yusuke1997/dblp-id-title huggingface dataset:
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach
Deep annotation of untargeted LC-MS metabolomics data with Binner
GTFtools: a software package for analyzing various features of gene models
Identification of protein-protein interaction bridges for multiple sclerosis
The CoFactor database: organic cofactors in enzyme catalysis
A network-based method for target selection in metabolic networks
KwARG: parsimonious reconstruction of ancestral recombination graphs with recurrent mutation
WebProtégé: a collaborative Web-based platform for editing biomedical ontologies
Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers
RAMONA: a Web application for gene set analysis on multilevel omics data
GO-Module : functional synthesis and improved interpretation of Gene Ontology patterns
OTUbase: an R infrastructure package for operational taxonomic unit data
Characterization of clinical signs in the human interactome
GGTyper: genotyping complex structural variants using short-read sequencing data
Peak selection from MALDI-TOF mass spectra using ant colony optimization
Detecting and removing multiplicative spatial bias in high-throughput screening technologies
Essentiality and damage in metabolic networks
sbgntikz - a TikZ library to draw SBGN maps
Aligning dynamic networks with DynaWAVE
Perceiver CPI: a nested cross-attention network for compound-protein interaction prediction
Clustering of temporal gene expression data with mixtures of mixed effects models with a penalized likelihood
Discovery of phosphorylation motif mixtures in phosphoproteomics data
Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction
ADDO: a comprehensive toolkit to detect, classify and visualize additive and non-additive quantitative trait loci
CHOYCE: a web server for constrained homology modelling with cryoEM maps
An APL procedure to estimate genotype by environment interaction when two environments are considered
Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations
Vivarium: an interface and engine for integrative multiscale modeling in computational biology
DockingPie: a consensus docking plugin for PyMOL
Message from ISCB: Outstanding contributions to ISCB award
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods
Analysis of expression profile using fuzzy adaptive resonance theory
Visual BLAST and visual FASTA: graphic workbenches for interactive analysis of full BLAST and FASTA outputs under Microsoft Windows 95/NT
A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps
Comparative analysis of tissue reconstruction algorithms for 3D histology
Adaptive settings for the nearest-neighbor particle tracking algorithm
MD-TASK: a software suite for analyzing molecular dynamics trajectories
MASIA: recognition of common patterns and properties in multiple aligned protein sequences
Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli
iBBiG: iterative binary bi-clustering of gene sets
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks
A min-cut algorithm for the consistency problem in multiple sequence alignment
Dot-plot comparisons by multivariate analysis (DOCMA): a tool for classifying protein sequences
Evolutionary trace report_maker: a new type of service for comparative analysis of proteins
CpGassoc: an R function for analysis of DNA methylation microarray data
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
Markers improve clustering of CGH data
ShinyBioHEAT: an interactive shiny app to identify phenotype driver genes in E.coli and B.subtilis
A procedure for RNA pseudoknot prediction
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
SNPTools: a software tool for visualization and analysis of microarray data
Xenome - a tool for classifying reads from xenograft samples
IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events
Simultaneous Gene Clustering and Subset Selection for Sample Classification Via MDL
Sparse kernel methods for high-dimensional survival data
Deconvolution and phylogeny inference of structural variations in tumor genomic samples
<tt>nipalsMCIA</tt> : flexible multi-block dimensionality reduction in R via nonlinear iterative partial least squares
SANS serif: alignment-free, whole-genome-based phylogenetic reconstruction
HOGMMNC: a higher order graph matching with multiple network constraints model for gene-drug regulatory modules identification
Medline search engine for finding genetic markers with biological significance
TRTools: a toolkit for genome-wide analysis of tandem repeats
PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Significance in scale space for Hi-C data
Filling annotation gaps in yeast genomes using genome-wide contact maps
DREAM: a webserver for the identification of editing sites in mature miRNAs using deep sequencing data
POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs
GLay: community structure analysis of biological networks
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
CheNER: chemical named entity recognizer
ProteinEvolverABC: coestimation of recombination and substitution rates in protein sequences by approximate Bayesian computation
Answer to the comments of K. Dobbin, J. Shih and R. Simon on the paper 'Evaluation of the gene-specific dye-bias in cDNA microarray experiments'
ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction
Chaos: principles and implications in biology
UniNovo: a universal tool for de novo peptide sequencing
A new approach for interpreting Random Forest models and its application to the biology of ageing
Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data
Prediction of protein functional residues from sequence by probability density estimation
Set cover-based methods for motif selection
PATRI-paternity inference using genetic data
Integrated profiling of three dimensional cell culture models and 3D microscopy
Multi-view methods for protein structure comparison using latent dirichlet allocation
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression
DeepTE: a computational method for de novo classification of transposons with convolutional neural network
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
NetRAX: accurate and fast maximum likelihood phylogenetic network inference
Using bioinformatics to predict the functional impact of SNVs
Predicting protein-peptide binding residues via interpretable deep learning
Monte Carlo algorithms for Brownian phylogenetic models
PAGER: constructing PAGs and new PAG-PAG relationships for network biology
A metadata approach to query interoperation between molecular biology databases
Design of endonuclease restriction sites into primers for PCR cloning
SPEX 2 : automated concise extraction of spatial gene expression patterns from Fly embryo ISH images
DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML
Structure similarity measure with penalty for close non-equivalent residues
A CoD-based reduction algorithm for designing stationary control policies on Boolean networks
R/DWD: distance-weighted discrimination for classification, visualization and batch adjustment
Recco: recombination analysis using cost optimization
TRANSDIRE: data-driven direct reprogramming by a pioneer factor-guided trans-omics approach
Gene-disease relationship discovery based on model-driven data integration and database view definition
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks
ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
Using manifold embedding for assessing and predicting protein interactions from high-throughput experimental data
Design of primers for PCR amplification of highly variable genomes
simuG: a general-purpose genome simulator
Message from the ISCB: 2017 ISCB Accomplishment by a Senior Scientist Award Given to Pavel Pevzner
PhyloJIVE: Integrating biodiversity data with the Tree of Life
Extending assembly of short DNA sequences to handle error
FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution
PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database
Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo
An integrated strategy for prediction uncertainty analysis
VikNGS: a C++ variant integration kit for next generation sequencing association analysis
Sequence-based prediction of protein interaction sites with an integrative method
PROMO: detection of known transcription regulatory elements using species-tailored searches
Comments on 'An empirical comparison of several recent epistatic interaction detection methods'
Predicting protein β-sheet contacts using a maximum entropy-based correlated mutation measure
FARVAT: a family-based rare variant association test
BlastAlign : a program that uses blast to align problematic nucleotide sequences
BACPI: a bi-directional attention neural network for compound-protein interaction and binding affinity prediction
DiNuP: a systematic approach to identify regions of differential nucleosome positioning
DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks
CONSTAX2: improved taxonomic classification of environmental DNA markers
Flower: extracting information from pyrosequencing data
CGH-Plotter: MATLAB toolbox for CGH-data analysis
GlyGen data model and processing workflow
Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features
SolidBin: improving metagenome binning with semi-supervised normalized cut
Computational space reduction and parallelization of a new clustering approach for large groups of sequences
HEAL: an automated deep learning framework for cancer histopathology image analysis
PASTAA: identifying transcription factors associated with sets of co-regulated genes
KOunt: a reproducible KEGG orthologue abundance workflow
IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data
SimReadUntil for benchmarking selective sequencing algorithms on ONT devices
MollDE: a homology modeling framework you can click with
Issues in incorporation semantic integrity in molecular biological object-oriented databases
ConDo: protein domain boundary prediction using coevolutionary information
Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data
INVEX - a web-based tool for integrative visualization of expression data
Inferring relative proportions of DNA variants from sequencing electropherograms
MultiGran-SMILES: multi-granularity SMILES learning for molecular property prediction
PconsC4: fast, accurate and hassle-free contact predictions
Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters
Fast Fourier transform-based correlation of DNA sequences using complex plane encoding
SYNCSA - R tool for analysis of metacommunities based on functional traits and phylogeny of the community components
O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique
PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq
2020 ISCB Overton Prize: Jian Peng
The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism
SOLQC: Synthetic Oligo Library Quality Control tool
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data
Linkage disequilibrium maps to guide contig ordering for genome assembly
An efficient algorithm for minimal primer set selection
REPuter: fast computation of maximal repeats in complete genomes
GRIL: genome rearrangement and inversion locator
UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase
A common layer of interoperability for biomedical ontologies based on OWL EL
Clustering microarray-derived gene lists through implicit literature relationships
Fast and robust ancestry prediction using principal component analysis
Pathview: an R/Bioconductor package for pathway-based data integration and visualization
A benchmark for comparison of cell tracking algorithms
Spatial clustering of protein binding sites for template based protein docking
SOLart: a structure-based method to predict protein solubility and aggregation
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model
Parametric Bayesian priors and better choice of negative examples improve protein function prediction
A simple and fast secondary structure prediction method using hidden neural networks
YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU
MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics
Multidimensional local false discovery rate for microarray studies
A divide-and-conquer approach to fragment assembly
A space-efficient algorithm for local similarities
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations
Reconstructing gene network structure and dynamics from single cell data
Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods
AbDesigner3D: a structure-guided tool for peptide-based antibody production
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data
A flexible forward simulator for populations subject to selection and demography
Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
Searching for tRNA genes in DNA sequences--an IBM microcomputer program
Benchmarking the performance of human antibody gene alignment utilities using a 454 sequence dataset
Efficient stochastic simulation of reaction-diffusion processes via direct compilation
2022 Outstanding Contributions to ISCB Award: Reinhard Schneider
copMEM: finding maximal exact matches via sampling both genomes
lga972: a cross-platform application for optimizing LD studies using a genetic algorithm
AMIGO, a toolbox for advanced model identification in systems biology using global optimization
Network orientation via shortest paths
Estimation and assessment of raw copy numbers at the single locus level
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
MDD-SOH: exploiting maximal dependence decomposition to identify S -sulfenylation sites with substrate motifs
Annotating genes and genomes with DNA sequences extracted from biomedical articles
IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions
Sparse redundancy analysis of high-dimensional genetic and genomic data
MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules
Easybiotics: a GUI for 3D physical modelling of multi-species bacterial populations
Determination and validation of principal gene products
ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model
Gene selection using support vector machines with non-convex penalty
Neuron tracing from light microscopy images: automation, deep learning and bench testing
Phosphate binding sites prediction in phosphorylation-dependent protein-protein interactions
AphidBase: a database for aphid genomic resources
A Statistical Problem for Inference to Regulatory Structure from Associations of Gene Expression Measurements with Microarrays
Inference of transcriptional regulatory network by bootstrapping patterns
Using meshes for MeSH term enrichment and semantic analyses
404 not found: the stability and persistence of URLs published in MEDLINE
Accurate prediction of orthologs in the presence of divergence after duplication
DIYA: a bacterial annotation pipeline for any genomics lab
FDR made easy in differential feature discovery and correlation analyses
HFSP: high speed homology-driven function annotation of proteins
Active learning for efficient analysis of high-throughput nanopore data
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Visualization of the entire surface of a protein by cartographic projection
Cancer therapy design based on pathway logic
MODELER4SIMCOAL2: A user-friendly, extensible modeler of demography and linked loci for coalescent simulations
Which is better for cDNA-microarray-based classification: ratios or direct intensities
Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites
Halvade: scalable sequence analysis with MapReduce
Identification of subfamily-specific sites based on active sites modeling and clustering
Domain-enhanced analysis of microarray data using GO annotations
The sequence context in poly-alanine regions: structure, function and conservation
DBSI server: DNA binding site identifier
VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data
MonaLisa - visualization and analysis of functional modules in biochemical networks
Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark
Random walk with restart on multiplex and heterogeneous biological networks
Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes
Interrogating local population structure for fine mapping in genome-wide association studies
PLPMDB: Pyridoxal-5'-phosphate dependent enzymes mutants database
Distinguishing prognostic and predictive biomarkers: an information theoretic approach
Quantile smoothing of array CGH data
Multivariate genome-wide association analysis by iterative hard thresholding
Trustworthy causal biomarker discovery: a multiomics brain imaging genetics-based approach
MeLAD: an integrated resource for metalloenzyme-ligand associations
A transition-based joint model for disease named entity recognition and normalization
Lacking alignments? The next-generation sequencing mapper segemehl revisited
A bioinformatic screen for novel A-I RNA editing sites reveals recoding editing in BC10
Clustering of highly homologous sequences to reduce the size of large protein databases
BioCoder: a benchmark for bioinformatics code generation with large language models
GenomeMixer: a complex genetic cross simulator
NetworkBLAST: comparative analysis of protein networks
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
A noise-robust classification method for cryo-ET subtomograms with out-of-distribution detection
The predictive power of the CluSTr database
AbCD: arbitrary coverage design for sequencing-based genetic studies
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics
Modeling genome evolution with a diffusion approximation of a birth-and-death process
BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone
The PSIPRED protein structure prediction server
Finding the fixed points of a Boolean network from a positive feedback vertex set
SeeVis - 3D space-time cube rendering for visualization of microfluidics image data
Structural variation analysis with strobe reads
DDIG-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels
CRAM 3.1: advances in the CRAM file format
DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins
Differential privacy-based evaporative cooling feature selection and classification with relief-F and random forests
MP-T: improving membrane protein alignment for structure prediction
Benchmarking algorithms for spatially variable gene identification in spatial transcriptomics
DualNetGO: a dual network model for protein function prediction via effective feature selection
A simple and fast method to determine the parameters for fuzzy c-means cluster analysis
CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks
The Cyni framework for network inference in Cytoscape
How independent are the appearances of n-mers in different genomes?
Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT
TRES predicts transcription control in embryonic stem cells
A comparison study: applying segmentation to array CGH data for downstream analyses
SLEMM: million-scale genomic predictions with window-based SNP weighting
Genome Analysis
PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing
Feature construction from synergic pairs to improve microarray-based classification
BLAD: A comprehensive database of widely circulated beta-lactamases
Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum
WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks
A better block partition and ligation strategy for individual haplotyping
BlueSNP: R package for highly scalable genome-wide association studies using Hadoop clusters
BIODICA: a computational environment for Independent Component Analysis of omics data
Bioclipse-R: integrating management and visualization of life science data with statistical analysis
A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data
Mouse model phenotypes provide information about human drug targets
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning
LVB: parsimony and simulated annealing in the search for phylogenetic trees
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results
Computing the shortest elementary flux modes in genome-scale metabolic networks
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Visualizing the geography of genetic variants
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes