yusuke1997/dblp-id-title huggingface dataset:
Identifying cis -regulatory modules by combining comparative and compositional analysis of DNA
CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices
Estimating and testing high-dimensional mediation effects in epigenetic studies
Computational prediction of novel components of lung transcriptional networks
Effects of small particle numbers on long-term behaviour in discrete biochemical systems
Defining the extent of gene function using ROC curvature
DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity
ProtorP: a protein-protein interaction analysis server
SMMB: a stochastic Markov blanket framework strategy for epistasis detection in GWAS
PTPan - overcoming memory limitations in oligonucleotide string matching for primer/probe design
DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
The 2024 ISCB Overton Prize Award - Dr Martin Steinegger
PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method
Expanding the toolkit for membrane protein modeling in Rosetta
Scupa: single-cell unified polarization assessment of immune cells using the single-cell foundation model
Is cross-validation better than resubstitution for ranking genes?
Identifying proteins controlling key disease signaling pathways
A quantitative model for linking two disparate sets of articles in MEDLINE
ECCB 2006 Organization
Using biologically interrelated experiments to identify pathway genes in Arabidopsis
Gretl - variation GRaph Evaluation TooLkit
Improved prediction of bacterial transcription start sites
Twine: display and analysis of cis -regulatory modules
Practical selection of representative sets of RNA-seq samples using a hierarchical approach
XMAn v2 - a database of Homo sapiens mutated peptides
NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets
Bayesian survival analysis in genetic association studies
On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library
TANDEM: integrating automated allele binning into genetics and genomics workflows
Integration of background knowledge for automatic detection of inconsistencies in gene ontology annotation
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data
Grand challenges in bioinformatics
caBIONet - A .NET wrapper to access and process genomic data stored at the National Cancer Institute's Center for Bioinformatics databases
On the significance of sequence alignments when using multiple scoring matrices
ESCARGOT: an AI agent leveraging large language models, dynamic graph of thoughts, and biomedical knowledge graphs for enhanced reasoning
HI-FEVER: a Nextflow pipeline for the high-throughput discovery and annotation of endogenous viral elements
Clustering of time-course gene expression data using a mixed-effects model with B-splines
MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data
Modeling and simulation of cancer immunoprevention vaccine
A readable and space-efficient DNA sequence representation: application to caulimoviral DNAs
Mapache: a flexible pipeline to map ancient DNA
Robustness analysis and tuning of synthetic gene networks
Revealing new therapeutic opportunities through drug target prediction: a class imbalance-tolerant machine learning approach
Support vector machine model of developmental brain gene expression data for prioritization of Autism risk gene candidates
A new data model for biological classification
MiRKAT: kernel machine regression-based global association tests for the microbiome
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
TCR3d: The T cell receptor structural repertoire database
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models
DoubleRecViz: a web-based tool for visualizing transcript-gene-species tree reconciliation
Interactive visualization software for exploring phylogenetic trees and clades
PDIviz: analysis and visualization of protein-DNA binding interfaces
SCARPA: scaffolding reads with practical algorithms
A rapid method for illustrating features in both coding and non-coding regions of a genome
Using a state-space model with hidden variables to infer transcription factor activities
PcircRNA_finder: a software for circRNA prediction in plants
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Comparison of six breast cancer classifiers using qPCR
GSearcher: Agile Attribute Querying for Biological Networks
hypeR: an R package for geneset enrichment workflows
Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction
Biomarker detection in the integration of multiple multi-class genomic studies
Pycellerator: an arrow-based reaction-like modelling language for biological simulations
HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling
MaGnET: Malaria Genome Exploration Tool
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations
Large-scale mammalian genome rearrangements coincide with chromatin interactions
Constrained multiple sequence alignment using XALIGN
Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data
DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
cddApp: a Cytoscape app for accessing the NCBI conserved domain database
Identification of genetic network dynamics with unate structure
Message from the ISCB: 2018 Outstanding Contributions to ISCB Award: Russ Altman
gff2aplot: Plotting sequence comparisons
Linear regression and two-class classification with gene expression data
PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes
Limits and potential of combined folding and docking
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions
A simple refined DNA minimizer operator enables 2-fold faster computation
Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development
tRanslatome: an R/Bioconductor package to portray translational control
Single-cell systems analysis: decision geometry in outliers
Phylogenetic Web Profiler
Detection of unusual RNA folding regions in HIV and SIV sequences
Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer
KGraph: a system for visualizing and evaluating complex genetic associations
DNAfan: a software tool for automated extraction and analysis of user-defined sequence regions
eCEO : an efficient Cloud Epistasis cOmputing model in genome-wide association study
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge
TCGA2STAT: simple TCGA data access for integrated statistical analysis in R
DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data
NetMatch: a Cytoscape plugin for searching biological networks
ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes
Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate
Consensus generation and variant detection by Celera Assembler
TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules
Expitope: a web server for epitope expression
SuccFind: a novel succinylation sites online prediction tool via enhanced characteristic strategy
An integrative pipeline for circular RNA quantitative trait locus discovery with application in human T cells
TCR-epiDiff: solving dual challenges of TCR generation and binding prediction
First and second moment of counts of words in random texts generated by Markov chains
Direct procedure for the determination of the number of replication forks and the reinitiation fraction in bacteria
Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance
Inference of temporally varying Bayesian Networks
High-throughput microbial population genomics using the Cortex variation assembler
DeepHINT: understanding HIV-1 integration via deep learning with attention
TileMap: create chromosomal map of tiling array hybridizations
CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data
Colour deconvolution: stain unmixing in histological imaging
A reference dataset for the analyses of membrane protein secondary structures and transmembrane residues using circular dichroism spectroscopy
A clustering linear combination approach to jointly analyze multiple phenotypes for GWAS
SETH detects and normalizes genetic variants in text
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework
TPMCalculator: one-step software to quantify mRNA abundance of genomic features
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch
Deep learning for survival analysis in breast cancer with whole slide image data
Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit
Automatic curation of large comparative animal MicroRNA datasets
VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data
Bayesian inference of distributed time delay in transcriptional and translational regulation
GraphClust: alignment-free structural clustering of local RNA secondary structures
Protein-protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique
CATMAID: collaborative annotation toolkit for massive amounts of image data
Structure-based prediction of protein- peptide binding regions using Random Forest
Quantitative PCR with internal controls
Finding new structural and sequence attributes to predict possible disease association of single amino acid polymorphism (SAP)
DRAGON View: information visualization for annotated microarray data
A graph regularized non-negative matrix factorization method for identifying microRNA-disease associations
Discovering transcription factor regulatory targets using gene expression and binding data
DrTransformer : heuristic cotranscriptional RNA folding using the nearest neighbor energy model
Gene symbol disambiguation using knowledge-based profiles
CrossTalkeR: analysis and visualization of ligand-receptorne tworks
Underground metabolism as a rich reservoir for pathway engineering
Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq
Multi-instance learning of graph neural networks for aqueous pKa prediction
Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis
Planning bioinformatics workflows using an expert system
The power of protein interaction networks for associating genes with diseases
Kohonen map as a visualization tool for the analysis of protein sequences: multiple alignments, domains and segments of secondary structures
SiPAN: simultaneous prediction and alignment of protein-protein interaction networks
The fiction of function
The SBW-CMATLAB interface
Compression of DNA sequence reads in FASTQ format
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality
PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping
Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites
Comparative evaluation of shape retrieval methods on macromolecular surfaces: an application of computer vision methods in structural bioinformatics
Extraction of regulatory gene/protein networks from Medline
A comprehensive SNP and indel imputability database
aPhyloGeo: a Python application for correlating genetic and climatic conditions
Automated analysis of biological oscillator models using mode decomposition
Inferring sequence regions under functional divergence in duplicate genes
Calibrating variant-scoring methods for clinical decision making
Discovering novel subsystems using comparative genomics
Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data
Filtering error from SOLiD Output
Expanding the coverage of spatial proteomics: a machine learning approach
Assessing the relationship between conservation of function and conservation of sequence using photosynthetic proteins
Functional association networks as priors for gene regulatory network inference
Faster exact maximum parsimony search with XMP
Nanopore base calling on the edge
Reactome and the Gene Ontology: digital convergence of data resources
MEPD: a resource for medaka gene expression patterns
RTNduals: an R/Bioconductor package for analysis of co-regulation and inference of dual regulons
Oligonucleotide frequency matrices addressed to recognizing functional DNA sites
Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing
ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease
The phers R package: using phenotype risk scores based on electronic health records to study Mendelian disease and rare genetic variants
ContEst: estimating cross-contamination of human samples in next-generation sequencing data
ELISA-BASE: an integrated bioinformatics tool for analyzing and tracking ELISA microarray data
Quantitative visualization of alternative exon expression from RNA-seq data
Evolutionary non-linear modelling for selecting vaccines against antigenically variable viruses
Primer Master: a new program for the design and analysis of PCR primers
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data
GenCLiP 3: mining human genes' functions and regulatory networks from PubMed based on co-occurrences and natural language processing
The DICS repository: module-assisted analysis of disease-related gene lists
A near-tight lower bound on the density of forward sampling schemes
PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling
MutHTP: mutations in human transmembrane proteins
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution
Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences
VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets
Comparative analysis of methods for representing and searching for transcription factor binding sites
A novel approach for drug response prediction in cancer cell lines via network representation learning
Identification of ribosomal RNA genes in metagenomic fragments
PyBEL: a computational framework for Biological Expression Language
Sensitivity and specificity of five abundance estimators for high-density oligonucleotide microarrays
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies
Profile Comparer: a program for scoring and aligning profile hidden Markov models
HitPick: a web server for hit identification and target prediction of chemical screenings
ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies
The Protein Feature Ontology: a tool for the unification of protein feature annotations
DSigDB: drug signatures database for gene set analysis
NetDS: a Cytoscape plugin to analyze the robustness of dynamics and feedforward/feedback loop structures of biological networks
MolArt: a molecular structure annotation and visualization tool
VCFShark: how to squeeze a VCF file
Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration
An optimal experimental design approach to model discrimination in dynamic biochemical systems
Improving position-specific predictions of protein functional sites using phylogenetic motifs
A Bayesian network model for protein fold and remote homologue recognition
Controlled noise: evidence of epigenetic regulation of single-cell expression variability
MetaCycle: an integrated R package to evaluate periodicity in large scale data
PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes
A new method for finding long consensus patterns in nucleic acid sequences
INCA: synonymous codon usage analysis and clustering by means of self-organizing map
Pseudoalignment for metagenomic read assignment
A Laboratory Information Management System (LIMS) for a high throughput genetic platform aimed at candidate gene mutation screening
Jasmine: a Java pipeline for isomiR characterization in miRNA-Seq data
Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts
Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology
Cross-species common regulatory network inference without requirement for prior gene affiliation
Mining heterogeneous causal effects for personalized cancer treatment
Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data
Retraction and replacement of: A deep learning architecture for metabolic pathway prediction
Kart: a divide-and-conquer algorithm for NGS read alignment
Evol and ProDy for bridging protein sequence evolution and structural dynamics
ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data
SSIPe: accurately estimating protein-protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function
Using association signal annotations to boost similarity network fusion
Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins
HAMPLE: deciphering TF-DNA binding mechanism in different cellular environments by characterizing higher-order nucleotide dependency
BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins
Corrigendum to: Utilizing image and caption information for biomedical document classification
A unified index of sequence quality and contig overlap for DNA barcoding
Computer video acquisition and analysis system for biological data
ECCB2020: the 19th European Conference on Computational Biology
Prediction of phosphorylation sites using SVMs
Learning directed acyclic graphical structures with genetical genomics data
Correction to: Targeted metabolomics analyses for brain tumor margin assessment during surgery
Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood
DeepAc4C: a convolutional neural network model with hybrid features composed of physicochemical patterns and distributed representation information for identification of N4-acetylcytidine in mRNA
Bendix: intuitive helix geometry analysis and abstraction
aCGH.Spline - an R package for aCGH dye bias normalization
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence
TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers
Multivariate correlation estimator for inferring functional relationships from replicated genome-wide data
CLAUDIO: automated structural analysis of cross-linking data
imDEV: a graphical user interface to R multivariate analysis tools in Microsoft Excel
BLTSA: pseudotime prediction for single cells by branched local tangent space alignment
Scalable clustering algorithms for continuous environmental flow cytometry
siRecords: an extensive database of mammalian siRNAs with efficacy ratings
Gapped sequence alignment using artificial neural networks: application to the MHC class I system
ESpritz: accurate and fast prediction of protein disorder
Importance-Penalized Joint Graphical Lasso (IPJGL): differential network inference via GGMs
Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles
Detecting differential peaks in ChIP-seq signals with ODIN
Seq2Feature: a comprehensive web-based feature extraction tool
The DNA methylation haplotype (mHap) format and mHapTools
Differential gene expression detection using penalized linear regression models: the improved SAM statistics
<tt>networkGWAS</tt> : a network-based approach to discover genetic associations
MapReduce for accurate error correction of next-generation sequencing data
Unraveling the role of low-frequency mutated genes in breast cancer
BS-SNPer: SNP calling in bisulfite-seq data
2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity
XPIWIT - an XML pipeline wrapper for the Insight Toolkit
mEBT: multiple-matching evidence-based translator of murine genomic responses for human immunity studies
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning
Exploiting pretrained biochemical language models for targeted drug design
Deep architectures for protein contact map prediction
vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data
Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager
Mining viral proteins for antimicrobial and cell-penetrating drug delivery peptides
A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values
MemBrain-contact 2.0: a new two-stage machine learning model for the prediction enhancement of transmembrane protein residue contacts in the full chain
Homologue series detection and management in LC-MS data with homologueDiscoverer
FusionLearn: a biomarker selection algorithm on cross-platform data
HaploBlockFinder: Haplotype Block Analyses
SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria
pyGenomeTracks: reproducible plots for multivariate genomic datasets
Prediction of the permeability of neutral drugs inferred from their solvation properties
Pathway-structured predictive modeling for multi-level drug response in multiple myeloma
ClicO FS: an interactive web-based service of Circos
RNA secondary structures: comparison and determination of frequently recurring substructures by consensus
LayerCake: a tool for the visual comparison of viral deep sequencing data
MiRonTop: mining microRNAs targets across large scale gene expression studies
Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
tRNAstudio: facilitating the study of human mature tRNAs from deep sequencing datasets
PseudoPipe: an automated pseudogene identification pipeline
Pvclust: an R package for assessing the uncertainty in hierarchical clustering
Plotgardener: cultivating precise multi-panel figures in R
CharGer: clinical Characterization of Germline variants
AcePrimer: automation of PCR primer design based on gene structure
CS-PSeq-Gen: Simulating the evolution of protein sequence under constraints