yusuke1997/dblp-id-title huggingface dataset:
Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics
Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources
Omilayers: a Python package for efficient data management to support multi-omic analysis
MotifClick: prediction of cis-regulatory binding sites via merging cliques
Process attributes in bio-ontologies
Gene prediction of aging-related diseases based on DNN and Mashup
SigFlux : A novel network feature to evaluate the importance of proteins in signal transduction networks
AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data
The dChip survival analysis module for microarray data
Helitron distribution in Brassicaceae and whole Genome Helitron density as a character for distinguishing plant species
MIPHENO: data normalization for high throughput metabolite analysis
Deep convolutional neural networks for mammography: advances, challenges and applications
Identifier mapping performance for integrating transcriptomics and proteomics experimental results
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics
EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers
Towards linked open gene mutations data
HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species
Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies
Normalizing for individual cell population context in the analysis of high-content cellular screens
Cheminformatics methods for novel nanopore analysis of HIV DNA termini
Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment
A Graph Feature Auto-Encoder for the prediction of unobserved node features on biological networks
Comparing somatic mutation-callers: Beyond Venn diagrams
GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms
A fast and effective dependency graph kernel for PPI relation extraction
Limit cycles in models of circular gene networks regulated by negative feedback loops
Length-dependent prediction of protein intrinsic disorder
DEDB: a database of Drosophila melanogaster exons in splicing graph form
An overlapping module identification method in protein-protein interaction networks
Learning the optimal scale for GWAS through hierarchical SNP aggregation
The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research
Analysis of associations between emotions and activities of drug users and their addiction recovery tendencies from social media posts using structural equation modeling
Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods
Identification of CD8 + T cell epitopes through proteasome cleavage site predictions
GEDI: a user-friendly toolbox for analysis of large-scale gene expression data
On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence
Structure-based substrate screening for an enzyme
RAPSearch: a Fast Protein Similarity Search Tool for Short Reads
Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique
Impact of concurrency on the performance of a whole exome sequencing pipeline
JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals
MS-kNN: protein function prediction by integrating multiple data sources
QPCR: Application for real-time PCR data management and analysis
Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM)
PCAN: phenotype consensus analysis to support disease-gene association
Decomposing the space of protein quaternary structures with the interface fragment pair library
Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons
A neural network multi-task learning approach to biomedical named entity recognition
Localizing triplet periodicity in DNA and cDNA sequences
EnvMine: A text-mining system for the automatic extraction of contextual information
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins
Distinguishing between enzyme sequences & non-enzymes without using alignments
A new method for exploring gene-gene and gene-environment interactions in GWAS with tree ensemble methods and SHAP values
AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions
Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
Gene family assignment-free comparative genomics
Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs)
IMMAN: an R/Bioconductor package for Interolog protein network reconstruction, mapping and mining analysis
VisANT: an online visualization and analysis tool for biological interaction data
Enhancing SVM for survival data using local invariances and weighting
KiNext: a portable and scalable workflow for the identification and classification of protein kinases
A deep learning-based framework for lung cancer survival analysis with biomarker interpretation
dsPIG: a tool to predict imprinted genes from the deep sequencing of whole transcriptomes
Leukocyte Nucleus Segmentation and Nucleus Lobe Counting
Agalma: an automated phylogenomics workflow
FitTetra 2.0 - improved genotype calling for tetraploids with multiple population and parental data support
Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy
Data structures and compression algorithms for high-throughput sequencing technologies
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data
A systematic study of genome context methods: calibration, normalization and combination
An integrative bioinformatic predictor of protein sub-cellular localisation in malaria
PyHLA: tests for the association between HLA alleles and diseases
Comparison of mode estimation methods and application in molecular clock analysis
dgfr: an R package to assess sequence diversity of gene families
RECOVIR: An application package to automatically identify some single stranded RNA viruses using capsid protein residues that uniquely distinguish among these viruses
Eye-color and Type-2 diabetes phenotype prediction from genotype data using deep learning methods
Discovering multiple realistic TFBS motifs based on a generalized model
Gene set-based module discovery in the breast cancer transcriptome
TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data
Semantic similarity in the biomedical domain: an evaluation across knowledge sources
Correction to: DeSP: a systematic DNA storage error simulation pipeline
Gene and pathway identification with L p penalized Bayesian logistic regression
Toward an interactive article: integrating journals and biological databases
Planning combinatorial disulfide cross-links for protein fold determination
Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
A study of quality measures for protein threading models
Genomic distance under gene substitutions
bioNMF: a versatile tool for non-negative matrix factorization in biology
A study on the flexibility of enzyme active sites
TADMaster: a comprehensive web-based tool for the analysis of topologically associated domains
AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments
Target SNP selection in complex disease association studies
Multi-label literature classification based on the Gene Ontology graph
xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation
Predicting protein functions by relaxation labelling protein interaction network
OrthoInspector: comprehensive orthology analysis and visual exploration
A simple approach for protein name identification: prospects and limits
RMDNet: RNA-aware dung beetle optimization-based multi-branch integration network for RNA-protein binding sites prediction
DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction
PASBio: predicate-argument structures for event extraction in molecular biology
GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model
DNA Molecule Classification Using Feature Primitives
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model
SMITH: a LIMS for handling next-generation sequencing workflows
PAWER: protein array web exploreR
Computational study of noise in a large signal transduction network
Bio-jETI: a framework for semantics-based service composition
Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines
A sequence embedding method for enzyme optimal condition analysis
On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors
The tumor as an organ: comprehensive spatial and temporal modeling of the tumor and its microenvironment
The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail
Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control
Comparative study of whole exome sequencing-based copy number variation detection tools
SRAdb: query and use public next-generation sequencing data from within R
Feature selection and classifier performance on diverse bio- logical datasets
Time-lagged Ordered Lasso for network inference
CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks
PredSTP: a highly accurate SVM based model to predict sequential cystine stabilized peptides
Fast and scalable neural embedding models for biomedical sentence classification
Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data
Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure
GeneSurrounder: network-based identification of disease genes in expression data
The curvHDR method for gating flow cytometry samples
tacg - a grep for DNA
Beef quality parameters estimation using ultrasound and color images
Approximate inference of gene regulatory network models from RNA-Seq time series data
Software tool for internal standard based normalization of lipids, and effect of data-processing strategies on resulting values
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network
Comparing K-mer based methods for improved classification of 16S sequences
PIXER: an automated particle-selection method based on segmentation using a deep neural network
ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data
An efficient pseudomedian filter for tiling microrrays
Large-scale clustering of CAGE tag expression data
ABCtoolbox: a versatile toolkit for approximate Bayesian computations
Entropy-based gene ranking without selection bias for the predictive classification of microarray data
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins
Improving the accuracy of high-throughput protein-protein affinity prediction may require better training data
Integration of relational and hierarchical network information for protein function prediction
Correcting scale distortion in RNA sequencing data
CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants
Mutanalyst, an online tool for assessing the mutational spectrum of epPCR libraries with poor sampling
Marmal-aid - a database for Infinium HumanMethylation450
MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations
Epigenetic control of signaling networks involved in interleukin-18-induced cardiac hypertrophy and its attenuation by pan-histone deacetylase inhibitors
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds
Advances in monolingual and crosslingual automatic disability annotation in Spanish
Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies
Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support
A benchmark study of sequence alignment methods for protein clustering
Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses
Highlights from the 1st ISCB Latin American Student Council Symposium 2014
KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences
Pleiotropy of tumor necrosis factor-alpha in C2C12 myotubes: in vitro studies on genes, networks and pathways involved in TNF-alpha induced skeletal muscle atrophy
Assessment of transfer methods for comparative genomics of regulatory networks in bacteria
Matching health information seekers' queries to medical terms
Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time
The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem
A full Bayesian hierarchical mixture model for the variance of gene differential expression
iRODS metadata management for a cancer genome analysis workflow
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases
LDA-SCGB: inferring lncRNA-disease associations based on condensed gradient boosting
Response network analysis of differential gene expression in human epithelial lung cells during avian influenza infections
An analysis of extensible modelling for functional genomics data
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
A reinforced merging methodology for mapping unique peptide motifs in members of protein families
Controlling false discoveries in high-dimensional situations: boosting with stability selection
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis
Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays
An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
Tumor classification and marker gene prediction by feature selection and fuzzy c-means clustering using microarray data
Reconstruction of human protein interolog network using evolutionary conserved network
Archetypal analysis of diverse Pseudomonas aeruginosa transcriptomes reveals adaptation in cystic fibrosis airways
Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation
Surface feature based classification of plant organs from 3D laserscanned point clouds for plant phenotyping
Automatic classification of registered clinical trials towards the Global Burden of Diseases taxonomy of diseases and injuries
Discrete structural features among interface residue-level classes
Identifying gene-specific subgroups: an alternative to biclustering
InterferenceAnalyzer: Tools for the analysis and simulation of multi-locus genetic data
Robust methods for population stratification in genome wide association studies
Enabling dynamic network analysis through visualization in TVNViewer
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila
The language of gene ontology: a Zipf's law analysis
Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
Identification of gene-drug interactions that impact patient survival in TCGA
Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support
Root Digger: a root placement program for phylogenetic trees
Building pathway clusters from Random Forests classification using class votes
Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)
inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons
GoWeb: a semantic search engine for the life science web
LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens
Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets
Multiplex methods provide effective integration of multi-omic data in genome-scale models
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε
Fast MCMC Sampling for Hidden Markov Models to Determine Copy Number Variations
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways
An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways
GsmPlot: a web server to visualize epigenome data in NCBI
A model-based information sharing protocol for profile Hidden Markov Models used for HIV-1 recombination detection
Secondary structure specific simpler prediction models for protein backbone angles
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis
Taxonomy based performance metrics for evaluating taxonomic assignment methods
The tissue microarray data exchange specification: implementation by the Cooperative Prostate Cancer Tissue Resource
A novel cell nuclei segmentation method for 3D C. elegans embryonic time-lapse images
bioSyntax: syntax highlighting for computational biology
VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database
Identification of metabolites from 2D 1 H- 13 C HSQC NMR using peak correlation plots
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data
iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features
Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment
Algorithms for effective querying of compound graph-based pathway databases
Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
RNA folding on the 3D triangular lattice
A model of pulldown alignments from SssI-treated DNA improves DNA methylation prediction
Joint pre-processing framework for two-dimensional gel electrophoresis images based on nonlinear filtering, background correction and normalization techniques
RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network
CANDLE/Supervisor: a workflow framework for machine learning applied to cancer research
xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria
Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data
Tiling array data analysis: a multiscale approach using wavelets
CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny
SAlign-a structure aware method for global PPI network alignment
Multiple sequence alignment accuracy and evolutionary distance estimation
UTAP: User-friendly Transcriptome Analysis Pipeline
ISSEC: inferring contacts among protein secondary structure elements using deep object detection
An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse
Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation
BPG: Seamless, automated and interactive visualization of scientific data
EDRMM: enhancing drug recommendation via multi-granularity and multi-attribute representation
Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments
A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences
Be-dataHIVE: a base editing database
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis
Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists
SNP-PHAGE - High throughput SNP discovery pipeline
Supervised topological data analysis for MALDI mass spectrometry imaging applications
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks
Reducing Boolean networks with backward equivalence
Topology independent protein structural alignment
GenRCA: a user-friendly rare codon analysis tool for comprehensive evaluation of codon usage preferences based on coding sequences in genomes
Generation and comparative genomics of synthetic dengue viruses
SLiMScape: a protein short linear motif analysis plugin for Cytoscape
Correction to: Evaluating the impact of topological protein features on the negative examples selection
Looking for chromosome spatial organization rules in microarray gene expression data
Design of a DNA-based shift register
puma: a Bioconductor package for propagating uncertainty in microarray analysis
A multiplex primer design algorithm for target amplification of continuous genomic regions
Computing preimages of Boolean networks
Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences
Blazing Signature Filter: a library for fast pairwise similarity comparisons
NMF-mGPU: non-negative matrix factorization on multi-GPU systems
ESTree db: a Tool for Peach Functional Genomics
Hinge Atlas: relating protein sequence to sites of structural flexibility
Towards practical privacy-preserving genome-wide association study
Efficient proximal gradient algorithm for inference of differential gene networks