yusuke1997/dblp-id-title huggingface dataset:
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project
Transcriptome assembly at single-cell resolution with Beaver
Hierarchical Analysis of Dependency in Metabolic Networks
DBToolkit: processing protein databases for peptide-centric proteomics
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions
StackDPPred: a stacking based prediction of DNA-binding protein from sequence
RTK: efficient rarefaction analysis of large datasets
MINRMS: an efficient algorithm for determining protein structure similarity using root-mean-squared-distance
MetaboLink: a web application for streamlined processing and analysis of large-scale untargeted metabolomics data
A logical model of HIV-1 interactions with the T-cell activation signalling pathway
Improving protein structure prediction using templates and sequence embedding
pLoc-mHum: predict subcellular localization of multi-location human proteins via general PseAAC to winnow out the crucial GO information
Recognition of ill-defined signals in nucleic acid sequences
CAMBerVis: visualization software to support comparative analysis of multiple bacterial strains
Similarity measures-based graph co-contrastive learning for drug-disease association prediction
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis
svtools: population-scale analysis of structural variation
Savant: genome browser for high-throughput sequencing data
Predicting biodegradation products and pathways: a hybrid knowledge- and machine learning-based approach
Optimized data fusion for K-means Laplacian clustering
A subspace method for the detection of transcription factor binding sites
ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data
SAMMI: a semi-automated tool for the visualization of metabolic networks
Plassembler: an automated bacterial plasmid assembly tool
The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs
Methrix: an R/Bioconductor package for systematic aggregation and analysis of bisulfite sequencing data
BSDE: barycenter single-cell differential expression for case-control studies
IDMap: facilitating the detection of potential leads with therapeutic targets
Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares
SwiSpot: modeling riboswitches by spotting out switching sequences
twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis
MotifMap: a human genome-wide map of candidate regulatory motif sites
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases
Optimal vaccination schedules using simulated annealing
An algorithm to detect and communicate the differences in computational models describing biological systems
mapDATAge: a ShinyR package to chart ancient DNA data through space and time
tmVar 2.0: integrating genomic variant information from literature with dbSNP and ClinVar for precision medicine
COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations
Power analysis and sample size estimation for sequence-based association studies
SynBioWave - a real-time communication platform for molecular and synthetic biology
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Predicting correlated outcomes from molecular data
Expertomica Cells: analysis of cell monolayer development
Can we recover a sequence, just knowing all its subsequences of given length?
TrExML: a maximum-likelihood approach for extensive tree-space exploration
Automated QuantMap for rapid quantitative molecular network topology analysis
TinGa: fast and flexible trajectory inference with Growing Neural Gas
LOT: a tool for linkage analysis of ordinal traits for pedigree data
NPIDB: a Database of Nucleic Acids-Protein Interactions
Drug-induced adverse events prediction with the LINCS L1000 data
MGAviewer: a desktop visualization tool for analysis of metagenomics alignment data
Local statistics allow quantification of cell-to-cell variability from high-throughput microscope images
A hypertext-like approach to navigating through the GCG sequence analysis package
Computational methods for diffusion-influenced biochemical reactions
LYCEUM: learning to call copy number variants on low-coverage ancient genomes
spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
Mining metabolic pathways through gene expression
Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs
TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers
LiPLike: towards gene regulatory network predictions of high certainty
Corrigendum for Elliott, B. et al. , 'PathCase pathways database system', Bioinformatics 2008, 24(21) 2526-2533
ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining
Database indexing for production MegaBLAST searches
Mining SARS-CoV protease cleavage data using non-orthogonal decision trees: a novel method for decisive template selection
Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters
Trajectory Inference with Cell-Cell Interactions (TICCI): intercellular communication improves the accuracy of trajectory inference methods
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data
GenePicker: replicate analysis of Affymetrix gene expression microarrays
Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA
Smooth orientation-dependent scoring function for coarse-grained protein quality assessment
gep2pep: a bioconductor package for the creation and analysis of pathway-based expression profiles
Automatic reading of hybridization filter images
Characteristics of 454 pyrosequencing data - enabling realistic simulation with flowsim
ONTO-PERL: An API for supporting the development and analysis of bio-ontologies
iATC-NRAKEL: an efficient multi-label classifier for recognizing anatomical therapeutic chemical classes of drugs
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Protease target prediction via matrix factorization
Protein ß-turn prediction using nearest-neighbor method
Automatic local resolution-based sharpening of cryo-EM maps
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification
MASCOT: multiple alignment system for protein sequences based on three- way dynamic programming
Capsule network for protein post-translational modification site prediction
A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life
proFIA: a data preprocessing workflow for flow injection analysis coupled to high-resolution mass spectrometry
jHeatmap: an interactive heatmap viewer for the web
dbDSM: a manually curated database for deleterious synonymous mutations
reDA: differential abundance testing on scATAC-seq data using random walk with restart
Stage prediction of embryonic stem cell differentiation from genome-wide expression data
Inferring orthologous gene regulatory networks using interspecies data fusion
Gap5 - editing the billion fragment sequence assembly
Multidimensional dot-matrices
MobilityTransformR: an R package for effective mobility transformation of CE-MS data
Predicting the trend of SARS-CoV-2 mutation frequencies using historical data
INPS-MD: a web server to predict stability of protein variants from sequence and structure
A structural homology approach for computational protein design with flexible backbone
Eukaryotic promoter recognition by binding sites for transcription factors
NITUMID: Nonnegative matrix factorization-based Immune-TUmor MIcroenvironment Deconvolution
Impact of allelic dropout on evidential value of forensic DNA profiles using RMNE
SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer
Integrative cancer patient stratification via subspace merging
Dataset-aware multi-task learning approaches for biomedical named entity recognition
Metabolic systems cost-benefit analysis for interpreting network structure and regulation
Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction
GeneTRACE - Reconstruction of Gene Content of Ancestral Species
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites
ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques
metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis
Gcluster: a simple-to-use tool for visualizing and comparing genome contexts for numerous genomes
A new approach for detecting riboswitches in DNA sequences
An informative approach on differential abundance analysis for time-course metagenomic sequencing data
Inferring nucleosome positions with their histone mark annotation from ChIP data
SNP calling using genotype model selection on high-throughput sequencing data
Statistical estimation of gene expression using multiple laser scans of microarrays
Group spike-and-slab lasso generalized linear models for disease prediction and associated genes detection by incorporating pathway information
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
D-Tailor: automated analysis and design of DNA sequences
Increasing the Impact of Bioinformatics
QuiCAT: a scalable and flexible framework for mapping synthetic sequences
ICARUS: flexible protein structural alignment based on Protein Units
VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution
Correction to: Rapid generation of high-quality structure figures for publication with PyMOL-PUB
Humanization of antibodies using a machine learning approach on large-scale repertoire data
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
Assessment of the probabilities for evolutionary structural changes in protein folds
GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes
shortran : a pipeline for small RNA-seq data analysis
fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs
The-more-the-better and the-less-the-better
SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays
A computational model to predict the immune system activation by citrus-derived vaccine adjuvants
PyIOmica: longitudinal omics analysis and trend identification
Utilizing gene pair orientations for HMM-based analysis of promoter array ChIP-chip data
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
Neural network prediction of peptide separation in strong anion exchange chromatography
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Co-evolving residues in membrane proteins
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing
BUSZ: compressed BUS files
SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts
Identifying differentially expressed genes from microarray experiments via statistic synthesis
ReCo: automated NGS re ad- co unting of single and combinatorial CRISPR gRNAs
StarPep Toolbox : an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
MosaicFinder: identification of fused gene families in sequence similarity networks
SphereCon - a method for precise estimation of residue relative solvent accessible area from limited structural information
GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture
GenVisR: Genomic Visualizations in R
PGMapper: a web-based tool linking phenotype to genes
An improved algorithm for stoichiometric network analysis: theory and applications
Clustering spatial transcriptomics data
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo
GLOGS: a fast and powerful method for GWAS of binary traits with risk covariates in related populations
Measuring the physical cohesiveness of proteins using physical interaction enrichment
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways
DeepChrome: deep-learning for predicting gene expression from histone modifications
Domain Interaction Footprint: a multi-classification approach to predict domain-peptide interactions
A descriptive marker gene approach to single-cell pseudotime inference
PGTdb: a database providing growth temperatures of prokaryotes
DACE: a scalable DP-means algorithm for clustering extremely large sequence data
U Subtle motifs: defining the limits of motif finding algorithms
Scaling multi-instance support vector machine to breast cancer detection on the BreaKHis dataset
Two- and three-dimensional image reconstructions from stained and autoradiographed histological sections
Aggressive assembly of pyrosequencing reads with mates
A Gaussian process-based definition reveals new and bona fide genetic interactions compared to a multiplicative model in the Gram-negative Escherichia coli
Model-based branching point detection in single-cell data by K-branches clustering
grünifai: interactive multiparameter optimization of molecules in a continuous vector space
CscoreTool-M infers 3D sub-compartment probabilities within cell population
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores
PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX
Affy exon tissues: exon levels in normal tissues in human, mouse and rat
EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy
FindGDPs: identification of primers for labeling microbial transcriptomes for DNA microarray analysis
Digital PCR cluster predictor: a universal R-package and shiny app for the automated analysis of multiplex digital PCR data
CompMap: a reference-based compression program to speed up read mapping to related reference sequences
EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes
MILVA: An interactive tool for the exploration of multidimensional microarray data
Identifying enhancer-promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism
PopABC: a program to infer historical demographic parameters
Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization
Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
RIFRAF: a frame-resolving consensus algorithm
Patpat: a public proteomics dataset search framework
Single-cell copy number calling and event history reconstruction
ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing
JOY: protein sequence-structure representation and analysis
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge
An iterative method for faster sum-of-pairs multiple sequence alignment
WEBMAP: radiation hybrid mapping on the WWW
CCIP: predicting CTCF-mediated chromatin loops with transitivity
Ensemble learning of genetic networks from time-series expression data
Microarray data mining with visual programming
MeDuSa: a multi-draft based scaffolder
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles
COMPADRE: an R and web resource for pathway activity analysis by component decompositions
Protein subcellular location pattern classification in cellular images using latent discriminative models
Building an abbreviation dictionary using a term recognition approach
Improved quality control processing of peptide-centric LC-MS proteomics data
BamToCov: an efficient toolkit for sequence coverage calculations
Subset scanning for multi-trait analysis using GWAS summary statistics
An XML message broker framework for exchange and integration of microarray data
AlpsNMR: an R package for signal processing of fully untargeted NMR-based metabolomics
Unsupervised segmentation of mass spectrometric ion images characterizes morphology of tissues
De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance
iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array
NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species
Interaction-based feature selection and classification for high-dimensional biological data
Microcomputer-based three-dimensional stereoscopic macromolecular graphics display
Fast model-based protein homology detection without alignment
A model for the expression of gap genes based on the Jeffreys-type equation
A computer-driven approach to PCR-based differential screening, alternative to differential display
The Database of Quantitative Cellular Signaling: management and analysis of chemical kinetic models of signaling networks
A pseudotemporal causality approach to identifying miRNA-mRNA interactions during biological processes
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps
PINBPA: Cytoscape app for network analysis of GWAS data
libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data
SVUPP: Pre-phasing long reads improves structural variant genotyping
Self-supervised feature extraction from image time series in plant phenotyping using triplet networks
Scoring protein sequence alignments using deep learning
TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing ChIP-seq datasets
Navigating the Brookhaven Protein Data Bank
Fine-tuning protein embeddings for functional similarity evaluation
Genetic Neural Networks: an artificial neural network architecture for capturing gene expression relationships
Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics
Robust design of microbial strains
multiclassPairs: an R package to train multiclass pair-based classifier
Automated extraction of information on protein-protein interactions from the biological literature
Comparative accuracy of methods for protein sequence similarity search
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
trfermikit: a tool to discover VNTR-associated deletions
RSSALib: a library for stochastic simulation of complex biochemical reactions
Fast randomization of large genomic datasets while preserving alteration counts
mkESA : enhanced suffix array construction tool
BlockFeST: Bayesian calculation of region-specific FST to detect local adaptation
MALDIquant: a versatile R package for the analysis of mass spectrometry data
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Deep neural networks for predicting restricted mean survival times
BioWareDB: the biomedical software and database search engine
Software package for automatic microarray image analysis (MAIA)
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data
An improved compound Poisson model for the number of motif hits in DNA sequences
Hybrid simulation of cellular behavior
Spliceman2: a computational web server that predicts defects in pre-mRNA splicing
VisioProt-MS: interactive 2D maps from intact protein mass spectrometry
Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array
ChromaX: a fast and scalable breeding program simulator
Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein-protein interfaces
oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language
datPAV - an online processing, analysis and visualization tool for exploratory investigation of experimental data
DPX: for the analysis of the protein core
Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network
Inferring statin-induced gene regulatory relationships in primary human hepatocytes
Computational quantification of metabolic fluxes from a single isotope snapshot: application to an animal biopsy
GenoFig: a user-friendly application for the visualization and comparison of genomic regions
Cross-type biomedical named entity recognition with deep multi-task learning
MDIPA: a microRNA-drug interaction prediction approach based on non-negative matrix factorization
Xper 2 : introducing e -taxonomy
Phylogenetic comparative analysis of RNA structure on Macintosh computers
Evolutionary relationship between the cysteine and histidine rich domains (CHORDs) and Btk-type zinc fingers
CALQ: compression of quality values of aligned sequencing data
GenePainter v. 2.0 resolves the taxonomic distribution of intron positions
Graph convolutional networks for epigenetic state prediction using both sequence and 3D genome data
InCroMAP: integrated analysis of cross-platform microarray and pathway data
Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum
Non-additivity in protein-DNA binding
ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases
Funmap: integrating high-dimensional functional annotations to improve fine-mapping
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins
The SNP ratio test: pathway analysis of genome-wide association datasets
Programmatic access to bacterial regulatory networks with regutools
EuGene-PP: a next-generation automated annotation pipeline for prokaryotic genomes
Simulating structurally variable nuclear pore complexes for microscopy
Mapping DNA by stochastic relaxation: a new approach to fragment sizes
Statistical inferences for isoform expression in RNA-Seq
Bartender: a fast and accurate clustering algorithm to count barcode reads
HDTD: analyzing multi-tissue gene expression data
Density-based hierarchical clustering of pyro-sequences on a large scale - the case of fungal ITS1