yusuke1997/dblp-id-title huggingface dataset:
Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization
Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing
StrongestPath: a Cytoscape application for protein-protein interaction analysis
Aber-OWL: a framework for ontology-based data access in biology
Identification of polymorphic inversions from genotypes
SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions
MLIP: using multiple processors to compute the posterior probability of linkage
BTR: training asynchronous Boolean models using single-cell expression data
Predicting bacterial resistance from whole-genome sequences using k-mers and stability selection
Biochemical systems identification by a random drift particle swarm optimization approach
Dependency-based long short term memory network for drug-drug interaction extraction
Novel and simple transformation algorithm for combining microarray data sets
Exploring effective approaches for haplotype block phasing
GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences
The Seventh Asia Pacific Bioinformatics Conference (APBC2009)
S3DB core: a framework for RDF generation and management in bioinformatics infrastructures
BioCreAtIvE Task 1A: gene mention finding evaluation
Fused inverse-normal method for integrated differential expression analysis of RNA-seq data
Sensitivity analysis of dynamic biological systems with time-delays
Studying the unfolding process of protein G and protein L under physical property space
Bayesian Inference of the Number of Factors in Gene-Expression Analysis: Application to Human Virus Challenge Studies
Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
Re-searcher: a system for recurrent detection of homologous protein sequences
SUNPLIN: Simulation with Uncertainty for Phylogenetic Investigations
Enhancer reprogramming in mammalian genomes
SitesIdentify: a protein functional site prediction tool
Novel methodology for construction and pruning of quasi-median networks
Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS)
OptNCMiner: a deep learning approach for the discovery of natural compounds modulating disease-specific multi-targets
Identifying term relations cross different gene ontology categories
A cascade computer model for mocrobicide diffusivity from mucoadhesive formulations
Phylogenetic convolutional neural networks in metagenomics
Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Identification of transcription factor high accumulation DNA zones
XML schemas for common bioinformatic data types and their application in workflow systems
Improved human disease candidate gene prioritization using mouse phenotype
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data
IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations
TabSQL: a MySQL tool to facilitate mapping user data to public databases
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes
A simple method for exploring adverse drug events in patients with different primary diseases using spontaneous reporting system
Early classification of multivariate temporal observations by extraction of interpretable shapelets
Highly accurate sigmoidal fitting of real-time PCR data by introducing a parameter for asymmetry
Classification of G-protein coupled receptors based on support vector machine with maximum relevance minimum redundancy and genetic algorithm
MendeLIMS: a web-based laboratory information management system for clinical genome sequencing
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation
JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies
Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset
CDSeqR: fast complete deconvolution for gene expression data from bulk tissues
Learning a peptide-protein binding affinity predictor with kernel ridge regression
PARE: A tool for comparing protein abundance and mRNA expression data
Protein function prediction using domain families
Statistical integration of two omics datasets using GO2PLS
Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level
Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions
The INTERPRET Decision-Support System version 3.0 for evaluation of Magnetic Resonance Spectroscopy data from human brain tumours and other abnormal brain masses
Discarding duplicate ditags in LongSAGE analysis may introduce significant error
Assessment of predictive models for chlorophyll-a concentration of a tropical lake
Correlation-maximizing surrogate gene space for visual mining of gene expression patterns in developing barley endosperm tissue
Gene trees and species trees: irreconcilable differences
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
Coordinates and intervals in graph-based reference genomes
On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
CERENKOV2: improved detection of functional noncoding SNPs using data-space geometric features
Expanding the taxonomic range in the fecal metagenome
A simple method for assessing sample sizes in microarray experiments
Application of a sensitive collection heuristic for very large protein families: Evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases
Machine learning models predicting multidrug resistant urinary tract infections using "DsaaS"
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE)
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model
Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data
Robust detection method for differential expression studies
iQuantitator: A tool for protein expression inference using iTRAQ
PC-TraFF: identification of potentially collaborating transcription factors using pointwise mutual information
T2DM-GeneMiner a web resource for meta-analysis and marker identification for type 2 diabetes mellitus
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014
Scan for Motifs: a webserver for the analysis of post-transcriptional regulatory elements in the 3[prime] untranslated regions (3[prime] UTRs) of mRNAs
GENOMEPOP: A program to simulate genomes in populations
Efficient Boolean implementation of universal sequence maps (bUSM)
Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex
Computer vision digitization of smartphone images of anesthesia paper health records from low-middle income countries
DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning
Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition
DiffCoEx: a simple and sensitive method to find differentially coexpressed gene modules
Viral quasispecies inference from 454 pyrosequencing
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction
Cancer survival prediction by learning comprehensive deep feature representation for multiple types of genetic data
A robust approach to 3D neuron shape representation for quantification and classification
Modularization of biochemical networks based on classification of Petri net t-invariants
The FBA solution space kernel: introduction and illustrative examples
Learning rule sets from survival data
Automatic prediction of catalytic residues by modeling residue structural neighborhood
Designs for the simultaneous inference of concentration-response curves
On the association analysis of CNV data: a fast and robust family-based association method
Biomimicry of quorum sensing using bacterial lifecycle model
Generating normal networks via leaf insertion and nearest neighbor interchange
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models
A robust two-way semi-linear model for normalization of cDNA microarray data
Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries
ErmineJ: Tool for functional analysis of gene expression data sets
SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units
isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation
Gene annotation and network inference by phylogenetic profiling
lifex-fiber: an open tool for myofibers generation in cardiac computational models
Analysis of promoter regions of co-expressed genes identified by microarray analysis
BPDA - A Bayesian peptide detection algorithm for mass spectrometry
Integrated analysis of the heterogeneous microarray data
Geena 2, improved automated analysis of MALDI/TOF mass spectra
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
Tremor assessment using smartphone sensor data and fuzzy reasoning
LPInsider: a webserver for lncRNA-protein interaction extraction from the literature
Empowering biologists to decode omics data: the Genekitr R package and web server
MolabIS - An Integrated Information System for Storing and Managing Molecular Genetics Data
A taxonomy of visualization tasks for the analysis of biological pathway data
CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
miRBaseConverter: an R/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase
HaploRec: efficient and accurate large-scale reconstruction of haplotypes
PPI-Graphomer: enhanced protein-protein affinity prediction using pretrained and graph transformer models
Experimental and computational analysis of mouse sleep-wake dynamics
pyHIVE, a health-related image visualization and engineering system using Python
Persistent memory as an effective alternative to random access memory in metagenome assembly
DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer
Predicting clinically promising therapeutic hypotheses using tensor factorization
PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3′-end sequencing
Fpocket: An open source platform for ligand pocket detection
Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching
LabPipe: an extensible bioinformatics toolkit to manage experimental data and metadata
Accurate and efficient gp120 V3 loop structure based models for the determination of HIV-1 co-receptor usage
Optimize data-driven multi-agent simulation for COVID-19 transmission
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management
The MoVIN server for the analysis of protein interaction networks
INFLECT: an R-package for cytometry cluster evaluation using marker modality
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach
Unaccounted uncertainty from qPCR efficiency estimates entails uncontrolled false positive rates
Group sparse canonical correlation analysis for genomic data integration
Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM)
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori
Global profile of genes regulated by securin
dBBQs: dataBase of Bacterial Quality scores
Correction to: SLR: a scaffolding algorithm based on long reads and contig classification
Machine learning and drug discovery for neglected tropical diseases
The EIPeptiDi tool: enhancing peptide discovery in ICAT-based LC MS/MS experiments
Extension of Lander-Waterman theory for sequencing filtered DNA libraries
Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface
Quality control for terms and definitions in ontologies and taxonomies
Discovering themes in biomedical literature using a projection-based algorithm
HiCmapTools: a tool to access HiC contact maps
Unsupervised segmentation of noisy electron microscopy images using salient watersheds and region merging
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction
Toxo: a library for calculating penetrance tables of high-order epistasis models
ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use
Correction to: Computational assembly of a human Cytomegalovirus vaccine upon experimental epitope legacy
Predicting disease-associated substitution of a single amino acid by analyzing residue interactions
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs
One-sample missing DNA-methylation value imputation
Supervised learning for the automated transcription of spacer classification from spoligotype films
M2PP: a novel computational model for predicting drug-targeted pathogenic proteins
Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R
Splice site identification using probabilistic parameters and SVM classification
XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
ICOR: improving codon optimization with recurrent neural networks
Visual analysis of biological data-knowledge networks
Detecting genomic deletions from high-throughput sequence data with unsupervised learning
Computing all hybridization networks for multiple binary phylogenetic input trees
EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search
Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation
Modeling Sage data with a truncated gamma-Poisson model
Boolean networks using the chi-square test for inferring large-scale gene regulatory networks
AttSec: protein secondary structure prediction by capturing local patterns from attention map
The BiSearch web server
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits
IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method
Prediction of beta-turns at over 80% accuracy based on an ensemble of predicted secondary structures and multiple alignments
Understanding the molecular basis of EGFR kinase domain/MIG-6 peptide recognition complex using computational analyses
Integrating protein structural dynamics and evolutionary analysis with Bio3D
categoryCompare: high-throughput data meta-analysis using gene annotations
CaliBayes: Integration of GRID based simulation and data resources for Bayesian calibration of biological models
Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data
Personalized Oncology Suite: integrating next-generation sequencing data and whole-slide bioimages
GibbsST: a Gibbs sampling method for motif discovery with enhanced resistance to local optima
Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method
mlstdbNet - distributed multi-locus sequence typing (MLST) databases
BitMapper: an efficient all-mapper based on bit-vector computing
Graph regularized L 2, 1 -nonnegative matrix factorization for miRNA-disease association prediction
A multiresolution approach to automated classification of protein subcellular location images
Extending the mutual information measure to rank inferred literature relationships
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
BioShell-Threading: versatile Monte Carlo package for protein 3D threading
Parameters for accurate genome alignment
An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system
Structural and functional-annotation of an equine whole genome oligoarray
Simcluster: clustering enumeration gene expression data on the simplex space
SmithHunter: a workflow for the identification of candidate smithRNAs and their targets
Euler diagrams drawn with ellipses area-proportionally (Edeap)
TreeSnatcher plus: capturing phylogenetic trees from images
Tree Edit Distance for Leaf-labelled trees on free leafset and its comparison with Frequent Subsplit dissimilarity and popular distance measures
Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq
An exploratory data analysis method to reveal modular latent structures in high-throughput data
Computational models of liver fibrosis progression for hepatitis C virus chronic infection
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases
Strategies for aggregating gene expression data: The collapseRows R function
A practical O(n log 2 n) time algorithm for computing the triplet distance on binary trees
Modeling the integration of bacterial rRNA fragments into the human cancer genome
GenoLink: a graph-based querying and browsing system for investigating the function of genes and proteins
A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification
Adverse drug reaction detection via a multihop self-attention mechanism
Deep multiview learning to identify imaging-driven subtypes in mild cognitive impairment
Identifying diseases that cause psychological trauma and social avoidance by GCN-Xgboost
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
Shotgun proteomic analysis of human head and neck squamous cell carcinoma cell line SQ20B with diminished AHSG expression
WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures
CRISPulator: a discrete simulation tool for pooled genetic screens
An automatic device for detection and classification of malaria parasite species in thick blood film
d-matrix - database exploration, visualization and analysis
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
Dynamic substrate preferences predict metabolic properties of a simple microbial consortium
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data
Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools
Detection of chromosomal regions showing differential gene expression in human skeletal muscle and in alveolar rhabdomyosarcoma
anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
Weighted analysis of general microarray experiments
Impact of variance components on reliability of absolute quantification using digital PCR
DePicT Melanoma Deep-CLASS: a deep convolutional neural networks approach to classify skin lesion images
Federated ontology-based queries over cancer data
Integrated visual analysis of protein structures, sequences, and feature data
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
HAHNet: a convolutional neural network for HER2 status classification of breast cancer
NOXclass: prediction of protein-protein interaction types
PPalign: optimal alignment of Potts models representing proteins with direct coupling information
Development and implementation of an algorithm for detection of protein complexes in large interaction networks
Accuracy of RNA-Seq and its dependence on sequencing depth
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
scMFF: a machine learning framework with multiple feature fusion strategies for cell type identification
PDBeCIF: an open-source mmCIF/CIF parsing and processing package
Empirical Bayes Analysis of Sequencing-based Transcriptional Profiling without Replicates
Simulated unbound structures for benchmarking of protein docking in the Dockground resource
Computational detection of genomic cis- regulatory modules applied to body patterning in the early Drosophila embryo
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states
A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents
An efficient protein complex mining algorithm based on Multistage Kernel Extension
LncRNA-protein interaction prediction with reweighted feature selection
Extending the evaluation of Genia Event task toward knowledge base construction and comparison to Gene Regulation Ontology task
Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization
Statistical distributions of optimal global alignment scores of random protein sequences
Bioinformatic challenges for proteomic biomarkers of cancer
EXPANDER - an integrative program suite for microarray data analysis
Meta-aligner: long-read alignment based on genome statistics
Missing value imputation for epistatic MAPs
How the Gene Ontology Evolves
Position dependent mismatch discrimination on DNA microarrays - experiments and model
Varia: a tool for prediction, analysis and visualisation of variable genes
Two-stage normalization using background intensities in cDNA microarray data
TmaDB: a repository for tissue microarray data
Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test
High-throughput peptide quantification using mTRAQ reagent triplex
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics
PLAST: parallel local alignment search tool for database comparison
Graph-based prediction of Protein-protein interactions with attributed signed graph embedding
Web-based analysis of the mouse transcriptome using Genevestigator
Protein-protein interaction extraction with feature selection by evaluating contribution levels of groups consisting of related features
Effective ambiguity checking in biosequence analysis
PRESTO: Rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies
Predicting protein functions by applying predicate logic to biomedical literature
Machine Learning for detection of viral sequences in human metagenomic datasets
Reverse engineering gene regulatory networks: Coupling an optimization algorithm with a parameter identification technique
Detecting overlapping protein complexes based on a generative model with functional and topological properties