yusuke1997/dblp-id-title huggingface dataset:
Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets
Feasible-metabolic-pathway-exploration technique using chemical latent space
Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA
Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia
A generalized framework for controlling FDR in gene regulatory network inference
TopoGSA: network topological gene set analysis
ASTRAL: genome-scale coalescent-based species tree estimation
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
ThreaDom: extracting protein domain boundary information from multiple threading alignments
pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC
Phigaro: high-throughput prophage sequence annotation
An improved microcomputer program for finding gene- or gene family-specific oligonucleotides suitable as primers for polymerase chain reactions or as probes
Probabilistic single-individual haplotyping
The gputools package enables GPU computing in R
Metabolic systems cost-benefit analysis for interpreting network structure and regulation - Erratum
PMIpred: a physics-informed web server for quantitative protein-membrane interaction prediction
The rise and fall of supervised machine learning techniques
Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization
For antibody sequence generative modeling, mixture models may be all you need
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs
A novel network-based method for measuring the functional relationship between gene sets
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
SnapDock - template-based docking by Geometric Hashing
Xdigitise: visualization of hybridization experiments
A robust DF-REML framework for variance components estimation in genetic studies
De-Bruijn graph partitioning for scalable and accurate DNA storage processing
Full-length de novo viral quasispecies assembly through variation graph construction
A robust clustering algorithm for identifying problematic samples in genome-wide association studies
Enzyme annotation in UniProtKB using Rhea
CURC: a CUDA-based reference-free read compressor
Tailored gene array databases: applications in mechanistic toxicology
ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes
DEFOR: depth- and frequency-based somatic copy number alteration detector
Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices
Correction to: Biomedical evidence engineering for data-driven discovery
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain
MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences
High-quality annotation of promoter regions for 913 bacterial genomes
Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens
SciDataFlow: a tool for improving the flow of data through science
Gene set analysis: limitations in popular existing methods and proposed improvements
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures
Mining sequence annotation databanks for association patterns
Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques
Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study
Numt identification and removal with RtN!
TARO: tree-aggregated factor regression for microbiome data integration
Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects
A simple statistical significance test of window scores in large dot matrices obtained from protein or nucleic acid sequences
HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly
R 2 C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter
OLIGOGET - a computerized database system for controlling oligonucleotide production
Metabolite fingerprinting: detecting biological features by independent component analysis
WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules
GATE: software for the analysis and visualization of high-dimensional time series expression data
MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs)
SCA db: spinocerebellar ataxia candidate gene database
The search for a grammatical theory of gene regulation is formally justified by showing the inadequacy of context-free grammars
EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences
Fast and robust optical flow for time-lapse microscopy using super-voxels
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression
DeepCoil - a fast and accurate prediction of coiled-coil domains in protein sequences
Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes
PCA-based spatial domain identification with state-of-the-art performance
SLGNN: synthetic lethality prediction in human cancers based on factor-aware knowledge graph neural network
bioDBnet: the biological database network
QuACN: an R package for analyzing complex biological networks quantitatively
PolyMarker: A fast polyploid primer design pipeline
A link between H3K27me3 mark and exon length in the gene promoters of pluripotent and differentiated cells
iRSpot-EL: identify recombination spots with an ensemble learning approach
The LCD-Composer webserver: high-specificity identification and functional analysis of low-complexity domains in proteins
TaxoNN: ensemble of neural networks on stratified microbiome data for disease prediction
H 3 M 2 : detection of runs of homozygosity from whole-exome sequencing data
Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities
CPRiL: compound-protein relationships in literature
Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis
Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets
Integrated search and alignment of protein structures
Curse: building expression atlases and co-expression networks from public RNA-Seq data
YaHS: yet another Hi-C scaffolding tool
Decombinator V4: an improved AIRR compliant-software package for T-cell receptor sequence annotation?
Inferring Boolean network structure via correlation
Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data
PSIKO2: a fast and versatile tool to infer population stratification on various levels in GWAS
RNA inter-nucleotide 3D closeness prediction by deep residual neural networks
Functional module identification in protein interaction networks by interaction patterns
Inferring dynamic gene networks under varying conditions for transcriptomic network comparison
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests
Integrative gene set analysis of multi-platform data with sample heterogeneity
In silico phenotyping via co-training for improved phenotype prediction from genotype
Introducing dAUTObase: a first step towards the global scale geoepidemiology of autoimmune syndromes and diseases
Applicability of the multiple alignment algorithm for detection of weak patterns: periodically distributed DNA pattern as a study case
Group SCAD regression analysis for microarray time course gene expression data
Finding recurrent copy number alterations preserving within-sample homogeneity
Human interactome resource and gene set linkage analysis for the functional interpretation of biologically meaningful gene sets
GeneTrack - a genomic data processing and visualization framework
DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets
Assembly scaffolding with PE-contaminated mate-pair libraries
A simulation program to display specific digestion products of predicted RNA foldings
K2 and K 2 * : efficient alignment-free sequence similarity measurement based on Kendall statistics
Chimira: analysis of small RNA sequencing data and microRNA modifications
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers
Census of halide-binding sites in protein structures
CCharPPI web server: computational characterization of protein-protein interactions from structure
pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks
Deconvoluting essential gene signatures for cancer growth from genomic expression in compound-treated cells
Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model
Advancing admixture graph estimation via maximum likelihood network orientation
A modified Chou and Fasman protein structure algorithm
Refinement of optical map assemblies
DFinder: a novel end-to-end graph embedding-based method to identify drug-food interactions
IlluminaGUI: Graphical User Interface for analyzing gene expression data generated on the Illumina platform
Normalized coefficient of variation (nCV): a method to evaluate circadian clock robustness in population scale data
Analysis of one-dimensional electrophoregrams
The strength of chemical linkage as a criterion for pruning metabolic graphs
QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images
DeepGOPlus: improved protein function prediction from sequence
Normalization and noise reduction for single cell RNA-seq experiments
Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes
In silico identification of rescue sites by double force scanning
Measuring the distance between multiple sequence alignments
gExcite: a start-to-end framework for single-cell gene expression, hashing, and antibody analysis
Selfish: discovery of differential chromatin interactions via a self-similarity measure
TALAIA: a 3D visual dictionary for protein structures
A note on the false discovery rate and inconsistent comparisons between experiments
SCell: integrated analysis of single-cell RNA-seq data
PALADIN: protein alignment for functional profiling whole metagenome shotgun data
ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins
Online interactive analysis of protein structure ensembles with Bio3D-web
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes
Computational inference of grammars for larger-than-gene structures from annotated gene sequences
A Macintosh program for the versatile generation of random nucleic acid sequences and their structural analysis
Screening novel drug candidates for Alzheimer's disease by an integrated network and transcriptome analysis
Biophysical informatics reveals distinctive phenotypic signatures and functional diversity of single-cell lineages
Coracle - a machine learning framework to identify bacteria associated with continuous variables
CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
Combining multiple tools outperforms individual methods in gene set enrichment analyses
PmliPred: a method based on hybrid model and fuzzy decision for plant miRNA-lncRNA interaction prediction
PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis
AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes
Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design
FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
Bayesian rule learning for biomedical data mining
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets
RNALoc-LM: RNA subcellular localization prediction using pre-trained RNA language model
Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families
CATH functional families predict functional sites in proteins
ManyFold: an efficient and flexible library for training and validating protein folding models
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness
SIRIUS: decomposing isotope patterns for metabolite identification
Analysis of transcription control signals using artificial neural networks
Noise Sampling Method: An ANOVA Approach Allowing Robust Selection of Differentially Regulated Genes Measured by DNA Microarrays
A cluster robustness score for identifying cell subpopulations in single cell gene expression datasets from heterogeneous tissues and tumors
PHOCOS: inferring multi-feature phenotypic crosstalk networks
Improved protein model quality assessment by integrating sequential and pairwise features using deep learning
KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways
Conditional generative adversarial network for gene expression inference
Deep graph representations embed network information for robust disease marker identification
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2): 229]
CoMeBack: DNA methylation array data analysis for co-methylated regions
LiveKraken--real-time metagenomic classification of illumina data
Covariate-adjusted heatmaps for visualizing biological data via correlation decomposition
MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
A computer program for the generation of problems in genetics for teaching purposes
Integrating physics in deep learning algorithms: a force field as a PyTorch module
Inferring gene regulatory networks by ANOVA
ReactPRED: a tool to predict and analyze biochemical reactions
An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions
LS Bound based gene selection for DNA microarray data
Easy NanoString nCounter data analysis with the NanoTube
A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis
dtangle: accurate and robust cell type deconvolution
EpiCompare: an online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features
fMLC: fast multi-level clustering and visualization of large molecular datasets
Good spaced seeds for homology search
Structure-based de novo prediction of zinc-binding sites in proteins of unknown function
Interactive data input into the GeneNet database
Ionmob: a Python package for prediction of peptide collisional cross-section values
Bioinformatics in Australia
Two-dimensional abstract representations (signatures) of proteins
BalestraWeb: efficient online evaluation of drug-target interactions
R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
Foldcomp: a library and format for compressing and indexing large protein structure sets
TFmodeller: comparative modelling of protein-DNA complexes
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
Q-RT-PCR: data analysis software for measurement of gene expression by competitive RT-PCR
G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss
GS-align for glycan structure alignment and similarity measurement
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data
Fast sinogram computation and the sinogram-based alignment of images
A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
DeepLGP: a novel deep learning method for prioritizing lncRNA target genes
Canvas SPW: calling de novo copy number variants in pedigrees
BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways
CovRadar: continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
Augmented training of hidden Markov models to recognize remote homologs via simulated evolution
DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network
SweepFinder2: increased sensitivity, robustness and flexibility
Enhancing predictions of protein stability changes induced by single mutations using MSA-based language models
Toward a statistically explicit understanding of de novo sequence assembly
A visual framework for sequence analysis using n -grams and spectral rearrangement
REJECTOR: software for population history inference from genetic data via a rejection algorithm
Effect of tokenization on transformers for biological sequences
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets
MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis
Robust joint clustering of multi-omics single-cell data via multi-modal high-order neighborhood Laplacian matrix optimization
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins
BooleSim: an interactive Boolean network simulator
NetworkView : 3D display and analysis of protein·RNA interaction networks
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments
GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes
Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks
Self-supervised semantic segmentation of retinal pigment epithelium cells in flatmount fluorescent microscopy images
Correction to: Integrative analysis of individual-level data and high-dimensional summary statistics
CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms
Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection
Protein intrinsically disordered regions have a non-random, modular architecture
Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding
SKINK: a web server for string kernel based kink prediction in α-helices
Graphical data mining of cancer mechanisms with SEMA
Cram-JS: reference-based decompression in node and the browser
Optimization of ribosomal RNA profile alignments
Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates
Improved performance in protein secondary structure prediction by inhomogeneous score combination
A statistical approach using network structure in the prediction of protein characteristics
Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif
FramePlus: aligning DNA to protein sequences
Engene: the processing and exploratory analysis of gene expression data
ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications
Base-pair resolution detection of transcription factor binding site by deep deconvolutional network
Assessing the fit of the multi-species network coalescent to multi-locus data
NetAcet: prediction of N-terminal acetylation sites
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination
The Journal Bioinformatics, key medium for computational biology
doubletD: detecting doublets in single-cell DNA sequencing data
The EBI SRS server-recent developments
HUM calculator and HUM package for R: easy-to-use software tools for multicategory receiver operating characteristic analysis
SpikePro: a webserver to predict the fitness of SARS-CoV-2 variants
Spot shape modelling and data transformations for microarrays
Isoform-level gene expression patterns in single-cell RNA-sequencing data
SCORPIO: a utility for defining and classifying mutation constellations of virus genomes
PyRanges: efficient comparison of genomic intervals in Python
Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks
Pokefind: a novel topological filter for use with protein structure prediction
The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR
Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions
Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform
CONICS integrates scRNA-seq with DNA sequencing to map gene expression to tumor sub-clones
Predicting G protein-coupled receptor downstream signaling by tissue expression
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification
Consistency enhancement of model prediction on document-level named entity recognition
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships
HOMGL - comparing genelists across species and with different accession numbers
Efficient RNA pairwise structure comparison by SETTER method
Optimal alignment between groups of sequences and its application to multiple sequence alignment
BIMA V3: an aligner customized for mate pair library sequencing
libRoadRunner 2.0: a high performance SBML simulation and analysis library
Discriminative and informative features for biomolecular text mining with ensemble feature selection
Pathway analysis of high-throughput biological data within a Bayesian network framework
COVID-19 Docking Server: a meta server for docking small molecules, peptides and antibodies against potential targets of COVID-19
Jenti: an efficient tool for mining complex inbred genealogies
High-order neural networks and kernel methods for peptide-MHC binding prediction
TRMP: a database of therapeutically relevant multiple pathways
Signaling gateway molecule pages - a data model perspective
pIPHULA - parallel inference of population parameters using a likelihood approach