yusuke1997/dblp-id-title huggingface dataset:
DNA reference alignment benchmarks based on tertiary structure of encoded proteins
AQUA: automated quality improvement for multiple sequence alignments
Methods for automatic reference trees and multilevel phylogenetic placement
START: an automated tool for serial analysis of chromatin occupancy data
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
Generating property-matched decoy molecules using deep learning
Predicting kinase substrates using conservation of local motif density
A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins
BRM: a statistical method for QTL mapping based on bulked segregant analysis by deep sequencing
girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads
BeCAS: biomedical concept recognition services and visualization
Genotype calling from next-generation sequencing data using haplotype information of reads
Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis
PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing
omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data
RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power
LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer
RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data
Gene structure identification with MyGV using cDNA evidence and protein homologs to improve ab initio predictions
WebMetabase: cleavage sites analysis tool for natural and unnatural substrates from diverse data source
scHinter: imputing dropout events for single-cell RNA-seq data with limited sample size
Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence
Fast databank searching with a reduced amino-acid alphabet
pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R
Pattern search in BioPAX models
KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis
REDItools: high-throughput RNA editing detection made easy
DLRS: gene tree evolution in light of a species tree
MR-Corr2: a two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants
Improved linking of motifs to their TFs using domain information
Efficient flexible backbone protein-protein docking for challenging targets
DeepEM3D: approaching human-level performance on 3D anisotropic EM image segmentation
microPred : effective classification of pre-miRNAs for human miRNA gene prediction
EVICAN - a balanced dataset for algorithm development in cell and nucleus segmentation
BatMis: a fast algorithm for k -mismatch mapping
Two novel pathway analysis methods based on a hierarchical model
Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM
Combinatorial image analysis of DNA microarray features
Generating linkage mapping files from Affymetrix SNP chip data
X-MATE: a flexible system for mapping short read data
Approximate probabilistic analysis of biopathway dynamics
Development of a robust classifier for quality control of reverse-phase protein arrays
DockNet: high-throughput protein-protein interface contact prediction
Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences
Detection of low level genomic alterations by comparative genomic hybridization based on cDNA micro-arrays
A de novo protein structure prediction by iterative partition sampling, topology adjustment and residue-level distance deviation optimization
CoCo: RNA-seq read assignment correction for nested genes and multimapped reads
BioASF: a framework for automatically generating executable pathway models specified in BioPAX
Designing a neural network simulator - the MENS modelling environment for network systems: II
DELLY: structural variant discovery by integrated paired-end and split-read analysis
glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
MMuFLR: missense mutation and frameshift location reporter
BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions
Cell population identification using fluorescence-minus-one controls with a one-class classifying algorithm
SynView: a GBrowse-compatible approach to visualizing comparative genome data
An attempt to define allergen-specific molecular surface features: a bioinformatic approach
Markov model plus k -word distributions: a synergy that produces novel statistical measures for sequence comparison
Efficient methods for identifying mutated driver pathways in cancer
scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model
A plant calmodulin-binding motor is part kinesin and part myosin
CIT: identification of differentially expressed clusters of genes from microarray data
SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis
Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing
Sequential feature selection and inference using multi-variate random forests
Estimating real cell size distribution from cross-section microscopy imaging
Disperse: a simple and efficient approach to parallel database searching
EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient
CSHAP: efficient haplotype frequency estimation based on sparse representation
A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics
Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
Statistical approaches for differential expression analysis in metatranscriptomics
MolCL-SP: a multimodal contrastive learning framework with non-overlapping substructure perturbations for molecular property prediction
Figure and caption extraction from biomedical documents
bioBakery: a meta'omic analysis environment
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties
E2FM: an encrypted and compressed full-text index for collections of genomic sequences
ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions
Robust synthetic biology design: stochastic game theory approach
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
FlexTaxD: flexible modification of taxonomy databases for improved sequence classification
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods
Regional and time-resolved mutation patterns of the human genome
Exploring protein domain organization by recognition of secondary structure packing interfaces
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
RepMaestro: scalable repeat detection on disk-based genome sequences
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm
Version 5 of the Mount-Conrad-Myers Sequence Analysis Software Package now available
hp-DPI: Helicobacter pylori Database of Protein Interactomes-embracing experimental and inferred interactions
YACHT : an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns
RecBic: a fast and accurate algorithm recognizing trend-preserving biclusters
HYLAS: program for generating H curves (abstract three-dimensional representations of long DNA sequences)
Autoregressive modeling and diagnostics for qPCR amplification
Quickomics: exploring omics data in an intuitive, interactive and informative manner
Convergent evolution of domain architectures (is rare)
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
Microarray-based classification and clinical predictors: on combined classifiers and additional predictive value
PySNV for complex intra-host variation detection
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
Threshold-seq: a tool for determining the threshold in short RNA-seq datasets
Taxonomic markup language: applying XML to systematic data
PDMDA: predicting deep-level miRNA-disease associations with graph neural networks and sequence features
DeepTrio: a ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks
CAPS: coevolution analysis using protein sequences
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment
SEQANALREF: a sequence analysis bibliographic reference databank
The DOMINO web-server for active module identification analysis
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells
Privacy-preserving construction of generalized linear mixed model for biomedical computation
Automated protein sequence pattern handling and PROSITE searching
Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction
Identifying mechanistic similarities in drug responses
PSIbase: a database of Protein Structural Interactome map (PSIMAP)
MPID-T2: a database for sequence-structure-function analyses of pMHC and TR/pMHC structures
BioQueue: a novel pipeline framework to accelerate bioinformatics analysis
A partition function algorithm for interacting nucleic acid strands
Bayesian inference using qualitative observations of underlying continuous variables
CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network
panRGP: a pangenome-based method to predict genomic islands and explore their diversity
Phage protein receptors have multiple interaction partners and high expressions
ExSPAnder: a universal repeat resolver for DNA fragment assembly
Bayesian network prior: network analysis of biological data using external knowledge
HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball
FRODOCK: a new approach for fast rotational protein-protein docking
Overseer: a nucleotide sequence searching tool
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data
Sprites: detection of deletions from sequencing data by re-aligning split reads
The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces
List-decoding methods for inferring polynomials in finite dynamical gene network models
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees
The K-mer File Format: a standardized and compact disk representation of sets of k -mers
Identification of function-associated loop motifs and application to protein function prediction
DNorm: disease name normalization with pairwise learning to rank
A BASIC program for the removal of noise from reaction traces using Fourier filtering
Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA)
DOLOP-database of bacterial lipoproteins
RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes
Recognition models to predict DNA-binding specificities of homeodomain proteins
Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules
scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data
PROTEIOS: an open source proteomics initiative
Model-based boosting in high dimensions
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data
GLOOME: gain loss mapping engine
EPoS: a modular software framework for phylogenetic analysis
Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells
PepGM: a probabilistic graphical model for taxonomic inference of viral proteome samples with associated confidence scores
Modeling promoter grammars with evolving hidden Markov models
Deep learning of protein sequence design of protein-protein interactions
RankGene: identification of diagnostic genes based on expression data
The spatiotemporal order of signaling events unveils the logic of development signaling
ADME-drug-likeness: enriching molecular foundation models via pharmacokinetics-guided multi-task learning for drug-likeness prediction
scVAE: variational auto-encoders for single-cell gene expression data
Integration of string and de Bruijn graphs for genome assembly
ASBench: benchmarking sets for allosteric discovery
DeepRank-GNN: a graph neural network framework to learn patterns in protein-protein interfaces
Extensions to gene set enrichment
Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection
Incremental generation of summarized clustering hierarchy for protein family analysis
PASTA for proteins
Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL
SwarmDock: a server for flexible protein-protein docking
Dominant spectral component analysis for transcriptional regulations using microarray time-series data
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
The SRS 3D module: integrating structures, sequences and features
CLANS: a Java application for visualizing protein families based on pairwise similarity
Aragonite-associated biomineralization proteins are disordered and contain interactive motifs
motifbreakR : an R/Bioconductor package for predicting variant effects at transcription factor binding sites
GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization
arcasHLA: high-resolution HLA typing from RNAseq
The Genomic Threading Database
Classification of oligonucleotide fingerprints: application for microbial community and gene expression analyses
GENEXPERT, a program system for nucleic acid sequence structural interpretation
Revealing hidden interval graph structure in STS-content data
Model aggregation: a building-block approach to creating large macromolecular regulatory networks
MitoTrack, a user-friendly semi-automatic software for lineage tracking in living embryos
Active learning to classify macromolecular structures in situ for less supervision in cryo-electron tomography
fastsimcoal2: demographic inference under complex evolutionary scenarios
NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction
Integration of metabolic networks and gene expression in virtual reality
POLINA: detection and evaluation of single amino acid substitutions in protein superfamilies
MaxCLK: discovery of cancer driver genes via maximal clique and information entropy of modules
DeepNOG: fast and accurate protein orthologous group assignment
The evolutionary forest algorithm
Motifs tree: a new method for predicting post-translational modifications
Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions
CePa: an R package for finding significant pathways weighted by multiple network centralities
Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
Multi-scale computational modeling of developmental biology
VISTAL - a new 2D visualization tool of protein 3D structural alignments
How Bayes tests of molecular phylogenies compare with frequentist approaches
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space
Generation of a consensus protein domain dictionary
Global alignment of protein-protein interaction networks by graph matching methods
GTExVisualizer: a web platform for supporting ageing studies
A bioinformatics analysis of the cell line nomenclature
TSGSIS: a high-dimensional grouped variable selection approach for detection of whole-genome SNP-SNP interactions
MatrixQCvis: shiny-based interactive data quality exploration for omics data
Pcons5: combining consensus, structural evaluation and fold recognition scores
Gener: a minimal programming module for chemical controllers based on DNA strand displacement
Enhancing scatterplots with smoothed densities
massiR : a method for predicting the sex of samples in gene expression microarray datasets
Hierarchical Access System for Sequence Libraries in Europe (HASSLE): a tool to access sequence databases remotely
SIMBSIG: similarity search and clustering for biobank-scale data
Discovering hospital admission patterns using models learnt from electronic hospital records
Cross species analysis of microarray expression data
RobNorm: model-based robust normalization method for labeled quantitative mass spectrometry proteomics data
ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins
Advanced Complex Trait Analysis
Gene Graphics: a genomic neighborhood data visualization web application
netGO: R-Shiny package for network-integrated pathway enrichment analysis
Detection of allele-specific methylation through a generalized heterogeneous epigenome model
The cell as a token: high-dimensional geometry in language models and cell embeddings
The global trace graph, a novel paradigm for searching protein sequence databases
SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
3DPatch: fast 3D structure visualization with residue conservation
Graphical methods for quantifying macromolecules through bright field imaging
CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing
Association studies for untyped markers with TUNA
Improved synapse detection for mGRASP-assisted brain connectivity mapping
SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network
Integrative analysis of individual-level data and high-dimensional summary statistics
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update
A generalized association test based on U statistics
Analyzing gene expression data in terms of gene sets: methodological issues
Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data
ADAM: another database of abbreviations in MEDLINE
VIRALpro: a tool to identify viral capsid and tail sequences
Metric learning for enzyme active-site search
CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features
ISMB/ECCB 2023 proceedings
A Bayesian missing value estimation method for gene expression profile data
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment
A method for estimating stochastic noise in large genetic regulatory networks
Artificial-cell-type aware cell-type classification in CITE-seq
Nanopype: a modular and scalable nanopore data processing pipeline
Reprohackathons: promoting reproducibility in bioinformatics through training
MMR: a tool for read multi-mapper resolution
SST: an algorithm for finding near-exact sequence matches in time proportional to the logarithm of the database size
Olorin: combining gene flow with exome sequencing in large family studies of complex disease
Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems
Optimal design of thermally stable proteins
A sequence family database built on ECOD structural domains
Simultaneous editing of multiple nucleic acid and protein sequences with ESEE
EBT: a statistic test identifying moderate size of significant features with balanced power and precision for genome-wide rate comparisons
CoPS: Comprehensive Peptide Signature Database
Boulder ALignment Editor (ALE): a web-based RNA alignment tool
Olga - oligonucleotide primer design program for the Atari ST
MFIB: a repository of protein complexes with mutual folding induced by binding
CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
Using spreadsheet languages to understand sequence analysis algorithms
Relative quantification of proteins and post-translational modifications in proteomic experiments with shared peptides: a weight-based approach
ALIBABA: PubMed as a graph
PRoMT: inferring demographic history from DNA sequences
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines
rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data
Calculation of Helix Packing Angles in Protein Structures
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Automated exploitation of deep learning for cancer patient stratification across multiple types
PatMaN: rapid alignment of short sequences to large databases
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer
DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity
FACTA: a text search engine for finding associated biomedical concepts
Automated workflow composition in mass spectrometry-based proteomics
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
DeepProtein: deep learning library and benchmark for protein sequence learning
GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions
PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors
CONCUR: quick and robust calculation of codon usage from ribosome profiling data
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing
Identification of protein binding surfaces using surface triplet propensities
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
RepLong: de novo repeat identification using long read sequencing data
GlycoEnzOnto: a GlycoEnzyme pathway and molecular function ontology
Zomit: biological data visualization and browsing
Assigning roles to DNA regulatory motifs using comparative genomics
BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures
A pathway-based data integration framework for prediction of disease progression
MODE-TASK: large-scale protein motion tools
Multispectral tracing in densely labeled mouse brain with nTracer
Software tool for gene mapping: gRanch
Exploring metabolic pathways in genome-scale networks via generating flux modes
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants