yusuke1997/dblp-id-title huggingface dataset:
Modeling cancer immunoediting in tumor microenvironment with system characterization through the ising-model Hamiltonian
Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package
Improving MetFrag with statistical learning of fragment annotations
FastMM: an efficient toolbox for personalized constraint-based metabolic modeling
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
BeEM: fast and faithful conversion of mmCIF format structure files to PDB format
Structure and function analysis of flexible alignment regions in proteins
An automated 3D modeling pipeline for constructing 3D models of MONOGENEAN HARDPART using machine learning techniques
Compact representation of k-mer de Bruijn graphs for genome read assembly
MGC: a metagenomic gene caller
Utilizing a mixed model approach to compare the lactating rat transcriptome against age-matched control virgins
GARNET - gene set analysis with exploration of annotation relations
Tpgen: a language model for stable protein design with a specific topology structure
TIDD: tool-independent and data-dependent machine learning for peptide identification
Discrete distributional differential expression (D 3 E) - a tool for gene expression analysis of single-cell RNA-seq data
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions
An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses
TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data
Comparing genetic pathways variation of immunoinhibitory receptor LAIR-1 in murine vs human internal organs
Pattern-driven neighborhood search for biclustering of microarray data
A study on fast calling variants from next-generation sequencing data using decision tree
B-cell epitope prediction through a graph model
Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter
Background correction using dinucleotide affinities improves the performance of GCRMA
Inference of single-cell network using mutual information for scRNA-seq data analysis
ASET: an end-to-end pipeline for quantification and visualization of allele specific expression
Improved shrunken centroid classifiers for high-dimensional class-imbalanced data
NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
The Yeast Resource Center Public Image Repository: A large database of fluorescence microscopy images
A framework for automated enrichment of functionally significant inverted repeats in whole genomes
Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development
An R Package that Automatically Collects and Archives Details for Reproducible Computing
Universal sequence map (USM) of arbitrary discrete sequences
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices
Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions
Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains
Query-based biclustering of gene expression data using Probabilistic Relational Models
How reliably can we predict the reliability of protein structure predictions?
Automated image computing reshapes computational neuroscience
Causal models and prediction in cell line perturbation experiments
Identifying target processes for microbial electrosynthesis by elementary mode analysis
Power analysis for RNA-Seq differential expression studies
Sparse multiple co-Inertia analysis with application to integrative analysis of multi -Omics data
Statistics for approximate gene clusters
Automated generation of genome-scale metabolic draft reconstructions based on KEGG
MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
A replica exchange Monte Carlo algorithm for protein folding in the HP model
New scoring schema for finding motifs in DNA Sequences
Multiple model species selection for transcriptomics analysis of non-model organisms
VFFVA: dynamic load balancing enables large-scale flux variability analysis
Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data
scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data
Protein sequence information extraction and subcellular localization prediction with gapped k-Mer method
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis
PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics
Deciphering hierarchical organization of topologically associated domains through change-point testing
Transcriptional interaction-assisted identification of dynamic nucleosome positioning
Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy
Strainer: software for analysis of population variation in community genomic datasets
Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)
ped_draw: pedigree drawing with ease
Differential diagnosis of pleural mesothelioma using Logic Learning Machine
SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis
MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model
Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets
Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver
The α2-HeremansSchmid glycoprotein (AHSG) promotes growth in head and neck squamous cell carcinoma (HNSCC)
TIA: algorithms for development of identity-linked SNP islands for analysis by massively parallel DNA sequencing
Sibe: a computation tool to apply protein sequence statistics to predict folding and design in silico
An automated method for finding molecular complexes in large protein interaction networks
Statistical analysis of real-time PCR data
MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers
G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
Vector analysis as a fast and easy method to compare gene expression responses between different experimental backgrounds
Towards human-computer synergetic analysis of large-scale biological data
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling
A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design
scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy
DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid
Drug repositioning of herbal compounds via a machine-learning approach
Visualizing Meta-Features in Proteomic Maps
Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text
PyPropel: a Python-based tool for efficiently processing and characterising protein data
Sampling the conformation of protein surface residues for flexible protein docking
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism
A theoretical approach to spot active regions in antimicrobial proteins
A hybrid clustering approach to recognition of protein families in 114 microbial genomes
jvenn: an interactive Venn diagram viewer
Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs
The predictive performance of short-linear motif features in the prediction of calmodulin-binding proteins
Phoenics: a novel statistical approach for longitudinal metabolomic pathway analysis
Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model
Accelerating metagenomic read classification on CUDA-enabled GPUs
β-empirical Bayes inference and model diagnosis of microarray data
In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform
Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses
Multidimensional scaling for large genomic data sets
Subcellular protein expression models for microsatellite instability in colorectal adenocarcinoma tissue images
Reconstructing DNA copy number by joint segmentation of multiple sequences
MBBC: an efficient approach for metagenomic binning based on clustering
An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage
CySBGN: A Cytoscape plug-in to integrate SBGN maps
A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data
ESTuber db: an online database for Tuber borchii EST sequences
A new mixture model approach to analyzing allelic-loss data using Bayes factors
A comparison of embedding aggregation strategies in drug-target interaction prediction
Predicting microbial interactions with approaches based on flux balance analysis: an evaluation
Robustness of signal detection in cryo-electron microscopy via a bi-objective-function approach
DTome: a web-based tool for drug-target interactome construction
Optimizing sequence data analysis using convolution neural network for the prediction of CNV bait positions
Time scale and dimension analysis of a budding yeast cell cycle model
A chemogenomics view on protein-ligand spaces
flippant-An R package for the automated analysis of fluorescence-based scramblase assays
The ontology of biological sequences
Identifying cancer prognostic modules by module network analysis
Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment
BitTorious volunteer: server-side extensions for centrally-managed volunteer storage in BitTorrent swarms
Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields
NRE: A tool for exploring neutral loci in the human genome
Identifying driver pathways based on a parameter-free model and a partheno-genetic algorithm
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
Harnessing pre-trained models for accurate prediction of protein-ligand binding affinity
A hidden two-locus disease association pattern in genome-wide association studies
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling
An empirical Bayesian approach for model-based inference of cellular signaling networks
EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration
Scoredist : A simple and robust protein sequence distance estimator
Semantic integration of isolation habitat and location in StrainInfo
The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes
Clustering cliques for graph-based summarization of the biomedical research literature
Correction to: Realizing drug repositioning by adapting a recommendation system to handle the process
PAIR: polymorphic Alu insertion recognition
Genome sequence-based species delimitation with confidence intervals and improved distance functions
MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators
HEC-ASD: a hybrid ensemble-based classification model for predicting autism spectrum disorder disease genes
A multi-task CNN learning model for taxonomic assignment of human viruses
Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations
Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction
A close examination of double filtering with fold change and t test in microarray analysis
muBLASTP: database-indexed protein sequence search on multicore CPUs
adabmDCA: adaptive Boltzmann machine learning for biological sequences
Expression analysis of RNA sequencing data from human neural and glial cell lines depends on technical replication and normalization methods
Integrating 400 million variants from 80, 000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts
Metabolomics variable selection and classification in the presence of observations below the detection limit using an extension of ERp
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks
A powerful score-based statistical test for group difference in weighted biological networks
RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences
MTAF-DTA: multi-type attention fusion network for drug-target affinity prediction
Using epigenomics data to predict gene expression in lung cancer
'Brukin2D': a 2D visualization and comparison tool for LC-MS data
GOSim - an R-package for computation of information theoretic GO similarities between terms and gene products
SVRMHC prediction server for MHC-binding peptides
bioWeb3D: an online webGL 3D data visualisation tool
Diminishing Return for Increased Mappability with Longer Sequencing Reads: Implications of the k-mer Distributions in the Human Genome
MS3ALIGN: an efficient molecular surface aligner using the topology of surface curvature
Parameterizing sequence alignment with an explicit evolutionary model
Mixture models for analysis of melting temperature data
Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity
kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R
Correction: Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss
Semantic Web Applications and Tools for Life Sciences, 2008 - Introduction
A unified approach to false discovery rate estimation
Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats
Predicting beta -turns and their types using predicted backbone dihedral angles and secondary structures
Neighborhood based computational approaches for the prediction of lncRNA-disease associations
Toward a more accurate 3D atlas of C. elegans neurons
Comprehensive ensemble in QSAR prediction for drug discovery
sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures
A multi-task graph deep learning model to predict drugs combination of synergy and sensitivity scores
Cleaning by clustering: methodology for addressing data quality issues in biomedical metadata
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept
Combining sequence and network information to enhance protein-protein interaction prediction
Alignment-free clustering of large data sets of unannotated protein conserved regions using minhashing
The gene normalization task in BioCreative III
Genephony: a knowledge management tool for genome-wide research
Wide coverage biomedical event extraction using multiple partially overlapping corpora
The TROVE module: A common element in Telomerase, Ro and Vault ribonucleoproteins
Broad-coverage biomedical relation extraction with SemRep
A Bayesian data fusion based approach for learning genome-wide transcriptional regulatory networks
Interaction prediction and classification of PDZ domains
MicroSyn: A user friendly tool for detection of microsynteny in a gene family
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool
ISHAPE: new rapid and accurate software for haplotyping
A fast and efficient path elimination algorithm for large-scale multiple common longest sequence problems
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods
Bayesian neural networks for detecting epistasis in genetic association studies
Single TNF alpha trimers mediating NF- kappa B activation: stochastic robustness of NF- kappa B signaling
Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels
Concept-based query expansion for retrieving gene related publications from MEDLINE
Applying Support Vector Machines for Gene ontology based gene function prediction
RASflow: an RNA-Seq analysis workflow with Snakemake
The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: bioinformatics towards translational applications
Detecting the stable point of therapeutic effect of chronic myeloid leukemia based on dynamic network biomarkers
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Exhaustive prediction of disease susceptibility to coding base changes in the human genome
An improved machine learning protocol for the identification of correct Sequest search results
Estimation of total mediation effect for high-dimensional omics mediators
An effective docking strategy for virtual screening based on multi-objective optimization algorithm
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information
Filtering of false positive microRNA candidates by a clustering-based approach
Magallanes: a web services discovery and automatic workflow composition tool
Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking model
Sample size and statistical power considerations in high-dimensionality data settings: a comparative study of classification algorithms
Comparison of evolutionary algorithms in gene regulatory network model inference
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses
The looks of an odour - Visualising neural odour response patterns in real time
The AnnoLite and AnnoLyze programs for comparative annotation of protein structures
FastGroup: A program to dereplicate libraries of 16S rDNA sequences
Slideflow: deep learning for digital histopathology with real-time whole-slide visualization
PyChelator: a Python-based Colab and web application for metal chelator calculations
PANDAseq: paired-end assembler for illumina sequences
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response
Unsupervised statistical clustering of environmental shotgun sequences
BayesMotif: de novo protein sorting motif discovery from impure datasets
Factor analysis for gene regulatory networks and transcription factor activity profiles
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
Automated vocabulary discovery for geo-parsing online epidemic intelligence
smORFunction: a tool for predicting functions of small open reading frames and microproteins
Automatic extraction of biomolecular interactions: an empirical approach
SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)
LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data
Equalizer reduces SNP bias in Affymetrix microarrays
MimoSA: a system for minimotif annotation
Learning pair-wise gene functional similarity by multiplex gene expression maps
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression
Estimating relative abundances of proteins from shotgun proteomics data
Prediction of GCRV virus-host protein interactome based on structural motif-domain interactions
A T-cell-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma based on transcriptomics and single-cell sequencing
PyMS: a Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools
Bacterial protein meta-interactomes predict cross-species interactions and protein function
AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures
is-rSNP: a novel technique for in silico regulatory SNP detection
Metric for Measuring the Effectiveness of Clustering of DNA Microarray Expression
siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
Phase change for the accuracy of the median value in estimating divergence time
Multi-level model for the investigation of oncoantigen-driven vaccination effect
CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences
Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
MDG-DDI: multi-feature drug graph for drug-drug interaction prediction
Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution
Correspondence on NanoVar's performance outlined by Jiang T. et al. in "Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation"
ET-GRU: using multi-layer gated recurrent units to identify electron transport proteins