yusuke1997/dblp-id-title huggingface dataset:
The CRASSS plug-in for integrating annotation data with hierarchical clustering results
RINQ: Reference-based Indexing for Network Queries
Exhaustive whole-genome tandem repeats search
The ModFOLD server for the quality assessment of protein structural models
WormExp: a web-based application for a Caenorhabditis elegans -specific gene expression enrichment analysis
modlAMP: Python for antimicrobial peptides
The application of a novel 'rising activity, multi-level mixed effects, indicator emphasis' (RAMMIE) method for syndromic surveillance in England
JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure
STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB
TFmiR2: constructing and analyzing disease-, tissue- and process-specific transcription factor and microRNA co-regulatory networks
Decoy-free protein-level false discovery rate estimation
Simulating the dynamics of targeted capture sequencing with CapSim
Computational analysis of kinase inhibitor selectivity using structural knowledge
Removing near-neighbour redundancy from large protein sequence collections
ncIDP-assign: a SPARKY extension for the effective NMR assignment of intrinsically disordered proteins
Defining transcription modules using large-scale gene expression data
A survey of across-target bioactivity results of small molecules in PubChem
Automated protein (re)sequencing with MS/MS and a homologous database yields almost full coverage and accuracy
Selection and validation of normalization methods for c-DNA microarrays using within-array replications
RefPlus: an R package extending the RMA Algorithm
Chemical structure informing statistical hypothesis testing in metabolomics
Aozan: an automated post-sequencing data-processing pipeline
Correction to: Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome
GS 2 : an efficiently computable measure of GO-based similarity of gene sets
Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
Recognition of 3'-processing sites of human mRNA precursors
Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames
Genomic island identification in Vibrio vulnificus reveals significant genome plasticity in this human pathogen
Learning meaningful representation of single-neuron morphology via large-scale pre-training
TopDraw: a sketchpad for protein structure topology cartoons
miRCancer: a microRNA-cancer association database constructed by text mining on literature
nf-core/pacvar: a pipeline for analyzing long-read PacBio whole genome and repeat expansion sequencing data
Deep learning improves antimicrobial peptide recognition
pDriver: a novel method for unravelling personalized coding and miRNA cancer drivers
ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting
Supporting tool suite for production proteomics
PuReD-MCL: a graph-based PubMed document clustering methodology
A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data
Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set
Walking the interactome for candidate prioritization in exome sequencing studies of Mendelian diseases
Integrating shotgun proteomics and mRNA expression data to improve protein identification
A Java API for working with PubChem datasets
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer
A Bayesian approach to targeted experiment design
A parallel neural network simulator on the connection machine CM-5
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
Integration of multiple terminology bases: a multi-view alignment method using the hierarchical structure
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
ClusterScan: simple and generalistic identification of genomic clusters
Using a measure of structural variation to define a core for the globins
LipidIMMS Analyzer: integrating multi-dimensional information to support lipid identification in ion mobility - mass spectrometry based lipidomics
aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction
Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis
DoriC: a database of oriC regions in bacterial genomes
METAL: fast and efficient meta-analysis of genomewide association scans
GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype
Global copy number profiling of cancer genomes
<tt>CREMSA</tt>: compressed indexing of (ultra) large multiple sequence alignments
TOPDOM: database of conservatively located domains and motifs in proteins
Combining many multiple alignments in one improved alignment
End-to-end learning of evolutionary models to find coding regions in genome alignments
Fold-specific substitution matrices for protein classification
Short-read aligner performance in germline variant identification
KASpOD - a web service for highly specific and explorative oligonucleotide design
sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts
G2P: a Genome-Wide-Association-Study simulation tool for genotype simulation, phenotype simulation and power evaluation
SKiM: accurately classifying metagenomic ONT reads in limited memory
A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data
A convolutional neural network for segmentation of yeast cells without manual training annotations
eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs
Ranked choice voting for representative transcripts with TRaCE
OpenBioLink: a benchmarking framework for large-scale biomedical link prediction
SENEX: a computer-based representation of cellular signal transduction processes in the central nervous system
MineBlast: a literature presentation service supporting protein annotation by data mining of BLAST results
ParaSAM: a parallelized version of the significance analysis of microarrays algorithm
Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure
Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi
Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data
ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect
Dissecting newly transcribed and old RNA using GRAND-SLAM
Assessing the validity and reproducibility of genome-scale predictions
Xenolog classification
BicAT: a biclustering analysis toolbox
SBML2Modelica: integrating biochemical models within open-standard simulation ecosystems
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants
Mytoe: automatic analysis of mitochondrial dynamics
Automated procedure for candidate compound selection in GC-MS metabolomics based on prediction of Kovats retention index
EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites
SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB
Joint registration of multiple point clouds for fast particle fusion in localization microscopy
GeneScape: a relational database of Escherichia coli genomic map data for Macintosh computers
UniProtJAPI: a remote API for accessing UniProt data
InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions
LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli
SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence
Detecting quantitative trait loci and exploring chromosomal pairing in autopolyploids using polyqtlR
Algorithms for large-scale genotyping microarrays
GSEA-P : a desktop application for Gene Set Enrichment Analysis
Fast and sensitive multiple sequence alignments on a microcomputer
RAGPOOLS: RNA-As-Graph-Pools - a web server for assisting the design of structured RNA pools for in vitro selection
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package
Pico-inplace-inversions between human and chimpanzee
Cascleave: towards more accurate prediction of caspase substrate cleavage sites
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
ISMB 2024 Proceedings
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Eigengene-based linear discriminant model for tumor classification using gene expression microarray data
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands
Advanced graph and sequence neural networks for molecular property prediction and drug discovery
Somatic variant analysis of linked-reads sequencing data with Lancet
Multi-omic integration by machine learning (MIMaL)
lumi : a pipeline for processing Illumina microarray
LTR_STRUC: a novel search and identification program for LTR retrotransposons
EBIC: an open source software for high-dimensional and big data analyses
RAG-Web: RNA structure prediction/design using RNA-As-Graphs
Leveraging known genomic variants to improve detection of variants, especially close-by Indels
Reveal - visual eQTL analytics
Pathways Database System: An Integrated System for Biological Pathways
Multimodal learning in clinical proteomics: enhancing antimicrobial resistance prediction models with chemical information
WGA-LP: a pipeline for whole genome assembly of contaminated reads
COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method
WikiNetworks: translating manually created biological pathways for topological analysis
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
BION web server: predicting non-specifically bound surface ions
MetaDCN: meta-analysis framework for differential co-expression network detection with an application in breast cancer
Calculation of daylength
ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots
2020 ISCB accomplishments by a Senior Scientist Award: Steven Salzberg
Trap spaces of multi-valued networks: definition, computation, and applications
PaxtoolsR: pathway analysis in R using Pathway Commons
CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets - application to peptide-MHC class II binding prediction
SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination
Increasing confidence of protein interactomes using network topological metrics
Removal of batch effects using distribution-matching residual networks
SumGNN: multi-typed drug interaction prediction via efficient knowledge graph summarization
VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies
Curators of the world unite: the International Society of Biocuration
A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry
PySeqLab: an open source Python package for sequence labeling and segmentation
ConceptGen: a gene set enrichment and gene set relation mapping tool
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
Epock: rapid analysis of protein pocket dynamics
SimBu : bias-aware simulation of bulk RNA-seq data with variable cell-type composition
Multi-objective tag SNPs selection using evolutionary algorithms
MagicMatch - cross-referencing sequence identifiers across databases
BioNetBuilder: automatic integration of biological networks
MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions
On the power of epigenome-wide association studies using a disease-discordant twin design
ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood
i GNM: a database of protein functional motions based on Gaussian Network Model
RDBridge: a knowledge graph of rare diseases based on large-scale text mining
Computing galled networks from real data
Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning
Partition function and base pairing probabilities for RNA-RNA interaction prediction
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
An analytical pipeline for genomic representations used for cytosine methylation studies
Deep learning of the tissue-regulated splicing code
MS2AI: automated repurposing of public peptide LC-MS data for machine learning applications
CPFP: a central proteomics facilities pipeline
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
OSCAR: One-class SVM for accurate recognition of cis -elements
CplexA: a Mathematica package to study macromolecular-assembly control of gene expression
Pedro: a configurable data entry tool for XML
Development of joint application strategies for two microbial gene finders
Tutorial on survival modeling with applications to omics data
Mega2: data-handling for facilitating genetic linkage and association analyses
MOSTPLAS: a self-correction multi-label learning model for plasmid host range prediction
MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample
BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains
Metingear: a development environment for annotating genome-scale metabolic models
Multimodal medical image fusion using adaptive co-occurrence filter-based decomposition optimization model
Cytoscape.js: a graph theory library for visualisation and analysis
Adjutant: an R-based tool to support topic discovery for systematic and literature reviews
Normalizing bead-based microRNA expression data: a measurement error model-based approach
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds
BIOESTIM: software for automatic design of estimators in bioprocess engineering
A Macintosh program for drawing circular plasmid maps
Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite
Paragraph - antibody paratope prediction using graph neural networks with minimal feature vectors
GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies
eHSCPr discriminating the cell identity involved in endothelial to hematopoietic transition
SVMQA: support-vector-machine-based protein single-model quality assessment
Bioinformatics needs to adopt statistical thinking - Editorial
StrAl: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
Optimization of probe coverage for high-resolution oligonucleotide aCGH
CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signalling and regulatory pathways
Learning with multiple pairwise kernels for drug bioactivity prediction
POLCA, a library running in a modern environment, implements a protocol for averaging randomly oriented images
CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure
ProtTest 3: fast selection of best-fit models of protein evolution
A graph-embedded deep feedforward network for disease outcome classification and feature selection using gene expression data
Integrating and annotating the interactome using the MiMI plugin for cytoscape
caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid
BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score
HapFlow: visualizing haplotypes in sequencing data
SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer
Rhapsody: predicting the pathogenicity of human missense variants
Ambiguous splice sites distinguish circRNA and linear splicing in the human genome
Tempel: time-series mutation prediction of influenza A viruses via attention-based recurrent neural networks
dsRBPBind: modeling the effect of RNA secondary structure on double-stranded RNA-protein binding
msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease
CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
clinker & clustermap.js: automatic generation of gene cluster comparison figures
ISMB/ECCB 2009 Stockholm
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data
Design of shortest double-stranded DNA sequences covering all k -mers with applications to protein-binding microarrays and synthetic enhancers
Identification of conserved protein complexes based on a model of protein network evolution
Bayesian feature selection for high-dimensional linear regression via the Ising approximation with applications to genomics
MVSO-PPIS: a structured objective learning model for protein-protein interaction sites prediction via multi-view graph information integration
Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors
Discriminating response groups in metabolic and regulatory pathway networks
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology
MolLM : a unified language model for integrating biomedical text with 2D and 3D molecular representations
Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations
A Bayesian estimator of protein-protein association probabilities
The 2024 Outstanding Contributions to ISCB Award - Dr Scott Markel
Compressed suffix tree - a basis for genome-scale sequence analysis
Computational cluster validation in post-genomic data analysis
SFA-SPA: a suffix array based short peptide assembler for metagenomic data
COPS - Cis/trans peptide bond conformation prediction of amino acids on the basis of secondary structure information
InstaPrism: an R package for fast implementation of BayesPrism
BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data
Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets
A computational pipeline for protein structure prediction and analysis at genome scale
DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer
Queueing theory model of Krebs cycle
LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities
OnD-CRF: prediciting order and disorder in proteins conditional random fields
EagleImp : fast and accurate genome-wide phasing and imputation in a single tool
DCDB: Drug combination database
A quantitative determination of multi-protein interactions by the analysis of confocal images using a pixel-by-pixel assessment algorithm
RefBool: a reference-based algorithm for discretizing gene expression data
VHMPT: a graphical viewer and editor for helical membrane protein topologies
Multiple alignment-free sequence comparison
SimPlot++: a Python application for representing sequence similarity and detecting recombination
vipR: variant identification in pooled DNA using R
ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence
Functional bioinformatics for Arabidopsis thaliana
Sub-dominant principal components inform new vaccine targets for HIV Gag
Correction to: On the feasibility of deep learning applications using raw mass spectrometry data
Predicting protein function from domain content
Conformational and physicochemical DNA features specific for transcription factor binding sites
OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches
Analysing microarray data using modular regulation analysis
SED-ML web tools: generate, modify and export standard-compliant simulation studies
LICRE: unsupervised feature correlation reduction for lipidomics
Improving gene quantification by adjustable spot-image restoration
Histones predate the split between bacteria and archaea
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
A statistical model providing comprehensive predictions for the mRNA differential display
Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling
Branch and bound computation of exact p -values
TIPR: transcription initiation pattern recognition on a genome scale
An improved algorithm for the prediction of optimum and suboptimum folding structures of long single-stranded RNA
DFprot: a webtool for predicting local chain deformability
Modeling RNA loops using sequence homology and geometric constraints
REET: robustness evaluation and enhancement toolbox for computational pathology
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data
PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data
A co-adaptive duality-aware framework for biomedical relation extraction
The EBI SRS server-new features
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads
pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data
An automated method for detecting alternatively spliced protein domains
Federated unsupervised random forest for privacy-preserving patient stratification
Variable selection and validation in multivariate modelling
GammaGateR: semi-automated marker gating for single-cell multiplexed imaging
CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
SCUM - simulation of cyanobacterial underwater movement
The generation of long telomere overhangs in human cells: a model and its implication
Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data
Sparsely correlated hidden Markov models with application to genome-wide location studies
Clustal W and Clustal X version 2.0
TITER: predicting translation initiation sites by deep learning
Poxvirus Orthologous Clusters (POCs)
Inferring protein interactions from phylogenetic distance matrices
Calign: aligning sequences with restricted affine gap penalties
Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases
Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields