yusuke1997/dblp-id-title huggingface dataset:
Discovering relational-based association rules with multiple minimum supports on microarray datasets
Spliceman - a computational web server that predicts sequence variations in pre-mRNA splicing
Estimating p -values in small microarray experiments
Elemental composition determination based on MS n
An integrative approach for fine-mapping chromatin interactions
RNA-seq differential expression studies: more sequence or more replication?
Learning gene regulatory networks from gene expression measurements using non-parametric molecular kinetics
Watermarking sexually reproducing diploid organisms
IDEOM: an Excel interface for analysis of LC-MS-based metabolomics data
DMDM: domain mapping of disease mutations
An improved encoding of genetic variation in a Burrows-Wheeler transform
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments
CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
metahdep : meta-analysis of hierarchically dependent gene expression studies
Finding consistent disease subnetworks using PFSNet
IntelliPy: a GUI for analyzing IntelliCage data
Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology
Dblox: a genome-wide test for ancient segmental duplication
ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data
An omnibus test for differential distribution analysis of microbiome sequencing data
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites
Phylogenomic inference of protein molecular function: advances and challenges
Inference of gene regulatory networks based on nonlinear ordinary differential equations
CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data
MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness
Identification of disease-associated loci using machine learning for genotype and network data integration
deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding
orfipy: a fast and flexible tool for extracting ORFs
Promoter modeling: the case study of mammalian histone promoters
A simple algorithm to infer gene duplication and speciation events on a gene tree
A weighted least-squares approach for inferring phylogenies from incomplete distance matrices
cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
Reconstructing 16S rRNA genes in metagenomic data
Recognition and analysis of protein-coding genes in severe acute respiratory syndrome associated coronavirus
Evolutionary profiles improve protein-protein interaction prediction from sequence
SuperDrug: a conformational drug database
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data
ENVIRON: a software package to compare protein three-dimensional structures with homologous sequences using local structural motifs
IMID: integrated molecular interaction database
Assembling short reads from jumping libraries with large insert sizes
survcomp : an R/Bioconductor package for performance assessment and comparison of survival models
PHI-DAC: protein homology database through dihedral angle conservation
PATO: genome-wide prediction of lncRNA-DNA triple helices
Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition
ViMRT: a text-mining tool and search engine for automated virus mutation recognition
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes
2dGBH: Two-dimensional group Benjamini-Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data
From pull-down data to protein interaction networks and complexes with biological relevance
Fast large-scale clustering of protein structures using Gauss integrals
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation
SVJedi: genotyping structural variations with long reads
GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk
Rotation equivariant and invariant neural networks for microscopy image analysis
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
MamMiBase: a mitochondrial genome database for mammalian phylogenetic studies
Universal dynamical properties preclude standard clustering in a large class of biochemical data
ROICellTrack: a deep learning framework for integrating cellular imaging modalities in subcellular spatial transcriptomic profiling of tumor tissues
NMJ Analyser: a novel method to quantify neuromuscular junction morphology in zebrafish
Padhoc: a computational pipeline for pathway reconstruction on the fly
The functional therapeutic chemical classification system
Performance of gene expression analyses using de novo assembled transcripts in polyploid species
Fast-SL: an efficient algorithm to identify synthetic lethal sets in metabolic networks
DEAttentionDTA: protein-ligand binding affinity prediction based on dynamic embedding and self-attention
ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage
Efficient gradient-based parameter estimation for dynamic models using qualitative data
AARDVARK: an automated reversion detector for variants affecting resistance kinetics
BacPaCS - Bacterial Pathogenicity Classification via Sparse-SVM
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks
Determining optical mapping errors by simulations
Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them
Quantification of fibrous spatial point patterns from single-molecule localization microscopy (SMLM) data
Hardware acceleration of processing of mass spectrometric data for proteomics
De novo pattern discovery enables robust assessment of functional consequences of non-coding variants
sInterBase: a comprehensive database of Escherichia coli sRNA-mRNA interactions
Manifold classification of neuron types from microscopic images
Genome measures used for quality control are dependent on gene function and ancestry
Web-based kinetic modelling using JWS Online
INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments
CMfinder - a covariance model based RNA motif finding algorithm
CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations
VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability
Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models
ISMB 2020 proceedings
Consensus features nested cross-validation
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures
GWAS quality score for evaluating associated regions in GWAS analyses
3Dmol.js: molecular visualization with WebGL
Reduced space hidden Markov model training
Designing patterns for profile HMM search
BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods
Using sequence compression to speedup probabilistic profile matching
Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings, with drug-repurposing applications in COVID-19
Bayesian estimation of genetic regulatory effects in high-throughput reporter assays
A computational method to preclude multistationarity in networks of interacting species
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data
Metapone: a Bioconductor package for joint pathway testing for untargeted metabolomics data
RNAiFold2T: Constraint Programming design of thermo-IRES switches
ProtEST: protein multiple sequence alignments from expressed sequence tags
Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays
De novo protein design by an energy function based on series expansion in distance and orientation dependence
GfaViz: flexible and interactive visualization of GFA sequence graphs
Rarity: discovering rare cell populations from single-cell imaging data
Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models
Automatic recognition of ligands in electron density by machine learning
PISCES: a protein sequence culling server
Graph convolutional network-based feature selection for high-dimensional and low-sample size data
WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering
The International Society for Computational Biology and WikiProject Computational Biology: celebrating 10 years of collaboration towards open access
On the bias of H-scores for comparing biclusters, and how to correct it
DESpace : spatially variable gene detection via differential expression testing of spatial clusters
BERT-GT: cross-sentence n-ary relation extraction with BERT and Graph Transformer
BDTcomparator: a program for comparing binary classifiers
Using credibility intervals instead of hypothesis tests in SAGE analysis
HiCLift: a fast and efficient tool for converting chromatin interaction data between genome assemblies
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
Comparing DNA integration site clusters with scan statistics
SecretSanta: flexible pipelines for functional secretome prediction
NetSets.js: a JavaScript framework for compositional assessment and comparison of biological networks through Venn-integrated network diagrams
Statistical inference of protein structural alignments using information and compression
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
NetAlign: a web-based tool for comparison of protein interaction networks
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach
DETECT - a Density Estimation Tool for Enzyme ClassificaTion and its application to Plasmodium falciparum
Probabilistic assignment of formulas to mass peaks in metabolomics experiments
FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals
RNA-Seq gene expression estimation with read mapping uncertainty
mLiftOver: harmonizing data across Infinium DNA methylation platforms
ProteinBERT: a universal deep-learning model of protein sequence and function
Nextstrain: real-time tracking of pathogen evolution
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
An efficient method to estimate the optimum regularization parameter in RLDA
Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles
MultiDTI: drug-target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network
estMOI: estimating multiplicity of infection using parasite deep sequencing data
Path2Surv: Pathway/gene set-based survival analysis using multiple kernel learning
SSLpheno: a self-supervised learning approach for gene-phenotype association prediction using protein-protein interactions and gene ontology data
Ultrafast SNP analysis using the Burrows-Wheeler transform of short-read data
MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data
Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data
Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network
Spatial quantification of the synaptic activity phenotype across large populations of neurons with Markov random fields
Drug repositioning with adaptive graph convolutional networks
A novel non-overlapping bi-clustering algorithm for network generation using living cell array data
A graph regularized generalized matrix factorization model for predicting links in biomedical bipartite networks
The Biopolymer Markup Language
Galaxy Portal: interacting with the galaxy platform through mobile devices
Empowering biologists with multi-omics data: colorectal cancer as a paradigm
Adaptive stochastic-deterministic chemical kinetic simulations
Sequence-structure relations of biopolymers
The Gene Interaction Miner: a new tool for data mining contextual information for protein-protein interaction analysis
PathScore: a web tool for identifying altered pathways in cancer data
Computer program Jamsek combining statistical and stereochemical rules for the prediction of protein secondary structure
BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications
Significance analysis of groups of genes in expression profiling studies
Integrated displays of aligned amino acid sequences and protein structures
A method for detection of differential gene expression in the presence of inter-individual variability in response
A new correlation clustering method for cancer mutation analysis
tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets
CVD: the intestinal crypt/villus in situ hybridization database
Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana
HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration
GenomeLaser: fast and accurate haplotyping from pedigree genotypes
limmaGUI: A graphical user interface for linear modeling of microarray data
CCPLS reveals cell-type-specific spatial dependence of transcriptomes in single cells
Thresher: an improved algorithm for peak height thresholding of microbial community profiles
Analysis of context of 5'-splice site sequences in mammalian mRNA precursors by subclass method
A unifying framework for rare variant association testing in family-based designs, including higher criticism approaches, SKATs, and burden tests
Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
Target-Decoy MineR for determining the biological relevance of variables in noisy datasets
3USS: a web server for detecting alternative 3′UTRs from RNA-seq experiments
Enhanced methods to detect haplotypic effects on gene expression
Efficient sorting of genomic permutations by translocation, inversion and block interchange
DART: a fast and accurate RNA-seq mapper with a partitioning strategy
Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations
MetBP: a software tool for detection of interaction between metal ion-RNA base pairs
Gene expression inference with deep learning
Profile scanning for three-dimensional structural patterns in protein sequences
Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools
Structural analogue-based protein structure domain assembly assisted by deep learning
Improving missing value estimation in microarray data with gene ontology
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems
Accurate and adaptive imputation of summary statistics in mixed-ethnicity cohorts
Detection of crossover points in detrended fluctuation analysis: an application to EEG signals of patients with epilepsy
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques
Classification in biological networks with hypergraphlet kernels
CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data
Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations
MIST: a user-friendly metabolic simulator
ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion
JBrowse Jupyter: a Python interface to JBrowse 2
A novel domain suggests a ciliary function for ASPM , a brain size determining gene
Vistla: identifying influence paths with information theory
Seed-based INTARNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
Reliable prediction of protein thermostability change upon double mutation from amino acid sequence
How frugal is mother nature with haplotypes?
ORCA: a comprehensive bioinformatics container environment for education and research
Thermodynamic properties of DNA sequences: characteristic values for the human genome
Probing the binding affinity of amyloids to reduce toxicity of oligomers in diabetes
Single-sample landscape entropy reveals the imminent phase transition during disease progression
RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality
GOfetcher: a database with complex searching facility for gene ontology
Measuring guide-tree dependency of inferred gaps in progressive aligners
PGAP: pan-genomes analysis pipeline
OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data
Automated inference of Boolean models from molecular interaction maps using CaSQ
Clustering FunFams using sequence embeddings improves EC purity
Eigenvalue analysis of amino acid substitution matrices reveals a sharp transition of the mode of sequence conservation in proteins
CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data
bbeaR: an R package and framework for epitope-specific antibody profiling
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data
SWAN: sliding window analysis of nucleotide sequence variability
SPLINDID: a semi-parametric, model-based method for obtaining transcription rates and gene regulation parameters from genomic and proteomic expression profiles
BioGuideSRS: querying multiple sources with a user-centric perspective
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes
Bayesian mixture model based clustering of replicated microarray data
CycSim - an online tool for exploring and experimenting with genome-scale metabolic models
HiTC: exploration of high-throughput 'C' experiments
A quantitative map of protein sequence space for the cis-defensin superfamily
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis
Nucleotide composition string selection in HIV-1 subtyping using whole genomes
Transcompp: understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions
Dro PhEA: Drosophila phenotype enrichment analysis for insect functional genomics
GAN-based data augmentation for transcriptomics: survey and comparative assessment
Using an alignment of fragment strings for comparing protein structures
JEPEG: a summary statistics based tool for gene-level joint testing of functional variants
Adding sequence context to a Markov background model improves the identification of regulatory elements
Robust prediction of clinical outcomes using cytometry data
Integrating phylogenetic and functional data in microbiome studies
Integrative mixture of experts to combine clinical factors and gene markers
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
Extracting 3D cell parameters from dense tissue environments: application to the development of the mouse heart
Modelling BioNano optical data and simulation study of genome map assembly
Deep learning identifies and quantifies recombination hotspot determinants
Unveil cis -acting combinatorial mRNA motifs by interpreting deep neural network
Hi-Enhancer: a two-stage framework for prediction and localization of enhancers based on Blending-KAN and Stacking-Auto models
Dissect: detection and characterization of novel structural alterations in transcribed sequences
svpluscnv: analysis and visualization of complex structural variation data
GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations
Improved VCF normalization for accurate VCF comparison
ProbeRating: a recommender system to infer binding profiles for nucleic acid-binding proteins
Site-specific evolutionary rates in proteins are better modeled as non-independent and strictly relative
MeltDB 2.0-advances of the metabolomics software system
PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways
Two-phase differential expression analysis for single cell RNA-seq
Context similarity scoring improves protein sequence alignments in the midnight zone
Power to detect selective allelic amplification in genome-wide scans of tumor data
SYMMETREE: whole-tree analysis of differential diversification rates
De novo transcriptome assembly with ABySS
EPO-KB: a searchable knowledge base of biomarker to protein links
Predicting survival from microarray data - a comparative study
Detecting subnetwork-level dynamic correlations
GaggleBridge : collaborative data analysis
A Bayesian approach to the alignment of mass spectra
DELFOS - drug efficacy leveraging forked and specialized networks - benchmarking scRNA-seq data in multi-omics-based prediction of cancer sensitivity
AFRbase: a database of protein mutations responsible for antifungal resistance
GT-Scan: identifying unique genomic targets
A wholly defined Agilent microarray spike-in dataset
Integrative random forest for gene regulatory network inference
Generalized random set framework for functional enrichment analysis using primary genomics datasets
Nebula - a web-server for advanced ChIP-seq data analysis
CMView: Interactive contact map visualization and analysis
Self-interaction of transmembrane helices representing pre-clusters from the human single-span membrane proteins
Tissue-specific prediction of directly regulated genes
TreesimJ: a flexible, forward time population genetic simulator
SCD Finder , a Web-based tool for the identification of putative novel ATM and ATR targets
Repulsive parallel MCMC algorithm for discovering diverse motifs from large sequence sets
Expression-based prediction of human essential genes and candidate lncRNAs in cancer cells
Reliability-Oriented bioinformatic networks visualization
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
An ensemble of K-local hyperplanes for predicting protein-protein interactions
HAPGEN2: simulation of multiple disease SNPs
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets
synbreed: a framework for the analysis of genomic prediction data using R
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Sul-BertGRU: an ensemble deep learning method integrating information entropy-enhanced BERT and directional multi-GRU for S-sulfhydration sites prediction
Bigmelon: tools for analysing large DNA methylation datasets
Genomic data visualization on the Web