yusuke1997/dblp-id-title huggingface dataset:
Tissue-specific deconvolution of immune cell composition by integrating bulk and single-cell transcriptomes
WarpSTR: determining tandem repeat lengths using raw nanopore signals
StructureMapper: a high-throughput algorithm for analyzing protein sequence locations in structural data
A rarefaction-based extension of the LDM for testing presence-absence associations in the microbiome
Visualization portal for genetic variation (VizGVar): a tool for interactive visualization of SNPs and somatic mutations in exons, genes and protein domains
PON-Sol: prediction of effects of amino acid substitutions on protein solubility
gSearch: a fast and flexible general search tool for whole-genome sequencing
FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector
Canonical, stable, general mapping using context schemes
Kernel hierarchical gene clustering from microarray expression data
Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy
Computational epigenetics
chainCleaner improves genome alignment specificity and sensitivity
A powerful framework for differential co-expression analysis of general risk factors
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma
Pathgroups, a dynamic data structure for genome reconstruction problems
Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms
A dual-rule encoding DNA storage system using chaotic mapping to control GC content
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data
ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization
Fiona: a parallel and automatic strategy for read error correction
A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches
An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics
EST clustering error evaluation and correction
Targeted projection pursuit for visualizing gene expression data classifications
MUTAGEN: Multi-User Tool for Annotating GENomes
MethylSig: a whole genome DNA methylation analysis pipeline
ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning
Causal reasoning on biological networks: interpreting transcriptional changes
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data
AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis
Simulating intervertebral disc cell behaviour within 3D multifactorial environments
ParaSurf: a surface-based deep learning approach for paratope-antigen interaction prediction
NAMOT2 - a redesigned nucleic acid modeling tool: construction of non-canonical DNA structures
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
Background correction for cDNA microarray images using the TV+ L 1 model
I2b2-etl: Python application for importing electronic health data into the informatics for integrating biology and the bedside platform
Mechanistic insights into SARS-CoV-2 epidemic via revealing the features of SARS-CoV-2 coding proteins and host responses upon its infection
Taxonomic weighting improves the accuracy of a gap-filling algorithm for metabolic models
Genome-wide in silico prediction of gene expression
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data
Correction to: Integrative data semantics through a model-enabled data stewardship
GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data
Genome-wide co-expression based prediction of differential expressions
SNPman: a program for genotype calling using run data from TaqMan allelic discrimination
ReLiance: a machine learning and literature-based prioritization of receptor - ligand pairings
An efficient algorithm for optimizing whole genome alignment with noise
Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems
Microarray R-based analysis of complex lysate experiments with MIRACLE
Modeling and comparing the organization of circular genomes
Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators
Optimizing a global alignment of protein interaction networks
TMQuery: a database of precomputed template modeling scores for assessment of protein structural similarity
WDSPdb: an updated resource for WD40 proteins
MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure
CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions
Accurate mapping of tRNA reads
Bayesian ontology querying for accurate and noise-tolerant semantic searches
LRFragLib: an effective algorithm to identify fragments for de novo protein structure prediction
Canto: an online tool for community literature curation
PyChimera: use UCSF Chimera modules in any Python 2.7 project
SBML-PET: a Systems Biology Markup Language-based parameter estimation tool
Exon Array Analyzer: a web interface for Affymetrix exon array analysis
Evidential meta-model for molecular property prediction
An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data
Identification of caveolin-1 domain signatures via machine learning and graphlet analysis of single-molecule super-resolution data
APPEX: analysis platform for the identification of prognostic gene expression signatures in cancer
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework
Dynamic exploration and editing of KEGG pathway diagrams
QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction
coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies
Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing
A modification of the ALIGN program to assist visual interpretation of mutated sequences
A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thaliana
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers
Hooke : an open software platform for force spectroscopy
ppBAM: ProteinPaint BAM track for read alignment visualization and variant genotyping
Chromatin accessibility prediction via convolutional long short-term memory networks with k-mer embedding
EVA: continuous automatic evaluation of protein structure prediction servers
Artefacts and biases affecting the evaluation of scoring functions on decoy sets for protein structure prediction
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data
monarchr: an R package for querying biomedical knowledge graphs
AFragmenter: schema-free, tuneable protein domain segmentation for AlphaFold protein structures
Construction of robust prognostic predictors by using projective adaptive resonance theory as a gene filtering method
Development of an integrated laboratory information management system for the maize mapping project
MicrobeDB: a locally maintainable database of microbial genomic sequences
Short read alignment with populations of genomes
Kinetochore tracking in 3D from lattice light-sheet imaging data with KiT
MAESTROweb: a web server for structure-based protein stability prediction
Multi-query sequence BLAST output examination with MuSeqBox
Deep Local Analysis deconstructs protein-protein interfaces and accurately estimates binding affinity changes upon mutation
VarMatch: robust matching of small variant datasets using flexible scoring schemes
Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization
Converting networks to predictive logic models from perturbation signalling data with CellNOpt
MDPbiome: microbiome engineering through prescriptive perturbations
nestly - a framework for running software with nested parameter choices and aggregating results
Disease association tests by inferring ancestral haplotypes using a hidden markov model
FlowGrid enables fast clustering of very large single-cell RNA-seq data
A Markov random field model for network-based analysis of genomic data
HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies
GUV-AP: multifunctional FIJI-based tool for quantitative image analysis of Giant Unilamellar Vesicles
GNN-based embedding for clustering scRNA-seq data
A cell-based simulation software for multi-cellular systems
Extracting relations between promoter sequences and their strengths from microarray data
BERN2: an advanced neural biomedical named entity recognition and normalization tool
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data
Temporal network alignment via GoT-WAVE
MAGUS: Multiple sequence Alignment using Graph clUStering
PDP: protein domain parser
UniAlign: protein structure alignment meets evolution
StrainDesign: a comprehensive Python package for computational design of metabolic networks
Prediction of survival risks with adjusted gene expression through risk-gene networks
Bayesian hierarchical model of protein-binding microarray k -mer data reduces noise and identifies transcription factor subclasses and preferred k -mers
NGSNGS: next-generation simulator for next-generation sequencing data
CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files
Towards a computational model for -1 eukaryotic frameshifting sites
Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
SALSA: improved protein database searching by a new algorithm for assembly of sequence fragments into gapped alignments
A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences
Corrected Small-sample Estimation of the Bayes Error
TARGET: a new method for predicting protein subcellular localization in eukaryotes
VoroContacts: a tool for the analysis of interatomic contacts in macromolecular structures
Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
MiNEApy: enhancing enrichment network analysis in metabolic networks
COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomics
Genome Runner : automating genome exploration
Analysis and identification of beta-turn types using multinomial logistic regression and artificial neural network
BioLayout-an automatic graph layout algorithm for similarity visualization
Refining carbon flux paths using atomic trace data
CLARIFY: cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics
Recomb-Mix: fast and accurate local ancestry inference
Moment invariants as shape recognition technique for comparing protein binding sites
Extracting morphologies from third harmonic generation images of structurally normal human brain tissue
NaViA: a program for the visual analysis of complex mass spectra
TiSAn: estimating tissue-specific effects of coding and non-coding variants
Cytocipher determines significantly different populations of cells in single-cell RNA-seq data
GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
JTK: targeted diploid genome assembler
Monte Carlo feature selection for supervised classification
iTOP: inferring the topology of omics data
The Cardiac Atlas Project - an imaging database for computational modeling and statistical atlases of the heart
TiltRec: an ultra-fast and open-source toolkit for cryo-electron tomographic reconstruction
PredMS: a random forest model for predicting metabolic stability of drug candidates in human liver microsomes
HUGIn: Hi-C Unifying Genomic Interrogator
PIR-ALN: a database of protein sequence alignments
CGLFold: a contact-assisted de novo protein structure prediction using global exploration and loop perturbation sampling algorithm
DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach
An algorithm to fit the Gompertz function to growth curves
iATC-mISF: a multi-label classifier for predicting the classes of anatomical therapeutic chemicals
Conservation analysis of large biochemical networks
MAGGIE: leveraging genetic variation to identify DNA sequence motifs mediating transcription factor binding and function
Leveraging a pharmacogenomics knowledgebase to formulate a drug response phenotype terminology for genomic medicine
HGTDR: Advancing drug repurposing with heterogeneous graph transformers
The SGN comparative map viewer
ViReMaShiny : an interactive application for analysis of viral recombination data
A test for the statistical significance of DNA sequence similarities for application in databank searches
VCF2Networks: applying genotype networks to single-nucleotide variants data
StatAlign 2.0: combining statistical alignment with RNA secondary structure prediction
An algorithm for identifying regions of a DNA sequence that satisfy a content requirement
Topology-driven negative sampling enhances generalizability in protein-protein interaction prediction
Using median sets for inferring phylogenetic trees
Heritability estimation for a linear combination of phenotypes via ridge regression
The HMMTOP transmembrane topology prediction server
APoc: large-scale identification of similar protein pockets
Alvira: comparative genomics of viral strains
CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes
Reducing the algorithmic variability in transcriptome-based inference
rMATS-DVR: rMATS discovery of differential variants in RNA
Object-oriented programming for the biosciences
Phage-bacterial contig association prediction with a convolutional neural network
Genome-wide analysis and visualization of copy number with CNVpytor in igv.js
Protein multiple sequence alignment benchmarking through secondary structure prediction
wapRNA: a web-based application for the processing of RNA sequences
GUESS: projecting machine learning scores to well-calibrated probability estimates for clinical decision-making
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
BiopLib and BiopTools - a C programming library and toolset for manipulating protein structure
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model
The DynDom Database of Protein Domain Motions
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs
Software tools for motif and pattern scanning: program descriptions including a universal sequence reading algorithm
PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection
Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method
Editing, validating and translating of SBGN maps
PreRBP-TL: prediction of species-specific RNA-binding proteins based on transfer learning
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships
VIMCO: variational inference for multiple correlated outcomes in genome-wide association studies
Detecting biological network organization and functional gene orthologs
TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs
MPP: a microarray-to-phylogeny pipeline for analysis of gene and marker content datasets
Variance adaptive shrinkage ( vash ): flexible empirical Bayes estimation of variances
A comprehensive comparison of association estimators for gene network inference algorithms
Snakemake - a scalable bioinformatics workflow engine
MOJITOO: a fast and universal method for integration of multimodal single-cell data
Inferring cluster-based networks from differently stimulated multiple time-course gene expression data
The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections
MCPeSe: Monte Carlo penalty selection for graphical lasso
mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling
DADP: the database of anuran defense peptides
mlegp : statistical analysis for computer models of biological systems using R
Inference of locus-specific ancestry in closely related populations
ArtiFuse - computational validation of fusion gene detection tools without relying on simulated reads
Do-calculus enables estimation of causal effects in partially observed biomolecular pathways
CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning
HyAsP, a greedy tool for plasmids identification
Towards reliable named entity recognition in the biomedical domain
Precrec: fast and accurate precision-recall and ROC curve calculations in R
NanoStringNormCNV: pre-processing of NanoString CNV data
Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach
LipidFun: a database of lipid functions
A multi-array multi-SNP genotyping algorithm for Affymetrix SNP microarrays
Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells
EGAN: exploratory gene association networks
GOTreePlus: an interactive gene ontology browser
Payao: a community platform for SBML pathway model curation
The ArrayExpress gene expression database: a software engineering and implementation perspective
CAAT-Box, contigs-Assembly and Annotation Tool-Box for genome sequencing projects
Extending P450 site-of-metabolism models with region-resolution data
Detect differentially methylated regions using non-homogeneous hidden Markov model for methylation array data
PathCluster: a framework for gene set-based hierarchical clustering
JAMSS: proteomics mass spectrometry simulation in Java
Improving and evaluating deep learning models of cellular organization
Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites
Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter
Cosi2: an efficient simulator of exact and approximate coalescent with selection
Structural interpretation of fluorescence resonance-energy transfer measurements
Regression analysis and modelling of data acquisition for SELDI-TOF mass spectrometry
Population-based change-point detection for the identification of homozygosity islands
DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis
PIDO: the primary immunodeficiency disease ontology
Integrating long-range connectivity information into de Bruijn graphs
Machine learning of functional class from phenotype data
Prioritising candidate genes causing QTL using hierarchical orthologous groups
FPSAC: fast phylogenetic scaffolding of ancient contigs
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data
TMRPres2D: high quality visual representation of transmembrane protein models
Biomarker discovery in microarray gene expression data with Gaussian processes
Redesigning, implementing and integrating Escherichia coli genome software tools with an object-oriented database system
SBILib: a handle for protein modeling and engineering
STRIKE-GOLDD 4.0: user-friendly, efficient analysis of structural identifiability and observability
GlycoGlyph: a glycan visualizing, drawing and naming application
Resolution-exchanged structural modeling and simulations jointly unravel that subunit rolling underlies the mechanism of programmed ribosomal frameshifting
CytoSimplex: visualizing single-cell fates and transitions on a simplex
Genome wide predictions of miRNA regulation by transcription factors
DAGchainer: a tool for mining segmental genome duplications and synteny
The epiGenomic Efficient Correlator (epiGeEC) tool allows fast comparison of user datasets with thousands of public epigenomic datasets
Computational modeling of in vivo and in vitro protein-DNA interactions by multiple instance learning
EUPAN enables pan-genome studies of a large number of eukaryotic genomes
CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA
varLD: a program for quantifying variation in linkage disequilibrium patterns between populations
MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions
Shufflet: shuffling sequences while conserving the k-let counts
wpLogicNet: logic gate and structure inference in gene regulatory networks
chimeraviz: a tool for visualizing chimeric RNA
Inference of transcriptional regulatory network by two-stage constrained space factor analysis
Simulation of aggregation in Dictyostelium using the Cell Programming Language
AIMIE: a web-based environment for detection and interpretation of significant sequence motifs in prokaryotic genomes
Repeat- and error-aware comparison of deletions