yusuke1997/dblp-id-title huggingface dataset:
Repetitive palindromic sequences in Escherichia coli. Detection and characterization with a new computer program
Incorporating prior information into association studies
Development of an animal genome database and its search system
Annotation confidence score for genome annotation: a genome comparison approach
OWEN: aligning long collinear regions of genomes
A Novel algorithm for identifying low-complexity regions in a protein sequence
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data
Assessing reproducibility of matrix factorization methods in independent transcriptomes
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
Determining functional specificity from protein sequences
pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination
DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments
Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information
GenomeVISTA - an integrated software package for whole-genome alignment and visualization
ChromoHub V2: cancer genomics
SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks
TotalReCaller: improved accuracy and performance via integrated alignment and base-calling
FoldAtlas: a repository for genome-wide RNA structure probing data
The Victor C++ library for protein representation and advanced manipulation
ggtranscript : an R package for the visualization and interpretation of transcript isoforms using ggplot2
Marker development for the genetic study of natural variation in Arabidopsis thaliana
mebipred : identifying metal-binding potential in protein sequence
LuxUS: DNA methylation analysis using generalized linear mixed model with spatial correlation
Can sugars be produced from fatty acids? A test case for pathway analysis tools
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms
EFICAz 2.5 : application of a high-precision enzyme function predictor to 396 proteomes
Integrative analysis reveals the direct and indirect interactions between DNA copy number aberrations and gene expression changes
QuICSeedR: an R package for analyzing fluorophore-assisted seed amplification assay data
Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA
TESD: a transposable element dynamics simulation environment
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
Learning to predict protein-protein interactions from protein sequences
Multiple sequence alignment in parallel on a workstation cluster
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference
aPRBind: protein-RNA interface prediction by combining sequence and I-TASSER model-based structural features learned with convolutional neural networks
findPC: An R package to automatically select the number of principal components in single-cell analysis
On representative and illustrative comparisons with real data in bioinformatics: response to the letter to the editor by Smith et al.
Glycan family analysis for deducing N -glycan topology from single MS
Statistical distance between texts and filtration methods in sequence comparison
mimicMe: a web server for prediction and analysis of host-like proteins in microbial pathogens
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways
PsiNorm: a scalable normalization for single-cell RNA-seq data
EzMap: a simple pipeline for reproducible analysis of the human virome
MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignment
OMEGA: a three-dimensional databank for protein structures (a complement to PDB)
Advanced Boolean modeling of biological networks applied to systems pharmacology
A comparison of scoring functions for protein sequence profile alignment
UCSC Cell Browser: visualize your single-cell data
contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples
Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS
XIBD: software for inferring pairwise identity by descent on the X chromosome
DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes
ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data
Robust rank aggregation for gene list integration and meta-analysis
Dealing with dimensionality: the application of machine learning to multi-omics data
A fully computational and reasonable representation for karyotypes
SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images
WIMOVAC: a software package for modelling the dynamics of plant leaf and canopy photosynthesis
Deep and wide digging for binding motifs in ChIP-Seq data
CobraMod: a pathway-centric curation tool for constraint-based metabolic models
bbcontacts: prediction of β -strand pairing from direct coupling patterns
VHost-Classifier: virus-host classification using natural language processing
Identification of causal genes for complex traits
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences
Graph convolution for predicting associations between miRNA and drug resistance
Bio-support vector machines for computational proteomics
MEICPS: substitution mutations to engineer intracellular protein stability
Gobe: an interactive, web-based tool for comparative genomic visualization
PyPore: a python toolbox for nanopore sequencing data handling
Memory-efficient RNA energy landscape exploration
Efficient network-guided multi-locus association mapping with graph cuts
Phylogenetic scanning: a computer-assisted algorithm for mapping gene conversions and other recombinational events
geneCo: a visualized comparative genomic method to analyze multiple genome structures
MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG
A BASIC microcomputer program for prediction of B and T cell epitopes in proteins
Primary sequence analysis and representation techniques in carbohydrates
Buchnera BASE: a post-genomic resource for Buchnera sp. APS
Observation of multiple folding pathways of beta -hairpin trpzip2 from independent continuous folding trajectories
Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival
RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution
Visualization and probability-based scoring of structural variants within repetitive sequences
Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference
MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals
ViralConsensus: a fast and memory-efficient tool for calling viral consensus genome sequences directly from read alignment data
Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data
HyperPCR: a Macintosh Hypercard program for the determination of optimal PCR annealing temperature
NetCAD: a network analysis tool for coronary artery disease-associated PPI network
Software support for SBGN maps: SBGN-ML and LibSBGN
Starcode: sequence clustering based on all-pairs search
Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland
Inferring global levels of alternative splicing isoforms using a generative model of microarray data
AuberGene - a sensitive genome alignment tool
Mosaic: making biological sense of complex networks
QU-GENE: a simulation platform for quantitative analysis of genetic models
Peptide set test: a peptide-centric strategy to infer differentially expressed proteins
RCSB PDB Mobile : iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank
Sparse representation and Bayesian detection of genome copy number alterations from microarray data
Integrated gene and species phylogenies from unaligned whole genome protein sequences
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily
nuScore: a web-interface for nucleosome positioning predictions
DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation
Highly accelerated feature detection in proteomics data sets using modern graphics processing units
Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?
iBioSim: a tool for the analysis and design of genetic circuits
Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001
A novel pipeline for computerized mouse spermatogenesis staging
An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis
Finding coexpressed genes in counts-based data: an improved measure with validation experiments
Robust and accurate data enrichment statistics via distribution function of sum of weights
DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences
An analysis of the Protein Data Bank in search of temporal and global trends
MEGA-GO: functions prediction of diverse protein sequence length using Multi-scalE Graph Adaptive neural network
Top-DTI: integrating topological deep learning and large language models for drug-target interaction prediction
MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis
Computational modelling of LY303511 and TRAIL-induced apoptosis suggests dynamic regulation of cFLIP
RCPedia: a database of retrocopied genes
Combining frequency and positional information to predict transcription factor binding sites
Accurately modeling biased random walks on weighted networks using node2vec+
Analysis of internal loops within the RNA secondary structure in almost quadratic time
In response to "On E -value for tandem MS scoring schemes"
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements
Pleiotropic mapping and annotation selection in genome-wide association studies with penalized Gaussian mixture models
Modified Nonparametric Approaches to Detecting Differentially Expressed Genes in Replicated Microarray Experiments
database.bio: a web application for interpreting human variations
A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes
Membranome 2.0: database for proteome-wide profiling of bitopic proteins and their dimers
NGSANE: a lightweight production informatics framework for high-throughput data analysis
dICC: distance-based intraclass correlation coefficient for metagenomic reproducibility studies
The European Bioinformatics Institute web site: a new view
Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
GradHC: highly reliable gradual hash-based clustering for DNA storage systems
Detecting time periods of differential gene expression using Gaussian processes: an application to endothelial cells exposed to radiotherapy dose fraction
Hotelling's T 2 multivariate profiling for detecting differential expression in microarrays
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
Discovering and visualizing indirect associations between biomedical concepts
ShapePheno: unsupervised extraction of shape phenotypes from biological image collections
Identifying cancer-related microRNAs based on gene expression data
The complexity of comparing reaction systems
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Correction: Surface ID: a geometry-aware system for protein molecular surface comparison
BRGenomics for analyzing high-resolution genomics data in R
ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data
ABRA: improved coding indel detection via assembly-based realignment
A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues
Differential network analysis of multiple human tissue interactomes highlights tissue-selective processes and genetic disorder genes
Incorporating prior knowledge into regularized regression
The Glycine Receptor Allosteric Ligands Library (GRALL)
Automatic prediction of polysaccharide utilization loci in Bacteroidetes species
RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA
RNAsolo: a repository of cleaned PDB-derived RNA 3D structures
A simple method for the removal of mains interference from pre-recorded electrophysiological data
Using genomic annotations increases statistical power to detect eGenes
Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap
3D GAN image synthesis and dataset quality assessment for bacterial biofilm
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs
SNPassoc: an R package to perform whole genome association studies
MitoProt, a Macintosh application for studying mitochondrial proteins
Studying 3D genome evolution using genomic sequence
GRASS: semi-automated NMR-based structure elucidation of saccharides
MIMIC: a Python package for simulating, inferring, and predicting microbial community interactions and dynamics
Indexed variation graphs for efficient and accurate resistome profiling
Accurate loop calling for 3D genomic data with cLoops
RaMWAS: fast methylome-wide association study pipeline for enrichment platforms
A new method for the high-precision assessment of tumor changes in response to treatment
Seave: a comprehensive web platform for storing and interrogating human genomic variation
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
DNAPlotter: circular and linear interactive genome visualization
PhyloProfile: dynamic visualization and exploration of multi-layered phylogenetic profiles
MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling
Modeling nucleosome position distributions from experimental nucleosome positioning maps
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)
Quantitative measurement of aging using image texture entropy
Compression and fast retrieval of SNP data
Joint sparse canonical correlation analysis for detecting differential imaging genetics modules
GiANT: gene set uncertainty in enrichment analysis
Probabilistic models of genetic variation in structured populations applied to global human studies
BLAST++: BLASTing queries in batches
NvAssign: protein NMR spectral assignment with NMRView
Geobase: a simple geographical information system on a personal computer
Updating annotations with the distributed annotation system and the automated sequence annotation pipeline
Incorporating prior information into differential network analysis using non-paranormal graphical models
Composition bias and the origin of ORFan genes
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations
Estimating the diversity of peptide populations from limited sequence data
A Web-based design center for vector-based siRNA and siRNA cassette
Estimating the order of mutations during tumorigenesis from tumor genome sequencing data
Permutation importance: a corrected feature importance measure
MemGen: a general web server for the setup of lipid membrane simulation systems
Flexible informatics for linking experimental data to mathematical models via DataRail
A Bayesian segmentation approach to ascertain copy number variations at the population level
Genome assembly from synthetic long read clouds
A DNA intercalation methodology for an efficient prediction of ligand binding pose and energetics
Leitmotif: protein motif scanning 2.0
pymzML - Python module for high-throughput bioinformatics on mass spectrometry data
A search for common patterns in many sequences
ADAN: a database for prediction of protein-protein interaction of modular domains mediated by linear motifs
S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank
Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions
HMMGEP: clustering gene expression data using hidden Markov models
Assumption weighting for incorporating heterogeneity into meta-analysis of genomic data
AbDiver: a tool to explore the natural antibody landscape to aid therapeutic design
Multivariate two-part statistics for analysis of correlated mass spectrometry data from multiple biological specimens
BAPS 2: enhanced possibilities for the analysis of genetic population structure
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection
Cell2Chem: mining explored and unexplored biosynthetic chemical spaces
An extensible application for assembling annotation for genomic data
A BASIC microcomputer program for data analysis of limiting dilution assays
SCLpred-EMS: subcellular localization prediction of endomembrane system and secretory pathway proteins by Deep N-to-1 Convolutional Neural Networks
Exploration and retrieval of whole-metagenome sequencing samples
MIRA: an R package for DNA methylation-based inference of regulatory activity
Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis
LipidPedia: a comprehensive lipid knowledgebase
ModDotPlot - rapid and interactive visualization of tandem repeats
MSX-3D: a tool to validate 3D protein models using mass spectrometry
MacT: Apple Macintosh programs for constructing phylogenetic trees
PEDL: extracting protein-protein associations using deep language models and distant supervision
Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments
MGAS: a powerful tool for multivariate gene-based genome-wide association analysis
BBC microcomputer controlled field inversion gel electrophoresis
SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics
Genome-by-genome approach for fast bacterial genealogical relationship evaluation
CDRUG: a web server for predicting anticancer activity of chemical compounds
Linking sequence patterns and functionality of alpha-helical antimicrobial peptides
FastTargetPred: a program enabling the fast prediction of putative protein targets for input chemical databases
PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model
KinVis: a visualization tool to detect cryptic relatedness in genetic datasets
Axe: rapid, competitive sequence read demultiplexing using a trie
CMF-Impute: an accurate imputation tool for single-cell RNA-seq data
ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data
A weight array method for splicing signal analysis
A cautionary note on using binary calls for analysis of DNA methylation
Continual knowledge infusion into pre-trained biomedical language models
Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data
gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks
rmRNAseq: differential expression analysis for repeated-measures RNA-seq data
MEPSA: minimum energy pathway analysis for energy landscapes
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
AutoCAT: automated cancer-associated TCRs discovery from TCR-seq data
Selecting targets for structural determination by navigating in a graph of protein families
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity
DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome
Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data
Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes
PopCluster: an algorithm to identify genetic variants with ethnicity-dependent effects
Parameter estimation for dynamical systems with discrete events and logical operations
A novel computational approach for drug repurposing using systems biology
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling
Flame (v2.0): advanced integration and interpretation of functional enrichment results from multiple sources
Comparison of human protein-protein interaction maps
A program for reordering coded data
Joint stage recognition and anatomical annotation of drosophila gene expression patterns
AFsample: improving multimer prediction with AlphaFold using massive sampling
PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution
GOLDsurfer: three dimensional display of linkage disequilibrium
Linking metabolic network features to phenotypes using sparse group lasso
DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
Automated classification of cytogenetic abnormalities in hematolymphoid neoplasms
Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data
Lengthening of 3′UTR increases with morphological complexity in animal evolution
OrthoGUI: graphical presentation of Orthostrapper results
Molecular basis for specificity in the druggable kinome: sequence-based analysis
Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization
Predicting Cancer Drug Response using a Recommender System
Parallelized multiple alignment
UnifiedGreatMod: a new holistic modelling paradigm for studying biological systems on a complete and harmonious scale
MitoFlex: an efficient, high-performance toolkit for animal mitogenome assembly, annotation and visualization
Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking
apLCMS - adaptive processing of high-resolution LC/MS data
An integrative approach to predicting the functional effects of non-coding and coding sequence variation
Statistical estimation of cluster boundaries in gene expression profile data
AliView: a fast and lightweight alignment viewer and editor for large datasets
Customizable views on semantically integrated networks for systems biology
Discovering transcriptional modules by Bayesian data integration
Unrealistic phylogenetic trees may improve phylogenetic footprinting
Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy
A regularized discriminative model for the prediction of protein-peptide interactions
FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
ECCB 2014: The 13 th European Conference on Computational Biology