yusuke1997/dblp-id-title huggingface dataset:
Alignment-free clustering of transcription factor binding motifs using a genetic-k-medoids approach
Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis
GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads
Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices
A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification
UVPAR: fast detection of functional shifts in duplicate genes
Optimizing graph-based patterns to extract biomedical events from the literature
Constructing a semantic predication gold standard from the biomedical literature
Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
Transparent mediation-based access to multiple yeast data sources using an ontology driven interface
MLPAstats: An R GUI package for the integrated analysis of copy number alterations using MLPA data
A question-entailment approach to question answering
Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access
TRain: T-cell receptor automated immunoinformatics
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context
Visualizing the genome: techniques for presenting human genome data and annotations
SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies
Robust consensus computation
Negative binomial additive model for RNA-Seq data analysis
HIV-phyloTSI: subtype-independent estimation of time since HIV-1 infection for cross-sectional measures of population incidence using deep sequence data
Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index
PyAGH: a python package to fast construct kinship matrices based on different levels of omic data
Testing the additional predictive value of high-dimensional molecular data
Topology-enhanced molecular graph representation for anti-breast cancer drug selection
Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
A systematic study on latent semantic analysis model parameters for mining biomedical literature
Protein structural similarity search by Ramachandran codes
A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization
Graphs in molecular biology
Correlation of cell membrane dynamics and cell motility
A fast least-squares algorithm for population inference
In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision
Core Hunter 3: flexible core subset selection
MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees
Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT
Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences
Next generation transcriptomes for next generation genomes using est2assembly
Environment specific substitution tables for thermophilic proteins
Comments on: fold change rank ordering statistics: a new method for detecting differentially expressed genes
BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies
cudaMap: a GPU accelerated program for gene expression connectivity mapping
Inferring protein function by domain context similarities in protein-protein interaction networks
Scaffold filling, contig fusion and comparative gene order inference
Dynamic model updating (DMU) approach for statistical learning model building with missing data
Automatic localization and identification of mitochondria in cellular electron cryo-tomography using faster-RCNN
Protein folding in HP model on hexagonal lattices with diagonals
AtPIN: Arabidopsis thaliana Protein Interaction Network
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Evaluation of pooling operations in convolutional architectures for drug-drug interaction extraction
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events
Integration of metabolomics, lipidomics and clinical data using a machine learning method
Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline
The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers
MFSPSSMpred: identifying short disorder-to-order binding regions in disordered proteins based on contextual local evolutionary conservation
Bounded search for de novo identification of degenerate cis-regulatory elements
Identification of physicochemical selective pressure on protein encoding nucleotide sequences
An extensive assessment of network alignment algorithms for comparison of brain connectomes
DBSecSys: a database of Burkholderia mallei secretion systems
Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning
Automated classification and characterization of the mitotic spindle following knockdown of a mitosis-related protein
Trends in the production of scientific data analysis resources
A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks
Contextualization of drug-mediator relations using evidence networks
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature
Lexical adaptation of link grammar to the biomedical sublanguage: a comparative evaluation of three approaches
Transcriptomic response to differentiation induction
Accounting for grouped predictor variables or pathways in high-dimensional penalized Cox regression models
Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization
DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle
Deep evolutionary fusion neural network: a new prediction standard for infectious disease incidence rates
ATAV: a comprehensive platform for population-scale genomic analyses
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability
MALDI imaging mass spectrometry: statistical data analysis and current computational challenges
The effects of early-life risperidone administration on forebrain neurotrophin expression during adulthood
poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening
Glycosylation site prediction using ensembles of Support Vector Machine classifiers
GenIO: a phenotype-genotype analysis web server for clinical genomics of rare diseases
Partial mixture model for tight clustering of gene expression time-course
Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets
GBCdb: RNA expression landscapes and ncRNA-mRNA interactions in gallbladder carcinoma
A new sequence logo plot to highlight enrichment and depletion
Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis
MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry
Combining gene prediction methods to improve metagenomic gene annotation
methCancer-gen: a DNA methylome dataset generator for user-specified cancer type based on conditional variational autoencoder
Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs
A microarray study of MPP + -treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates
Background frequencies for residue variability estimates: BLOSUM revisited
Proceedings of the 2017 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
MADA: a web service for analysing DNA methylation array data
Spatial quorum sensing modelling using coloured hybrid Petri nets and simulative model checking
ArkMAP: integrating genomic maps across species and data sources
Mutational Signatures in Cancer (MuSiCa): a web application to implement mutational signatures analysis in cancer samples
ReUseData: an R/Bioconductor tool for reusable and reproducible genomic data management
De novo profile generation based on sequence context specificity with the long short-term memory network
Evaluation of variant calling tools for large plant genome re-sequencing
New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background
Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration
Inversion-based genomic signatures
Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline
Drug-target interaction prediction via class imbalance-aware ensemble learning
More robust detection of motifs in coexpressed genes by using phylogenetic information
IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
afterParty: turning raw transcriptomes into permanent resources
Computational analysis of gene expression space associated with metastatic cancer
Improving prediction of phenotypic drug response on cancer cell lines using deep convolutional network
Mapping proteins in the presence of paralogs using units of coevolution
Deep learning architectures for prediction of nucleosome positioning from sequences data
PAnalyzer: A software tool for protein inference in shotgun proteomics
The volatile compound BinBase mass spectral database
A Network of SCOP Hidden Markov Models and Its Analysis
ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments
Bayesian models and meta analysis for multiple tissue gene expression data following corticosteroid administration
HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data
Methodology capture: discriminating between the "best" and the rest of community practice
Prediction of heart disease and classifiers' sensitivity analysis
Sensei: how many samples to tell a change in cell type abundance?
Roar: detecting alternative polyadenylation with standard mRNA sequencing libraries
Automatic classification of nerve discharge rhythms based on sparse auto-encoder and time series feature
HAPSIMU: a genetic simulation platform for population-based association studies
Computational modeling of the immune response in multiple sclerosis using epimod framework
Core module biomarker identification with network exploration for breast cancer metastasis
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation
Removing duplicate reads using graphics processing units
A fixed-point algorithm for estimating amplification efficiency from a polymerase chain reaction dilution series
Genome Expression Pathway Analysis Tool - Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
Computational verification of protein-protein interactions by orthologous co-expression
Genomic and proteomic characterization of multi-drug resistant Acinetobacter baumannii
GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data
Analysis of single-cell RNA sequencing data based on autoencoders
RNA editing-based classification of diffuse gliomas: predicting isocitrate dehydrogenase mutation and chromosome 1p/19q codeletion
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
A Semantic Web for bioinformatics: goals, tools, systems, applications
Statistical implications of pooling RNA samples for microarray experiments
GIFtS: annotation landscape analysis with GeneCards
Genome comparison without alignment using shortest unique substrings
Sensitivity analysis on protein-protein interaction networks through deep graph networks
BNDB - The Biochemical Network Database
MapMi: automated mapping of microRNA loci
A personalized computational model of edema formation in myocarditis based on long-axis biventricular MRI images
Conditional independence relations among biological markers may improve clinical decision as in the case of triple negative breast cancers
Metadag: a web tool to generate and analyse metabolic networks
Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis
INBIA: a boosting methodology for proteomic network inference
AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides
Missing value imputation improves clustering and interpretation of gene expression microarray data
Wide-coverage relation extraction from MEDLINE using deep syntax
Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
Joint embedding-classifier learning for interpretable collaborative filtering
StatiCAL: an interactive tool for statistical analysis of biomedical data and scientific valorization
Effective normalization for copy number variation in Hi-C data
eSTGt: a programming and simulation environment for population dynamics
Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures
Moment estimators of relatedness from low-depth whole-genome sequencing data
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides
Automatic generation of pseudoknotted RNAs taxonomy
A heuristic approach to determine an appropriate number of topics in topic modeling
CorrelaGenes: a new tool for the interpretation of the human transcriptome
Prediction of indirect interactions in proteins
ABrowse - a customizable next-generation genome browser framework
Probabilistic prediction and ranking of human protein-protein interactions
Partial inhibition and bilevel optimization in flux balance analysis
Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA
BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
Euclidean distance-optimized data transformation for cluster analysis in biomedical data (EDOtrans)
Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models
multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data
Shared transcriptional correlations in seed formation and in plants response to drought
Functional site prediction selects correct protein models
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
Synaptic plasticity in infralimbic cortex mediates socially-acquired nicotine self-administration
Automatic categorization of diverse experimental information in the bioscience literature
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Visualizing complex feature interactions and feature sharing in genomic deep neural networks
New Words in Human Mutagenesis
RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags
Aspects of coverage in medical DNA sequencing
Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions
Differential expression analysis for paired RNA-seq data
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
GOAL: A software tool for assessing biological significance of genes groups
Evaluating concentration estimation errors in ELISA microarray experiments
Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory
Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding
Inferring new indications for approved drugs via random walk on drug-disease heterogenous networks
Comparative analysis of microbiome measurement platforms using latent variable structural equation modeling
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science
Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles
GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease
A site specific model and analysis of the neutral somatic mutation rate in whole-genome cancer data
OGO: an ontological approach for integrating knowledge about orthology
SperMD: the expression atlas of sperm maturation
ESLpred2: improved method for predicting subcellular localization of eukaryotic proteins
GSAMDA: a computational model for predicting potential microbe-drug associations based on graph attention network and sparse autoencoder
Statistical inference for a quasi birth-death model of RNA transcription
A statistical network pre-processing method to improve relevance and significance of gene lists in microarray gene expression studies
A machine learning-based service for estimating quality of genomes using PATRIC
Multi-scale agent-based brain cancer modeling and prediction of TKI treatment response: Incorporating EGFR signaling pathway and angiogenesis
PON-SC - program for identifying steric clashes caused by amino acid substitutions
Visualization and analysis of microarray and gene ontology data with treemaps
Exploring biological interaction networks with tailored weighted quasi-bicliques
Assessing probe-specific dye and slide biases in two-color microarray data
Improving classification in protein structure databases using text mining
fastJT: An R package for robust and efficient feature selection for machine learning and genome-wide association studies
Predicting MHC class I epitopes in large datasets
SpliceFinder: ab initio prediction of splice sites using convolutional neural network
The poly-omics of ageing through individual-based metabolic modelling
CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes
SNA - a toolbox for the stoichiometric analysis of metabolic networks
DNA as a medium for hiding data
PDTD: a web-accessible protein database for drug target identification
Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays
Tri-model classifiers for EEG based mental task classification: hybrid optimization assisted framework
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy
Identifying miRNA synergism using multiple-intervention causal inference
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
A2A: a platform for research in biomedical literature search
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis
Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs)
Artificial neural network models for prediction of intestinal permeability of oligopeptides
Convolutional neural network for automated mass segmentation in mammography
Identification and analysis of structurally critical fragments in HopS2
Highly sensitive feature detection for high resolution LC/MS
H2V: a database of human genes and proteins that respond to SARS-CoV-2, SARS-CoV, and MERS-CoV infection
Predicting protein functions using incomplete hierarchical labels
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Visualization of comparative genomic analyses by BLAST score ratio
Mining protein function from text using term-based support vector machines
G-Aligner: a graph-based feature alignment method for untargeted LC-MS-based metabolomics
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration
Odyssey: a semi-automated pipeline for phasing, imputation, and analysis of genome-wide genetic data
Correction: Path-level interpretation of Gaussian graphical models using the pair-path subscore
Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats
Extraction, integration and analysis of alternative splicing and protein structure distributed information
MScanner: a classifier for retrieving Medline citations
HiComet: a high-throughput comet analysis tool for large-scale DNA damage assessment
CLIP-EZ: a computational tool for HITS-CLIP data analysis
Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases
Learning-based parallel acceleration for HaplotypeCaller
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models
A computational approach for detecting peptidases and their specific inhibitors at the genome level
Discovering and mapping chromatin states using a tree hidden Markov model
MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding
Evaluation of methods for detection of fluorescence labeled subcellular objects in microscope images
Genomic multiple sequence alignments: refinement using a genetic algorithm
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees
BayesianSSA: a Bayesian statistical model based on structural sensitivity analysis for predicting responses to enzyme perturbations in metabolic networks
PharmacoMicrobiomics or how bugs modulate drugs: an educational initiative to explore the effects of human microbiome on drugs
Computational prediction of inter-species relationships through omics data analysis and machine learning
Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach
Large scale hierarchical clustering of protein sequences
Identifying differential exon splicing using linear models and correlation coefficients
scCapsNet-mask: an updated version of scCapsNet with extended applicability in functional analysis related to scRNA-seq data