yusuke1997/dblp-id-title huggingface dataset:
Prediction of Golgi Type II membrane proteins based on their transmembrane domains
MedTator: a serverless annotation tool for corpus development
Identifying tumor clones in sparse single-cell mutation data
Benchmark problems for dynamic modeling of intracellular processes
RobustClone: a robust PCA method for tumor clone and evolution inference from single-cell sequencing data
CGO: utilizing and integrating gene expression microarray data in clinical research and data management
Functional microRNA targets in protein coding sequences
A novel hybrid gene prediction method employing protein multiple sequence alignments
Nucleic acid and protein sequence databases
obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology
MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis
The effect of sequence quality on sequence alignment
LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model
Hierarchical boosting: a machine-learning framework to detect and classify hard selective sweeps in human populations
In silico grouping of peptide/HLA class I complexes using structural interaction characteristics
Discovering a sparse set of pairwise discriminating features in high-dimensional data
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
Weighted minimizer sampling improves long read mapping
Bayesian hierarchical error model for analysis of gene expression data
PLATCOM: a Platform for Computational Comparative Genomics
HoSeqI: automated homologous sequence identification in gene family databases
The GPMDB REST interface
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure
Computing biological functions using BioPsi, a formal description of biological processes based on elementary bricks of actions
Pocket to concavity: a tool for the refinement of protein-ligand binding site shape from alpha spheres
Inference of viral quasispecies with a paired de Bruijn graph
MDiNE: a model to estimate differential co-occurrence networks in microbiome studies
Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions
HaptenDB: a comprehensive database of haptens, carrier proteins and anti-hapten antibodies
GOChase: correcting errors from Gene Ontology-based annotations for gene products
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses
PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events
Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions
UbE3-APA: a bioinformatic strategy to elucidate ubiquitin E3 ligase activities in quantitative proteomics study
WASPS: web-assisted symbolic plasmid synteny server
Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence
Improved tools for DNA comparison and clustering
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Searching protein structure databases with DaliLite v.3
A new gene selection procedure based on the covariance distance
CLEAVAGE: a microcomputer program for predicting signal sequence cleavage sites
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data
LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs
TACTICS, an interactive platform for customized high-content bioimaging analysis
TargetDB: a target registration database for structural genomics projects
PaperMaker: validation of biomedical scientific publications
Test set bias affects reproducibility of gene signatures
Set of approaches based on 3D structure and position specific-scoring matrix for predicting DNA-binding proteins
GLAD: a mixed-membership model for heterogeneous tumor subtype classification
SPar-K: a method to partition NGS signal data
Gene sequence signatures revealed by mining the UniGene affiliation network
Prowler: a novel trimming algorithm for Oxford Nanopore sequence data
Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty
KEA: kinase enrichment analysis
Two distinct SSB protein families in nucleo-cytoplasmic large DNA viruses
rRNA: mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments
quantiNemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Porter, PaleAle 4.0: high-accuracy prediction of protein secondary structure and relative solvent accessibility
Generalized Read-Across prediction using genra-py
Regional analysis to delineate intrasample heterogeneity with RegionalST
MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network
Bio Simulators: a web UI for biological simulation
SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)
An integer programming framework for inferring disease complexes from network data
annoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq
pcaMethods - a bioconductor package providing PCA methods for incomplete data
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences
KMC 3: counting and manipulating k-mer statistics
Very Fast Tree: speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions
FABIA: factor analysis for bicluster acquisition
Towards unified quality verification of synthetic count data with countsimQC
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
BioStructMap: a Python tool for integration of protein structure and sequence-based features
Current structure predictors are not learning the physics of protein folding
Broad-Enrich: functional interpretation of large sets of broad genomic regions
VIBE 2.0: Visual Integration for Bayesian Evaluation
TEXtopo: shaded membrane protein topology plots in LATEX2
3D-Jury: A Simple Approach to Improve Protein Structure Predictions
XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences
EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards
Why neural networks should not be used for HIV-1 protease cleavage site prediction
Alternative splicing and co-option of transposable elements: the case of TMPO/LAP2α and ZNF451 in mammals
Molecular property prediction by contrastive learning with attention-guided positive sample selection
Mixtures of common t -factor analyzers for clustering high-dimensional microarray data
Prokka: rapid prokaryotic genome annotation
An error model for protein quantification
Simplified user poll and experience report language (SUPER): implementation and application
13CFLUX - third-generation high-performance engine for isotopically (non)stationary 13C metabolic flux analysis
minMLST: machine learning for optimization of bacterial strain typing
Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNA-seq data with SCANet
A general method of curve fitting and error analysis using a spreadsheet: determination of the binding constants of tight binding ligands in variable volume assays
Extending traditional query-based integration approaches for functional characterization of post-genomic data
Unipept CLI 2.0: adding support for visualizations and functional annotations
rTANDEM, an R/Bioconductor package for MS/MS protein identification
MEDUSA: large scale automatic selection and visual assessment of PCR primer pairs
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
A LASSO-based approach to sample sites for phylogenetic tree search
Improved datasets and evaluation methods for the automatic prediction of DNA-binding proteins
Systematic inference of functional phosphorylation events in yeast metabolism
Stochastic EM-based TFBS motif discovery with MITSU
BITES: balanced individual treatment effect for survival data
AmiGO: online access to ontology and annotation data
Align human interactome with phenome to identify causative genes and networks underlying disease families
Online synonymous codon usage analyses with the ade4 and seqinR packages
Analysis of DNA curvature using artificial neural networks
doubletrouble : an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications
Realfreq: real-time base modification analysis for nanopore sequencing
Identification of hidden relationships from the coupling of Hydrophobic Cluster Analysis and Domain Architecture information
Ngila: global pairwise alignments with logarithmic and affine gap costs
Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data
The FunCoup Cytoscape App: multi-species network analysis and visualization
Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers
A scalable and portable framework for massively parallel variable selection in genetic association studies
An intrinsically interpretable neural network architecture for sequence-to-function learning
RAREMETAL: fast and powerful meta-analysis for rare variants
CypRules: a rule-based P450 inhibition prediction server
Hyperbolic regression analysis for kinetics, electrophoresis, ELISA, RIA, Bradford, Lowry, and other applications
Multi-label classifier based on histogram of gradients for predicting the anatomical therapeutic chemical class/classes of a given compound
The optimal discovery procedure for significance analysis of general gene expression studies
Clustering single-cell RNA-seq data by rank constrained similarity learning
Pathogen detection using short-RNA deep sequencing subtraction and assembly
MELINA: motif extraction from promoter regions of potentially co-regulated genes
Revisiting drug-protein interaction prediction: a novel global-local perspective
Large-scale prediction of adverse drug reactions-related proteins with network embedding
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
Quasi-Entropy Closure: a fast and reliable approach to close the moment equations of the Chemical Master Equation
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples
A spatial attention guided deep learning system for prediction of pathological complete response using breast cancer histopathology images
SOAP: short oligonucleotide alignment program
Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning
Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer
Structure prediction meta server
Protein subcellular localization of fluorescence imagery using spatial and transform domain features
AbPredict 2: a server for accurate and unstrained structure prediction of antibody variable domains
Cooperative development of logical modelling standards and tools with CoLoMoTo
CircaCompare: a method to estimate and statistically support differences in mesor, amplitude and phase, between circadian rhythms
Correction to: ELIXIR biovalidator for semantic validation of life science metadata
adephylo : new tools for investigating the phylogenetic signal in biological traits
MODELTEST: testing the model of DNA substitution
Proteomic mass spectra classification using decision tree based ensemble methods
Interactive network-based clustering and investigation of multimorbidity association matrices with associationSubgraphs
A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings
NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources
GSOAP: a tool for visualization of gene set over-representation analysis
ST-Steiner: a spatio-temporal gene discovery algorithm
Learning embedding features based on multisense-scaled attention architecture to improve the predictive performance of anticancer peptides
A mixture model-based approach to the clustering of microarray expression data
MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees
PconsFold: improved contact predictions improve protein models
GNN-SubNet: disease subnetwork detection with explainable graph neural networks
Binary Interval Search: a scalable algorithm for counting interval intersections
A web-based tool for principal component and significance analysis of microarray data
Mutate and observe: utilizing deep neural networks to investigate the impact of mutations on translation initiation
Fast and accurate correction of optical mapping data via spaced seeds
Network-based inference from complex proteomic mixtures using SNIPE
Estimating node degree in bait-prey graphs
CATANA: a tool for generating comprehensive annotations of alternative transcript events
Isomorphic semantic mapping of variant call format (VCF2RDF)
Exploiting sample variability to enhance multivariate analysis of microarray data
Binding peptide generation for MHC Class I proteins with deep reinforcement learning
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades
MeCorS: Metagenome-enabled error correction of single cell sequencing reads
Detection and characterization of novel sequence insertions using paired-end next-generation sequencing
EBIC: an evolutionary-based parallel biclustering algorithm for pattern discovery
Further Steps in TANGO: improved taxonomic assignment in metagenomics
CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
PyNAST: a flexible tool for aligning sequences to a template alignment
Columba: fast approximate pattern matching with optimized search schemes
A closed formula relevant to 'Theory of local k-mer selection with applications to long-read alignment' by Jim Shaw and Yun William Yu
Exploring classification strategies with the CoEPrA 2006 contest
Virxicon: a lexicon of viral sequences
Navigating protected genomics data with UCSC Genome Browser in a Box
Towards self-learning based hypotheses generation in biomedical text domain
MPSS: an integrated database system for surveying a set of proteins
Attention-based approach to predict drug-target interactions across seven target superfamilies
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition
Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites
Computational prediction of N-linked glycosylation incorporating structural properties and patterns
Distinction immune genes of hepatitis-induced heptatocellular carcinoma
H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs
SNP2NMD: A database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
DeepLoc: prediction of protein subcellular localization using deep learning
Java editor for biological pathways
A new method for designing degenerate primers and its use in the identification of sequences in Brachiaria showing similarity to apomixis-associated genes
HGC: fast hierarchical clustering for large-scale single-cell data
An integrated toolkit for accurate prediction and analysis of cis- regulatory motifs at a genome scale
Optimizing reduced-space sequence analysis
Accurate extraction of functional associations between proteins based on common interaction partners and common domains
Family relationships: should consensus reign? - consensus clustering for protein families
Evolution of biosequence search algorithms: a brief survey
Deep kernel learning improves molecular fingerprint prediction from tandem mass spectra
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks
An introduction to deep learning on biological sequence data: examples and solutions
Computational prediction of human proteins that can be secreted into the bloodstream
Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays
A Bayesian framework for the inference of gene regulatory networks from time and pseudo-time series data
SNPP: automating large-scale SNP genotype data management
Accelerated protein structure comparison using TM-score-GPU
Synergy of human Pol II core promoter elements revealed by statistical sequence analysis
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH terms
Bayesian model-based clustering of temporal gene expression using autoregressive panel data approach
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering
Stable H3K4me3 is associated with transcription initiation during early embryo development
famCNV: copy number variant association for quantitative traits in families
A structure-based protocol for learning the family-specific mechanisms of membrane-binding domains
BlastXtract - a new way of exploring translated searches
PTID: an integrated web resource and computational tool for agrochemical discovery
The systems biology simulation core library
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data
Toxicology Analysis by Means of the JSM-method
VIPER: a web application for rapid expert review of variant calls
Detection of sputum by interpreting the time-frequency distribution of respiratory sound signal using image processing techniques
Scalable integration of multiomic single-cell data using generative adversarial networks
SurvCurv database and online survival analysis platform update
Corrigendum to: Decombinator V4: an improved AIRR-C compliant software package for T-cell receptor sequence annotation
contamDE-lm: linear model-based differential gene expression analysis using next-generation RNA-seq data from contaminated tumor samples
MRGCN: cancer subtyping with multi-reconstruction graph convolutional network using full and partial multi-omics dataset
ProteinFishing: a protein complex generator within the ModelX toolsuite
SEQSEE: a comprehensive program suite for protein sequence analysis
SQUARE-determining reliable regions in sequence alignments
Poly(A) motif prediction using spectral latent features from human DNA sequences
Polyphest: fast polyploid phylogeny estimation
seXY: a tool for sex inference from genotype arrays
Drawing mitochondrial genomes with circularMT
RWEN: response-weighted elastic net for prediction of chemosensitivity of cancer cell lines
Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences
SurvJamda: an R package to predict patients' survival and risk assessment using joint analysis of microarray gene expression data
Correction to: GIL: a python package for designing custom indexing primers
SHICEDO: single-cell Hi-C data enhancement with reduced over-smoothing
S1000: a better taxonomic name corpus for biomedical information extraction
The effects of feedback loops on disease comorbidity in human signaling networks
Correction to: FASTRAL: improving scalability of phylogenomic analysis
deTS: tissue-specific enrichment analysis to decode tissue specificity
GeOKG: geometry-aware knowledge graph embedding for Gene Ontology and genes
Predicting subcellular localization of proteins in a hybridization space
CSM-AB: graph-based antibody-antigen binding affinity prediction and docking scoring function
RT States: systematic annotation of the human genome using cell type-specific replication timing programs
RPdb: a database of experimentally verified cellular reprogramming records
Decoupling dynamical systems for pathway identification from metabolic profiles
A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome
mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data
CROC: finding chromosomal clusters in eukaryotic genomes
Efficient toolkit implementing best practices for principal component analysis of population genetic data
Using repeated measurements to validate hierarchical gene clusters
DaTeR: error-correcting phylogenetic chronograms using relative time constraints
BackCLIP: a tool to identify common background presence in PAR-CLIP datasets
DBFE: distribution-based feature extraction from structural variants in whole-genome data
Geometry-complete perceptron networks for 3D molecular graphs
scGraph: a graph neural network-based approach to automatically identify cell types
Genetic association analysis with FAMHAP: a major program update
A graph based algorithm for generating EST consensus sequences
Dealing with errors in interactive sequencing by hybridization
Improved data-driven likelihood factorizations for transcript abundance estimation
Gene specific siRNA selector
A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
Gene-gene interaction analysis for the survival phenotype based on the Cox model
TROVE: a user-friendly tool for visualizing and analyzing cancer hallmarks in signaling networks
MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition
PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes
ELISL: early-late integrated synthetic lethality prediction in cancer
Computing the maximum similarity bi-clusters of gene expression data
BATMAN - an R package for the automated quantification of metabolites from nuclear magnetic resonance spectra using a Bayesian model
Powerful and interpretable control of false discoveries in two-group differential expression studies
Measuring and comparing structural fluctuation patterns in large protein datasets
Microcomputer assisted identification of Bacillus species
Learning a mixture of microbial networks using minorization-maximization
RabbitSketch: a high-performance sketching library for genome analysis
Agent-based modeling reveals benefits of heterogeneous and stochastic cell populations during cGAS-mediated IFNβ production
JADOPPT: java based AutoDock preparing and processing tool
Engineering support vector machine kernels that recognize translation initiation sites
DMAP: differential methylation analysis package for RRBS and WGBS data
Efficient spatial segmentation of large imaging mass spectrometry datasets with spatially aware clustering
Synthetic biology - putting engineering into biology
R3D Align: global pairwise alignment of RNA 3D structures using local superpositions
Gene Interaction in DNA Microarray Data Is Decomposed by Information Geometric Measure
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules
RPEMHC: improved prediction of MHC-peptide binding affinity by a deep learning approach based on residue-residue pair encoding
The Taverna Interaction Service: enabling manual interaction in workflows
KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics