yusuke1997/dblp-id-title huggingface dataset:
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
Shepherd: accurate clustering for correcting DNA barcode errors
FLYCOP: metabolic modeling-based analysis and engineering microbial communities
Caleydo: connecting pathways and gene expression
Reversible jump MCMC for multi-model inference in Metabolic Flux Analysis
Integration of SNP genotyping confidence scores in IBD inference
ScanNeo: identifying indel-derived neoantigens using RNA-Seq data
An efficient gene-gene interaction test for genome-wide association studies in trio families
A Siamese neural network model for the prioritization of metabolic disorders by integrating real and simulated data
PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy
regioneReloaded: evaluating the association of multiple genomic region sets
Accurate confidence aware clustering of array CGH tumor profiles
Building structural models of peptides: a semi-automatic software
DistanceScan: a tool for promoter modeling
aGEM: an integrative system for analyzing spatial-temporal gene-expression information
Inference of biochemical network models in S-system using multiobjective optimization approach
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
Efficient multiple biomedical events extraction via reinforcement learning
Analysis of case-control association studies with known risk variants
Inferring gene expression networks with hubs using a degree weighted Lasso approach
Identification of plant microRNA homologs
A proposal for a standard CORBA interface for genome maps
MCQTL: multi-allelic QTL mapping in multi-cross design
Interoperability between phenotype and anatomy ontologies
ExperimentSubset: an R package to manage subsets of Bioconductor Experiment objects
Isolating structural errors in reaction networks in systems biology
Echo LOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations
Regression trees for analysis of mutational spectra in nucleotide sequences
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
A multivariate Bernoulli model to predict DNaseI hypersensitivity status from haplotype data
Penalized co-inertia analysis with applications to -omics data
Identification of genetic outliers due to sub-structure and cryptic relationships
SpecEncoder: deep metric learning for accurate peptide identification in proteomics
Gene recognition by combination of several gene-finding programs
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
Advancing mRNA subcellular localization prediction with graph neural network and RNA structure
GREP: genome for REPositioning drugs
Error correction of high-throughput sequencing datasets with non-uniform coverage
PCP: a program for supervised classification of gene expression profiles
PREDDIMER: a web server for prediction of transmembrane helical dimers
Overcoming biases in causal inference of molecular interactions
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
Protein contact prediction using metagenome sequence data and residual neural networks
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
ipd: an R package for conducting inference on predicted data
Investigation of the BERT model on nucleotide sequences with non-standard pre-training and evaluation of different k-mer embeddings
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
SINC: a scale-invariant deep-neural-network classifier for bulk and single-cell RNA-seq data
DTF: Deep Tensor Factorization for predicting anticancer drug synergy
Physics-based gene identification: proof of concept for Plasmodium falciparum
Flexible analysis of RNA-seq data using mixed effects models
TCRBuilder: multi-state T-cell receptor structure prediction
How to reconstruct a large genetic network from n gene perturbations in fewer than n2 easy steps
MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
gpDB: a database of GPCRs, G-proteins, effectors and their interactions
Peak bagging for peptide mass fingerprinting
BicOverlapper 2.0: visual analysis for gene expression
SiNVICT: ultra-sensitive detection of single nucleotide variants and indels in circulating tumour DNA
nhmmer: DNA homology search with profile HMMs
Artemis: sequence visualization and annotation
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data
Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data
GeneEvolve: a fast and memory efficient forward-time simulator of realistic whole-genome sequence and SNP data
Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis
Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge
Detecting hypermutations in viral sequences with an emphasis on G A hypermutation
Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies
Novo&Stitch: accurate reconciliation of genome assemblies via optical maps
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening
The HIB database of annotated UniGene clusters
TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic
Sample size for gene expression microarray experiments
PanCGH: a genotype-calling algorithm for pangenome CGH data
COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Intramolecular surface contacts contain information about protein-protein interface regions
OMGProm: a database of orthologous mammalian gene promoters
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA)
ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices
A web-based software system for dynamic gene cluster comparison across multiple genomes
INSECT 2.0: a web-server for genome-wide cis -regulatory modules prediction
Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data
Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation
Learning probabilistic models of cis -regulatory modules that represent logical and spatial aspects
deML: robust demultiplexing of Illumina sequences using a likelihood-based approach
Susceptibility of the human pathways graphs to fragmentation by small sets of microRNAs
SequencEnG: an interactive knowledge base of sequencing techniques
Integrative network alignment reveals large regions of global network similarity in yeast and human
A fast graphics printing program for neurophysiological data
PySFD: comprehensive molecular insights from significant feature differences detected among many simulated ensembles
QMSim: a large-scale genome simulator for livestock
The MUSC DNA Microarray Database
Correction to: The 2024 ISCB Innovator Award - Dr Su-In Lee
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
MAVG: locating non-overlapping maximum average segments in a given sequence
CRNET: an efficient sampling approach to infer functional regulatory networks by integrating large-scale ChIP-seq and time-course RNA-seq data
pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra
SUPERTRIPLETS: a triplet-based supertree approach to phylogenomics
Efficient exact motif discovery
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores
Target space for structural genomics revisited
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)
GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization
LoRA-DR-suite: adapted embeddings predict intrinsic and soft disorder from protein sequences
MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning
Apollo: a community resource for genome annotation editing
2023 ISCB accomplishments by a senior scientist award: Mark Gerstein
COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures
QUAST: quality assessment tool for genome assemblies
IsoMIF Finder: online detection of binding site molecular interaction field similarities
Open Agile text mining for bioinformatics: the PubAnnotation ecosystem
Network-principled deep generative models for designing drug combinations as graph sets
PIUS: peptide identification by unbiased search
DPMIND: degradome-based plant miRNA-target interaction and network database
CytoPacq: a web-interface for simulating multi-dimensional cell imaging
A predictive model for identifying proteins by a single peptide match
SiGN-SSM: open source parallel software for estimating gene networks with state space models
Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection
Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies
metaboprep: an R package for preanalysis data description and processing
Local structure-based sequence profile database for local and global protein structure predictions
Revana: a comprehensive tool for regulatory variant analysis and visualization of cancer genomes
TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates
Phylogeny-independent detection of functional residues
SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data
GNET2: an R package for constructing gene regulatory networks from transcriptomic data
Point estimates in phylogenetic reconstructions
SASpy: a PyMOL plugin for manipulation and refinement of hybrid models against small angle X-ray scattering data
Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics
A tale of two tails: why are terminal residues of proteins exposed?
A task framework for the web interface W2H
Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k -mer sets
Ultrafast and ultralarge multiple sequence alignments using TWILIGHT
GELENT: a sequence gel entry program for keyboard and sonic digitizer input
EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals
REGGAE: a novel approach for the identification of key transcriptional regulators
Biskit - A software platform for structural bioinformatics
OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases
A C version of Fourier-derived affinity spectrum analysis (FASA) to resolve binding heterogeneity
Toward community standards in the quest for orthologs
Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network
The qBED track: a novel genome browser visualization for point processes
PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context
Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Finding relevant references to genes and proteins in Medline using a Bayesian approach
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows
STREME: accurate and versatile sequence motif discovery
Querying and computing with BioCyc databases
A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT
DISTREE: a tool for estimating genetic distances between aligned DNA sequences
AMADA: analysis of microarray data
Web-igloo: a web based platform for multivariate data visualization
Constructing an enzyme-centric view of metabolism
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer
Unequal group variances in microarray data analyses
Bellman's GAP - a language and compiler for dynamic programming in sequence analysis
Compression of quantification uncertainty for scRNA-seq counts
Quick selection of representative protein chain sets based on customizable requirements
Processing and population genetic analysis of multigenic datasets with ProSeq3 software
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Bioimage informatics: a new category in Bioinformatics
Compensation for nucleotide bias in a genome by representation as a discrete channel with noise
vcfgl: a flexible genotype likelihood simulator for VCF/BCF files
Towards a piRNA prediction using multiple kernel fusion and support vector machine
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics
Automated ordering of fingerprinted clones
Accelerated off-target search algorithm for siRNA
RReportGenerator: automatic reports from routine statistical analysis using R
PathwayNexus: a tool for interactive metabolic data analysis
Training for translation between disciplines: a philosophy for life and data sciences curricula
BAlaS: fast, interactive and accessible computational alanine-scanning using BudeAlaScan
Knowledge-based simulation of DNA metabolism: prediction of enzyme action
HERSIM: a microcomputer program designed to compute the limits of conversion for real homogeneous isothermal enzymic reactors
AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality
TIPP: taxonomic identification and phylogenetic profiling
MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions
An alignment-free test for recombination
DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments
TIN-X: target importance and novelty explorer
Quantitative assessment of filter-based cDNA microarrays: gene expression profiles of human T-lymphoma cell lines
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
Ka-me: a Voronoi image analyzer
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
PFGE MAPPER: a tool to aid in the analysis of pulse field gel electrophoresis maps
MolMVC: Enhancing molecular representations for drug-related tasks through multi-view contrastive learning
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control
New approach for segmentation and quantification of two-dimensional gel electrophoresis images
A score matrix to reveal the hidden links in glycans
GWASpro: a high-performance genome-wide association analysis server
Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific reference panels
tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks
Gene expression: Quick calculation for sample size while controlling false discovery rate with application to microarray analysis
Collaborative analysis of multi-gigapixel imaging data using Cytomine
De novo identification of replication-timing domains in the human genome by deep learning
Correction to: Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms
An atlas of human viruses provides new insights into diversity and tissue tropism of human viruses
mirtronDB: a mirtron knowledge base
NETAL: a new graph-based method for global alignment of protein-protein interaction networks
MetaMarker: a pipeline for de novo discovery of novel metagenomic biomarkers
HTT-DB: Horizontally transferred transposable elements database
Kernelized rank learning for personalized drug recommendation
LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening
myGenomeBrowser: building and sharing your own genome browser
A simple algorithm for averaging multiple cycles of waveforms having varying cycle periods
Roary: rapid large-scale prokaryote pan genome analysis
OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action
De novo peptide sequencing using ion peak intensity and amino acid cleavage intensity ratio
Logistic regression for disease classification using microarray data: model selection in a large p and small n case
Finding enzyme cofactors in Protein Data Bank
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
IGLOSS: iterative gapless local similarity search
Integrative data analysis for functional prediction: a multi-objective optimization approach
Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics
Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
Fast protein fold estimation from NMR-derived distance restraints
Time-optimized analysis of slit-scan chromosome profiles on a general- purpose personal computer
Automated analysis of interatomic contacts in proteins
Transcriptor: a comprehensive platform for annotation of the enzymatic functions of transcripts
BNPMDA: Bipartite Network Projection for MiRNA-Disease Association prediction
bWGR: Bayesian whole-genome regression
Integrated genome browser: visual analytics platform for genomics
Prediction of human protein function according to Gene Ontology categories
AGORA: organellar genome annotation from the amino acid and nucleotide references
pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification
The VCBS superfamily forms a third supercluster of β-propellers that includes tachylectin and integrins
COPICAT: a software system for predicting interactions between proteins and chemical compounds
Discovery of tandem and interspersed segmental duplications using high-throughput sequencing
Benchmarking homology detection procedures with low complexity filters
Large-scale motif discovery using DNA Gray code and equiprobable oligomers
Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra
BAGET: a web server for the effortless retrieval of prokaryotic gene context and sequence
iFoldRNA: three-dimensional RNA structure prediction and folding
DNA-BAR: distinguisher selection for DNA barcoding
InterVelo: a mutually enhancing model for estimating pseudotime and RNA velocity in multi-omic single-cell data
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS
Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data
GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes
AQUA-DUCT 1.0: structural and functional analysis of macromolecules from an intramolecular voids perspective
mRNAStab - a web application for mRNA stability analysis
tmVar: a text mining approach for extracting sequence variants in biomedical literature
wenda_gpu: fast domain adaptation for genomic data
Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data
Discoal: flexible coalescent simulations with selection
GTRAC: fast retrieval from compressed collections of genomic variants
Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)
Dynamic simulation of the human red blood cell metabolic network
POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
RNA-RNA interaction prediction based on multiple sequence alignments
MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability
Large-scale inference of conjunctive Bayesian networks
MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation
swga: a primer design toolkit for selective whole genome amplification
Development of an expert system for amino acid sequence identification
Energy landscape of k -point mutants of an RNA molecule
Lep-MAP: fast and accurate linkage map construction for large SNP datasets
An evolution based classifier for prediction of protein interfaces without using protein structures
Kmer-db: instant evolutionary distance estimation
Human recombination rates are increased around accelerated conserved regions - evidence for continued selection?
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants
TOPAL: recombination detection in DNA and protein sequences
The BioPAX Validator
VisualGraphX: interactive graph visualization within Galaxy
Sight: automating genomic data-mining without programming skills
Identifying novel associations between small molecules and miRNAs based on integrated molecular networks
mpMoRFsDB: a database of molecular recognition features in membrane proteins
Qxpak: a versatile mixed model application for genetical genomics and QTL analyses
Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems
NxTrim: optimized trimming of Illumina mate pair reads
FrameD: framework for DNA-based data storage design, verification, and validation
Characterization of the N-ATPase, a distinct, laterally transferred Na + -translocating form of the bacterial F-type membrane ATPase
Repseek, a tool to retrieve approximate repeats from large DNA sequences
Interfacing Seurat with the R tidy universe
An RNA pattern matching program with enhanced performance and portability
Accurate determination of DNA in agarose gels using the novel algorithm GelScann(1.0)
Expected gene-order distances and model selection in bacteria
SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles
Near-optimal experimental design for model selection in systems biology
Specific alignment of structured RNA: stochastic grammars and sequence annealing
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes
Predicting a set of minimal free energy RNA secondary structures common to two sequences
A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes
Modeling mechanistic biological networks: An advanced Boolean approach
Mining gene expression data for positive and negative co-regulated gene clusters
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams
Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment
A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes