yusuke1997/dblp-id-title huggingface dataset:
SPI: a tool for incorporating gene expression data into a four-dimensional database of Caenorhabditis elegans embryogenesis
Automatic generation of protein structure cartoons with Pro-origami
Modularity of cellular networks shows general center-periphery polarization
iEnhancer-EL: identifying enhancers and their strength with ensemble learning approach
ITFP: an integrated platform of mammalian transcription factors
MedKit: a helper toolkit for automatic mining of MEDLINE/PubMed citations
Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs
A multi-algorithm, multi-timescale method for cell simulation
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
Application of the cghRA framework to the genomic characterization of Diffuse Large B-Cell Lymphoma
InterMineR: an R package for InterMine databases
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
Web-based exchange of biochemical information
IRscope: an online program to visualize the junction sites of chloroplast genomes
Ribosome occupancy profiles are conserved between structurally and evolutionarily related yeast domains
Optimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms
Genesis: cluster analysis of microarray data
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
ESG: extended similarity group method for automated protein function prediction
Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition
PlanNET: homology-based predicted interactome for multiple planarian transcriptomes
SNiPA : an interactive, genetic variant-centered annotation browser
Prediction of quaternary structure from primary structure
tsRNAsearch: a pipeline for the identification of tRNA and ncRNA fragments from small RNA-sequencing data
Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity
Deep profiling of multitube flow cytometry data
Treenome Browser: co-visualization of enormous phylogenies and millions of genomes
CandiSNPer: a web tool for the identification of candidate SNPs for causal variants
WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy
Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution
On the representativeness and stability of a set of EFMs
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC
Coalescent simulation in continuous space
Computational identification of piRNA targets on mouse mRNAs
Bioinformatics challenges for genome-wide association studies
ESTprep: Preprocessing CDNA Sequence Reads
Simulated linear test applied to quantitative proteomics
flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data
SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric
A dissimilarity matrix between protein atom classes based on Gaussian mixtures
psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression
Protein-ensemble-RNA docking by efficient consideration of protein flexibility through homology models
TE Displayer for post-genomic analysis of transposable elements
VIZARD: analysis of Affymetrix Arabidopsis GeneChi® data
An online literature mining tool for protein phosphorylation
HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences
APID2NET: unified interactome graphic analyzer
Design of long oligonucleotide probes for functional gene detection in a microbial community
gemBS: high throughput processing for DNA methylation data from bisulfite sequencing
Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes
Speeding up whole-genome alignment by indexing frequency vectors
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
pyTWMR: transcriptome-wide Mendelian randomization in python
Robust identification of temporal biomarkers in longitudinal omics studies
METREE: a program package for inferring and testing minimum-evolution trees
Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods
Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis
RNApuzzler: efficient outerplanar drawing of RNA-secondary structures
MARSI: metabolite analogues for rational strain improvement
Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data
Effectively addressing complex proteomic search spaces with peptide spectrum matching
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets
Explainable nucleus classification using Decision Tree Approximation of Learned Embeddings
Automat: a novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS
Deep models for brain EM image segmentation: novel insights and improved performance
ORFanFinder: automated identification of taxonomically restricted orphan genes
Analysis of finite mixture of distributions: a statistical tool for biological classification problems
CProMG: controllable protein-oriented molecule generation with desired binding affinity and drug-like properties
Bias from removing read duplication in ultra-deep sequencing experiments
Searching for distantly related protein sequences in large databases by parallel processing on a transputer machine
Versatile genome assembly evaluation with QUAST-LG
An efficient method to identify differentially expressed genes in microarray experiments
MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning
RNA tertiary structure determination: NOE pathways construction by tabu search
mCSEA: detecting subtle differentially methylated regions
deTELpy: Python package for high-throughput detection of amino acid substitutions in mass spectrometry datasets
POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules
SHARP 2 : protein-protein interaction predictions using patch analysis
CONTRA: copy number analysis for targeted resequencing
A historical perspective on gene/protein functional assignment
QUASAR - scoring and ranking of sequence-structure alignments
FasParser2: a graphical platform for batch manipulation of tremendous amount of sequence data
ClutrFree: cluster tree visualization and interpretation
Knowledge-based gene expression classification via matrix factorization
Examining clustered somatic mutations with SigProfilerClusters
The ENDS of assumptions: an online tool for the epistemic non-parametric drug-response scoring
GPO-VAE: modeling explainable gene perturbation responses utilizing GRN-aligned parameter optimization
SVIM-asm: structural variant detection from haploid and diploid genome assemblies
ETAscape: analyzing protein networks to predict enzymatic function and substrates in Cytoscape
InteractiveROSETTA: a graphical user interface for the PyRosetta protein modeling suite
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
MPI-LIT: a literature-curated dataset of microbial binary protein--protein interactions
Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers
A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: application to human breast cancer
Ecological applications using a novel expert system shell
Hypercard-based data management tools for molecular biologists
Data-based identifiability analysis of non-linear dynamical models
scGrapHiC: deep learning-based graph deconvolution for Hi-C using single cell gene expression
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome
quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics
Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters
Neither random nor censored: estimating intensity-dependent probabilities for missing values in label-free proteomics
An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences
Using GOstats to test gene lists for GO term association
Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics
Discovering network phenotype between genetic risk factors and disease status via diagnosis-aligned multi-modality regression method in Alzheimer's disease
CMV: visualization for RNA and protein family models and their comparisons
Optimal Bayesian supervised domain adaptation for RNA sequencing data
Covariate-modulated local false discovery rate for genome-wide association studies
CaNDis: a web server for investigation of causal relationships between diseases, drugs and drug targets
Best templates outperform homology models in predicting the impact of mutations on protein stability
The WHy domain mediates the response to desiccation in plants and bacteria
An algorithm to determine protein sequence alignment by utilizing data obtained from a peptide mixture and individual peptides
S-leaping: an efficient downsampling method for large high-throughput sequencing data
cyvcf2: fast, flexible variant analysis with Python
Testing multiple gene interactions by the ordered combinatorial partitioning method in case-control studies
A machine learning-based method for prediction of macrocyclization patterns of polyketides and non-ribosomal peptides
Detecting host factors involved in virus infection by observing the clustering of infected cells in siRNA screening images
Dynamic compression schemes for graph coloring
Expression of Concern: Cleavage-Stage Embryo Segmentation Using SAM-Based Dual Branch Pipeline: Development and Evaluation with the CleavageEmbryo Dataset
Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
Rank order metrics for quantifying the association of sequence features with gene regulation
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping
SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments
ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting
PHYSEAN: PHYsical SEquence ANalysis for the identification of protein domains on the basis of physical and chemical properties of amino acids
COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome
Parameter estimation of kinetic models from metabolic profiles: two-phase dynamic decoupling method
The effect of replication on gene expression microarray experiments
Diamond: a multi-modal DIA mass spectrometry data processing pipeline
Using combined evidence from replicates to evaluate ChIP-seq peaks
TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference
libAnnotationSBML: a library for exploiting SBML annotations
cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs
zfRegeneration: a database for gene expression profiling during regeneration
Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach
SChiSM: creating interactive web page annotations of molecular structure models using Chime
GDASC: a GPU parallel-based web server for detecting hidden batch factors
2Struc: the secondary structure server
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data
Merging of distance matrices and classification by dynamic clustering
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data
SECA: SNP effect concordance analysis using genome-wide association summary results
PHISTO: pathogen-host interaction search tool
PyKnot: a PyMOL tool for the discovery and analysis of knots in proteins
A novel method of protein sequence classification based on oligopeptide frequency analysis and its application to search for functional sites and to domain localization
The ESID Online Database network
HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
DP2: Distributed 3D image segmentation using micro-labor workforce
Imputing gene expression to maximize platform compatibility
Parallel hardware for sequence comparison and alignment
Ragas: integration and enhanced visualization for single cell subcluster analysis
SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
Probabilistic alignment of motifs with sequences
Identification of sub-Golgi protein localization by use of deep representation learning features
ACE: adaptive cluster expansion for maximum entropy graphical model inference
MotifScorer: using a compendium of microarrays to identify regulatory motifs
SAMBLASTER : fast duplicate marking and structural variant read extraction
Allosite: a method for predicting allosteric sites
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
Using traveling salesman problem algorithms for evolutionary tree construction
Post-processing of BLAST results using databases of clustered sequences
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)
Development and evaluation of a deep learning model for protein-ligand binding affinity prediction
An integrated approach utilizing artificial neural networks and SELDI mass spectrometry for the classification of human tumours and rapid identification of potential biomarkers
Pan-genomic analysis provides novel insights into the association of E.coli with human host and its minimal genome
<tt>spillR</tt> : spillover compensation in mass cytometry data
Prediction of zinc-binding sites in proteins from sequence
Covariate-dependent negative binomial factor analysis of RNA sequencing data
miniMDS: 3D structural inference from high-resolution Hi-C data
Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products
Towards patterns tree of gene coexpression in eukaryotic species
Cellular proliferation biases clonal lineage tracing and trajectory inference
Incorporating prior knowledge into Gene Network Study
NMRb: a web-site repository for raw NMR datasets
ESPript: analysis of multiple sequence alignments in PostScript
Using the biological taxonomy to access biological literature with PathBinderH
Combinatorial therapy discovery using mixed integer linear programming
A hybrid bayesian approach for genome-wide association studies on related individuals
ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices
NucleusJ : an ImageJ plugin for quantifying 3D images of interphase nuclei
ROBNCA: robust network component analysis for recovering transcription factor activities
CAP: Conformation Angles Package - Displaying the Conformation Angles of Side Chains in Proteins
Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues
HYSTRUC: hydropathy and secondary structure prediction
Improving SNP prioritization and pleiotropic architecture estimation by incorporating prior knowledge using graph-GPA
EBARDenovo: highly accurate de novo assembly of RNA-Seq with efficient chimera-detection
Learning temporal difference embeddings for biomedical hypothesis generation
Learning sparse log-ratios for high-throughput sequencing data
Correcting sequencing errors in DNA coding regions using a dynamic programming approach
Transcriptome network component analysis with limited microarray data
RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures
Metadata retrieval from sequence databases with ffq
Jalview Version 2 - a multiple sequence alignment editor and analysis workbench
Literature mining and database annotation of protein phosphorylation using a rule-based system
OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA
SBGNview: towards data analysis, integration and visualization on all pathways
PSiFR: an integrated resource for prediction of protein structure and function
Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification
BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations
HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data
A new index to find regions showing an unexpected variability or conservation in sequence alignments
Grape RNA-Seq analysis pipeline environment
Predicting the linkage sites in glycoproteins using bio-basis function neural network
Substring selection for biomedical document classification
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
Comparison of approaches for parameter identifiability analysis of biological systems
LeafCutterMD: an algorithm for outlier splicing detection in rare diseases
Using language models and ontology topology to perform semantic mapping of traits between biomedical datasets
inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data
Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model
Two Hypercard calculators for molecular biology
Identifying diagnosis-specific genotype-phenotype associations via joint multitask sparse canonical correlation analysis and classification
MMnc: multi-modal interpretable representation for non-coding RNA classification and class annotation
A tool for RNA sequencing sample identity check
An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins
PROFcon: novel prediction of long-range contacts
A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
ScisorWiz: visualizing differential isoform expression in single-cell long-read data
A weighting system and algorithm for aligning many phylogenetically related sequences
Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM
Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease
Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment
Statistical compression of protein sequences and inference of marginal probability landscapes over competing alignments using finite state models and Dirichlet priors
OpenPhi: an interface to access Philips iSyntax whole slide images for computational pathology
Simulating genetic networks made easy: network construction with simple building blocks
Memory-efficient dynamic programming backtrace and pairwise local sequence alignment
TiSGeD: a database for tissue-specific genes
Prediction of locally stable RNA secondary structures for genome-wide surveys
Link-HD: a versatile framework to explore and integrate heterogeneous microbial communities
A context-sensitive framework for the analysis of human signalling pathways in molecular interaction networks
Exchangeable random variables
cisExpress : motif detection in DNA sequences
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information
FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human
Imprint of evolutionary conservation and protein structure variation on the binding function of protein tyrosine kinases
WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) - a web application for visualization of wastewater pathogen sequencing results
MultiGuideScan: a multi-processing tool for designing CRISPR guide RNA libraries
Prediction of biologically significant components from microarray data: Independently Consistent Expression Discriminator (ICED)
Unified methods for feature selection in large-scale genomic studies with censored survival outcomes
Persistent minimal sequences of SARS-CoV-2
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins
Browsing protein families via the 'Rich Family Description' format
SNAPper: gene order predicts gene function
Cardinal : an R package for statistical analysis of mass spectrometry-based imaging experiments
FERAL: network-based classifier with application to breast cancer outcome prediction
MOSAIC: segmenting multiple aligned DNA sequences
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images
Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: do mutations of H1N1 from 1918 to 2009 affect much on this binding?
Identification of linked regions using high-density SNP genotype data in linkage analysis
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems
A space and time-efficient index for the compacted colored de Bruijn graph
Programs for reference library managing
Construction of restriction maps
MeganServer: facilitating interactive access to metagenomic data on a server
spolTools: online utilities for analyzing spoligotypes of the Mycobacterium tuberculosis complex
Accurate prediction of human essential genes using only nucleotide composition and association information
Reasoning with bio-ontologies: using relational closure rules to enable practical querying
ProQ2: estimation of model accuracy implemented in Rosetta
FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis
CodonLogo: a sequence logo-based viewer for codon patterns
Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation
SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models