yusuke1997/dblp-id-title huggingface dataset:
Obtaining insights from high-dimensional data: sparse principal covariates regression
Finding an appropriate equation to measure similarity between binary vectors: case studies on Indonesian and Japanese herbal medicines
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space
A factorization method for the classification of infrared spectra
LncDisAP: a computation model for LncRNA-disease association prediction based on multiple biological datasets
Biomarker interaction selection and disease detection based on multivariate gain ratio
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects
Combining feature selection and shape analysis uncovers precise rules for miRNA regulation in Huntington's disease mice
ContDist: a tool for the analysis of quantitative gene and promoter properties
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise
NoGOA: predicting noisy GO annotations using evidences and sparse representation
Live neighbor-joining
Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments
Kernel-imbedded Gaussian processes for disease classification using microarray gene expression data
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma
Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
NeatMap - non-clustering heat map alternatives in R
A novel nonparametric computational strategy for identifying differential methylation regions
Mining expressed sequence tags identifies cancer markers of clinical interest
Refining gene signatures: a Bayesian approach
Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions
CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms
A novel approach for predicting protein S-glutathionylation
Enzyme classification with peptide programs: a comparative study
Finishing bacterial genome assemblies with Mix
Uncovering the prognostic gene signatures for the improvement of risk stratification in cancers by using deep learning algorithm coupled with wavelet transform
Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β-aggregate forming peptide sequences
FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium
MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data
A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure
A multi-omics approach for identifying important pathways and genes in human cancer
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment
A scalable method for identifying frequent subtrees in sets of large phylogenetic trees
FiatFlux - a software for metabolic flux analysis from 13 C-glucose experiments
Machine learning approach informs biology of cancer drug response
GOTrapper: a tool to navigate through branches of gene ontology hierarchy
Deep learning methods for protein torsion angle prediction
Multiallelic models for QTL mapping in diverse polyploid populations
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
Fast Empirical Bayesian LASSO for Multiple Quantitative Trait Locus Mapping
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering
Cell cycle control and environmental response by second messengers in Caulobacter crescentus
DiviK: divisive intelligent K-means for hands-free unsupervised clustering in big biological data
Collocation analysis for UMLS knowledge-based word sense disambiguation
ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification
Efficient estimation of grouped survival models
Rank-invariant resampling based estimation of false discovery rate for analysis of small sample microarray data
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease
Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system
A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
Missing value imputation for microarray gene expression data using histone acetylation information
A modular framework for biomedical concept recognition
Efficient computation of absent words in genomic sequences
MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony
A new alignment-free method: K-mer Subsequence Natural Vector (K-mer SNV) for classification of fungi
Evaluation of properties over phylogenetic trees using stochastic logics
Multi-CAR: a tool of contig scaffolding using multiple references
Constructing a meaningful evolutionary average at the phylogenetic center of mass
Discover Protein Complexes in Protein-Protein Interaction Networks Using Parametric Local Modularity
A local average distance descriptor for flexible protein structure comparison
InDel marker detection by integration of multiple softwares using machine learning techniques
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
Cluster-based assessment of protein-protein interaction confidence
Identifying health related occupations of Twitter users through word embedding and deep neural networks
Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine 2020
Predicting protein-protein interface residues using local surface structural similarity
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs
Additive methods for genomic signatures
Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
leBIBI QBPP : a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences
Variant detection sensitivity and biases in whole genome and exome sequencing
Predicting population coverage of T-cell epitope-based diagnostics and vaccines
Semi-supervised COVID-19 CT image segmentation using deep generative models
Illumina WG-6 BeadChip strips should be normalized separately
LASAGNA: A novel algorithm for transcription factor binding site alignment
Automated analysis of phylogenetic clusters
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes
Identification of histone modifications in biomedical text for supporting epigenomic research
Prediction of miRNA-disease associations based on PCA and cascade forest
Classification based on extensions of LS-PLS using logistic regression: application to clinical and multiple genomic data
A systematic approach to detecting transcription factors in response to environmental stresses
Impact of explicit area scaling on kinetic models involving multiple compartments
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data
PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships
REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies
PURE: A webserver for the prediction of domains in unassigned regions in proteins
Comparative functional genomic study of substrate specificity evolution of the SABATH family of methyltransferases in plants
SGFSC: speeding the gene functional similarity calculation based on hash tables
Theme discovery from gene lists for identification and viewing of multiple functional groups
Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations
Predicting changes in protein thermostability brought about by single- or multi-site mutations
KinMap: a web-based tool for interactive navigation through human kinome data
Improving read mapping using additional prefix grams
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST
Visualization of large influenza virus sequence datasets using adaptively aggregated trees with sampling-based subscale representation
FastPop: a rapid principal component derived method to infer intercontinental ancestry using genetic data
An overview of the CellML API and its implementation
An imaging system for standardized quantitative analysis of C. elegans behavior
Identifying genes with tri-modal association with survival and tumor grade in cancer patients
Molecular modeling and lead design of substituted zanamivir derivatives as potent anti-influenza drugs
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia
Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective
Prediction of enzyme function by combining sequence similarity and protein interactions
Ceph-X: development and evaluation of 2D cephalometric system
iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data
VarioML framework for comprehensive variation data representation and exchange
ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining
Towards an Age-Phenome Knowledge-base
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays
BactoGeNIE: a large-scale comparative genome visualization for big displays
Comparative structural analysis of haemagglutinin proteins from type A influenza viruses: conserved and variable features
PKIS: computational identification of protein Kinases for experimentally discovered protein Phosphorylation sites
DBBP: database of binding pairs in protein-nucleic acid interactions
Feature selection using Haar wavelet power spectrum
Sortal anaphora resolution to enhance relation extraction from biomedical literature
FUSIM: a software tool for simulating fusion transcripts
IPRStats: visualization of the functional potential of an InterProScan run
Detecting overlapping coding sequences in virus genomes
In silico segmentations of lentivirus envelope sequences
Clustering of circular consensus sequences: accurate error correction and assembly of single molecule real-time reads from multiplexed amplicon libraries
Knowledge-based annotation of small molecule binding sites in proteins
binomialRF: interpretable combinatoric efficiency of random forests to identify biomarker interactions
Indel PDB: A database of structural insertions and deletions derived from sequence alignments of closely related proteins
Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data
Learning gene regulatory networks from only positive and unlabeled data
Block-based characterization of protease specificity from substrate sequence profile
Flexible taxonomic assignment of ambiguous sequencing reads
Gene function prediction using labeled and unlabeled data
Using Comparative Genomics & RNA Structure to Find RNA Editing Sites
SigsPack, a package for cancer mutational signatures
Spatial pattern analysis of nuclear migration in remodelled muscles during Drosophila metamorphosis
Accelerated large-scale multiple sequence alignment
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
Presenting and exploring biological pathways with PathVisio
Proceedings of the 2013 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
Using individual barcodes to increase quantification power of massively parallel reporter assays
Predicting Receptor-Ligand Pairs through Kernel Learning
VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
Visualising biological data: a semantic approach to tool and database integration
Fast network centrality analysis using GPUs
GPFrontend and GPGraphics: graphical analysis tools for genetic association studies
mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines
Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications
HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics
Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses
stpm: an R package for stochastic process model
Predicting enzyme targets for cancer drugs by profiling human Metabolic reactions in NCI-60 cell lines
Determining minimum set of driver nodes in protein-protein interaction networks
Estimating developmental states of tumors and normal tissues using a linear time-ordered model
Coral: an integrated suite of visualizations for comparing clusterings
A fast tool for minimum hybridization networks
Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis
Accounting for overlapping annotations in genomic prediction models of complex traits
Detect the early-warning signals of diseases based on signaling pathway perturbations on a single sample
The discriminant power of RNA features for pre-miRNA recognition
TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology
HormoNet: a deep learning approach for hormone-drug interaction prediction
LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data
HuntMi: an efficient and taxon-specific approach in pre-miRNA identification
Integrating water exclusion theory into βcontacts to predict binding free energy changes and binding hot spots
A methodological approach for using high-level Petri Nets to model the immune system response
A generic algorithm for layout of biological networks
Design and implementation of a generalized laboratory data model
Computational approaches for Cancer 2017 workshop overview
QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
Functional analysis of novel SNPs and mutations in human and mouse genomes
Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information
A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns
MQAPRank: improved global protein model quality assessment by learning-to-rank
Effective computational detection of piRNAs using n-gram models and support vector machine
FISH Amyloid - a new method for finding amyloidogenic segments in proteins based on site specific co-occurence of aminoacids
TIde: a software for the systematic scanning of drug targets in kinetic network models
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series
Development of tools for the automated analysis of spectra generated by tandem mass spectrometry
The Distributed Annotation System
Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes
Prioritizing biological pathways by recognizing context in time-series gene expression data
BRNI: Modular analysis of transcriptional regulatory programs
geneRFinder: gene finding in distinct metagenomic data complexities
ScreenSifter: analysis and visualization of RNAi screening data
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
LLAMA: a robust and scalable machine learning pipeline for analysis of large scale 4D microscopy data: analysis of cell ruffles and filopodia
HiTSEE KNIME: a visualization tool for hit selection and analysis in high-throughput screening experiments for the KNIME platform
The "etiome": identification and clustering of human disease etiological factors
ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification
DualGCN: a dual graph convolutional network model to predict cancer drug response
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation
Network-based de-noising improves prediction from microarray data
Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data
Haplotype based testing for a better understanding of the selective architecture
Discovering biological connections between experimental conditions based on common patterns of differential gene expression
Flexible and efficient genome tiling design with penalized uniqueness score
Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers
A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies
Modern simulation utilities for genetic analysis
Variable cellular decision-making behavior in a constant synthetic network topology
RegCloser: a robust regression approach to closing genome gaps
decompTumor2Sig: identification of mutational signatures active in individual tumors
EnsembleFam: towards more accurate protein family prediction in the twilight zone
Combining word embeddings to extract chemical and drug entities in biomedical literature
BayesMetab: treatment of missing values in metabolomic studies using a Bayesian modeling approach
Phenotype Recognition with Combined Features and Random Subspace Classifier Ensemble
LMAP: Lightweight Multigene Analyses in PAML
WholeCellViz: data visualization for whole-cell models
Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks
Topological characterization of neuronal arbor morphology via sequence representation: II - global alignment
t2prhd: a tool to study the patterns of repeat evolution
Evaluation of normalization methods for cDNA microarray data by k -NN classification
Graph regularized non-negative matrix factorization with L 2,1 norm regularization terms for drug-target interactions prediction
MetaMQAP: A meta-server for the quality assessment of protein models
An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data
Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform
MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment
Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles
Computational workflow for analysis of gain and loss of genes in distantly related genomes
SVhound: detection of regions that harbor yet undetected structural variation
Fast automatic quantitative cell replication with fluorescent live cell imaging
CLEAN: CLustering Enrichment ANalysis
DFAST_QC: quality assessment and taxonomic identification tool for prokaryotic Genomes
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior
Performance evaluation of lossy quality compression algorithms for RNA-seq data
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
ADEPT, a dynamic next generation sequencing data error-detection program with trimming
Convex-hull voting method on a large data set
Hierarchical Parallelization of Gene Differential Association Analysis
HEnRY: a DZIF LIMS tool for the collection and documentation of biomaterials in multicentre studies
Structural descriptor database: a new tool for sequence-based functional site prediction
SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information
Semantic annotation of morphological descriptions: an overall strategy
Mitochondrial Genome Sequence Analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy
GCOD - GeneChip Oncology Database
Coupling effects on turning points of infectious diseases epidemics in scale-free networks
How genome complexity can explain the difficulty of aligning reads to genomes
VPAC: Variational projection for accurate clustering of single-cell transcriptomic data
Integrative, multi-omics, analysis of blood samples improves model predictions: applications to cancer
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities
Implications for domain fusion protein-protein interactions based on structural information
The relationship between the L1 and L2 domains of the insulin and epidermal growth factor receptors and leucine-rich repeat modules
BioAssay Ontology (BAO): A Semantic Description of Bioassays and High-Throughput Screening Results
Structural motifs recurring in different folds recognize the same ligand fragments
Robust detection and verification of linear relationships to generate metabolic networks using estimates of technical errors
Correction to: Towards pixel-to-pixel deep nucleus detection in microscopy images
digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes
HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses
EpiFire: An open source C++ library and application for contact network epidemiology
Prediction of glycosylation sites using random forests
A genome alignment algorithm based on compression
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma
Yeast pheromone pathway modeling using Petri nets