yusuke1997/dblp-id-title huggingface dataset:
BranchClust: a phylogenetic algorithm for selecting gene families
Automatic discovery of cross-family sequence features associated with protein function
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing
Fast activation maximization for molecular sequence design
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules
GSAR: Bioconductor package for Gene Set analysis in R
Thawing Frozen Robust Multi-array Analysis (fRMA)
RevEcoR: an R package for the reverse ecology analysis of microbiomes
Predicting existing targets for new drugs base on strategies for missing interactions
Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions
GSVA: gene set variation analysis for microarray and RNA-Seq data
SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences
Realizing drug repositioning by adapting a recommendation system to handle the process
CBESW: Sequence Alignment on the Playstation 3
CoolBox: a flexible toolkit for visual analysis of genomics data
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation
mtDNAcombine: tools to combine sequences from multiple studies
A comparison of methods for differential expression analysis of RNA-seq data
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data
Systematic calibration of a cell signaling network model
Analyzing gene expression data for pediatric and adult cancer diagnosis using logic learning machine and standard supervised methods
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling
Species-specific analysis of protein sequence motifs using mutual information
An ontology-based search engine for protein-protein interactions
PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine
The Genome Reverse Compiler: an explorative annotation tool
Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes
Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types
A systems biology approach to elucidating epigenetic regulation of cardiac hypertrophy
Cross-validation for training and testing co-occurrence network inference algorithms
Assessments of Affymetrix GeneChip Microarray Quality for Laboratories and Single Samples
Phenotype forecasting with SNPs data through gene-based Bayesian networks
Parallel multiple instance learning for extremely large histopathology image analysis
Classification of genomic signals using dynamic time warping
Bioinformatics analysis of transcriptional regulation of circadian genes in rat liver
BioRel: towards large-scale biomedical relation extraction
A text-mining system for extracting metabolic reactions from full-text articles
SODa: An Mn/Fe superoxide dismutase prediction and design server
Bayesian semi-supervised classification of bacterial samples using MLST databases
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
Computational discovery and annotation of conserved small open reading frames in fungal genomes
R-Gada: a fast and flexible pipeline for copy number analysis in association studies
A simple method to combine multiple molecular biomarkers for dichotomous diagnostic classification
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer
Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA
HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction
BAMQL: a query language for extracting reads from BAM files
BLAST+: architecture and applications
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets
Determination of the minimum number of microarray experiments for discovery of gene expression patterns
SFSSClass: an integrated approach for miRNA based tumor classification
RLFDDA: a meta-path based graph representation learning model for drug-disease association prediction
Regularized Least Squares Cancer Classifiers from DNA microarray data
GenEpi: gene-based epistasis discovery using machine learning
MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments
PoPLAR: Portal for Petascale Lifescience Applications and Research
Implementing sequence-based antigenic distance calculation into immunological shape space model
Exploiting the bootstrap method to analyze patterns of gene expression
TEES 2.2: Biomedical Event Extraction for Diverse Corpora
A perspective for biomedical data integration: Design of databases for flow cytometry
Critique of the pairwise method for estimating qPCR amplification efficiency: beware of correlated data!
Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal
Dynamic epigenetic mode analysis using spatial temporal clustering
Task-driven knowledge graph filtering improves prioritizing drugs for repurposing
Parameter estimation in models of biological oscillators: an automated regularised estimation approach
metaX: a flexible and comprehensive software for processing metabolomics data
HTQC: a fast quality control toolkit for Illumina sequencing data
Improving the performance of beta-turn prediction using predicted shape strings and a two-layer support vector machine model
ENTRNA: a framework to predict RNA foldability
PSSM-based prediction of DNA binding sites in proteins
VAIV bio-discovery service using transformer model and retrieval augmented generation
Dependency parsing of biomedical text with BERT
Using distances between Top-n-gram and residue pairs for protein remote homology detection
A Poisson reduced-rank regression model for association mapping in sequencing data
A novel method detecting the key clinic factors of portal vein system thrombosis of splenectomy & cardia devascularization patients for cirrhosis & portal hypertension
Oqtans: a multifunctional workbench for RNA-seq data analysis
An investigation into inter- and intragenomic variations of graphic genomic signatures
Signal transduction pathway profiling of individual tumor samples
Bayesian inference of biochemical kinetic parameters using the linear noise approximation
Prediction of heterogeneous differential genes by detecting outliers to a Gaussian tight cluster
Comparison of pathway and gene-level models for cancer prognosis prediction
Identifying protein complexes based on node embeddings obtained from protein-protein interaction networks
A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants
NITPicker: selecting time points for follow-up experiments
Multiple organism algorithm for finding ultraconserved elements
GenomeBlast: a web tool for small genome comparison
Data-driven normalization strategies for high-throughput quantitative RT-PCR
Design of lung nodules segmentation and recognition algorithm based on deep learning
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions
Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks
ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA-protein interactions
The BioLexicon: a large-scale terminological resource for biomedical text mining
A molecular structure matching approach to efficient identification of endogenous mammalian biochemical structures
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
A mesh generation and machine learning framework for Drosophila gene expression pattern image analysis
HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes
The systems biology format converter
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models
Predicting deleterious nsSNPs: an analysis of sequence and structural attributes
Analysis of interactions between ribosomal proteins and RNA structural motifs
Liver tumor segmentation in CT volumes using an adversarial densely connected network
Detailed estimation of bioinformatics prediction reliability through the Fragmented Prediction Performance Plots
Discovering biclusters in gene expression data based on high-dimensional linear geometries
ScRNAbox: empowering single-cell RNA sequencing on high performance computing systems
Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly
Validating Clustering of Molecular Dynamics Simulations Using Polymer Models
Identifying named entities from PubMed®; for enriching semantic categories
An alignment-free method for phylogeny estimation using maximum likelihood
Improving performance of mammalian microRNA target prediction
MICA: desktop software for comprehensive searching of DNA databases
DECA: scalable XHMM exome copy-number variant calling with ADAM and Apache Spark
TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction
Identification of ATP binding residues of a protein from its primary sequence
Empirical codon substitution matrix
Polynomial superlevel set representation of the multistationarity region of chemical reaction networks
A new insight into underlying disease mechanism through semi-parametric latent differential network model
CSA: An efficient algorithm to improve circular DNA multiple alignment
Probabilistic ancestry maps: a method to assess and visualize population substructures in genetics
Variable-order sequence modeling improves bacterial strain discrimination for Ion Torrent DNA reads
Computational investigation of DNA packing in confinement
Predicting drug-protein interactions by preserving the graph information of multi source data
Accurate splice site prediction using support vector machines
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences
A minimal descriptor of an ancestral recombinations graph
Serendipitous discoveries in microarray analysis
Demonstration of two novel methods for predicting functional siRNA efficiency
MultiChIPmixHMM: an R package for ChIP-chip data analysis modeling spatial dependencies and multiple replicates
scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis
Combining transcriptional datasets using the generalized singular value decomposition
Sorting genomes with rearrangements and segmental duplications through trajectory graphs
A straightforward method to compute average stochastic oscillations from data samples
GeneralizedDTA: combining pre-training and multi-task learning to predict drug-target binding affinity for unknown drug discovery
optimalFlow: optimal transport approach to flow cytometry gating and population matching
Rational discovery of new capsaicin analogues as TRPV1 activators
ConCysFind: a pipeline tool to predict conserved amino acids of protein sequences across the plant kingdom
Robust and accurate prediction of noncoding RNAs from aligned sequences
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets
Exploratory visual analysis of conserved domains on multiple sequence alignments
ColonyTrak: a web tool and database system for managing experimental animal models
R/parallel - speeding up bioinformatics analysis with R
CountASAP: a lightweight, easy to use python package for processing ASAPseq data
Giving raw data a chance to talk: A demonstration of de-identified Pediatric Research Database (PRD) and exploratory analysis techniques for possible research cohort discovery and identifiable high risk factors for readmission
A computational approach for ordering signal transduction pathway components from genomics and proteomics Data
MPDA: Microarray pooled DNA analyzer
A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer
CNVind: an open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi Diagrams
ProphNet: A generic prioritization method through propagation of information
BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus
Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences
Computational algorithms to predict Gene Ontology annotations
How interacting pathways are regulated by miRNAs in breast cancer subtypes
EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
A robust measure of correlation between two genes on a microarray
An approach for clustering gene expression data with error information
Machine learning to analyse omic-data for COVID-19 diagnosis and prognosis
Disk-based k-mer counting on a PC
CMAGN: circRNA-miRNA association prediction based on graph attention auto-encoder and network consistency projection
Compartmentalization of the Edinburgh Human Metabolic Network
CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments
Expression pattern divergence of duplicated genes in rice
EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics
Identification and utilization of copy number information for correcting Hi-C contact map of cancer cell lines
GPAT: Retrieval of genomic annotation from large genomic position datasets
Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists
WormTensor: a clustering method for time-series whole-brain activity data from C. elegans
A semantic web framework to integrate cancer omics data with biological knowledge
Data-driven biological network alignment that uses topological, sequence, and functional information
OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies
Detection of attractors of large Boolean networks via exhaustive enumeration of appropriate subspaces of the state space
Reconstructing genome trees of prokaryotes using overlapping genes
Deep learning based DNA: RNA triplex forming potential prediction
Bioinformatics screening of biomarkers related to liver cancer
NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly
Manananggal - a novel viewer for alternative splicing events
Spatial segmentation and feature selection for desi imaging mass spectrometry data with spatially-aware sparse clustering
NanoStriDE: normalization and differential expression analysis of NanoString nCounter data
MitoTox: a comprehensive mitochondrial toxicity database
SPRINT: A new parallel framework for R
IHCP: interpretable hepatitis C prediction system based on black-box machine learning models
VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences
Multivariate meta-analysis of proteomics data from human prostate and colon tumours
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions
SKPDB: a structural database of shikimate pathway enzymes
Comparison and improvement of algorithms for computing minimal cut sets
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Regularized estimation of large-scale gene association networks using graphical Gaussian models
Kernel-based distance metric learning for microarray data classification
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring
Structural characterization of genomes by large scale sequence-structure threading: application of reliability analysis in structural genomics
QuaDMutNetEx: a method for detecting cancer driver genes with low mutation frequency
Aneuvis: web-based exploration of numerical chromosomal variation in single cells
POPISK: T-cell reactivity prediction using support vector machines and string kernels
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes
Gene expression data classification using topology and machine learning models
SVExpress: identifying gene features altered recurrently in expression with nearby structural variant breakpoints
A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks
NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model
Can geometric combinatorics improve RNA branching predictions?
An improved classification of G-protein-coupled receptors using sequence-derived features
Gene and protein nomenclature in public databases
TIGER: tiled iterative genome assembler
PEPOP 2.0: new approaches to mimic non-continuous epitopes
Initial steps towards a production platform for DNA sequence analysis on the grid
ANINet: a deep neural network for skull ancestry estimation
A haplotype-based normalization technique for the analysis and detection of allele specific expression
Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data
Identification of clustered microRNAs using an ab initio prediction method
The Autoimmune Disease Database: a dynamically compiled literature-derived database
Gene processing control loops suggested by sequencing, splicing, and RNA folding
Capturing coevolutionary signals inrepeat proteins
Consensus clustering for Bayesian mixture models
Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves
A method for exploring implicit concept relatedness in biomedical knowledge network
Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments
Age-adjusted nonparametric detection of differential DNA methylation with case-control designs
Identification of plant vacuole proteins by using graph neural network and contact maps
Prediction of guide strand of microRNAs from its sequence and secondary structure
Assessing the quality of annotations in asthma gene expression experiments
Adaptable, high recall, event extraction system with minimal configuration
AllerTOP - a server for in silico prediction of allergens
Computational determination of hERG-related cardiotoxicity of drug candidates
Identification of monotonically differentially expressed genes for non-small cell lung cancer
Extending pathways based on gene lists using InterPro domain signatures
EnClaSC: a novel ensemble approach for accurate and robust cell-type classification of single-cell transcriptomes
Moments of genome evolution by Double Cut-and-Join
HHMMiR: efficient de novo prediction of microRNAs using hierarchical hidden Markov models
PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum
Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations
QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
Userscripts for the Life Sciences
Novel methods for secondary structure determination using low wavelength (VUV) circular dichroism spectroscopic data
Predicting genetic interactions with random walks on biological networks
Coloring the Mu transpososome
Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015
BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data
Weighted minimum feedback vertex sets and implementation in human cancer genes detection
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I
Establishing a protocol for single cell transcriptome sequencing of the rat brain
Prediction of host - pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs
Gene network interconnectedness and the generalized topological overlap measure
Towards accurate characterization of clonal heterogeneity based on structural variation
Identifying differentially regulated subnetworks from phosphoproteomic data
Hierarchical shared transfer learning for biomedical named entity recognition
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model
A novel subgradient-based optimization algorithm for blockmodel functional module identification
Vestige: Maximum likelihood phylogenetic footprinting
Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application
A neural network model to screen feature genes for pancreatic cancer
INTEGRATOR: interactive graphical search of large protein interactomes over the Web
Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns
Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains
A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms
Adaptiveness of RGB-image derived algorithms in the measurement of fractional vegetation coverage
Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs
Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies
DeepFrag-k: a fragment-based deep learning approach for protein fold recognition
VIGOR, an annotation program for small viral genomes
Building protein-protein interaction networks for Leishmania species through protein structural information
Density-reducing Jaccard estimators for sketch-based long read applications
A p-Median approach for predicting drug response in tumour cells
An optimized TOPS+ comparison method for enhanced TOPS models
STAR: predicting recombination sites from amino acid sequence
A structural approach for finding functional modules from large biological networks
Interpolation based consensus clustering for gene expression time series
Benchmarking of different molecular docking methods for protein-peptide docking
Differential coexpression network modules observed in human hepatocellular carcinoma progression
Ttn as a likely causal gene for QTL of alcohol preference on mouse chromosome 2
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data
Fuzzy association rules for biological data analysis: A case study on yeast