yusuke1997/dblp-id-title huggingface dataset:
Metal-MACiE: a database of metals involved in biological catalysis
ColorHOR-novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome
Allowing mutations in maximal matches boosts genome compression performance
A benchmark for Affymetrix GeneChip expression measures
Profile-based detection of microRNA precursors in animal genomes
FlexiDot: highly customizable, ambiguity-aware dotplots for visual sequence analyses
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach
MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework
AEGS: identifying aberrantly expressed gene sets for differential variability analysis
UpSetR: an R package for the visualization of intersecting sets and their properties
MotGen: a closed-loop bacterial motility control framework using generative adversarial networks
Disease-specific genomic analysis: identifying the signature of pathologic biology
Exon discovery by genomic sequence alignment
@MInter: automated text-mining of microbial interactions
Conpair: concordance and contamination estimator for matched tumor-normal pairs
DNABERT-S: pioneering species differentiation with species-aware DNA embeddings
mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clustering
Rail-RNA: scalable analysis of RNA-seq splicing and coverage
Expert systems: frames, rules or logic for species identification?
DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance
CellAnimation: an open source MATLAB framework for microscopy assays
Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs
Cell-level somatic mutation detection from single-cell RNA sequencing
cisASE: a likelihood-based method for detecting putative cis -regulated allele-specific expression in RNA sequencing data
PriorsEditor: a tool for the creation and use of positional priors in motif discovery
Learning graph representations of biochemical networks and its application to enzymatic link prediction
Gencube: centralized retrieval and integration of multi-omics resources from leading databases
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization
HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif
Reconstruction of DNA sequencing by hybridization
Teaching bioinformatics through the analysis of SARS-CoV-2: project-based training for computer science students
PleioGRiP: genetic risk prediction with pleiotropy
Chimera: construction of chimeric sequences for phylogenetic analysis
SNAP predicts effect of mutations on protein function
Rigorous assessment of gene set enrichment tests
optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis
The rapid generation of mutation data matrices from protein sequences
EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes
Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions
DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra
Flexible parsing, interpretation, and editing of technical sequences with splitcode
Correction to: SBbadger: biochemical reaction networks with definable degree distributions
PIVOT: Protein Interacions VisualizatiOn Tool
ProAcePred: prokaryote lysine acetylation sites prediction based on elastic net feature optimization
IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains
Bi-De: an application for simulating phylogenetic processes
MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP
Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules
Sequence pattern matching on a massively parallel computer
BART: a transcription factor prediction tool with query gene sets or epigenomic profiles
ARBitrator: a software pipeline for on-demand retrieval of auto-curated nifH sequences from GenBank
AVA: visual analysis of gene expression microarray data
TORMES: an automated pipeline for whole bacterial genome analysis
Chemical rule-based filtering of MS/MS spectra
pegas: an R package for population genetics with an integrated-modular approach
ntHash: recursive nucleotide hashing
Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans
Identification of protein complexes by integrating multiple alignment of protein interaction networks
ReMILO: reference assisted misassembly detection algorithm using short and long reads
Automatic selection of verification tools for efficient analysis of biochemical models
Improving metabolic flux estimation via evolutionary optimization for convex solution space
Alignment of possible secondary structures in multiple RNA sequences using simulated annealing
Topology-based classification of tetrads and quadruplex structures
KOnezumi: a web application for automating gene disruption strategies to generate knockout mice
Exact quantification of cellular robustness in genome-scale metabolic networks
Combining pattern discovery and discriminant analysis to predict gene co-regulation
SBbadger: biochemical reaction networks with definable degree distributions
PyBoolNet: a python package for the generation, analysis and visualization of boolean networks
pcnaDeep: a fast and robust single-cell tracking method using deep-learning mediated cell cycle profiling
Development and validation of a consistency based multiple structure alignment algorithm
Retraction of: Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants
Estimating the proportion of true null hypotheses when the statistics are discrete
HiTEC: accurate error correction in high-throughput sequencing data
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
The SMAL web server: global multiple network alignment from pairwise alignments
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
Fast and exact gap-affine partial order alignment with POASTA
Automatically identifying and annotating mouse embryo gene expression patterns
HDMC: a novel deep learning-based framework for removing batch effects in single-cell RNA-seq data
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
Causal network inference using biochemical kinetics
PROF_ PAT 1.3: Updated database of patterns used to detect local similarities
Microarray blob-defect removal improves array analysis
Personal Cancer Genome Reporter: variant interpretation report for precision oncology
Distance measures for tumor evolutionary trees
Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data
GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs
Computational enhancement of single-cell sequences for inferring tumor evolution
BioBlend: automating pipeline analyses within Galaxy and CloudMan
JaMBW 1.1: Java-based Molecular Biologists' Workbench
PopGLen - a Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods
Application of a deductive database system to search for topological and similar three-dimensional structures in protein
Latent sequence periodicity of some oncogenes and DNA-binding protein genes
Increasing confidence in proteomic spectral deconvolution through mass defect
Stable Iterative Variable Selection
MultiQC: summarize analysis results for multiple tools and samples in a single report
AVIS: AJAX viewer of interactive signaling networks
AGRA: analysis of gene ranking algorithms
Minimally overlapping words for sequence similarity search
FAME: fast and memory efficient multiple sequences alignment tool through compatible chain of roots
Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum
RelateAdmix: a software tool for estimating relatedness between admixed individuals
AISAIC: a software suite for accurate identification of significant aberrations in cancers
CompareM2 is a genomes-to-report pipeline for comparing microbial genomes
Position-wise binding preference is important for miRNA target site prediction
Antibody complementarity determining region design using high-capacity machine learning
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS)
Dysregulated ligand-receptor interactions from single-cell transcriptomics
A simple convolutional neural network for prediction of enhancer-promoter interactions with DNA sequence data
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data
Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies
BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task
NUVIEW: software for display and interactive manipulation of nucleic acid models
A knowledge-based experimental design system for nucleic acid engineering
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways
MethylMix: an R package for identifying DNA methylation-driven genes
OpenStructure: a flexible software framework for computational structural biology
AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies
PharaCon: a new framework for identifying bacteriophages via conditional representation learning
CHRONOS : a time-varying method for microRNA-mediated subpathway enrichment analysis
MPBind: a multitask protein binding site predictor using protein language models and equivariant GNNs
flexiMAP: a regression-based method for discovering differential alternative polyadenylation events in standard RNA-seq data
Genome inhomogeneity is determined mainly by WW and SS dinucleotides
Efficient privacy-preserving whole-genome variant queries
Repair-FunMap: a functional database of proteins of the DNA repair systems
NET-SYNTHESIS: a software for synthesis, inference and simplification of signal transduction networks
Computing chemical organizations in biological networks
ENDscript: a workflow to display sequence and structure information
Training HMM structure with genetic algorithm for biological sequence analysis
Compressive genomics for protein databases
Susceptibility of non-linear systems as an approach to metabolic responses
FAST (Flexible Analysis by Software Tool) and CHAMP (CHemico-physical AMinoacidic Parameter data bank): a new tool to investigate protein structure
Inhibition of HIV-1 protease: the rigidity perspective
Plasmid permissiveness of wastewater microbiomes can be predicted from 16S rRNA sequences by machine learning
jORCA: easily integrating bioinformatics Web Services
Unbiased pattern detection in microarray data series
Automated benchmarking of peptide-MHC class I binding predictions
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis
Reno: regularized non-parametric analysis of protein lysate array data
UPP2: fast and accurate alignment of datasets with fragmentary sequences
Globally, unrelated protein sequences appear random
Segmentation of yeast DNA using hidden Markov models
PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Rapid protein fragment search using hash functions based on the Fourier transform
Multitask learning for host-pathogen protein interactions
GeneReporter - sequence-based document retrieval and annotation
Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
ExTopoDB: a database of experimentally derived topological models of transmembrane proteins
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data
ASIAN: a website for network inference
NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration
A new representation for protein secondary structure prediction based on frequent patterns
HQAlign: aligning nanopore reads for SV detection using current-level modeling
Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae
HESAS: HERVs Expression and Structure Analysis System
Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis
POPdemog: visualizing population demographic history from simulation scripts
Further improvement in methods of group-to-group sequence alignment with generalized profile operations
Sequence optimization as an alternative to de novo analysis of tandem mass spectrometry data
Open Bioinformatics
SCSsim: an integrated tool for simulating single-cell genome sequencing data
PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables
SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches
SSMART: sequence-structure motif identification for RNA-binding proteins
NetGen: generating phylogenetic networks with diploid hybrids
CloudPhylo: a fast and scalable tool for phylogeny reconstruction
VeriNA3d: an R package for nucleic acids data mining
A Mixture model with random-effects components for clustering correlated gene-expression profiles
Optimization of primer design for the detection of variable genomic lesions in cancer
A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains
TREECON: a software package for the construction and drawing of evolutionary trees
MNMO: discover driver genes from a multi-omics data based-multi-layer network
GlycoPattern: a web platform for glycan array mining
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus
Optimal stepwise experimental design for pairwise functional interaction studies
Boosting for Tumor Classification with Gene Expression Data
Weighted mutual information analysis substantially improves domain-based functional network models
Computing optimal factories in metabolic networks with negative regulation
BYASE: a Python library for estimating gene and isoform level allele-specific expression
Colorstock, SScolor, Ratón: RNA alignment visualization tools
CrossIsoFun: predicting isoform functions using the integration of multi-omics data
Phylogenetic diversity statistics for all clades in a phylogeny
PRIMEX: rapid identification of oligonucleotide matches in whole genomes
EpIC: a rational pipeline for epitope immunogenicity characterization
pez : phylogenetics for the environmental sciences
Statistical tests for detecting variance effects in quantitative trait studies
LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks
MSRCall: a multi-scale deep neural network to basecall Oxford Nanopore sequences
Information-theoretic analysis and prediction of protein atomic burials: on the search for an informational intermediate between sequence and structure
VIDHOP, viral host prediction with deep learning
Label-guided seed-chain-extend alignment on annotated De Bruijn graphs
Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined
DepLogo: visualizing sequence dependencies in R
scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets
Better diagnostic signatures from RNAseq data through use of auxiliary co-data
EGAD: ultra-fast functional analysis of gene networks
From cell lines to cancer patients: personalized drug synergy prediction
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level
Procom: a web-based tool to compare multiple eukaryotic proteomes
Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage
From high-throughput evaluation to wet-lab studies: advancing mutation effect prediction with a retrieval-enhanced model
PLCOjs, a FAIR GWAS web SDK for the NCI Prostate, Lung, Colorectal and Ovarian Cancer Genetic Atlas project
Restriction site mapping for three or more enzymes
bnglViz: online visualization of rule-based models
methylclock: a Bioconductor package to estimate DNA methylation age
ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text
Chaining for accurate alignment of erroneous long reads to acyclic variation graphs
Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
Model quality assessment for membrane proteins
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling
Topology of functional networks predicts physical binding of proteins
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data
The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects
Alignment free sequence comparison methods and reservoir host prediction
RevUP: an online scoring system for regulatory variants implicated in rare diseases
Bagging to Improve the Accuracy of A Clustering Procedure
Towards detection of orthologues in sequence databases
Ensemble non-negative matrix factorization methods for clustering protein-protein interactions
Inferring functional information from domain co-evolution
Swissknife - 'lazy parsing' of SWISS-PROT entries
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data
Integrative analysis of cross-modal features for the prognosis prediction of clear cell renal cell carcinoma
treePL: divergence time estimation using penalized likelihood for large phylogenies
SPRING: a kinetic interface for visualizing high dimensional single-cell expression data
PCR designer for restriction analysis of various types of sequence mutation
Model building and intelligent acquisition with application to protein subcellular location classification
Primer3_masker: integrating masking of template sequence with primer design software
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification
iFad: an integrative factor analysis model for drug-pathway association inference
iNucs: inter-nucleosome interactions
An update from the Bioinformatics Editors
A nonparametric significance test for sampled networks
HOMED: a homologous sequence editor
Rosetta error model for gene expression analysis
Evoker: a visualization tool for genotype intensity data
Marker selection strategies for circulating tumor DNA guided by phylogenetic inference
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides
ICPS: an integrative cancer profiler system
Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study
FUGE: an analytical ultracentrifuge simulation for teaching purposes
DeepSol: a deep learning framework for sequence-based protein solubility prediction
Deterministic identification of specific individuals from GWAS results
A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive
A dynamic programming algorithm for binning microbial community profiles
FIVEx: an interactive eQTL browser across public datasets
A model-based hierarchical Bayesian approach to Sholl analysis
Likelihood-based complex trait association testing for arbitrary depth sequencing data
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
PurityEst: estimating purity of human tumor samples using next-generation sequencing data
CoMutDB: the landscape of somatic mutation co-occurrence in cancers
OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts
Improving sequence-based modeling of protein families using secondary-structure quality assessment
Variable-selection ANOVA Simultaneous Component Analysis (VASCA)
Selecton: a server for detecting evolutionary forces at a single amino-acid site
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences
INfORM: Inference of NetwOrk Response Modules
Efficient functional clustering of protein sequences using the Dirichlet process
Hive Panel Explorer: an interactive network visualization tool
FactorialHMM: fast and exact inference in factorial hidden Markov models
Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices
PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods
DELPHI: accurate deep ensemble model for protein interaction sites prediction
pyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells
A machine-learning approach to combined evidence validation of genome assemblies
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish
Ontological function annotation of long non-coding RNAs through hierarchical multi-label classification
Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series
Selection of models for the analysis of risk-factor trees: leveraging biological knowledge to mine large sets of risk factors with application to microbiome data
ProDDO: a database of disordered proteins from the Protein Data Bank (PDB)
A Bayesian linear mixed model for prediction of complex traits
Unsupervised Feature Selection Via Two-way Ordering in Gene Expression Analysis
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties
MSDRP: a deep learning model based on multisource data for predicting drug response
Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation
ALES: Cell Lineage Analysis and Mapping of Developmental Events
RiboDiffusion: tertiary structure-based RNA inverse folding with generative diffusion models
A toolkit for creating three-dimensional RNA pencil models
MaHCO: an ontology of the major histocompatibility complex for immunoinformatic applications and text mining
Selecting a classification function for class prediction with gene expression data
Menu-driven cloud computing and resource sharing for R and Bioconductor
solarius: an R interface to SOLAR for variance component analysis in pedigrees