yusuke1997/dblp-id-title huggingface dataset:
A novel variational Bayes multiple locus Z -statistic for genome-wide association studies with Bayesian model averaging
Pathway-based visualization of cross-platform microarray datasets
Topology-based sparsification of graph annotations
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data
Functional topology in a network of protein interactions
Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories
MamPhEA: a web tool for mammalian phenotype enrichment analysis
GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families
Collaborative intra-tumor heterogeneity detection
Gapsplit: efficient random sampling for non-convex constraint-based models
OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers
Assessing concordance among human, in silico predictions and functional assays on genetic variant classification
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R
Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language models
BaiHui: cross-species brain-specific network built with hundreds of hand-curated datasets
Combining multiple approaches for gene microarray classification
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
Classification of DNA sequences using Bloom filters
relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data
PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes
Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps
The use of missing values in proteomic data-independent acquisition mass spectrometry to enable disease activity discrimination
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics
SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity
DeepDTA: deep drug-target binding affinity prediction
tcpl: the ToxCast pipeline for high-throughput screening data
FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets
DREAM-Yara: an exact read mapper for very large databases with short update time
EXPANDS: expanding ploidy and allele frequency on nested subpopulations
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction
Scalable machine learning-assisted model exploration and inference using Sciope
ChemDB: a public database of small molecules and related chemoinformatics resources
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling
Analysis of densitometric data obtained from electrophoretic analysis
Analysis of variance components in gene expression data
InfoTrac TFD: a microcomputer implementation of the Transcription Factor Database TFD with a graphical user interface
RNA-TorsionBERT: leveraging language models for RNA 3D torsion angles prediction
GAPSCORE: finding gene and protein names one word at a time
A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data
Increasing the accuracy of single sequence prediction methods using a deep semi-supervised learning framework
VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis
BIAS: Bioinformatics Integrated Application Software
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
What should be expected from feature selection in small-sample settings
gwasrapidd: an R package to query, download and wrangle GWAS catalog data
Prediction of protein secondary structures by a neural network
MENDB: a database of polymorphic loci from natural populations
CHROMA: consensus-based colouring of multiple alignments for publication
Adaptive multiorientation resolution analysis of complex filamentous network images
Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome
Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer
LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq
Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data
BiXGBoost: a scalable, flexible boosting-based method for reconstructing gene regulatory networks
PredHPI: an integrated web server platform for the detection and visualization of host-pathogen interactions using sequence-based methods
Improving evolutionary models of protein interaction networks
Distribution patterns of over-represented k-mers in non-coding yeast DNA
Clustering protein sequences-structure prediction by transitive homology
DEOD: uncovering dominant effects of cancer-driver genes based on a partial covariance selection method
Bioconductor toolchain for reproducible bioinformatics pipelines using Rcwl and RcwlPipelines
mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes
Prediction of neuropeptide cleavage sites in insects
Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
FoldX 5.0: working with RNA, small molecules and a new graphical interface
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes
i DeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences
BCrystal: an interpretable sequence-based protein crystallization predictor
A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data
An algorithm for searching restriction maps
SBAL: a practical tool to generate and edit structure-based amino acid sequence alignments
DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins
AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data
Constraint-based functional similarity of metabolic genes: going beyond network topology
IntegrAlign: a comprehensive tool for multi-immunofluorescence panel integration through image alignment
Accurate identification of alternatively spliced exons using support vector machine
Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs
NanoPack: visualizing and processing long-read sequencing data
GToTree: a user-friendly workflow for phylogenomics
On what to permute in test-based approaches for variable importance measures in Random Forests
Palo: spatially aware color palette optimization for single-cell and spatial data
VisuStatR: visualizing motility and morphology statistics on images in R
tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression
Interpreting protein abundance in Saccharomyces cerevisiae through relational learning
Computer aided design of pellets for fixed-bed reactors performing Michaelis-Menten reactions
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
PrecisionProDB: improving the proteomics performance for precision medicine
SVDMAN-singular value decomposition analysis of microarray data
A statistical framework for the design of microarray experiments and effective detection of differential gene expression
Falco: a quick and flexible single-cell RNA-seq processing framework on the cloud
Command line tool for calculating theoretical MS spectra for given sequences
Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets
OBO Explorer: an editor for open biomedical ontologies in OWL
JPred: a consensus secondary structure prediction server
Protein Homeostasis Database: protein quality control in E.coli
TwisTranscripT: stochastic simulation of the transcription-supercoiling coupling
A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs
DeepAntigen: a novel method for neoantigen prioritization via 3D genome and deep sparse learning
SPA-STOCSY: an automated tool for identifying annotated and non-annotated metabolites in high-throughput NMR spectra
PROMOT: a FORTRAN program to scan protein sequences against a library of known motifs
SplitsTree: analyzing and visualizing evolutionary data
A soft kinetic data structure for lesion border detection
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data
Gaia: automated quality assessment of protein structure models
CNVRuler: a copy number variation-based case-control association analysis tool
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure
Inferring parental genomic ancestries using pooled semi-Markov processes
Sample size for FDR-control in microarray data analysis
Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network
Joint reconstruction of multiple gene networks by simultaneously capturing inter-tumor and intra-tumor heterogeneity
Improved NSGA-II algorithms for multi-objective biomarker discovery
Mocca: semi-automatic method for domain hunting
Accurate detection of short and long active ORFs using Ribo-seq data
Cuttlefish: fast, parallel and low-memory compaction of de Bruijn graphs from large-scale genome collections
A probabilistic measure for alignment-free sequence comparison
A public website for the automated assessment and validation of SARS-CoV-2 diagnostic PCR assays
XDIA: improving on the label-free data-independent analysis
BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry
Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway
nVenn: generalized, quasi-proportional Venn and Euler diagrams
cBrother: relaxing parental tree assumptions for Bayesian recombination detection
CoD: inferring immune-cell quantities related to disease states
poRe GUIs for parallel and real-time processing of MinION sequence data
DRUDIT: web-based DRUgs DIscovery Tools to design small molecules as modulators of biological targets
von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
FeatureStack: Perl module for comparative visualization of gene features
When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks
JUCHMME: a Java Utility for Class Hidden Markov Models and Extensions for biological sequence analysis
MARDy: Mycology Antifungal Resistance Database
Bias correction for selecting the minimal-error classifier from many machine learning models
GenomeVx: simple web-based creation of editable circular chromosome maps
Predicting disulfide bond connectivity in proteins by correlated mutations analysis
VeTra: a tool for trajectory inference based on RNA velocity
Easy-HLA: a validated web application suite to reveal the full details of HLA typing
Sipros Ensemble improves database searching and filtering for complex metaproteomics
CABS-flex predictions of protein flexibility compared with NMR ensembles
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
Expertomica metabolite profiling: getting more information from LC-MS using the stochastic systems approach
ET viewer: an application for predicting and visualizing functional sites in protein structures
dCAS: a desktop application for cDNA sequence annotation
Autoregressive modeling of analytical sensor data can yield classifiers in the predictor coefficient parameter space
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data
Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder
PyHMMER: a Python library binding to HMMER for efficient sequence analysis
Computer monitoring, capture and analysis of gas/liquid chromatograph traces
TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter
Computing topological parameters of biological networks
Aligning short reads to reference alignments and trees
GRAST: a new way of genome reduction analysis using comparative genomics
Gene regulatory network inference methodology for genomic and transcriptomic data acquired in genetically related heterozygote individuals
IMMerge: merging imputation data at scale
Prioritizing genetic variants in GWAS with lasso using permutation-assisted tuning
Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites
BioMAJ: a flexible framework for databanks synchronization and processing
Multiple sequence alignment based on deep reinforcement learning with self-attention and positional encoding
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
Genome rearrangement with gene families
Computational approaches towards understanding human long non-coding RNA biology
Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing
cBinderDB: a covalent binding agent database
Deep learning with word embeddings improves biomedical named entity recognition
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets
A new ensemble-based algorithm for identifying breath gas marker candidates in liver disease using ion molecule reaction mass spectrometry
M 3 : an improved SNP calling algorithm for Illumina BeadArray data
MULTAN (2), a multiple string alignment program for nucleic acids and proteins
Notes on the implementation of the mass-radius method of fractal dimension estimation
miRAnno - network-based functional microRNA annotation
HCS-Analyzer: open source software for high-content screening data correction and analysis
GeNGe: systematic generation of gene regulatory networks
Trev: a DNA trace editor and viewer
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations
TargetFinder: searching annotated sequence databases for target genes of transcription factors
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS
Enrichment analysis with EpiAnnotator
gkmSVM: an R package for gapped-kmer SVM
PLIDA: cross-platform gene expression normalization using perturbed topic models
Phenotypic clustering of yeast mutants based on kinetochore microtubule dynamics
RNASeqMetaDB: a database and web server for navigating metadata of publicly available mouse RNA-Seq datasets
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions
IRSOM, a reliable identifier of ncRNAs based on supervised self-organizing maps with rejection
A software package for the manipulation, display and analysis of electron and light microscope data
G-SQZ: compact encoding of genomic sequence and quality data
GlycoBase and autoGU: tools for HPLC-based glycan analysis
NLR-parser: rapid annotation of plant NLR complements
MOSAIC: a joint modeling methodology for combined circadian and non-circadian analysis of multi-omics data
Copy number variant detection in inbred strains from short read sequence data
A microcomputer program to evaluate the saturation of complex solutions with respect to biominerals
Bayesian linear mixed model with multiple random effects for prediction analysis on high-dimensional multi-omics data
HiChIP-Peaks: a HiChIP peak calling algorithm
MIRACH: efficient model checker for quantitative biological pathway models
PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries
ViralWasm: a client-side user-friendly web application suite for viral genomics
Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration
Predicting single-cell cellular responses to perturbations using cycle consistency learning
GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor
Fractionation, rearrangement and subgenome dominance
MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed search logs for zero-shot biomedical information retrieval
BPP: a sequence-based algorithm for branch point prediction
Spresso: an ultrafast compound pre-screening method based on compound decomposition
PCIG: a web-based application to explore immune-genomics interactions across cancer types
Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data
PedSplit: pedigree management for stratified analysis
Systematic comparison of RNA-Seq normalization methods using measurement error models
Stability analysis of phylogenetic trees
GARLIC: Genomic Autozygosity Regions Likelihood-based Inference and Classification
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing
Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level
Protein-protein binding affinity prediction from amino acid sequence
SPEAR: Systematic ProtEin AnnotatoR
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction
ProtNote: a multimodal method for protein-function annotation
Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies
LDB2000: sequence-based integrated maps of the human genome
Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)
Gene selection in cancer classification using sparse logistic regression with Bayesian regularization
SUBSIS: DNASIS/PROSIS subdirectory management
BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
DANN: a deep learning approach for annotating the pathogenicity of genetic variants
PASTASpark: multiple sequence alignment meets Big Data
A distributed system for two-dimensional gel analysis
Automated gene-model curation using global discriminative learning
Multimodal mechanistic signatures for neurodegenerative diseases (NeuroMMSig): a web server for mechanism enrichment
Inheritance and variability of kinetic gene expression parameters in microbial cells: modeling and inference from lineage tree data
A framework for space-efficient variable-order Markov models
Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x
GEInfo: an R package for gene-environment interaction analysis incorporating prior information
Causality and pathway search in microarray time series experiment
Comparing transmembrane protein structures with ATOLL
Predicting fold novelty based on ProtoNet hierarchical classification
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays
Explainable Multilayer Graph Neural Network for cancer gene prediction
BIOSITE: a program for the interactive comparison of aligned homologous protein sequences
Kfits: a software framework for fitting and cleaning outliers in kinetic measurements
DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies
Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities
Analysis of gene evolution: the software AGE
SVAMP: sequence variation analysis, maps and phylogeny
New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation
Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
The string decomposition problem and its applications to centromere analysis and assembly
A platform for integrating threading results with protein family analyses
From phenotype to genotype: an association study of longitudinal phenotypic markers to Alzheimer's disease relevant SNPs
deltaGseg: macrostate estimation via molecular dynamics simulations and multiscale time series analysis
Rapid and sensitive dot-matrix methods for genome analysis
DyNetViewer: a Cytoscape app for dynamic network construction, analysis and visualization
An algorithm for discriminating sequences and its application to yeast transfer RNA
scDMV: a zero-one inflated beta mixture model for DNA methylation variability with scBS-seq data
GIFT: Guided and Interpretable Factorization for Tensors with an application to large-scale multi-platform cancer analysis
Mixture modelling of gene expression data from microarray experiments
TransPPMP: predicting pathogenicity of frameshift and non-sense mutations by a Transformer based on protein features
Computation Method to Identify Differential Allelic Gene Expression and Novel Imprinted Genes
Missing value estimation for DNA microarray gene expression data: local least squares imputation
Admix'em: a flexible framework for forward-time simulations of hybrid populations with selection and mate choice
MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data
Quasi-consensus-based comparison of profile hidden Markov models for protein sequences
DNA sequence quality trimming and vector removal
Ergatis: a web interface and scalable software system for bioinformatics workflows
IIFDTI: predicting drug-target interactions through interactive and independent features based on attention mechanism
Transducers: an emerging probabilistic framework for modeling indels on trees
Probabilistic pathway-based multimodal factor analysis
GAIT: Gene expression Analysis for Interval Time
Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells
An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures
Supervised cluster analysis for microarray data based on multivariate Gaussian mixture
DiPhiSeq: robust comparison of expression levels on RNA-Seq data with large sample sizes
Distance-based differential analysis of gene curves
kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
A toolkit for analysing large-scale plant small RNA datasets
TIVAN-indel: a computational framework for annotating and predicting non-coding regulatory small insertions and deletions
A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny
Phylogenetic inference using generative adversarial networks
Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis
Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction
Efficient initial volume determination from electron microscopy images of single particles
Protein function prediction using the Protein Link EXplorer (PLEX)
Convergent Island Statistics: a fast method for determining local alignment score significance
The SNPMaP package for R: a framework for genome-wide association using DNA pooling on microarrays