of excised introns
SYCAMORE - a systems biology computational analysis and modeling research environment
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool
HD-eXplosion: visualization of hydrogen-deuterium exchange data as chiclet and volcano plots with statistical filtering
GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
AlphaPulldown - a python package for protein-protein interaction screens using AlphaFold-Multimer
Time correction for computing Michaelis-Menten kinetics
LEHM: a convenient non-linear regression microcomputer program for fitting Michaelis-Menten and Hill models to enzyme kinetic data
scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets
NMPP: a user-customized NimbleGen microarray data processing pipeline
Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms
screenwerk: a modular tool for the design and analysis of drug combination screens
PESTAS: a web server for EST analysis and sequence mining
ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth
A new approach to bias correction in RNA-Seq
Understanding hydrogen-bond patterns in proteins using network motifs
eFORGE v2.0: updated analysis of cell type-specific signal in epigenomic data
Application of the Bayesian MMSE estimator for classification error to gene expression microarray data
A systematic comparison and evaluation of biclustering methods for gene expression data
SAMF: a self-adaptive protein modeling framework
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Bpipe: a tool for running and managing bioinformatics pipelines
NIEND: neuronal image enhancement through noise disentanglement
Phylonium: fast estimation of evolutionary distances from large samples of similar genomes
Complex heatmaps reveal patterns and correlations in multidimensional genomic data
EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings
Identifying cellular cancer mechanisms through pathway-driven data integration
Generating multiple alignments on a pangenomic scale
Co-regulation in embryonic stem cells via context-dependent binding of transcription factors
Hunting down zinc(II)-binding sites in proteins with distance matrices
RF-Net 2: fast inference of virus reassortment and hybridization networks
Seq2Struct: a resource for establishing sequence-structure links
Ovarian cancer identification based on dimensionality reduction for high-throughput mass spectrometry data
pIRS: Profile-based Illumina pair-end reads simulator
AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver
Hidden Markov models for sequence analysis: extension and analysis of the basic method
ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks
Differential expression of genes coding for ribosomal proteins in different human tissues
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data
Real Time Metagenomics: Using k -mers to annotate metagenomes
Quantifying biological samples using Linear Poisson Independent Component Analysis for MALDI-ToF mass spectra
Pharokka: a fast scalable bacteriophage annotation tool
GenXref. VI: Automatic generation of links between two heterogeneous databases
The SuMo server: 3D search for protein functional sites
Adding unaligned sequences into an existing alignment using MAFFT and LAST
MetaSpark: a spark-based distributed processing tool to recruit metagenomic reads to reference genomes
PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods
Protein motif extraction with neuro-fuzzy optimization
Rapid generation of high-quality structure figures for publication with PyMOL-PUB
RSDB: representative protein sequence databases have high information content
WEbcoli: an interactive and asynchronous web application for in silico design and analysis of genome-scale E.coli model
HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data
Exact Significance Levels for the Maximum 2 Method of Detecting Recombination
Which Genetic Loci Have Greater Population Assignment Power?
shinyGEO : a web-based application for analyzing gene expression omnibus datasets
Supervised normalization of microarrays
Stem Trace: an interactive visual tool for comparative RNA structure analysis
Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries
MSQT for choosing SNP assays from multiple DNA alignments
Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics
Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction
CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments
BASIC: BCR assembly from single cells
Refined phylogenetic profiles method for predicting protein-protein interactions
sBGC-hm: an atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome
GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway-pathway interaction network
VizStruct: exploratory visualization for gene expression profiling
BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server
AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting
GABAC: an arithmetic coding solution for genomic data
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data
Somatic selection distinguishes oncogenes and tumor suppressor genes
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold
Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq
SPV: a JavaScript Signaling Pathway Visualizer
Assimilating genome-scale metabolic reconstructions with modelBorgifier
IBDkin: fast estimation of kinship coefficients from identity by descent segments
How to get your goat: automated identification of species from MALDI-ToF spectra
Simple sequence-based kernels do not predict protein-protein interactions
SChiSM2: creating interactive web page annotations of molecular structure models using Jmol
ALIGNMENT SERVICE: creation and processing of alignments of sequences of unlimited length
ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation
PlayMolecule BindScope: large scale CNN-based virtual screening on the web
Discovering simple DNA sequences by the algorithmic significance method
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning
GeneVetter: a web tool for quantitative monogenic assessment of rare diseases
CNEFinder: finding conserved non-coding elements in genomes
Penalized and weighted K -means for clustering with scattered objects and prior information in high-throughput biological data
GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses
METIS: multiple extraction techniques for informative sentences
Integrative gene network construction for predicting a set of complementary prostate cancer genes
Using semantic web rules to reason on an ontology of pseudogenes
New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region
Weighted quality estimates in machine learning
SEQ-ED: an interactive computer program for editing, analysis and storage of long DNA sequences
SBMLToolbox: an SBML toolbox for MATLAB users
Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference
Predicting protein-protein interactions through sequence-based deep learning
Robust adjustment of sequence tag abundance
AllerCatPro - prediction of protein allergenicity potential from the protein sequence
Information Concept in Biology
Model-free unsupervised gene set screening based on information enrichment in expression profiles
Soffritto: a deep learning model for predicting high-resolution replication timing
ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes
ACT: the Artemis comparison tool
SOS: online probability estimation and generation of T-and B-cell receptors
UMI-VarCal: a new UMI-based variant caller that efficiently improves low-frequency variant detection in paired-end sequencing NGS libraries
NEAR: neural embeddings for amino acid relationships
ToxAssay: a hierarchical model-driven tool for advanced toxicogenomics biomarker discovery
PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources
SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases
CLigOpt: controllable ligand design through target-specific optimization
FluxModeCalculator: an efficient tool for large-scale flux mode computation
DIA-MCIS: an importance sampling network randomizer for network motif discovery and other topological observables in transcription networks
A generic methodological framework for studying single cell motility in high-throughput time-lapse data
Statistical Adjustment of Signal Censoring in Gene Expression Experiments
Benchmarking time-series data discretization on inference methods
Potentially functional regions of nucleic acids recognized by a Kohonen's self-organizing map
Peakhood: individual site context extraction for CLIP-seq peak regions
EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing
Gene-Expression Omnibus integration and clustering Tools in SeqExpress
An educator framework for organizing Wikipedia editathons for computational biology
COMPARE, a multi-organism system for cross-species data comparison and transfer of information
HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape
Inferring transcriptional logic from multiple dynamic experiments
SCOT: Rethinking the classification of secondary structure elements
Modelling biological processes using workflow and Petri Net models
Site identification in high-throughput RNA-protein interaction data
Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Differential gene expression analysis for multi-subject single-cell RNA-sequencing studies with aggregateBioVar
Analysis of correlated mutations in HIV-1 protease using spectral clustering
MedlineR: an open source library in R for Medline literature data mining
Beyond the central dogma
Theory of local k-mer selection with applications to long-read alignment
Random forest of perfect trees: concept, performance, applications and perspectives
Predicting anti-cancer drug response by finding optimal subset of drugs
Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing
RSIR: regularized sliced inverse regression for motif discovery
Practical FDR-based sample size calculations in microarray experiments
Statistical modeling of isoform splicing dynamics from RNA-seq time series data
Efficient identification and analysis of chemical exchange in biomolecules by R 1ρ relaxation dispersion with Amaterasu
Simulating Illumina metagenomic data with InSilicoSeq
ViSiBooL - visualization and simulation of Boolean networks with temporal constraints
STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data
BEReX: Biomedical Entity-Relationship eXplorer
Improving subcellular localization prediction using text classification and the gene ontology
CG2AA: backmapping protein coarse-grained structures
Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations
ScripTree: scripting phylogenetic graphics