yusuke1997/dblp-id-title huggingface dataset:
Polytomy refinement for the correction of dubious duplications in gene trees
The NEW ESID online database network
Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models
Analysis of array CGH data for cancer studies using fused quantile regression
BAIUCAS: a novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome
ViewDock TDW: high-throughput visualization of virtual screening results
Assessment of cancer and virus antigens for cross-reactivity in human tissues
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images
A key for freshwater invertebrates using fuzzy logic
Comparison of variance between correlated samples
FCP: functional coverage of the proteome by structures
PatGen - a consolidated resource for searching genetic patent sequences
Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation
CONDOP: an R package for CONdition-Dependent Operon Predictions
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins
CiteFuse enables multi-modal analysis of CITE-seq data
Hubness reduction improves clustering and trajectory inference in single-cell transcriptomic data
A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
KeBABS: an R package for kernel-based analysis of biological sequences
Unsupervised segmentation of continuous genomic data
Inferring epigenetic and transcriptional regulation during blood cell development with a mixture of sparse linear models
Inferring transcriptional regulatory networks from high-throughput data
fastNGSadmix: admixture proportions and principal component analysis of a single NGS sample
A hybrid model for robust detection of transcription factor binding sites
Statistical method for predicting protein coding regions in nucleic acid sequences
HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling
Structural flexibility in proteins: impact of the crystal environment
Accessibility of covariance information creates vulnerability in Federated Learning frameworks
MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters
myVCF: a desktop application for high-throughput mutations data management
Modularity and directionality in genetic interaction maps
E-MEM: efficient computation of maximal exact matches for very large genomes
Increasing the accuracy of protein loop structure prediction with evolutionary constraints
Large-scale learning of combinatorial transcriptional dynamics from gene expression
Topology-independent and global protein structure alignment through an FFT-based algorithm
PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data
JASPAR RESTful API: accessing JASPAR data from any programming language
Statistical expression deconvolution from mixed tissue samples
PhosphoNetworks: a database for human phosphorylation networks
HISSTA: a human in situ single-cell transcriptome atlas
MorphoScript: a dedicated analysis to assess the morphology and contractile structures of cardiomyocytes derived from stem cells
An improved algorithm for nucleic acid secondary structure display
Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading
IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels
Haplotype-based linkage disequilibrium mapping via direct data mining
PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families
Discovering patterns to extract protein-protein interactions from full texts
Enhancement of DNA sequence computer programs by using digitized voice output
RapidRMSD: rapid determination of RMSDs corresponding to motions of flexible molecules
ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases
GFPE: gene-finding program evaluation
A hidden Markov model for progressive multiple alignment
SBMLDiagrams: a python package to process and visualize SBML layout and render
A general method for accurate estimation of false discovery rates in identification of differentially expressed genes
On a common structure of intelligence in biological and technical systems
FINEMAP: efficient variable selection using summary data from genome-wide association studies
PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm
rMTA: robust metabolic transformation analysis
iATC-FRAKEL: a simple multi-label web server for recognizing anatomical therapeutic chemical classes of drugs with their fingerprints only
Comparative Network Reconstruction using mixed integer programming
nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis
Parsimony and likelihood reconstruction of human segmental duplications
PhyloDraw: a phylogenetic tree drawing system
Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis
Extensive feature detection of N-terminal protein sorting signals
PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
NetRaVE: constructing dependency networks using sparse linear regression
Tibanna: software for scalable execution of portable pipelines on the cloud
PINALOG: a novel approach to align protein interaction networks - implications for complex detection and function prediction
EnsembleDesign: messenger RNA design minimizing ensemble free energy via probabilistic lattice parsing
Reconciling differential gene expression data with molecular interaction networks
CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data
Programming strategy for efficient modeling of dynamics in a population of heterogeneous cells
Comprehensive estimation of input signals and dynamics in biochemical reaction networks
Trace alignment and some of its applications
Applications of Tree-Maps to hierarchical biological data
Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing
A Java applet for visualizing protein-protein interaction
ExactFDR: exact computation of false discovery rate estimate in case-control association studies
Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian regeneration
Interfacing similarity search software with the sequence retrieval system ACNUC
ParTIES: a toolbox for Paramecium interspersed DNA elimination studies
Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data
DataDTA: a multi-feature and dual-interaction aggregation framework for drug-target binding affinity prediction
Using uncertainty to link and rank evidence from biomedical literature for model curation
A cell-level discriminative neural network model for diagnosis of blood cancers
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures
AnnoGen: annotating genome-wide pragmatic features
Improving dictionary-based named entity recognition with deep learning
Application of distance geometry to 3D visualization of sequence relationships
A simple method for accessing and transferring nucleotide database files
Ligand-binding site prediction of proteins based on known fragment-fragment interactions
SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application
A distribution free summarization method for Affymetrix GeneChip ® arrays
Decoding properties of tRNA leave a detectable signal in codon usage bias
A simple model predicts UGT-mediated metabolism
EC_oligos: automated and whole-genome primer design for exons within one or between two genomes
A knowledge-based approach to predict intragenic deletions or duplications
AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins
Mapping PDB chains to UniProtKB entries
Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence
ProtNAff: protein-bound Nucleic Acid filters and fragment libraries
G4Killer web application: a tool to design G-quadruplex mutations
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control
ALP & FALP: C++ libraries for pairwise local alignment E -values
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding
Assessing consistency across functional screening datasets in cancer cells
RED-T: utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events
Detecting independent and recurrent copy number aberrations using interval graphs
mlr3proba: an R package for machine learning in survival analysis
Correction to: Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment
Privacy-preserving microbiome analysis using secure computation
A hidden Markov model to identify combinatorial epigenetic regulation patterns for estrogen receptor α target genes
Long-range control of expression in yeast
TRITON: in silico construction of protein mutants and prediction of their activities
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments
SPINAL: scalable protein interaction network alignment
G-PRIMER: greedy algorithm for selecting minimal primer set
Fast multiple sequence alignment via multi-armed bandits
Modular Modeling of Cellular Systems with ProMoT/Diva
Next generation software for functional trend analysis
PSSV: a novel pattern-based probabilistic approach for somatic structural variation identification
LRLoop: a method to predict feedback loops in cell-cell communication
FIMO: scanning for occurrences of a given motif
PROFILEGRAPH: an interactive graphical tool for protein sequence analysis
Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods
Refinement strategies for Tangram for reliable single-cell to spatial mapping
AWOT and CWOT for genotype and genotype-by-treatment interaction joint analysis in pharmacogenetics GWAS
MOLI: multi-omics late integration with deep neural networks for drug response prediction
Genome-wide DNA sequence polymorphisms facilitate nucleosome positioning in yeast
Analysis of longitudinal metabolomics data
Understanding the sources of performance in deep drug response models reveals insights and improvements
MyBioNet: interactively visualize, edit and merge biological networks on the Web
ChemoPy: freely available python package for computational biology and chemoinformatics
Bayesian inference on stochastic gene transcription from flow cytometry data
MetOSite: an integrated resource for the study of methionine residues sulfoxidation
Identification of copy number variations and translocations in cancer cells from Hi-C data
ODS: ordering DNA sequences - a physical mapping algorithm based on simulated annealing
HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology
PTGL - a web-based database application for protein topologies
FNV: light-weight flash-based network and pathway viewer
quincunx: an R package to query, download and wrangle PGS Catalog data
Myriads: P-value-based multiple testing correction
AlphaPulldown2 - a general pipeline for high-throughput structural modeling
siRNA specificity searching incorporating mismatch tolerance data
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis
DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout
SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells
PanCGHweb: a web tool for genotype calling in pangenome CGH data
scMaSigPro: differential expression analysis along single-cell trajectories
FRETraj: integrating single-molecule spectroscopy with molecular dynamics
Augur - a computational pipeline for whole genome microbial surface protein prediction and classification
MoNET: an R package for multi-omic network analysis
Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method
Accelerated nanopore basecalling with SLOW5 data format
SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies
Educating biologists in the 21st century: bioinformatics scientists versus bioinformatics technicians
Fec: a fast error correction method based on two-rounds overlapping and caching
Imbalanced classification for protein subcellular localization with multilabel oversampling
SOMAP: a novel interactive approach to multiple protein sequences alignment
AllerTool: a web server for predicting allergenicity and allergic cross-reactivity in proteins
Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
APL program for evaluation of heat processes for spherical foods
Predicting human microbe-drug associations via graph convolutional network with conditional random field
Predicted function of the vaccinia virus G5R protein
The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies
Marker2sequence, mine your QTL regions for candidate genes
PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment
Quantifying the complexity of medical research
The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics
COMBOSA3D: combining sequence alignments with three-dimensional structures
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer
IVA: accurate de novo assembly of RNA virus genomes
dNEMO: a tool for quantification of mRNA and punctate structures in time-lapse images of single cells
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
Complexity reduction in context-dependent DNA substitution models
COMER2: GPU-accelerated sensitive and specific homology searches
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures
FLUSYS: a software package for the collection and analysis of kinetic and scanning data from Perkin-Elmer fluorimeters
An overview of the wcd EST clustering tool
Predicting dynamic signaling network response under unseen perturbations
Ancestors 1.0: a web server for ancestral sequence reconstruction
Che Shift-2: graphic validation of protein structures
Extending MapMan: application to legume genome arrays
Whiteboard : a framework for the programmatic visualization of complex biological analyses
CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways
Similarity-based prediction for Anatomical Therapeutic Chemical classification of drugs by integrating multiple data sources
lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection
FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads
Benchmarking optimization methods for parameter estimation in large kinetic models
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers
Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data
greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
CistromeFinder for ChIP-seq and DNase-seq data reuse
SCHIP: statistics for chromosome interphase positioning based on interchange data
The BioCatalog
Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction
GECA: a fast tool for gene evolution and conservation analysis in eukaryotic protein families
GOAnno: GO annotation based on multiple alignment
The statistical significance of nucleotide position-weight matrix matches
VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays
mcmc_clib-an advanced MCMC sampling package for ode models
LaGAT: link-aware graph attention network for drug-drug interaction prediction
SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data
Inferring combined CNV/SNP haplotypes from genotype data
XiP: a computational environment to create, extend and share workflows
Primerize-2D: automated primer design for RNA multidimensional chemical mapping
Robust estimators for expression analysis
ProteomeExpert: a Docker image-based web server for exploring, modeling, visualizing and mining quantitative proteomic datasets
PhosIDN: an integrated deep neural network for improving protein phosphorylation site prediction by combining sequence and protein-protein interaction information
Biographer: web-based editing and rendering of SBGN compliant biochemical networks
BioSCAN: a network sharable computational resource for searching biosequence databases
A practical method for exact computation of subtree prune and regraft distance
Disulfide connectivity prediction using recursive neural networks and evolutionary information
runBNG: a software package for BioNano genomic analysis on the command line
A non-negative matrix factorization based method for predicting disease-associated miRNAs in miRNA-disease bilayer network
Identification of conserved evolutionary trajectories in tumors
Multi-omics data integration by generative adversarial network
Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase
Fast and accurate search for non-coding RNA pseudoknot structures in genomes
Cost function network-based design of protein-protein interactions: predicting changes in binding affinity
vulcanSpot: a tool to prioritize therapeutic vulnerabilities in cancer
Gnome - an Internet-based sequence analysis tool
Context awareness and embedding for biomedical event extraction
Predicting protein structure classes from function predictions
Searching RNA motifs and their intermolecular contacts with constraint networks
APOPTO-CELL - a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis
BATL: Bayesian annotations for targeted lipidomics
DNA fragment size determination on agarose gel by using the application GEL
HiCARN: resolution enhancement of Hi-C data using cascading residual networks
DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments
Genetic algorithm optimization for pre-processing and variable selection of spectroscopic data
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data
Maximum likelihood inference of imprinting and allele-specific expression from EST data
HaploForge: a comprehensive pedigree drawing and haplotype visualization web application
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank
Discrete mixture modeling to address genetic heterogeneity in time-to-event regression
Using Sybil for interactive comparative genomics of microbes on the web
A distance-based approach for testing the mediation effect of the human microbiome
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process
Simulation of heterogeneous tumour genomes with HeteroGenesis and in silico whole exome sequencing
PIML: the Pathogen Information Markup Language
A new approach to prediction of short-range conformational propensities in proteins
POIBM: batch correction of heterogeneous RNA-seq datasets through latent sample matching
ProAffiMuSeq: sequence-based method to predict the binding free energy change of protein-protein complexes upon mutation using functional classification
Correcting log ratios for signal saturation in cDNA microarrays
Motif comparison based on similarity of binding affinity profiles
MView: a web-compatible database search or multiple alignment viewer
The neXtProt peptide uniqueness checker: a tool for the proteomics community
A fixed-point alignment technique for detection of recurrent and common sequence motifs associated with biological features
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
Ontology-based validation and identification of regulatory phenotypes
iMotifs: an integrated sequence motif visualization and analysis environment
Improved prediction of breast cancer outcome by identifying heterogeneous biomarkers
PBOOST: a GPU-based tool for parallel permutation tests in genome-wide association studies
ESS ++: a C++ objected-oriented algorithm for Bayesian stochastic search model exploration
Fuzzy optimization for detecting enzyme targets of human uric acid metabolism
glmgraph: an R package for variable selection and predictive modeling of structured genomic data
Omic space: coordinate-based integration and analysis of genomic phenomic interactions
A novel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
OLTA: Optimizing bait seLection for TArgeted sequencing
ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arrays
Detecting presence of mutational signatures in cancer with confidence
TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments
Comparative modeling without implicit sequence alignments
SpliceLauncher: a tool for detection, annotation and relative quantification of alternative junctions from RNAseq data
Machine-OlF-Action: a unified framework for developing and interpreting machine-learning models for chemosensory research
VizRank: finding informative data projections in functional genomics by machine learning
A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes
EpiVar Browser: advanced exploration of epigenomics data under controlled access
A polynomial-time algorithm for a class of protein threading problems
Quantitative computer analysis of signal sequence homologies in DNA
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data