yusuke1997/dblp-id-title huggingface dataset:
BioCichlid: central dogma-based 3D visualization system of time-course microarray data on a hierarchical biological network
ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models
GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population
GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences
fimpera : drastic improvement of Approximate Membership Query data-structures with counts
Interpretation of ANOVA models for microarray data using PCA
TileProbe: modeling tiling array probe effects using publicly available data
Estimating chain length for time delays in dynamical systems using profile likelihood
Inherent limitations in protein-protein docking procedures
String graph construction using incremental hashing
ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data
Accurate and efficient estimation of small P-values with the cross-entropy method: applications in genomic data analysis
Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction
The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15
A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio
MLDSP-GUI: an alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis
The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community
HIV-1 genotypic resistance: automated sequence analysis and interpretation
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes
Multiscale adaptive differential abundance analysis in microbial compositional data
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps
A generic deep convolutional neural network framework for prediction of receptor-ligand interactions - NetPhosPan: application to kinase phosphorylation prediction
LanceOtron: a deep learning peak caller for genome sequencing experiments
cooccurNet: an R package for co-occurrence network construction and analysis
Secondary structure computer prediction of the poliovirus 5' non-coding region is improved by a genetic algorithm
ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data
ROptimus: a parallel general-purpose adaptive optimization engine
Integrative structural and dynamical biology with PLUMED-ISDB
Representing inter-residue dependencies in protein sequences with probabilistic networks
Gene tree and species tree reconciliation with endosymbiotic gene transfer
Adjustment for local ancestry in genetic association analysis of admixed populations
libSRES: a C library for stochastic ranking evolution strategy for parameter estimation
Two-Tier Mapper, an unbiased topology-based clustering method for enhanced global gene expression analysis
Exploring high-dimensional biological data with sparse contrastive principal component analysis
KEGGParser: parsing and editing KEGG pathway maps in Matlab
CoLoRMap: Correcting Long Reads by Mapping short reads
Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions
The minimum evolution problem is hard: a link between tree inference and graph clustering problems
Tangent normalization for somatic copy-number inference in cancer genome analysis
iPAC: a genome-guided assembler of isoforms via phasing and combing paths
Computational analysis of transcriptional regulatory elements: a field in flux
aRNApipe: a balanced, efficient and distributed pipeline for processing RNA-seq data in high-performance computing environments
Quark enables semi-reference-based compression of RNA-seq data
LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection
Bias in the intervention in prediction measure in random forests: illustrations and recommendations
SNPhood : investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data
A folding algorithm for extended RNA secondary structures
CoSIA: an R Bioconductor package for CrOss Species Investigation and Analysis
SIBIS: a Bayesian model for inconsistent protein sequence estimation
Methods to define and locate patterns of motifs in sequences
Sparse group factor analysis for biclustering of multiple data sources
powmic: an R package for power assessment in microbiome case-control studies
ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data
Drug-drug interaction extraction via hierarchical RNNs on sequence and shortest dependency paths
Deep graph learning of inter-protein contacts
NARWHAL, a primary analysis pipeline for NGS data
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies
WebBLAST 2.0: an integrated solution for organizing and analyzing sequence data
Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies
SynQuant: an automatic tool to quantify synapses from microscopy images
Parkour LIMS: high-quality sample preparation in next generation sequencing
Geno3D: automatic comparative molecular modelling of protein
The Bioinformatics Open Access option
GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies
Identification of mixups among DNA sequencing plates
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data
Figure mining for biomedical research
Exploring protein fold space by secondary structure prediction using data distribution method on Grid platform
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
Distributions of pI versus pH provide prior information for the design of crystallization screening experiments: response to comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'
CoCoa: a software tool for estimating the coefficient of coancestry from multilocus genotype data
A workbench for large-scale sequence homology analysis
Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly
Cytoscape Web: an interactive web-based network browser
Gene Set Expression Comparison kit for BRB-ArrayTools
Vacceed : a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease
Seeksv: an accurate tool for somatic structural variation and virus integration detection
BPRMeth: a flexible Bioconductor package for modelling methylation profiles
Inferring causality in biological oscillators
Picante: R tools for integrating phylogenies and ecology
KISS for STRAP: user extensions for a protein alignment editor
DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing
Large-scale model quality assessment for improving protein tertiary structure prediction
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
DichroCalc - circular and linear dichroism online
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries
Least absolute regression network analysis of the murine osteoblast differentiation network
EM-random forest and new measures of variable importance for multi-locus quantitative trait linkage analysis
A statistical method for the detection of variants from next-generation resequencing of DNA pools
rCGH: a comprehensive array-based genomic profile platform for precision medicine
PRONET: a microcomputer program for predicting the secondary structure of proteins with a neural network
Modeling metastatic progression from cross-sectional cancer genomics data
Over-optimism in bioinformatics research
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments
ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations
Phylogenetic exploration of bacterial genomic rearrangements
Adaptive quality-based clustering of gene expression profiles
Time to defend what we have won
Comparing multiple RNA secondary structures using tree comparisons
SPRINT: an SNP-free toolkit for identifying RNA editing sites
ProkSeq for complete analysis of RNA-Seq data from prokaryotes
WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing
Effective and efficient active learning for deep learning-based tissue image analysis
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data
EcoProDB: the Escherichia coli protein database
Understanding the complementarity and plasticity of antibody-antigen interfaces
State reduction for network intervention in probabilistic Boolean networks
Bayesian inference of the sites of perturbations in metabolic pathways via Markov chain Monte Carlo
Scbean: a python library for single-cell multi-omics data analysis
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images
MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
Prediction of protein interdomain linker regions by a hidden Markov model
Microarray Standard Data Set and Figures of Merit for Comparing Data Processing Methods and Experiment Designs
To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data
Spectrum: fast density-aware spectral clustering for single and multi-omic data
Poisson hurdle model-based method for clustering microbiome features
Figmop: a profile HMM to identify genes and bypass troublesome gene models in draft genomes
Measuring the spatial correlations of protein binding sites
MetaADEDB 2.0: a comprehensive database on adverse drug events
Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions
3D-equivariant graph neural networks for protein model quality assessment
SUBIM: a program for analysing the Kabat database and determining the variability subgroup of a new immunoglobulin sequence
Identification of metabolic network models from incomplete high-throughput datasets
Message from the ISCB: 2018 ISCB Accomplishments by a Senior Scientist Award
Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar
Fast protein binding site comparisons using visual words representation
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins
A heuristic algorithm solving the mutual-exclusivity-sorting problem
Analyzing user-generated online content for drug discovery: development and use of MedCrawler
Gemini: memory-efficient integration of hundreds of gene networks with high-order pooling
LogBTF: gene regulatory network inference using Boolean threshold network model from single-cell gene expression data
Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping
Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions
PathMiner: predicting metabolic pathways by heuristic search
Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris : zero-inflated Poisson regression models to predict abundance of undetected proteins
Oncotree2vec - a method for embedding and clustering of tumor mutation trees
ggCyto: next generation open-source visualization software for cytometry
DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network
ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Deciphering associations between gut microbiota and clinical factors using microbial modules
A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets
Sequence features of DNA binding sites reveal structural class of associated transcription factor
gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python
SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts
Characterizing and ranking computed metabolic engineering strategies
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences
Reconstruction of transcriptional dynamics from gene reporter data using differential equations
HCABAND: a computer program for the 2D-helical representation of protein sequences
Discrimination of outer membrane proteins using support vector machines
TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets
Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble
KIMI: Knockoff Inference for Motif Identification from molecular sequences with controlled false discovery rate
MatrixEpistasis: ultrafast, exhaustive epistasis scan for quantitative traits with covariate adjustment
Inferring delays in partially observed gene regulation processes
PROMALS: towards accurate multiple sequence alignments of distantly related proteins
Predicting functionality of protein-DNA interactions by integrating diverse evidence
FunImageJ: a Lisp framework for scientific image processing
MISS: a non-linear methodology based on mutual information for genetic association studies in both population and sib-pairs analysis
Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments
Markov chains improve the significance computation of overlapping genome annotations
SNAP: workbench management tool for evolutionary population genetic analysis
AMPA: an automated web server for prediction of protein antimicrobial regions
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics
Leveraging large language models to predict antibiotic resistance in Mycobacterium tuberculosis
Genetic Simulation Resources and the GSR Certification Program
RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures
ATV: display and manipulation of annotated phylogenetic
Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures
netClass: an R-package for network based, integrative biomarker signature discovery
Dalliance: interactive genome viewing on the web
Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes
An accurate paired sample test for count data
Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Steady-state modelling of metabolic flux between the tricarboxylic acid cycle and the glyoxylate bypass in Escherichia coli
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
HTSinfer: inferring metadata from bulk Illumina RNA-Seq libraries
Identification and visualization of differential isoform expression in RNA-seq time series
A suite of Perl modules for handling microarray data
Powerful differential expression analysis incorporating network topology for next-generation sequencing data
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation
J-Express: exploring gene expression data using Java
Identifying correct bacteriological vocabulary: software to look up RKC codes and statements
Updating RNA-Seq analyses after re-annotation
A blind and independent benchmark study for detecting differentially methylated regions in plants
A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity
FPV: Fast Protein Visualization Using Java 3DTM
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads
Spectral clustering of single-cell multi-omics data on multilayer graphs
PLncDB: plant long non-coding RNA database
Unraveling spatial domain characterization in spatially resolved transcriptomics with robust graph contrastive clustering
Post-translational modifications induce significant yet not extreme changes to protein structure
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
PanTools v3: functional annotation, classification and phylogenomics
ALTRE: workflow for defining ALTered Regulatory Elements using chromatin accessibility data
GMNN2CD: identification of circRNA-disease associations based on variational inference and graph Markov neural networks
Protein docking model evaluation by 3D deep convolutional neural networks
COMPASS: the COMPletely Arbitrary Sequence Simulator
Mouse Quantitative Proteomics Knowledgebase: reference protein concentration ranges in 20 mouse tissues using 5000 quantitative proteomics assays
ACTINN: automated identification of cell types in single cell RNA sequencing
A unifying network modeling approach for codon optimization
Panoptes: web-based exploration of large scale genome variation data
BioVAE: a pre-trained latent variable language model for biomedical text mining
Pathway discovery in metabolic networks by subgraph extraction
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data
MathSBML: a package for manipulating SBML-based biological models
Selection of human tissue-specific elementary flux modes using gene expression data
Large-scale entity representation learning for biomedical relationship extraction
A stochastic automaton model for simulating kinesin processivity
A hybrid machine-learning approach for segmentation of protein localization data
A robust peak detection method for RNA structure inference by high-throughput contact mapping
The FASTQ+ format and PISA
A dynamically growing self-organizing tree (DGSOT) for hierarchical clustering gene expression profiles
MACAT - microarray chromosome analysis tool
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
UniProt archive
nCal: an R package for non-linear calibration
bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks
A change-point model for identifying 3′UTR switching by next-generation RNA sequencing
Qualitative translation of relations from BioPAX to SBML qual
Aclust2.0: a revamped unsupervised R tool for Infinium methylation beadchips data analyses
Data reduction of isotope-resolved LC-MS spectra
Evolutionary inaccuracy of pairwise structural alignments
Message from the ISCB: 2017 ISCB Overton Prize Awarded to Christoph Bock
Multiple testing in genome-wide association studies via hidden Markov models
smallWig: parallel compression of RNA-seq WIG files
Protein structure topological comparison, discovery and matching service
Difference detection in LC-MS data for protein biomarker discovery
Graphic and DNA sequence interface for the pCP123 database system for managing recombinant DNA data
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification
CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
mFASD: a structure-based algorithm for discriminating different types of metal-binding sites
DeepMSPeptide: peptide detectability prediction using deep learning
ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes
High-dimensional quantile mediation analysis with application to a birth cohort study of mother-newborn pairs
Probability Map Viewer: near real-time probability map generator of serial block electron microscopy collections
FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data
Shaping the interaction landscape of bioactive molecules
Matrix completion with side information and its applications in predicting the antigenicity of influenza viruses
RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity
PGAT: a multistrain analysis resource for microbial genomes
Semi-automated update and cleanup of structural RNA alignment databases
GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data
CoC: a database of universally conserved residues in protein folds
PGA: post-GWAS analysis for disease gene identification
Digital extractor: analysis of digital differential display output
Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments
CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
Prediction of probable genes by Fourier analysis of genomic sequences
Systematic parameter estimation in data-rich environments for cell signalling dynamics
OnlineCall: fast online parameter estimation and base calling for illumina's next-generation sequencing
SRV: an open-source toolbox to accelerate the recovery of metabolic biomarkers and correlations from metabolic phenotyping datasets
MARD: a new method to detect differential gene expression in treatment-control time courses
GTC: how to maintain huge genotype collections in a compressed form
Structure-guided sequence representation learning for generalizable protein function prediction
VarNMF: non-negative probabilistic factorization with source variation
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions
spatialGE: quantification and visualization of the tumor microenvironment heterogeneity using spatial transcriptomics
Identification of deleterious synonymous variants in human genomes
Detecting putative orthologs
Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation
Identifying disease-associated SNP clusters via contiguous outlier detection
PASHEMOS: a versatile program written in Pascal to simulate patterns on the shells of molluscs, according to the Meinhardt model
VERA: agent-based modeling transmission of antibiotic resistance between human pathogens and gut microbiota
Spatial regulation dominates gene function in the ganglia chain
The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster
Gene recognition in eukaryotic DNA by comparison of genomic sequences
Codon adaptation index as a measure of dominating codon bias
Application of Bayesian Decomposition for analysing microarray data
Sample classification from protein mass spectrometry, by 'peak probability contrasts'