yusuke1997/dblp-id-title huggingface dataset:
Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees
ezGeno: an automatic model selection package for genomic data analysis
GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function
Merging microarray cell synchronization experiments through curve alignment
Simulation of large-scale rule-based models
GGtools: analysis of genetics of gene expression in bioconductor
dSreg: a Bayesian model to integrate changes in splicing and RNA-binding protein activity
Folding RNA/DNA hybrid duplexes
VDNA: The virtual DNA plug-in for VMD
EpiToolKit - a web-based workbench for vaccine design
ViTraM: visualization of transcriptional modules
FTIP: an accurate and efficient method for global protein surface comparison
DEF: an automated dead-end filling approach based on quasi-endosymbiosis
A computer program to aid the sequencing of peptides in collision- activated decomposition experiments
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors
Exploiting disjointness axioms to improve semantic similarity measures
QuasR: quantification and annotation of short reads in R
A new measure of the robustness of biochemical networks
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites
IMG ER: a system for microbial genome annotation expert review and curation
Combining multiple microarrays in the presence of controlling variables
SCooP: an accurate and fast predictor of protein stability curves as a function of temperature
Discovering tightly regulated and differentially expressed gene sets in whole genome expression data
hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework
AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes
Predicting protein-protein interactions using signature products
PSI-Search: iterative HOE-reduced profile SSEARCH searching
Interactive gene-order comparison for multiple small genomes
KEC: unique sequence search by K-mer exclusion
YAdumper: extracting and translating large information volumes from relational databases to structured flat files
FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes
The automation of Nested Clade Phylogeographic Analysis
Optimized atomic statistical potentials: assessment of protein interfaces and loops
Development of the receptor database (RDB): application to the endocrine disruptor problem
Molecular property prediction by semantic-invariant contrastive learning
PIRD: Pan Immune Repertoire Database
Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data
A web application and service for imputing and visualizing missense variant effect maps
Identifying informative subsets of the Gene Ontology with information bottleneck methods
Searching for protein loops in parallel
Hierarchical modelling of microbial communities
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
Paving the future: finding suitable ISMB venues
Identifying centromeric satellites with dna-brnn
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks
Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server
Proteome coverage prediction with infinite Markov models
MBG: Minimizer-based sparse de Bruijn Graph construction
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation
Gaussian mixture clustering and imputation of microarray data
Circoletto: visualizing sequence similarity with Circos
Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space
Inferring combinatorial association logic networks in multimodal genome-wide screens
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
DISC: DISulfide linkage Characterization from tandem mass spectra
Gearing up to handle the mosaic nature of life in the quest for orthologs
A classification of tasks in bioinformatics
CRISPRL and: Interpretable large-scale inference of DNA repair landscape based on a spectral approach
Efficient change point detection for genomic sequences of continuous measurements
MetaboCraft: building a Minecraft plugin for metabolomics
iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis
Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array
DISTAN--a program which detects significant distances between short oligonucleotides
BioStructures.jl: read, write and manipulate macromolecular structures in Julia
The Economic Value of Bioinformation
do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations
Ontology patterns for tabular representations of biomedical knowledge on neglected tropical diseases
The interplay between microRNA and alternative splicing of linear and circular RNAs in eleven plant species
HIDE: hierarchical cell-type deconvolution
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support
DistilProtBert: a distilled protein language model used to distinguish between real proteins and their randomly shuffled counterparts
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks
A novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers
vcfpp: a C++ API for rapid processing of the variant call format
A reference peptide database for proteome quantification based on experimental mass spectrum response curves
Structure clustering features on the Sfold Web server
CisML: an XML-based format for sequence motif detection software
FATSLiM: a fast and robust software to analyze MD simulations of membranes
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks
NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference
PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure
EpiDope: a deep neural network for linear B-cell epitope prediction
ANDY: a general, fault-tolerant tool for database searching on computer clusters
Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation
IndexToolkit: an open source toolbox to index protein databases for high-throughput proteomics
Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data
ACNUC - a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage
TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities
PALI: a database of alignments and phylogeny of homologous protein structures
Identifying sequence regions undergoing conformational change via predicted continuum secondary structure
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection
On the trail of protein sequences
PathWalks: identifying pathway communities using a disease-related map of integrated information
Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays
Systematic analysis of synchronized oscillatory neuronal networks reveals an enrichment for coupled direct and indirect feedback motifs
scphaser: haplotype inference using single-cell RNA-seq data
Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules
Exploring biological network structure using exponential random graph models
minimac2: faster genotype imputation
A statistical method for identifying differential gene-gene co-expression patterns
Adapt-Mix: learning local genetic correlation structure improves summary statistics-based analyses
Coala: an R framework for coalescent simulation
Blue: correcting sequencing errors using consensus and context
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
Hum-mPLoc 3.0: prediction enhancement of human protein subcellular localization through modeling the hidden correlations of gene ontology and functional domain features
Optimal spliced alignment of homologous cDNA to a genomic DNA template
PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades
SPADEVizR: an R package for visualization, analysis and integration of SPADE results
An image-processing approach to dotplots: an X-Window-based program for interactive analysis of dotplots derived from sequence and structural data
Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients
NeoFuse: predicting fusion neoantigens from RNA sequencing data
MAGOS: multiple alignment and modelling server
ConFind: a robust tool for conserved sequence identification
Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation
A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays
CACONET: a novel classification framework for microbial correlation networks
Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis
insilicoSV: a flexible grammar-based framework for structural variant simulation and placement
expa: a program for calculating extreme pathways in biochemical reaction networks
circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs
Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences
Moderated statistical tests for assessing differences in tag abundance
The reduction of large molecular profiles to informative components using a Genetic Algorithm
New Analytical Techniques for the Interpretation of Microarray Data
Complete genomes in WWW Entrez: data representation and analysis
An astonishing wealth of new proteasome homologs
LongISLND: in silico sequencing of lengthy and noisy datatypes
ViaComplex: software for landscape analysis of gene expression networks in genomic context
Systematic replication enables normalization of high-throughput imaging assays
Phylogeny inferred from codon usage pattern in 31 organisms
NanoASV: a snakemake workflow for reproducible field-based Nanopore full-length 16S metabarcoding amplicon data analysis
Scaling neighbor joining to one million taxa with dynamic and heuristic neighbor joining
mmsearch: a motif arrangement language and search program
Computational, experimental analysis reveals a novel Src family kinase in the C. elegans genome
Maximum likelihood reconstruction of ancestral networks by integer linear programming
The application of SSADM to modelling the logical structure of proteins
The translation of DNA primary base sequence into three-dimensional structure
openBIS ELN-LIMS: an open-source database for academic laboratories
Arioc: GPU-accelerated alignment of short bisulfite-treated reads
Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease
TADA: phylogenetic augmentation of microbiome samples enhances phenotype classification
FastMEDUSA: a parallelized tool to infer gene regulatory networks
The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models
iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC
Automatic term list generation for entity tagging
Scalable CNN-based classification of selective sweeps using derived allele frequencies
Assessing gene-level translational control from ribosome profiling
Phylolink: phylogenetically-based profiling, visualisations and metrics for biodiversity
Automated neuron tracing using probability hypothesis density filtering
Effective cluster-based seed design for cross-species sequence comparisons
WAVECLOCK: wavelet analysis of circadian oscillation
SERPENT - an information storage and analysis resource for protein sequences
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data
deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks
Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences
Domain adaptation for semantic role labeling in the biomedical domain
NanoPack2: population-scale evaluation of long-read sequencing data
MSC: a metagenomic sequence classification algorithm
A novel normalization and differential abundance test framework for microbiome data
peakPantheR, an R package for large-scale targeted extraction and integration of annotated metabolic features in LC-MS profiling datasets
RNAenrich: a web server for non-coding RNA enrichment
CIIPro: a new read-across portal to fill data gaps using public large-scale chemical and biological data
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology
Clustalnet: the joining of Clustal and CORBA
Adapters, shims, and glue - service interoperability for in silico experiments
FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data
A probabilistic approach for collective similarity-based drug-drug interaction prediction
DeepSynergy: predicting anti-cancer drug synergy with Deep Learning
EW_dmGWAS: edge-weighted dense module search for genome-wide association studies and gene expression profiles
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing
Tropical - parameter estimation and simulation of reaction-diffusion models based on spatio-temporal microscopy images
SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences
Modeling T-cell activation using gene expression profiling and state-space models
GRIMM: genome rearrangements web server
Reference bias in the Illumina Isaac aligner
Automatic evaluation of protein sequence functional patterns
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters
BioThings SDK: a toolkit for building high-performance data APIs in biomedical research
FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
PTMint database of experimentally verified PTM regulation on protein-protein interaction
Ligandbook: an online repository for small and drug-like molecule force field parameters
Discovering significant evolutionary trajectories in cancer phylogenies
Estimation of the intrinsic rate of natural increase and its error by both algebraic and resampling approaches
The Delphic boat or what the genomic texts tell us
Mining and integration of pathway diagrams from imaging data
When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality
Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome
Classifying tumors by supervised network propagation
Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression
SANPolyA: a deep learning method for identifying Poly(A) signals
PPIXpress: construction of condition-specific protein interaction networks based on transcript expression
VSS: variance-stabilized signals for sequencing-based genomic signals
Estimating the strength of expression conservation from high throughput RNA-seq data
amplimap: a versatile tool to process and analyze targeted NGS data
Machine learning-based quantification for disease uncertainty increases the statistical power of genetic association studies
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs
ISMB/ECCB 2017 PROCEEDINGS PAPERS COMMITTEE
BhGLM: Bayesian hierarchical GLMs and survival models, with applications to genomics and epidemiology
The 2025 ISCB Overton Prize Award - Dr James Zou
A computationally efficient modular optimal discovery procedure
GAGE-B: an evaluation of genome assemblers for bacterial organisms
BioJS: an open source JavaScript framework for biological data visualization
Mathematical characterization of three-dimensional gene expression patterns
FFPopSim: an efficient forward simulation package for the evolution of large populations
Support vector machines for prediction of dihedral angle regions
Detection of significant patterns by compression algorithms: the case of approximate tandem repeats in DNA sequences
Identification of DNA regulatory motifs using Bayesian variable selection
Few-shot biomedical named entity recognition via knowledge-guided instance generation and prompt contrastive learning
The MGED Ontology: a resource for semantics-based description of microarray experiments
Semi-supervised learning of Hidden Markov Models for biological sequence analysis
GalaxyCloudRunner: enhancing scalable computing for Galaxy
LinkageMapView - rendering high-resolution linkage and QTL maps
Protein Peeling 3D: new tools for analyzing protein structures
Optimal alignments of biological sequences on a microcomputer
A weighted exact test for mutually exclusive mutations in cancer
FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications
Identification of cell-type-specific spatially variable genes accounting for excess zeros
Nearest-neighbor Projected-Distance Regression (NPDR) for detecting network interactions with adjustments for multiple tests and confounding
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary
The Glycome Analytics Platform: an integrative framework for glycobioinformatics
McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences
Probabilistic inference of molecular networks from noisy data sources
bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
A Search for H/ACA SnoRNAs in Yeast Using MFE Secondary Structure Prediction
MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks
Identification of prokaryotic small proteins using a comparative genomic approach
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Two C++ libraries for counting trees on a phylogenetic terrace
Neural Collective Matrix Factorization for integrated analysis of heterogeneous biomedical data
Statistical methods of translating microarray data into clinically relevant diagnostic information in colorectal cancer
CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction
Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence
On the quality of tree-based protein classification
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes
Analysis of array CGH data: from signal ratio to gain and loss of DNA regions
uBioRSS: Tracking taxonomic literature using RSS
Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes
Correction to: Improving annotation propagation on molecular networks through random walks: introducing ChemWalker
chromswitch: a flexible method to detect chromatin state switches
A novel knowledge-based approach to design inorganic-binding peptides
Correction to: PEMT: a patent enrichment tool for drug discovery
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
MAVisto: a tool for the exploration of network motifs
PIGS: automatic prediction of antibody structures
CGManalyzer: an R package for analyzing continuous glucose monitoring studies
SKmDB: an integrated database of next generation sequencing information in skeletal muscle
Accelerating flux balance calculations in genome-scale metabolic models by localizing the application of loopless constraints
KORP-PL: a coarse-grained knowledge-based scoring function for protein-ligand interactions
Decision tree-based formation of consensus protein secondary structure prediction
Efficient implementation of convolutional neural networks in the data processing of two-photon in vivo imaging
Integrating multi-OMICS data through sparse canonical correlation analysis for the prediction of complex traits: a comparison study
A new method to improve network topological similarity search: applied to fold recognition
Adaptive intervention in probabilistic boolean networks
Analysis of disturbed images
A special-purpose processor for gene sequence analysis
Morpheus: a fragment-based algorithm to predict fold-switching behaviour in proteins across proteomes
Alloscore: a method for predicting allosteric ligand-protein interactions
Non-linear PCA: a missing data approach
Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data
An automated genotyping system for analysis of HIV-1 and other microbial sequences
Extraction of fluorescent cell puncta by adaptive fuzzy segmentation
The UCSC Known Genes
HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs
HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences
DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs
Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
RNA-SeQC 2: efficient RNA-seq quality control and quantification for large cohorts
Using Genome Query Language to uncover genetic variation
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization
Testing multiple biological mediators simultaneously
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data
Polylink: to support two-point linkage analysis in autotetraploids
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
Ontoclick: a web browser extension to facilitate biomedical knowledge curation
CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data
Joint eQTL mapping and inference of gene regulatory network improves power of detecting both cis- and trans-eQTLs
CNV-guided multi-read allocation for ChIP-seq
MLGL-MP: a Multi-Label Graph Learning framework enhanced by pathway interdependence for Metabolic Pathway prediction
Multiple spaced seeds for homology search
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
SplamiR - prediction of spliced miRNAs in plants
SQuAPP - simple quantitative analysis of proteins and PTMs
SED88: a Pascal program for the analysis of sedimentation equilibrium data
PyCoTools: a Python toolbox for COPASI
GASSST: global alignment short sequence search tool