yusuke1997/dblp-id-title huggingface dataset:
Fast and scalable querying of eukaryotic linear motifs with gget elm
Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks
Polynomial model approach for resynchronization analysis of cell-cycle gene expression data
On the effectiveness of compact biomedical transformers
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data
Editorial. The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB'99)
Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
Information-optimal genome assembly via sparse read-overlap graphs
MetWork: a web server for natural products anticipation
mRMRe: an R package for parallelized mRMR ensemble feature selection
SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names
A collaborative filtering-based approach to biomedical knowledge discovery
BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics
Adjustment of systematic microarray data biases
BNArray : an R package for constructing gene regulatory networks from microarray data by using Bayesian network
CGAS: comparative genomic analysis server
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
Sequencing data discovery with MetaSeek
Automated exploration of gene ontology term and pathway networks with ClueGO-REST
Simulation-based estimation of branching models for LTR retrotransposons
Mining complex genotypic features for predicting HIV-1 drug resistance
Bayesian robust analysis for genetic architecture of quantitative traits
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Contextual analysis of RNAi-based functional screens using interaction networks
SM2miR: a database of the experimentally validated small molecules' effects on microRNA expression
Generalizable sgRNA design for improved CRISPR/Cas9 editing efficiency
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
Improving conformational searches by geometric screening
Diffusion maps for high-dimensional single-cell analysis of differentiation data
The COVID-19 Ontology
Neural inductive matrix completion with graph convolutional networks for miRNA-disease association prediction
FastLSU: a more practical approach for the Benjamini-Hochberg FDR controlling procedure for huge-scale testing problems
Removing redundancy in SWISS-PROT and TrEMBL
Prediction of unfolded segments in a protein sequence based on amino acid composition
PARODS - a study of parallel algorithms for ordering DNA sequences
Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
A deep learning method to predict bacterial ADP-ribosyltransferase toxins
CellTrack: an open-source software for cell tracking and motility analysis
EMBL-search: a CD-ROM based database query system
Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites
Term-BLAST-like alignment tool for concept recognition in noisy clinical texts
The role of proteosome-mediated proteolysis in modulating potentially harmful transcription factor activity in Saccharomyces cerevisiae
SNPsnap: a Web-based tool for identification and annotation of matched SNPs
The SEQANAL and SEQTALK programs: a new method of access to high- resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer
pyDockEneRes: per-residue decomposition of protein-protein docking energy
al3c : high-performance software for parameter inference using Approximate Bayesian Computation
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations
Study of coordinative gene expression at the biological process level
Incorporating hierarchical information into multiple instance learning for patient phenotype prediction with single-cell RNA-sequencing data
Measuring the similarity of protein structures by means of the universal similarity metric
RETRACTED: LFQC: a lossless compression algorithm for FASTQ files
nEASE: a method for gene ontology subclassification of high-throughput gene expression data
TRAP: automated classification, quantification and annotation of tandemly repeated sequences
Identification of novel phosphorylation modification sites in human proteins that originated after the human-chimpanzee divergence
Estimating the posterior probability that genome-wide association findings are true or false
FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
A simple method of hidden-line removal in three-dimensional modelling: hiding the problem behind filled polygons
TALC: Transcript-level Aware Long-read Correction
phylostratr: a framework for phylostratigraphy
Parallelization of a local similarity algorithm
miMsg: a target enrichment algorithm for predicted miR-mRNA interactions based on relative ranking of matched expression data
GOSLING: a rule-based protein annotator using BLAST and GO
The database of epoxide hydrolases and haloalkane dehalogenases: one structure, many functions
LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines
Heterogeneous networks integration for disease-gene prioritization with node kernels
GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank
Transcript structure and domain display: a customizable transcript visualization tool
Optimal phylogenetic reconstruction of insertion and deletion events
PubMed Assistant: a biologist-friendly interface for enhanced PubMed search
Dragon Promoter Mapper (DPM): a Bayesian framework for modelling promoter structures
A new progressive-iterative algorithm for multiple structure alignment
TVAR: assessing tissue-specific functional effects of non-coding variants with deep learning
SEED: efficient clustering of next-generation sequences
PATO: Pangenome Analysis Toolkit
Comment on 'protein-protein binding affinity prediction from amino acid sequence'
Effective similarity measures for expression profiles
Estimation of dynamic SNP-heritability with Bayesian Gaussian process models
GEL: a novel genotype calling algorithm using empirical likelihood
SpliceAI-10k calculator for the prediction of pseudoexonization, intron retention, and exon deletion
LONGO: an R package for interactive gene length dependent analysis for neuronal identity
Prediction of kinetics of protein folding with non-redundant contact information
IS: a web-site for intron statistics
circlize implements and enhances circular visualization in R
PopGeV: a web-based large-scale population genome browser
scRMD: imputation for single cell RNA-seq data via robust matrix decomposition
TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction
A curated rotamer library for common post-translational modifications of proteins
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks
ActivePPI: quantifying protein-protein interaction network activity with Markov random fields
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats
A mathematical model describing the mechanical kinetics of kinesin stepping
Using isoelectric point to determine the pH for initial protein crystallization trials
Gene-based association tests using GWAS summary statistics
Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings
Evaluating contributions of natural language parsers to protein-protein interaction extraction
Megadepth: efficient coverage quantification for BigWigs and BAMs
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
The START App: a web-based RNAseq analysis and visualization resource
Oligodb-interactive design of oligo DNA for transcription profiling of human genes
TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators
Dot2dot: accurate whole-genome tandem repeats discovery
Oncopression: gene expression compendium for cancer with matched normal tissues
PhenoRank: reducing study bias in gene prioritization through simulation
Motif Tool Manager: a web-based framework for motif discovery
Chromatin accessibility prediction via a hybrid deep convolutional neural network
A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy
Adaptive gene- and pathway-trait association testing with GWAS summary statistics
SAD - a normalized structural alignment database: improving sequence-structure alignments
Bisque: a platform for bioimage analysis and management
Empirical profile mixture models for phylogenetic reconstruction
Convex hull as diagnostic tool in single-molecule localization microscopy
Predicting target genes of non-coding regulatory variants with IRT
Automatic prediction of protein domains from sequence information using a hybrid learning system
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations
SPRISS: approximating frequent k -mers by sampling reads, and applications
SAMNetWeb: identifying condition-specific networks linking signaling and transcription
DPre: computational identification of differentiation bias and genes underlying cell type conversions
An extensible network query unification system for biological databases
Fast parametric time warping of peak lists
aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences
GreedyMini: generating low-density DNA minimizers
KMC 2: fast and resource-frugal k -mer counting
NextGenMap: fast and accurate read mapping in highly polymorphic genomes
PROBE: analysis and visualization of protein block-level evolution
MetAmp: combining amplicon data from multiple markers for OTU analysis
MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform
Genetic Simulation Library
VAGUE: a graphical user interface for the Velvet assembler
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
Detecting interspecific recombination with a pruned probabilistic divergence measure
OrfM: a fast open reading frame predictor for metagenomic data
Simulome: a genome sequence and variant simulator
PaVESy: Pathway Visualization and Editing System
Automatically classifying sentences in full-text biomedical articles into Introduction, Methods, Results and Discussion
Optimization-based decoding of Imaging Spatial Transcriptomics data
Nonparametric Bayesian inference for perturbed and orthologous gene regulatory networks
REVCOM: a robust Bayesian method for evolutionary rate estimation
MinReact: a systematic approach for identifying minimal metabolic networks
Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries
Comment on 'Evaluation of the gene-specific dye bias in cDNA microarray experiments'
COSMOS: Python library for massively parallel workflows
On patterns and re-use in bioinformatics databases
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data
Optimization of alignment-based methods for taxonomic binning of metagenomics reads
SeeCiTe: a method to assess CNV calls from SNP arrays using trio data
FDM: a graph-based statistical method to detect differential transcription using RNA-seq data
ClonArch: visualizing the spatial clonal architecture of tumors
Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics
SOPanG: online text searching over a pan-genome
Natural similarity measures between position frequency matrices with an application to clustering
Recognition of CRISPR/Cas9 off-target sites through ensemble learning of uneven mismatch distributions
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
rqt: an R package for gene-level meta-analysis
An evaluation of new criteria for CpG islands in the human genome as gene markers
Logical transformation of genome-scale metabolic models for gene level applications and analysis
Model-based detection of alternative splicing signals
NMRNet: a deep learning approach to automated peak picking of protein NMR spectra
Simple and fast alignment of metabolic pathways by exploiting local diversity
Predicting colorectal cancer tumor mutational burden from histopathological images and clinical information using multi-modal deep learning
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses
Antimony: a modular model definition language
Tagging gene and protein names in biomedical text
VISAR: an interactive tool for dissecting chemical features learned by deep neural network QSAR models
LFQC: A lossless compression algorithm for FASTQ files
BiC: a web server for calculating bimodality of coexpression between gene and protein networks
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data
DeepSec: a deep learning framework for secreted protein discovery in human body fluids
iAnn: an event sharing platform for the life sciences
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images
Two or three myths about bioinformatics
A novel copy number variants kernel association test with application to autism spectrum disorders studies
Molecular signatures that can be transferred across different omics platforms
IsomiR Bank: a research resource for tracking IsomiRs
MAFin: motif detection in multiple alignment files
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks
Minimizing the overlap problem in protein NMR: a computational framework for precision amino acid labeling
A framework for gene expression analysis
Pathway analysis through mutual information
Building protein structure-specific rotamer libraries
Bandage: interactive visualization of de novo genome assemblies
Cell type matching across species using protein embeddings and transfer learning
Domain organization within repeated DNA sequences: application to the study of a family of transposable elements
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data
Graph accordance of next-generation sequence assemblies
LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications
TEclass - a tool for automated classification of unknown eukaryotic transposable elements
Empirical Bayes conditional independence graphs for regulatory network recovery
A de novo metagenomic assembly program for shotgun DNA reads
MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets
Fast and scalable Wasserstein-1 neural optimal transport solver for single-cell perturbation prediction
PartiGene-constructing partial genomes
PEPred-Suite: improved and robust prediction of therapeutic peptides using adaptive feature representation learning
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
MutBERT: probabilistic genome representation improves genomics foundation models
EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks
Polyketide synthase genes and the natural products potential of Dictyostelium discoideum
Dasty3, a WEB framework for DAS
Fast and sensitive taxonomic assignment to metagenomic contigs
A knowledge-based approach for predicting gene-disease associations
Improving false discovery rate estimation
DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species
A novel specific edge effect correction method for RNA interference screenings
MP-GeneticSynth: inferring biological network regulations from time series
DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence
Fuzzy J-Means and VNS methods for clustering genes from microarray data
Full-length de novo protein structure determination from cryo-EM maps using deep learning
Meta-DP: domain prediction meta-server
An interactive power analysis tool for microarray hypothesis testing and generation
Accurate detection of chimeric contigs via Bionano optical maps
MLNGCF: circRNA-disease associations prediction with multilayer attention neural graph-based collaborative filtering
SCOP: a novel scaffolding algorithm based on contig classification and optimization
Computational probing protein-protein interactions targeting small molecules
mCSM: predicting the effects of mutations in proteins using graph-based signatures
Modeling multi-cellular behavior in epidermal tissue homeostasis via finite state machines in multi-agent systems
Batch effects correction for microbiome data with Dirichlet-multinomial regression
integrOmics: an R package to unravel relationships between two omics datasets
Bonnie Berger named ISCB 2019 ISCB Accomplishments by a Senior Scientist Award recipient
TopEnzyme: a framework and database for structural coverage of the functional enzyme space
Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
Model annotation for synthetic biology: automating model to nucleotide sequence conversion
DysRegSig: an R package for identifying gene dysregulations and building mechanistic signatures in cancer
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps
AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology
Hybrid spatial Gillespie and particle tracking simulation
Gene selection in microarray survival studies under possibly non-proportional hazards
G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes
SynLinker: an integrated system for designing linkers and synthetic fusion proteins
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information
In silico error correction improves cfDNA mutation calling
HIVID2: an accurate tool to detect virus integrations in the host genome
Estimation and filtering of potential protein-protein docking positions
SNPdbe: constructing an nsSNP functional impacts database
Comparing clustering and pre-processing in taxonomy analysis
Multiple-rule bias in the comparison of classification rules
Similarities and differences of gene expression in yeast stress conditions
VEF: a variant filtering tool based on ensemble methods
FASTRAL: improving scalability of phylogenomic analysis
SKSV: ultrafast structural variation detection from circular consensus sequencing reads
Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity
SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells
EvoEF2: accurate and fast energy function for computational protein design
Predicting protein function: a versatile tool for the Apple Macintosh
VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization
Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data
RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads
A novel sequence alignment algorithm based on deep learning of the protein folding code
A new summarization method for affymetrix probe level data
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
OMA Browser - Exploring orthologous relations across 352 complete genomes
A simple add-on algorithm to extend one-dimensional finite difference diffusion calculations to include charge coupling
An efficient method for the detection and elimination of systematic error in high-throughput screening
Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing
tCal: transcriptional probability calculator using thermodynamic model
Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach
Structural exon database, SEDB, mapping exon boundaries on multiple protein structures
CAMIL: channel attention-based multiple instance learning for whole slide image classification
A simple tool to search for sequence motifs that are conserved in BLAST outputs
The locality dilemma of Sankoff-like RNA alignments
Cancer survival prediction based on soft-label guided contrastive learning and global feature fusion
Sincell : an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq
ProteoDisco: a flexible R approach to generate customized protein databases for extended search space of novel and variant proteins in proteogenomic studies
Modularized learning of genetic interaction networks from biological annotations and mRNA expression data
ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring
A multivariate test of association
Correction to: Online bias-aware disease module mining with ROBUST-Web
Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data
BioModels Parameters: a treasure trove of parameter values from published systems biology models
PineSAP - sequence alignment and SNP identification pipeline
Scaffolding low quality genomes using orthologous protein sequences
In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'
Bayesian ranking of biochemical system models
Computational modeling of the expansion of human cord blood CD133 + hematopoietic stem/progenitor cells with different cytokine combinations
Intensity quantile estimation and mapping - a novel algorithm for the correction of image non-uniformity bias in HCS data
Tracing evolutionary pressure
GeneHuggers: database mining and application connectivity tools for subsequence analyses of the human genome
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors
Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials
Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays
Divisive Correlation Clustering Algorithm (DCCA) for grouping of genes: detecting varying patterns in expression profiles
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases
Metagenomic binning through low-density hashing
Ensemble-based evaluation for protein structure models
Mendel: the Swiss army knife of genetic analysis programs