yusuke1997/dblp-id-title huggingface dataset:
Cancer drug response prediction with surrogate modeling-based graph neural architecture search
Survival analysis on rare events using group-regularized multi-response Cox regression
Small RNA gene identification and mRNA target predictions in bacteria
TomoEED: fast edge-enhancing denoising of tomographic volumes
Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison
IsoCor: isotope correction for high-resolution MS labeling experiments
A conditional neural fields model for protein threading
Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities
Knowledge-driven geospatial location resolution for phylogeographic models of virus migration
WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures
Modeling the percolation of annotation errors in a database of protein sequences
Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library
A non-parametric approach to translating gene region heterogeneity associated with phenotype into location heterogeneity
Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data
Support vector machines for separation of mixed plant?Cpathogen EST collections based on codon usage
Expected 10-anonymity of HyperLogLog sketches for federated queries of clinical data repositories
The variant call format and VCFtools
ResistoMap - online visualization of human gut microbiota antibiotic resistome
Identification of regulatory elements using a feature selection method
FLAMS: Find Lysine Acylations and other Modification Sites
Con-AAE: contrastive cycle adversarial autoencoders for single-cell multi-omics alignment and integration
Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries
MCAST: scanning for cis -regulatory motif clusters
PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption
SEQanswers: an open access community for collaboratively decoding genomes
A Boolean network inference from time-series gene expression data using a genetic algorithm
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
Probabilistic suffix array: efficient modeling and prediction of protein families
Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases
Fingerprinting protein structures effectively and efficiently
Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry
D-ASSIRC: distributed program for finding sequence similarities in genomes
Sparse combinatorial inference with an application in cancer biology
Computational identification of micro-structural variations and their proteogenomic consequences in cancer
SOAP2: an improved ultrafast tool for short read alignment
JAMM: a peak finder for joint analysis of NGS replicates
iTagPlot: an accurate computation and interactive drawing tool for tag density plot
Correction to: Damsel: analysis and visualisation of DamID sequencing in R
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach
Protein family annotation in a multiple alignment viewer
dnadna : a deep learning framework for population genetics inference
Varying coefficient model for gene-environment interaction: a non-linear look
Seeder: discriminative seeding DNA motif discovery
PfamAlyzer: domain-centric homology search
Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
VRmol: an integrative web-based virtual reality system to explore macromolecular structure
Chromothripsis detection with multiple myeloma patients based on deep graph learning
Predicting methylation status of CpG islands in the human brain
SBOannotator: a Python tool for the automated assignment of systems biology ontology terms
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
Construction of a reference gene association network from multiple profiling data: application to data analysis
Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure
GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach
The 2024 ISCB Innovator Award - Dr Su-In Lee
A fast algorithm for exact sequence search in biological sequences using polyphase decomposition
Prediction of drug-likeness using graph convolutional attention network
TFRank: network-based prioritization of regulatory associations underlying transcriptional responses
FUpred: detecting protein domains through deep-learning-based contact map prediction
Assessing sequence comparison methods with the average precision criterion
The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio
Detection of hydrogen-bond signature patterns in protein families
FinaleDB: a browser and database of cell-free DNA fragmentation patterns
Developing optimal non-linear scoring function for protein design
RNA Solutions: Synthesizing Information to Support Transcriptomics (RNASSIST)
Understanding the evolution of functional redundancy in metabolic networks
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis
SNAP: Combine and Map modules for multilocus population genetic analysis
Determination of stoichiometric association constants by a non- iterative computational method
Automatic computation of enzyme kinetics by HPLC
Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature
EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks
Determination of sample size in genome-scale RNAi screens
Regularized ROC method for disease classification and biomarker selection with microarray data
The DNA walk and its demonstration of deterministic chaos - relevance to genomic alterations in lung cancer
FACT: Feature Aggregation and Convolution with Transformers for predicting drug classification code
Assembly and reasoning over semantic mappings at scale for biomedical data integration
Inferring the perturbation time from biological time course data
Chemometric Modelling based on 2D-Fluorescence Spectra without a Calibration Measurement
InterLig: improved ligand-based virtual screening using topologically independent structural alignments
cneViewer: a database of conserved non-coding elements for studies of tissue-specific gene regulation
Cheetah-MS: a web server to model protein complexes using tandem cross-linking mass spectrometry data
LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking
SUBSTRA: Supervised Bayesian Patient Stratification
Disk-based compression of data from genome sequencing
SD2: spatially resolved transcriptomics deconvolution through integration of dropout and spatial information
HieRFIT: a hierarchical cell type classification tool for projections from complex single-cell atlas datasets
bmVAE: a variational autoencoder method for clustering single-cell mutation data
On the inference of spatial structure from population genetics data
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores
Analysis of microdensitometric data in terms of probability of cleavage of DNA
Pandora, a PAthway and Network DiscOveRy Approach based on common biological evidence
The identification of short linear motif-mediated interfaces within the human interactome
digeR: a graphical user interface R package for analyzing 2D-DIGE data
repfdr: a tool for replicability analysis for genome-wide association studies
Idéfix: identifying accidental sample mix-ups in biobanks using polygenic scores
COCOMAPS 2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes
UniBLAST: a system to filter, cluster, and display BLAST results and assign unique gene annotation
AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
Thermodynamics of RNA-RNA binding
NeSSie: a tool for the identification of approximate DNA sequence symmetries
PathBuilder - open source software for annotating and developing pathway resources
Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity
Naive binning improves phylogenomic analyses
G-BLASTN: accelerating nucleotide alignment by graphics processors
FGCNSurv: dually fused graph convolutional network for multi-omics survival prediction
Detection of a tandem BRCT in Nbs1 and Xrs2 with functional implications in the DNA damage response
DMLE+: Bayesian linkage disequilibrium gene mapping
The minimizer Jaccard estimator is biased and inconsistent
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
Two-pass alignment improves novel splice junction quantification
DNAssist: the integrated editing and analysis of molecular biology sequences in Windows
Subclonal variant calling with multiple samples and prior knowledge
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
PROBER: oligonucleotide FISH probe design software
Complex event extraction at PubMed scale
SynBrowse: a synteny browser for comparative sequence analysis
methyLImp2: faster missing value estimation for DNA methylation data
ClassifyR: an R package for performance assessment of classification with applications to transcriptomics
BigDataProcessor2: a free and open-source Fiji plugin for inspection and processing of TB sized image data
PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition
PeakBot: machine-learning-based chromatographic peak picking
Computational deconvolution of transcriptomics data from mixed cell populations
TreeEFM: calculating elementary flux modes using linear optimization in a tree-based algorithm
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances
pfsearchV3: a code acceleration and heuristic to search PROSITE profiles
Alignment-free Genomic Analysis via a Big Data Spark Platform
FastqCLS: a FASTQ compressor for long-read sequencing via read reordering using a novel scoring model
REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability
SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets
Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets
Optimal sequencing budget allocation for trajectory reconstruction of single cells
Object-oriented biological system integration: a SARS coronavirus example
XGSA: A statistical method for cross-species gene set analysis
Predicting protein stability changes upon mutation using a simple orientational potential
Modelling signalling networks from perturbation data
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization
Estimation of eosinophil cells in cord blood with references based on blood in adults via Bayesian measurement error modeling
Transformation distances: a family of dissimilarity measures based on movements of segments
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family
Testing hypotheses about the microbiome using the linear decomposition model (LDM)
Mass-balanced randomization of metabolic networks
CellTracker (not only) for dummies
ImmuCellAI-mouse: a tool for comprehensive prediction of mouse immune cell abundance and immune microenvironment depiction
SPEQ: quality assessment of peptide tandem mass spectra with deep learning
Message from the ISCB: 2016 Outstanding Contributions to ISCB Award: Burkhard Rost
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data
Two computer programs for the generation of problems in transmission genetics for teaching purposes
VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL
GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads
CEMAsuite: open source degenerate PCR primer design
EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography
Statistical distribution of amino acid sequences: a proof of Darwinian evolution
Narrative scientific data visualization in an immersive environment
Alignment-free clustering of UMI tagged DNA molecules
OMBlast: alignment tool for optical mapping using a seed-and-extend approach
Systematic tracking of dysregulated modules identifies novel genes in cancer
P3BSseq: parallel processing pipeline software for automatic analysis of bisulfite sequencing data
CAMR: cross-aligned multimodal representation learning for cancer survival prediction
Shark: fishing relevant reads in an RNA-Seq sample
MACS: automatic counting of objects based on shape recognition
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes
Erratum: Evaluation of methods for the prediction of membrane spanning regions
RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor
HCPM - program for hierarchical clustering of protein models
SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing
TiPs: a database of therapeutic targets in pathogens and associated tools
FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies
DREAM: an R package for druggability evaluation of human complex diseases
Reducing the variability in cDNA microarray image processing by Bayesian inference
Phytest: quality control for phylogenetic analyses
Alpha-Tri: a deep neural network for scoring the similarity between predicted and measured spectra improves peptide identification of DIA data
Synthetic microarray data generation with RANGE and NEMO
OBO to OWL: a protégé OWL tab to read/save OBO ontologies
Prediction of the phenotypic effects of non-synonymous single nucleotide polymorphisms using structural and evolutionary information
WebGBrowse - a web server for GBrowse
Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris : a non-linear model to predict abundance of undetected proteins
B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle
CASCC: a co-expression-assisted single-cell RNA-seq data clustering method
PriSM: a primer selection and matching tool for amplification and sequencing of viral genomes
TeachEnG: a Teaching Engine for Genomics
Approximating edit distances between complex tandem repeats efficiently
NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Domain-adversarial multi-task framework for novel therapeutic property prediction of compounds
Solvated docking: introducing water into the modelling of biomolecular complexes
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes
Improving MEME via a two-tiered significance analysis
Genome U-Plot: a whole genome visualization
MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature
Topology of gene expression networks as revealed by data mining and modeling
ReGeNNe: genetic pathway-based deep neural network using canonical correlation regularizer for disease prediction
Metrics for comparing regulatory sequences on the basis of pattern counts
CONTRABASS: exploiting flux constraints in genome-scale models for the detection of vulnerabilities
ConsensuSV - from the whole-genome sequencing data to the complete variant list
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity
Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies
Increasing the efficiency and accuracy of the ABACUS protein sequence design method
scTPC: a novel semisupervised deep clustering model for scRNA-seq data
Relation between weight matrix and substitution matrix: motif search by similarity
Estimating the predictability of cancer evolution
Event trigger identification for biomedical events extraction using domain knowledge
CAPG: comprehensive allopolyploid genotyper
Random walk and gap plots of DNA sequences
SAPA tool: finding protein regions by combination of amino acid composition, scaled profiles, patterns and rules
CAME: identification of chromatin accessibility from nucleosome occupancy and methylome sequencing
GraphGONet: a self-explaining neural network encapsulating the Gene Ontology graph for phenotype prediction on gene expression
Sequence database versioning for command line and Galaxy bioinformatics servers
Partial RNA design
gff2ps: visualizing genomic annotations
An assessment of substitution scores for protein profile-profile comparison
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm
Bioinformatics pipeline using JUDI: Just Do It!
Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants
compleasm: a faster and more accurate reimplementation of BUSCO
Searching for virus phylotypes
Discovering drug-drug interactions: a text-mining and reasoning approach based on properties of drug metabolism
TeSS: a platform for discovering life-science training opportunities
Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology
Visualization of genomic data with the Hilbert curve
Factorized embeddings learns rich and biologically meaningful embedding spaces using factorized tensor decomposition
VisCoSe: visualization and comparison of consensus sequences
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Identifying transcription factor complexes and their roles
CoCAS: a ChIP-on-chip analysis suite
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes
Colocalization analyses of genomic elements: approaches, recommendations and challenges
EDITtoTrEMBL: a distributed approach to high-quality automated protein sequence annotation
Parallel content-based sub-image retrieval using hierarchical searching
PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R
orthAgogue: an agile tool for the rapid prediction of orthology relations
Conformational analysis of alternative protein structures
A graph layout algorithm for drawing metabolic pathways
Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping
Interpool: interpreting smart-pooling results
BEST: a Shiny/R web-based application to easily retrieve cross-related enzyme functional parameters and information from BRENDA
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts
omiXcore: a web server for prediction of protein interactions with large RNA
Gradient matching accelerates mixed-effects inference for biochemical networks
Taxator-tk : precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats
An approach of gene regulatory network construction using mixed entropy optimizing context-related likelihood mutual information
HUME: large-scale detection of causal genetic factors of adverse drug reactions
A linear programming approach for identifying a consensus sequence on DNA sequences
Detecting high-order interactions of single nucleotide polymorphisms using genetic programming
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides
SUSPECTS: enabling fast and effective prioritization of positional candidates
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model
Transcription factor binding site identification using the self-organizing map
Neighbourhoods in the yeast regulatory network in different physiological states
A coordinate descent approach for sparse Bayesian learning in high dimensional QTL mapping and genome-wide association studies
EPPS: mining the COG database by an extended phylogenetic patterns search
baerhunter: an R package for the discovery and analysis of expressed non-coding regions in bacterial RNA-seq data
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing
Secondary structure prediction with support vector machines
Matrix (factorization) reloaded: flexible methods for imputing genetic interactions with cross-species and side information
Assessing statistical significance in multivariable genome wide association analysis
Incorporating gene functions as priors in model-based clustering of microarray gene expression data
AgIn: measuring the landscape of CpG methylation of individual repetitive elements
TransGEM: a molecule generation model based on Transformer with gene expression data
ChromoZoom: a flexible, fluid, web-based genome browser
MIDAS2: Metagenomic Intra-species Diversity Analysis System
PyDREAM: high-dimensional parameter inference for biological models in python
Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis
MuTATE - an R package for comprehensive multi-objective molecular modeling
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes
SPICi: a fast clustering algorithm for large biological networks
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences
Generating Consensus Sequences from Partial Order Multiple Sequence Alignment Graphs
Uncertainty-aware single-cell annotation with a hierarchical reject option
Characterization and prediction of residues determining protein functional specificity
Global importance of RNA secondary structures in protein-coding sequences
KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
WinPCA: a package for windowed principal component analysis
Multimodal reasoning based on knowledge graph embedding for specific diseases
Broom: application for non-redundant storage of high throughput sequencing data
cat RAPID omics : a web server for large-scale prediction of protein-RNA interactions
Response to comments on 'Empirical comparison of web-based antimicrobial peptide prediction tools'
Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints