yusuke1997/dblp-id-title huggingface dataset:
Development of a protein-ligand extended connectivity (PLEC) fingerprint and its application for binding affinity predictions
mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics
NetBioV: an R package for visualizing large network data in biology and medicine
STRUM: structure-based prediction of protein stability changes upon single-point mutation
Solubis: optimize your protein
A graph-theoretic approach for the separation of b and y ions in tandem mass spectra
The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations
ToolShop: prerelease inspections for protein structure prediction servers
Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses
Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities
Alignment of dynamic networks
HALPER facilitates the identification of regulatory element orthologs across species
Charting the structure-sequence landscape of light chain amyloids
Babel's tower revisited: a universal resource for cross-referencing across annotation databases
Sequence-structure specificity of a knowledge based energy function at the secondary structure level
Modelling capture efficiency of single-cell RNA-sequencing data improves inference of transcriptome-wide burst kinetics
Hierarchical reinforcement learning for automatic disease diagnosis
Association of nucleotide patterns with gene function classes: application to human 3' untranslated sequences
MutationFinder: a high-performance system for extracting point mutation mentions from text
GenomeDiagram: a python package for the visualization of large-scale genomic data
Heterogeneous entity representation for medicinal synergy prediction
NETASA: neural network based prediction of solvent accessibility
RiboD: a comprehensive database for prokaryotic riboswitches
Viruses selectively mutate their CD8+ T-cell epitopes - a large-scale immunomic analysis
A Comparison of Parametric Versus Permutation Methods with Applications to General and Temporal Microarray Gene Expression Data
Distinct profiling of antimicrobial peptide families
ChaperISM: improved chaperone binding prediction using position-independent scoring matrices
Associative database of protein sequences
CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks
Nonlinear regression on a microcomputer: which program?
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
ceas: an R package for Seahorse data analysis and visualization
Drug-target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism
LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation
Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental Mueller matrices
Evolution of gene neighborhoods within reconciled phylogenies
Feature selection using a one dimensional naïve Bayes' classifier increases the accuracy of support vector machine classification of CDR3 repertoires
OCSANA+: optimal control and simulation of signaling networks from network analysis
Unsupervised discovery of information structure in biomedical documents
Characterization and identification of long non-coding RNAs based on feature relationship
Haplotype inference by maximum parsimony
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
ATEN: And/Or tree ensemble for inferring accurate Boolean network topology and dynamics
Mining gene expression databases for association rules
RSVSim: an R/Bioconductor package for the simulation of structural variations
RelEx - Relation extraction using dependency parse trees
HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS
Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web
miRNAmeConverter: an R/bioconductor package for translating mature miRNA names to different miRBase versions
VariantTools: an extensible framework for developing and testing variant callers
SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles
Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions
GABI-Kat SimpleSearch: A Flanking Sequence Tag (FST) Database for the Identification of T-DNA Insertion Mutants in Arabidopsis Thaliana
Investigating microbial co-occurrence patterns based on metagenomic compositional data
Nsite, NsiteH and NsiteM computer tools for studying transcription regulatory elements
A web application to perform linkage disequilibrium and linkage analyses on a computational grid
TALENoffer: genome-wide TALEN off-target prediction
Lossy compression of quality scores in genomic data
Model-based prediction of sequence alignment quality
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data
PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics
Comparison of observation-based and model-based identification of alert concentrations from concentration-expression data
Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features
iHMMune-align: hidden Markov model-based alignment and identification of germline genes in rearranged immunoglobulin gene sequences
AMiGA: the arthropodan mitochondrial genomes accessible database
Fast characterization of segmental duplications in genome assemblies
SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis
Bridging the gaps in statistical models of protein alignment
SuperSpot: coarse graining spatial transcriptomics data into metaspots
PedVizApi: a Java API for the interactive, visual analysis of extended pedigrees
MOSS: multi-omic integration with sparse value decomposition
ChEMBLSpace - a graphical explorer of the chemogenomic space covered by the ChEMBL database
scRNAss: a single-cell RNA-seq assembler via imputing dropouts and combing junctions
Detecting differential protein expression in large-scale population proteomics
MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues
GMHCC: high-throughput analysis of biomolecular data using graph-based multiple hierarchical consensus clustering
Fast, clash-free RNA conformational morphing using molecular junctions
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks
Exploring chromatin conformation and gene co-expression through graph embedding
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging
Kaviar: an accessible system for testing SNV novelty
FSelector: a Ruby gem for feature selection
Association testing of bisulfite-sequencing methylation data via a Laplace approximation
QuickLIMS: facilitating the data management for DNA-microarray fabrication
Hierarchical Bayesian models of transcriptional and translational regulation processes with delays
methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing
Structure-dependent sequence alignment for remotely related proteins
Genome-wide pre-miRNA discovery from few labeled examples
Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface
MINDG: a drug-target interaction prediction method based on an integrated learning algorithm
Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art
Rfold: an exact algorithm for computing local base pairing probabilities
AskBeacon - performing genomic data exchange and analytics with natural language
LSTSQ: a module for reliable constrained and unconstrained nonlinear regression
EMBLSCAN: fast approximate DNA database searches on compact disc
iCarPS: a computational tool for identifying protein carbonylation sites by novel encoded features
Comprehensive, comprehensible, distributed and intelligent databases: current status
Faster sequence homology searches by clustering subsequences
ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes
PINSPlus: a tool for tumor subtype discovery in integrated genomic data
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
Using Lotus 1-2-3 to determine correlation of linearly related method comparison data
MatArray: a Matlab toolbox for microarray data
The product of C9orf72, a gene strongly implicated in neurodegeneration, is structurally related to DENN Rab-GEFs
Multi-class cancer classification via partial least squares with gene expression profiles
DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia
Bayesian model averaging: development of an improved multi-class, gene selection and classification tool for microarray data
Morphologically constrained spectral unmixing by dictionary learning for multiplex fluorescence microscopy
GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework
EpiDISH web server: Epigenetic Dissection of Intra-Sample-Heterogeneity with online GUI
Statistical detection of cooperative transcription factors with similarity adjustment
AmyLoad: website dedicated to amyloidogenic protein fragments
Dissecting differential signals in high-throughput data from complex tissues
An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization
NEREL-BIO: a dataset of biomedical abstracts annotated with nested named entities
cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens
STRAP: editor for STRuctural Alignments of Proteins
DASMI: exchanging, annotating and assessing molecular interaction data
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling
UDock2 : interactive real-time multi-body protein-protein docking software
Evidence for the dissemination of cryptic non-coding RNAs transcribed from intronic and intergenic segments by retroposition
Pandit: a database of protein and associated nucleotide domains with inferred trees
Interpretable meta-learning of multi-omics data for survival analysis and pathway enrichment
A computer program to display codon changes caused by mutagenesis
HoPhage: an ab initio tool for identifying hosts of phage fragments from metaviromes
Validation of electron microscopy initial models via small angle X-ray scattering curves
SBML2L A T E X: Conversion of SBML files into human-readable reports
Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information
ensembldb: an R package to create and use Ensembl-based annotation resources
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns
DNA structure constraint is probably a fundamental factor inducing CpG deficiency in bacteria
regSNPs: a strategy for prioritizing regulatory single nucleotide substitutions
MinIONQC: fast and simple quality control for MinION sequencing data
OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem
Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning
Rclick: a web server for comparison of RNA 3D structures
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
Prediction of mRNA subcellular localization using deep recurrent neural networks
RNASAlign: RNA Structural Alignment System
Fast computation of 3D radon transform via a direct Fourier method
KCMBT: a k -mer Counter based on Multiple Burst Trees
Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression
rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples
Ab-CoV: a curated database for binding affinity and neutralization profiles of coronavirus-related antibodies
MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins
Vargas: heuristic-free alignment for assessing linear and graph read aligners
An exact test for comparing a fixed quantitative property between gene sets
Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package
ELECANS - an integrated model development environment for multiscale cancer systems biology
Read count approach for DNA copy number variants detection
ELLIPSIS: robust quantification of splicing in scRNA-seq
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
SPOT-ligand 2: improving structure-based virtual screening by binding-homology search on an expanded structural template library
Systematic analysis of gene properties influencing organ system phenotypes in mammalian perturbations
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis
Applying signal theory to the analysis of biomolecules
ChimeraUGEM: unsupervised gene expression modeling in any given organism
iSwathX: an interactive web-based application for extension of DIA peptide reference libraries
MDQC: a new quality assessment method for microarrays based on quality control reports
MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment
Predicting potential domain homologies from FASTA search results
Confirmation of data mining based predictions of protein function
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks
Digital reviews in molecular biology: approaches to structured digital publication
Limbform: a functional ontology-based database of limb regeneration experiments
Detecting spatially co-expressed gene clusters with functional coherence by graph-regularized convolutional neural network
Signed Distance Correlation (SiDCo): an online implementation of distance correlation and partial distance correlation for data-driven network analysis
A Survey of the Predictive Toxicology Challenge 2000-2001
Microcomputers and neurobiology: a short review
ORCA: a COBRA toolbox extension for model-driven discovery and analysis
PUMA: PANDA Using MicroRNA Associations
BCSExplorer: a customized biosynthetic chemical space explorer with multifunctional objective function analysis
Improved transcript isoform discovery using ORF graphs
Interactive analysis of large cancer copy number studies with Copy Number Explorer
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection
TOBMI: trans-omics block missing data imputation using a k-nearest neighbor weighted approach
Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data
Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates
MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya
Short inversions and conserved gene cluster
SynergyFinder: a web application for analyzing drug combination dose-response matrix data
BLANT - fast graphlet sampling tool
3D-MSNet: a point cloud-based deep learning model for untargeted feature detection and quantification in profile LC-HRMS data
Bistability in cell signalling and its significance in identifying potential drug-targets
A novel feature-based approach to extract drug-drug interactions from biomedical text
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination
CSynth: an interactive modelling and visualization tool for 3D chromatin structure
HIPred: an integrative approach to predicting haploinsufficient genes
On reverse engineering of gene interaction networks using time course data with repeated measurements
Evaluating disease similarity based on gene network reconstruction and representation
LDpred2: better, faster, stronger
ROCCO : a robust method for detection of open chromatin via convex optimization
FIRE: functional inference of genetic variants that regulate gene expression
GENOTRACE: cDNA-based local GENOme assembly from TRACE archives
Bambus 2: scaffolding metagenomes
Identifying Property Based Sequence Motifs in Protein Families and Superfamilies: Application to DNase-1 Related Endonucleases
Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes
Estimating replicate time shifts using Gaussian process regression
DynaPho: a web platform for inferring the dynamics of time-series phosphoproteomics
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
Zerg: A Very Fast BLAST Parser Library
Generalizing biomedical relation classification with neural adversarial domain adaptation
A flexible rank-based framework for detecting copy number aberrations from array data
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data
Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6
Equivalent binding sites reveal convergently evolved interaction motifs
Unmixing biological fluorescence image data with sparse and low-rank Poisson regression
seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data
Compression of nucleic acid and protein sequence data
BioMercator V3: an upgrade of genetic map compilation and quantitative trait loci meta-analysis algorithms
Associating microbiome composition with environmental covariates using generalized UniFrac distances
Model-based clustering for RNA-seq data
Cox regression is robust to inaccurate EHR-extracted event time: an application to EHR-based GWAS
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum
Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion
KIND-a non-redundant protein database
The GenBank nucleic acid sequence database
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms
MuDCoD: multi-subject community detection in personalized dynamic gene networks from single-cell RNA sequencing
Global snapshot of a protein interaction network - a percolation based approach
Visualization of protein sequence features using JavaScript and SVG with pViz.js
A computational strategy for the prediction of functional linear peptide motifs in proteins
2LD, GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species
Compositional variations in DNA sequences
nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments
Parametric alignment of ordered trees
PYCHEM: a multivariate analysis package for python
Frameshift alignment: statistics and post-genomic applications
Interactive exploration of RNA22 microRNA target predictions
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks
RDP2: recombination detection and analysis from sequence alignments
Sparse allele vectors and the savvy software suite
Network-guided sparse regression modeling for detection of gene-by-gene interactions
Scanning protein sequence databanks using a distributed processing workstation network
Bayesian Network Webserver: a comprehensive tool for biological network modeling
A four-dimensional digital image archiving system for cell lineage tracing and retrospective embryology
FISH: a guide to protein-coding DNA sequences in the GenBank database
TSAPA: identification of tissue-specific alternative polyadenylation sites in plants
PhyloCorrelate: inferring bacterial gene-gene functional associations through large-scale phylogenetic profiling
A computer program for the analysis of protein complex formation
MetaboReport: from metabolomics data analysis to comprehensive reporting
Object-oriented data handler for sequence analysis software development
Chemical-protein interaction extraction via Gaussian probability distribution and external biomedical knowledge
An improved method for computing q-values when the distribution of effect sizes is asymmetric
epic2 efficiently finds diffuse domains in ChIP-seq data
Efficient estimation of graphlet frequency distributions in protein-protein interaction networks
MARS: a motif-based autoregressive model for retrosynthesis prediction
Utopia documents: linking scholarly literature with research data
A Macintosh Hypercard stack to simulate the pharmacokinetics of infusion of intravenous anesthetic drugs (NarSim)
Grouped graphical Granger modeling for gene expression regulatory networks discovery
On entropy and information in gene interaction networks
Index suffix-prefix overlaps by (w, k)-minimizer to generate long contigs for reads compression
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Text processing through Web services: calling Whatizit
STOP: searching for transcription factor motifs using gene expression
twilight; a Bioconductor package for estimating the local false discovery rate
Towards optimal alignment of protein structure distance matrices
The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries
BHap: a novel approach for bacterial haplotype reconstruction
tcplfit2: an R-language general purpose concentration-response modeling package
CD-HIT Suite: a web server for clustering and comparing biological sequences
GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype
A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes
Vizardous: interactive analysis of microbial populations with single cell resolution
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function
CAM-CM: a signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues
Reconstructing spatiotemporal gene expression data from partial observations
iHam and pyHam: visualizing and processing hierarchical orthologous groups
A system for exact and approximate genetic linkage analysis of SNP data in large pedigrees
Multiple structural alignment and clustering of RNA sequences
TabPath: interactive tables for metabolic pathway analysis
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments
PrepMS: TOF MS data graphical preprocessing tool
ngsTools : methods for population genetics analyses from next-generation sequencing data
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins