yusuke1997/dblp-id-title huggingface dataset:
Joint epitope selection and spacer design for string-of-beads vaccines
Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence
Analysis of repeating oligonucleotide sequences in ribonucleic acids using an Apple II microcomputer
Textual data compression in computational biology: a synopsis
Exploring the role of human miRNAs in virus-host interactions using systematic overlap analysis
An unsupervised hierarchical dynamic self-organizing approach to cancer class discovery and marker gene identification in microarray data
Large scale microbiome profiling in the cloud
Evitar: designing anti-viral RNA therapies against future RNA viruses
Classification and review of free PCR primer design software
TimeTree2: species divergence times on the iPhone
SCOOP: a simple method for identification of novel protein superfamily relationships
Artificial neural network method for discriminating coding regions of eukaryotic genes
Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics
Analysis of high density expression microarrays with signed-rank call algorithms
A novel method for data fusion over entity-relation graphs and its application to protein-protein interaction prediction
Recognizing the fold of a protein structure
ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments
Codelink: an R package for analysis of GE healthcare gene expression bioarrays
CONTROL: software for the analysis of the control of metabolic networks
Evolutionary simulations to detect functional lineage-specific genes
Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy
TIGER: inferring DNA replication timing from whole-genome sequence data
Inferring genetic regulatory logic from expression data
DeepCDA: deep cross-domain compound-protein affinity prediction through LSTM and convolutional neural networks
MissForest - non-parametric missing value imputation for mixed-type data
SemGen: a tool for semantics-based annotation and composition of biosimulation models
An interactive genome browser of association results from the UK10K cohorts project
Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
me-PCR: a refined ultrafast algorithm for identifying sequence-defined genomic elements
OLIN: optimized normalization, visualization and quality testing of two-channel microarray data
PROXIMO - a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)
Extraction of protein interaction information from unstructured text using a context-free grammar
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization
Improved survival analysis by learning shared genomic information from pan-cancer data
Occupancy spectrum distribution: application for coalescence simulation with generic mergers
RBind: computational network method to predict RNA binding sites
Detection and interpretation of metabolite-transcript coresponses using combined profiling data
r2cat: synteny plots and comparative assembly
NMRpQuant : an automated software for large scale urinary total protein quantification by one-dimensional 1H NMR profiles
StackCPPred: a stacking and pairwise energy content-based prediction of cell-penetrating peptides and their uptake efficiency
pyBedGraph: a python package for fast operations on 1D genomic signal tracks
Efficient querying of genomic reference databases with gget
Capturing non-local interactions by long short-term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility
riboCleaner: a pipeline to identify and quantify rRNA read contamination from RNA-seq data in plants
GEMtractor: extracting views into genome-scale metabolic models
scatterbar: an R package for visualizing proportional data across spatially resolved coordinates
Joint analysis of individual-level and summary-level GWAS data by leveraging pleiotropy
BELMM: Bayesian model selection and random walk smoothing in time-series clustering
DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters
Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences
A data processing pipeline for the AACR project GENIE biopharma collaborative data with the {genieBPC} R package
??Harvester??: a fast meta search engine of human protein resources
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
TopoLink: evaluation of structural models using chemical crosslinking distance constraints
SVM-HUSTLE - an iterative semi-supervised machine learning approach for pairwise protein remote homology detection
Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study
MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization
GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution
Finding regulatory modules through large-scale gene-expression data analysis
ELIXIR: providing a sustainable infrastructure for life science data at European scale
scRNABatchQC: multi-samples quality control for single cell RNA-seq data
Scool: a new data storage format for single-cell Hi-C data
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs
The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction
Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
Probabilistic graphlets capture biological function in probabilistic molecular networks
FUEL-mLoc: feature-unified prediction and explanation of multi-localization of cellular proteins in multiple organisms
DIVAA: analysis of amino acid diversity in multiple aligned protein sequences
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ
Direct AUC optimization of regulatory motifs
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci
Matching relational patterns in nucleic acid sequences
SimLoRD: Simulation of Long Read Data
A complete, yet flexible, system for DNA/protein sequence analysis using VAX/VMS computers
Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation
HELIQUEST: a web server to screen sequences with specific alpha-helical properties
affylmGUI: a graphical user interface for linear modeling of single channel microarray data
SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences
Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit
LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism
CNVDetector: locating copy number variations using array CGH data
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring
Metrics for rapid quality control in RNA structure probing experiments
TargetNet: functional microRNA target prediction with deep neural networks
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
SBtab: a flexible table format for data exchange in systems biology
ProteoMix: an integrated and flexible system for interactively analyzing large numbers of protein sequences
snoStrip: a snoRNA annotation pipeline
tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes
Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe
HSEpred: predict half-sphere exposure from protein sequences
CRAVE: a database, middleware and visualization system for phenotype ontologies
3D-Cell-Annotator: an open-source active surface tool for single-cell segmentation in 3D microscopy images
G3viz: an R package to interactively visualize genetic mutation data using a lollipop-diagram
Image enhancement to leverage the 3D morphological reconstruction of single-cell neurons
eMPRess: a systematic cophylogeny reconciliation tool
Correction to: ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes
DNA Translator and Aligner: HyperCard utilities to aid phylogenetic analysis of molecules
PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities
Predicting enzymatic function of protein sequences with attention
Predicting serious rare adverse reactions of novel chemicals
Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations
DOMIRE: a web server for identifying structural domains and their neighbors in proteins
PyMethylProcess - convenient high-throughput preprocessing workflow for DNA methylation data
LncVar: a database of genetic variation associated with long non-coding genes
ExplorATE: a new pipeline to explore active transposable elements from RNA-seq data
The CroCo cross-link converter: a user-centred tool to convert results from cross-linking mass spectrometry experiments
Bioinformatics-the necessity of the quest for 'first principles' in life
SNPStats: a web tool for the analysis of association studies
Identification of context-specific gene regulatory networks with GEMULA - gene expression modeling using LAsso
An object model and database for functional genomics
EPIC-CoGe: managing and analyzing genomic data
Supercomputing for the parallelization of whole genome analysis
Using deep learning to associate human genes with age-related diseases
Group-combined P -values with applications to genetic association studies
EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites
Quartet Inference from SNP Data Under the Coalescent Model
HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data
NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug-target binding affinity prediction
BIPA: a database for protein-nucleic acid interaction in 3D structures
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences
PredMP: a web server for de novo prediction and visualization of membrane proteins
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
SNP-o-matic
SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences
VICTOR: genome-based phylogeny and classification of prokaryotic viruses
MDTips: a multimodal-data-based drug-target interaction prediction system fusing knowledge, gene expression profile, and structural data
Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems
Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+
RazerS 3: Faster, fully sensitive read mapping
ShinySOM: graphical SOM-based analysis of single-cell cytometry data
cypress : an R/Bioconductor package for cell-type-specific differential expression analysis power assessment
Metric learning on expression data for gene function prediction
From structure to dynamics of metabolic pathways: application to the plant mitochondrial TCA cycle
Smarter clustering methods for SNP genotype calling
cpPredictor: a web server for template-based prediction of RNA secondary structure
Group testing for pathway analysis improves comparability of different microarray datasets
CoCoNat: a novel method based on deep learning for coiled-coil prediction
A nearest-neighboring-end algorithm for genetic mapping
SPEM: a parser for EMBL style flat file database entries
Accurate PROTAC-targeted degradation prediction with DegradeMaster
Fundamental gene network rewiring at the second order within and across mammalian systems
SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer
A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
Predicting HIV drug resistance with neural networks
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data
BioGranat-IG: a network analysis tool to suggest mechanisms of genetic heterogeneity from exome-sequencing data
BigDataScript: a scripting language for data pipelines
Pretrained transformer models for predicting the withdrawal of drugs from the market
Meta-analysis of Caenorhabditis elegans single-cell developmental data reveals multi-frequency oscillation in gene activation
PrInCE: an R/Bioconductor package for protein-protein interaction network inference from co-fractionation mass spectrometry data
Improving protein fold recognition with hybrid profiles combining sequence and structure evolution
ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms
LIAN 3.0: detecting linkage disequilibrium in multilocus data
PRODIGY: personalized prioritization of driver genes
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees
Privacy preserving identification of population stratification for collaborative genomic research
Modification of DNA ends and detection of restriction enzyme recognition sequences in their ligated junctions
HoTResDB: host transcriptional response database for viral hemorrhagic fevers
corto: a lightweight R package for gene network inference and master regulator analysis
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes
Local sequence alignments with monotonic gap penalties
Resolving complex tandem repeats with long reads
KEDDY: a knowledge-based statistical gene set test method to detect differential functional protein-protein interactions
Outcome signature genes in breast cancer: is there a unique set?
Concepts to automate the theoretical design of effective antisense oligonucleotides
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life
Computer-aided construction of nucleic acid restriction maps using defined vectors
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies
Genozip: a universal extensible genomic data compressor
Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
A novel approach for increasing sensitivity and correcting saturation artifacts of radioactively labeled cDNA arrays
LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips
High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0
Generation of a database containing discordant intron positions in eukaryotic genes (MIDB)
Correction to: Continuous chromatin state feature annotation of the human epigenome
PanViz: interactive visualization of the structure of functionally annotated pangenomes
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts
Balancing protein similarity and gene co-expression reveals new links between genetic conservation and developmental diversity in invertebrates
Exploiting the past and the future in protein secondary structure prediction
To permute or not to permute
MeSHLabeler: improving the accuracy of large-scale MeSH indexing by integrating diverse evidence
canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS
VirPipe: an easy-to-use and customizable pipeline for detecting viral genomes from Nanopore sequencing
Class discovery and classification of tumor samples using mixture modeling of gene expression data - a unified approach
Precise charge-coupling calculations for finite difference diffusion problems using a modification of the add-on algorithm Q-COUPLE
CrossPlan: systematic planning of genetic crosses to validate mathematical models
MAFFIN: metabolomics sample normalization using maximal density fold change with high-quality metabolic features and corrected signal intensities
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks
SpecAlign - processing and alignment of mass spectra datasets
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups
Visualization of unfavorable interactions in protein folds
Regression trees for regulatory element identification
INTEGRALL: a database and search engine for integrons, integrases and gene cassettes
CCmiR: a computational approach for competitive and cooperative microRNA binding prediction
RNASeqGUI: a GUI for analysing RNA-Seq data
Cross-species queries of large gene expression databases
model.it : building three dimensional DNA models from sequence data
SRmapper: a fast and sensitive genome-hashing alignment tool
Mining HIV protease cleavage data using genetic programming with a sum-product function
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization
Disperse - a software system for design of selector probes for exon resequencing applications
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions
PDB2CD: a web-based application for the generation of circular dichroism spectra from protein atomic coordinates
libOmexMeta: enabling semantic annotation of models to support FAIR principles
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing
UniBioDicts: Unified access to Biological Dictionaries
RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies
Interfering contexts of regulatory sequence elements
Genquire: genome annotation browser/editor
Telescoper: de novo assembly of highly repetitive regions
Inference with viral quasispecies diversity indices: clonal and NGS approaches
DRTF: a database of rice transcription factors
LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis
ASCIIGenome: a command line genome browser for console terminals
SmashCommunity: a metagenomic annotation and analysis tool
Detection of potential enzyme targets by metabolic modelling and optimization: Application to a simple enzymopathy
Haystack: systematic analysis of the variation of epigenetic states and cell-type specific regulatory elements
Improved estimation of model quality using predicted inter-residue distance
A new statistical framework to assess structural alignment quality using information compression
The Distance Precision Matrix: computing networks from non-linear relationships
<tt>tstrait</tt> : a quantitative trait simulator for ancestral recombination graphs
Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data
A simple fold with variations: the pacifastin inhibitor family
TreeWiz: interactive exploration of huge trees
A non-linear optimization procedure to estimate distances and instantaneous substitution rate matrices under the GTR model
Introducing variable gap penalties to sequence alignment in linear space
Evaluating bacterial gene-finding HMM structures as probabilistic logic programs
ISMB 2008 conference report
METALGEN.DB: metabolism linked to the genome of Escherichia coli, a graphics-oriented database
Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development
Matching experiments across species using expression values and textual information
ViTO: tool for refinement of protein sequence-structure alignments
SimShift: Identifying structural similarities from NMR chemical shifts
deBGA: read alignment with de Bruijn graph-based seed and extension
Application of support vector machines for T-cell epitopes prediction
Ruffus: a lightweight Python library for computational pipelines
Joint embedding of biological networks for cross-species functional alignment
BlendMol: advanced macromolecular visualization in Blender
Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering
Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data
Approximating the set of local minima in partial RNA folding landscapes
SliceMap: an algorithm for automated brain region annotation
dbgap2x: an R package to explore and extract data from the database of Genotypes and Phenotypes (dbGaP)
Bayesian sampling of genomic rearrangement scenarios via double cut and join
miR2GO: comparative functional analysis for microRNAs
A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity
A comparison of algorithms for the pairwise alignment of biological networks
ISMB/ECCB 2015
Gene List significance at-a-glance with GeneValorization
The UniMarker (UM) method for synteny mapping of large genomes
Easy and interactive taxonomic profiling with Metabuli App
Predicting protein interactions via parsimonious network history inference
Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics
AlphaMPSim: flexible simulation of multi-parent crosses
A parallel algorithm to compute chemical organizations in biological networks
SHAPE directed RNA folding
Fast and accurate imputation of summary statistics enhances evidence of functional enrichment
A principal skeleton algorithm for standardizing confocal images of fruit fly nervous systems
SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks
Inductive matrix completion for predicting gene-disease associations
MP-LAMP: parallel detection of statistically significant multi-loci markers on cloud platforms
MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction
Human cell structure-driven model construction for predicting protein subcellular location from biological images
Molecular evaluation using in silico protein interaction profiles
mTM-align: an algorithm for fast and accurate multiple protein structure alignment
DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network
PROSOFT: a general purpose software in protein chemistry
Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences
FALCON: a toolbox for the fast contextualization of logical networks