yusuke1997/dblp-id-title huggingface dataset:
iFoldRNA v2: folding RNA with constraints
Murlet: a practical multiple alignment tool for structural RNA sequences
CellMix: a comprehensive toolbox for gene expression deconvolution
U-Compare: share and compare text mining tools with UIMA
Finding antibodies in cryo-EM maps with <tt>CrAI</tt>
webMGR: an online tool for the multiple genome rearrangement problem
GenFrag 2.1: new features for more robust fragment assembly benchmarks
Speeding up tandem mass spectral identification using indexes
Mariner: explore the Hi-Cs
An evaluation of ß-turn prediction methods
A discrete view on fold space
Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection
Going from where to why - interpretable prediction of protein subcellular localization
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
Shortest path analysis using partial correlations for classifying gene functions from gene expression data
Viola: a structural variant signature extractor with user-defined classifications
Probalign: multiple sequence alignment using partition function posterior probabilities
MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification
Clustering proteins into families using artificial neural networks [published erratum appears in Comput Appl Biosci 1992 Jun;8(3): 305]
Virtual PCR
TEFOOL/2: a program for theoretical drug design on microcomputers
Inferring causal relationships among intermediate phenotypes and biomarkers: a case study of rheumatoid arthritis
A comprehensive assessment of long intrinsic protein disorder from the DisProt database
genipe : an automated genome-wide imputation pipeline with automatic reporting and statistical tools
FUNGI: FUsioN Gene Integration toolset
Low folding propensity and high translation efficiency distinguish in vivo substrates of GroEL from other Escherichia coli proteins
Identification and characterization of moonlighting long non-coding RNAs based on RNA and protein interactome
Knotty: efficient and accurate prediction of complex RNA pseudoknot structures
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server
Large-scale comparative analysis of microbial pan-genomes using PanOCT
easyLINKAGE: a PERL script for easy and automated two-/multi-point linkage analyses
Concerning the accuracy of MAST E-values
pyFoldX: enabling biomolecular analysis and engineering along structural ensembles
Interactive exploration of heterogeneous biological networks with Biomine Explorer
Phylotyper: in silico predictor of gene subtypes
Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease
COVID-KOP: integrating emerging COVID-19 data with the ROBOKOP database
SHIP: identifying antimicrobial resistance gene transfer between plasmids
EpicPred: predicting phenotypes driven by epitope-binding TCRs using attention-based multiple instance learning
The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures
A graphical interface for correlated mutations and other protein structure prediction methods
Identification of cancer fusion drivers using network fusion centrality
Identification of potential HIV-1 targets of minocycline
PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir
DINAMO: interactive protein alignment and model building
VariantQC: a visual quality control report for variant evaluation
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure
Identifying good diagnostic gene groups from gene expression profiles using the concept of emerging patterns
Metagenomic functional profiling: to sketch or not to sketch?
AlloSigMA: allosteric signaling and mutation analysis server
Clonality inference in multiple tumor samples using phylogeny
AutoSite: an automated approach for pseudo-ligands prediction - from ligand-binding sites identification to predicting key ligand atoms
A framework for group-wise summarization and comparison of chromatin state annotations
SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data
Correction to: USNAP : fast unique dense region detection and its application to lung cancer
RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families
ABIF Manager: simple reading and editing of ABIF formatted files
An unbiased evaluation of gene prioritization tools
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits
DDN3.0: determining significant rewiring of biological network structure with differential dependency networks
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks
IonGAP: integrative bacterial genome analysis for Ion Torrent sequence data
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy
Ge N Nius : an ultrafast drug-target interaction inference method based on graph neural networks
Visualization of circular RNAs and their internal splicing events from transcriptomic data
Integrative analysis of multiple genomic variables using a hierarchical Bayesian model
SDRS - an algorithm for analyzing large-scale dose-response data
Unipept Visualizations: an interactive visualization library for biological data
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads
dbTEU: a protein database of trace element utilization
A framework to refine particle clusters produced by EMAN
SPDI: data model for variants and applications at NCBI
Gene-set integrative analysis of multi-omics data using tensor-based association test
PBRpredict-Suite: a suite of models to predict peptide-recognition domain residues from protein sequence
Exact computation of pattern probabilities in random sequences generated by Markov chains
SPRINT: side-chain prediction inference toolbox for multistate protein design
Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder TM
A new modeling method in feature construction for the HSQC spectra screening problem
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly
ExPrimer: to design primers from exon-exon junctions
simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data
Prediction of HIV sensitivity to monoclonal antibodies using aminoacid sequences and deep learning
Inference of historical migration rates via haplotype sharing
A bank of protein family patterns for rapid identification of possible functions of amino acid sequences
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
AcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks
A weighted distance-based approach for deriving consensus tumor evolutionary trees
Prediction of contact matrix for protein-protein interaction
ISDB: a database toolkit for storing and analyzing viral integration site data
Genescript: DNA Sequence Annotation Pipeline
Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses
JIND: joint integration and discrimination for automated single-cell annotation
Inference of combinatorial Boolean rules of synergistic gene sets from cancer microarray datasets
AtlasXplore: a web platform for visualizing and sharing spatial epigenome data
PUmPER: phylogenies updated perpetually
FANCY: fast estimation of privacy risk in functional genomics data
A back-step algorithm for simulation of Monod-type models
Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks
KORP: knowledge-based 6D potential for fast protein and loop modeling
gofasta: command-line utilities for genomic epidemiology research
Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning
Methods for the detection and assembly of novel sequence in high-throughput sequencing data
MAMMOT - a set of tools for the design, management and visualization of genomic tiling arrays
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking
Sampling ARG of multiple populations under complex configurations of subdivision and admixture
The software for interactive evaluation of mass spectra stability and reproducibility
Swelfe: a detector of internal repeats in sequences and structures
The Simmune Modeler visual interface for creating signaling networks based on bi-molecular interactions
A faster circular binary segmentation algorithm for the analysis of array CGH data
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis
The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data
DrugCVar: a platform for evidence-based drug annotation for genetic variants in cancer
Haplotype-based membership inference from summary genomic data
Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens
Integrating 5hmC and gene expression data to infer regulatory mechanisms
Structural discrimination analysis for constraint selection in protein modeling
Denoising genome-wide histone ChIP-seq with convolutional neural networks
Epidemiological modeling in StochSS Live!
Promoter2.0: for the recognition of PolII promoter sequences
rBiopaxParser - an R package to parse, modify and visualize BioPAX data
Semi-supervised protein classification using cluster kernels
isONform: reference-free transcriptome reconstruction from Oxford Nanopore data
Benchmarks for identification of ordinary differential equations from time series data
GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes
D'or: deep orienter of protein-protein interaction networks
AMC: accurate mutation clustering from single-cell DNA sequencing data
pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences
Protein-protein binding affinity prediction on a diverse set of structures
Adversarial deconfounding autoencoder for learning robust gene expression embeddings
Tandem repeat interval pattern identifies animal taxa
Extraction of knowledge on protein-protein interaction by association rule discovery
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting
The elucidation of protein function by sequence motif analysis
DeepPerVar: a multi-modal deep learning framework for functional interpretation of genetic variants in personal genome
On the calculation of signal transduction ability of signaling transduction pathways in intracellular communication: systematic approach
EasyGDB: a low-maintenance and highly customizable system to develop genomics portals
Hand-held computer program for field-capture and analysis of herbage yield and composition data using a modified dry-weight-rank and yield estimate method
Weighted rank aggregation of cluster validation measures: a Monte Carlo cross-entropy approach
Management of personal bibliographic reference using a simple database program
The hidden factor: accounting for covariate effects in power and sample size computation for a binary trait
ConKit: a python interface to contact predictions
Python interfaces for the Smoldyn simulator
Drug target prediction using adverse event report systems: a pharmacogenomic approach
ANARCI: antigen receptor numbering and receptor classification
SysBiolPGWAS: simplifying post-GWAS analysis through the use of computational technologies and integration of diverse omics datasets
Multiscale part mutual information for quantifying nonlinear direct associations in networks
In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder
Inference of gene regulatory networks using pseudo-time series data
InteroPORC: automated inference of highly conserved protein interaction networks
An innovative peptide toxicity prediction model based on multi-scale convolutional neural network and residual connection
DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics
Commonly misunderstood parameters of NCBI BLAST and important considerations for users
rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications
BioWeka - extending the Weka framework for bioinformatics
Phylogenetic trees: visualizing, customizing and detecting incongruence
TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates
P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher's meta-analysis method in omics applications
Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana
S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection
heatmaply: an R package for creating interactive cluster heatmaps for online publishing
Fully-sensitive seed finding in sequence graphs using a hybrid index
Efficient change-points detection for genomic sequences via cumulative segmented regression
CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data
Chull.sas: an SAS macro to construct the convex hull of one (or more) finite sets of points in a plane
Metadata-guided feature disentanglement for functional genomics
Efficient construction and utilization of k -ordered FM-indexes with kISS for ultra-fast read mapping in large genomes
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes
Fast and accurate phylogeny reconstruction using filtered spaced-word matches
IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets
Many-core algorithms for statistical phylogenetics
Gene Ontology-driven inference of protein-protein interactions using inducers
pystablemotifs: Python library for attractor identification and control in Boolean networks
Efficient simulation under a population genetics model of carcinogenesis
HeteroGGM: an R package for Gaussian graphical model-based heterogeneity analysis
BioPartsDB: a synthetic biology workflow web-application for education and research
ECCB2024: The 23rd European Conference on Computational Biology
ChromatinDB: a database of genome-wide histone modification patterns for Saccharomyces cerevisiae
BBID: the biological biochemical image database
Visual DSD: a design and analysis tool for DNA strand displacement systems
MaBoSS 2.0: an environment for stochastic Boolean modeling
CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism
GRiP: a computational tool to simulate transcription factor binding in prokaryotes
BWA-MEME: BWA-MEM emulated with a machine learning approach
LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins
MetaMDA: explainable prediction of microbe-drug association utilizing random walks on a microbe-metabolite-drug heterogeneous network
SCANCell reveals diverse inter-cluster interaction patterns in systemic lupus erythematosus across the disease spectrum
A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences
Monte Carlo simulations of ionic channel selectivity
3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion
Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing
PanGP: A tool for quickly analyzing bacterial pan-genome profile
Genotype transposer: automated genotype manipulation for linkage disequilibrium analysis
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification
HPID: The Human Protein Interaction Database
Robust network inference using response logic
Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates
On the use of qualitative reasoning to simulate and identify metabolic pathway
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles
A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism
Modelling G×E with historical weather information improves genomic prediction in new environments
Exploiting sequence-based features for predicting enhancer-promoter interactions
Image-based spatiotemporal causality inference for protein signaling networks
Poretools: a toolkit for analyzing nanopore sequence data
Message from the ISCB: The 5th ISCB Wikipedia competition: coming to a classroom near you?
Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models
PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants
Bipartite graph-based approach for clustering of cell lines by gene expression-drug response associations
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays
A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays
HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA
A convex optimization approach for identification of human tissue-specific interactomes
ChromDMM: a Dirichlet-multinomial mixture model for clustering heterogeneous epigenetic data
SynaptomeDB: an ontology-based knowledgebase for synaptic genes
High quality SNP calling using Illumina data at shallow coverage
PRAWNS: compact pan-genomic features for whole-genome population genomics
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
seeQTL: a searchable database for human eQTLs
ARBitR: an overlap-aware genome assembly scaffolder for linked reads
Intelligent Systems for Molecular Biology: review of the first international conference [published erratum appears in Comput Appl Biosci 1994 10(3)]
Statistical tests for identifying differentially expressed genes in time-course microarray experiments
VarMap: a web tool for mapping genomic coordinates to protein sequence and structure and retrieving protein structural annotations
Mediante: a web-based microarray data manager
CGDM: collaborative genomic data model for molecular profiling data using NoSQL
methscore: a comprehensive R function for DNA methylation-based health predictors
Variable selection for discriminant analysis with Markov random field priors for the analysis of microarray data
Evaluating recommender systems for AI-driven biomedical informatics
Evaluating individual genome similarity with a topic model
Automated annotation of Drosophila gene expression patterns using a controlled vocabulary
Calibrating E -values for hidden Markov models using reverse-sequence null models
RIBFIND: a web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps
OMTools: a software package for visualizing and processing optical mapping data
Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets
ISEApeaks: an Excel platform for GeneScan and Immunoscope data retrieval, management and analysis
MOST: a software environment for constraint-based metabolic modeling and strain design
IslandViewer: an integrated interface for computational identification and visualization of genomic islands
A hidden Ising model for ChIP-chip data analysis
Shimmer: detection of genetic alterations in tumors using next-generation sequence data
Discovering patterns to extract protein-protein interactions from the literature: Part II
Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins
Annotation of selection strengths in viral genomes
MRDagent: iterative and adaptive parameter optimization for stable ctDNA-based MRD detection in heterogeneous samples
Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences
e-LiSe - an online tool for finding needles in the "(Medline) haystack"
Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices
A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers
scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single-cell data
Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data
GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
SIFORM: shared informative factor models for integration of multi-platform bioinformatic data
DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data
CellTracker: an automated toolbox for single-cell segmentation and tracking of time-lapse microscopy images
The directory of P450-containing systems on WorldWide Web
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2
SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses
BEAUTY-X: enhanced BLAST searches for DNA queries
Tools for the SBML Community
Biological assessment of robust noise models in microarray data analysis
ELIXIR biovalidator for semantic validation of life science metadata
Radié: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree
The human genome contracts again
PSiTE: a Phylogeny guided Simulator for Tumor Evolution
NRPSsp: non-ribosomal peptide synthase substrate predictor
Towards precise PICO extraction from abstracts of randomized controlled trials using a section-specific learning approach
Reliable ABC model choice via random forests
CAARS: comparative assembly and annotation of RNA-Seq data
fastANCOM: a fast method for analysis of compositions of microbiomes
A program for verification of phylogenetic network models
EpiCombFlu: exploring known influenza epitopes and their combination to design a universal influenza vaccine
DeepEfflux: a 2D convolutional neural network model for identifying families of efflux proteins in transporters
TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases
pgRNAFinder: a web-based tool to design distance independent paired-gRNA
Building chromosome-wide LD maps
A bioinformatic strategy to rapidly characterize cDNA libraries
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction
ScaleQC: a scalable lossy to lossless solution for NGS data compression
ANGES: reconstructing ANcestral GEnomeS maps
linemodels: clustering effects based on linear relationships