yusuke1997/dblp-id-title huggingface dataset:
Novel probabilistic models of spatial genetic ancestry with applications to stratification correction in genome-wide association studies
Co-design protein sequence and structure in discrete space via generative flow
iPTM-mLys: identifying multiple lysine PTM sites and their different types
Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development
Improving bacterial genome assembly using a test of strand orientation
Highly significant improvement of protein sequence alignments with AlphaFold2
CLEVER: clique-enumerating variant finder
GlycanFormatConverter: a conversion tool for translating the complexities of glycans
MoDMaps3D: an interactive webtool for the quantification and 3D visualization of interrelationships in a dataset of DNA sequences
Four-Body Scoring Function for Mutagenesis
Simple high-throughput annotation pipeline (SHAP)
ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process
IslandPath: aiding detection of genomic islands in prokaryotes
A new concept of sequence data distribution on wide area networks
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains
OrthologID: automation of genome-scale ortholog identification within a parsimony framework
On E -values for tandem MS scoring schemes
GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping
HiLight-PTM: an online application to aid matching peptide pairs with isotopically labelled PTMs
BioCaster: detecting public health rumors with a Web-based text mining system
GenPlay, a multipurpose genome analyzer and browser
Predicting protein-protein interactions from primary structure
simPATHy: a new method for simulating data from perturbed biological PATHways
Characterizing therapeutic signatures of transcription factors in cancer by incorporating profiles in compound treated cells
HIG-Syn: a hypergraph and interaction-aware multigranularity network for predicting synergistic drug combinations
Mining literature for protein-protein interactions
Accurate assembly of multiple RNA-seq samples with Aletsch
Bioinformatics - The new home for protein sequence motifs
CompariMotif: quick and easy comparisons of sequence motifs
GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
The latent geometry of the human protein interaction network
On the Use of Permutation in and the Performance of A Class of Nonparametric Methods to Detect Differential Gene Expression
ESPClust: unsupervised identification of modifiers for the effect size profile in omics association studies
AlphaFamImpute: high-accuracy imputation in full-sib families from genotype-by-sequencing data
DINGO: differential network analysis in genomics
Biophysical informatics approach for quantifying phenotypic heterogeneity in cancer cell migration in confined microenvironments
Dasty and UniProt DAS: a perfect pair for protein feature visualization
WIST: toolkit for rapid, customized LIMS development
Morphing projections: a new visual technique for fast and interactive large-scale analysis of biomedical datasets
M-path: a compass for navigating potential metabolic pathways
cat RAPID signature : identification of ribonucleoproteins and RNA-binding regions
KaMRaT : a C++ toolkit for k -mer count matrix dimension reduction
GARN2: coarse-grained prediction of 3D structure of large RNA molecules by regret minimization
MCScanX-transposed : detecting transposed gene duplications based on multiple colinearity scans
RCSB Protein Data Bank 1D tools and services
ISMB 2022 proceedings
Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution
ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs
A generative model for the behavior of RNA polymerase
MARS: a program to find potential restriction sites [published erratum appears in Comput Appl Biosci 1991 Jul;7(3): 415]
Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus
Exploring automatic inconsistency detection for literature-based gene ontology annotation
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
GMCheck: Bayesian error checking for pedigreegenotypes and phenotypes
i2d: an R package for simulating data from images and the implications in biomedical research
MetATT: a web-based metabolomics tool for analyzing time-series and two-factor datasets
Boosting for high-dimensional time-to-event data with competing risks
Structured crowdsourcing enables convolutional segmentation of histology images
TITAN: T-cell receptor specificity prediction with bimodal attention networks
Survival analysis of longitudinal microarrays
GOAT: Gene-level biomarker discovery from multi-Omics data using graph ATtention neural network for eosinophilic asthma subtype
A hybrid constrained continuous optimization approach for optimal causal discovery from biological data
PERFUMES: pipeline to extract RNA functional motifs and exposed structures
Protein evolution along phylogenetic histories under structurally constrained substitution models
SpaRC: scalable sequence clustering using Apache Spark
Computational clustering for viral reference proteomes
Calculations of protein volumes: sensitivity analysis and parameter database
EPS-LASSO: test for high-dimensional regression under extreme phenotype sampling of continuous traits
QTLMiner: QTL database curation by mining tables in literature
grabseqs: simple downloading of reads and metadata from multiple next-generation sequencing data repositories
pepKalc: scalable and comprehensive calculation of electrostatic interactions in random coil polypeptides
ICN: extracting interconnected communities in gene co-expression networks
APOLLO: a quality assessment service for single and multiple protein models
Interactive visualization of nanopore sequencing signal data with Squigualiser
TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees
DDAffinity: predicting the changes in binding affinity of multiple point mutations using protein 3D structure
MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks
Global FDR control across multiple RNAseq experiments
GELYMAC: a Macintosh application for calculating DNA fragment size from gel electrophoresis migration data
PyRice: a Python package for querying Oryza sativa databases
Antibody interface prediction with 3D Zernike descriptors and SVM
SGN Sim, a Stochastic Genetic Networks Simulator
Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)
Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
DNABIND: an interactive microcomputer program searching for nucleotide sequences that may code for conserved DNA-binding protein motifs
Uncertainty estimation of predictions of peptides' chromatographic retention times in shotgun proteomics
Viral quasispecies reconstruction via tensor factorization with successive read removal
Systematic exploration of error sources in pyrosequencing flowgram data
Cerebro: interactive visualization of scRNA-seq data
A novel method SEProm for prokaryotic promoter prediction based on DNA structure and energetics
QuCo: quartet-based co-estimation of species trees and gene trees
arrayQualityMetrics - a bioconductor package for quality assessment of microarray data
New GO-based measures in multiple network alignment
DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes
A library of coiled-coil domains: from regular bundles to peculiar twists
Sample size calculation, power analysis and randomization: research project design in Windows
PathFinder: reconstruction and dynamic visualization of metabolic pathways
popSTR2 enables clinical and population-scale genotyping of microsatellites
Reading the book of life
Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'
Exact hypothesis testing for shrinkage-based Gaussian graphical models
Comparative assembly hubs: Web-accessible browsers for comparative genomics
COBREXA 2: tidy and scalable construction of complex metabolic models
Retrieval of Enterobacteriaceae drug targets using singular value decomposition
phyloMeta : a program for phylogenetic comparative analyses with meta-analysis
Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies
CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing
Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments
A method for identifying splice sites and translational start sites in eukaryotic mRNA
NSF4SL: negative-sample-free contrastive learning for ranking synthetic lethal partner genes in human cancers
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer
Conditional random pattern algorithm for LOH inference and segmentation
Founder reconstruction enables scalable and seamless pangenomic analysis
NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange
Characterization of biofilm structure and properties via processing of 2D optical coherence tomography images in BISCAP
The RNASeq-er API - a gateway to systematically updated analysis of public RNA-seq data
Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster
Robust inference of positive selection from recombining coding sequences
M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models
Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches
WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization
Concept and prototype of protein-ligand docking simulator with force feedback technology
A package of computer programs for handling taxonomic databases
ECCB 2018: The 17th European Conference on Computational Biology
Modelling haplotypes with respect to reference cohort variation graphs
Construction of optimal quality control for oligo arrays
GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models
WemIQ: an accurate and robust isoform quantification method for RNA-seq data
Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes
LongSAGE analysis revealed the presence of a large number of novel antisense genes in the mouse genome
MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data
ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population, and perturbation from time-series single-cell data
Designing robust watermark barcodes for multiplex long-read sequencing
ViraPipe: scalable parallel pipeline for viral metagenome analysis from next generation sequencing reads
Transcriptional landscape estimation from tiling array data using a model of signal shift and drift
ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster
LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario
MolFCL: predicting molecular properties through chemistry-guided contrastive and prompt learning
FastAlert - an automatic search system to alert about new entries in biological sequence databanks
treeheatr: an R package for interpretable decision tree visualizations
Common denominator procedure: a novel approach to gene-expression data mining for identification of phenotype-specific genes
Bacteriophage classification for assembled contigs using graph convolutional network
CoABind: a novel algorithm for Coenzyme A (CoA)- and CoA derivatives-binding residues prediction
ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data
Threading Using Neural nEtwork (TUNE): the measure of protein sequence-structure compatibility
Ligand Depot: a data warehouse for ligands bound to macromolecules
HiSCF: leveraging higher-order structures for clustering analysis in biological networks
Representation of functional information in the SWISS-PROT Data Bank
Entropy-accelerated exact clustering of protein decoys
JAWAMix5: an out-of-core HDF5-based java implementation of whole-genome association studies using mixed models
Computational modeling of mRNA degradation dynamics using deep neural networks
Tachyon search speeds up retrieval of similar sequences by several orders of magnitude
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models
WFA-GPU: gap-affine pairwise read-alignment using GPUs
GEOSEQ: a Pascal program to calculate statistical geometry parameters of aligned nucleic acid sequences
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis
On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data
CSAM: Compressed SAM format
A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury
CancerCellTracker: a brightfield time-lapse microscopy framework for cancer drug sensitivity estimation
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA
Circles: automating the comparative analysis of RNA secondary structure
AJGM: joint learning of heterogeneous gene networks with adaptive graphical model
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes
SPEED: a molecular-evolution-based database of mammalian orthologous groups
A semi-supervised fracture-attention model for segmenting tubular objects with improved topological connectivity
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data
Variations on probabilistic suffix trees: statistical modeling and prediction of protein families
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources
Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences
NFTest: automated testing of Nextflow pipelines
xMWAS: a data-driven integration and differential network analysis tool
Bayesian joint analysis of heterogeneous genomics data
Redundancy-weighting for better inference of protein structural features
DEPD: a novel database for differentially expressed proteins
How networks change with time
Multiple gene expression profile alignment for microarray time-series data clustering
Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts
BioSwitch: a tool for the detection of bistability and multi-steady state behaviour in signalling and gene regulatory networks
GEM: scalable and flexible gene-environment interaction analysis in millions of samples
BioProfiling.jl: profiling biological perturbations with high-content imaging in single cells and heterogeneous populations
A unified approach for sparse dynamical system inference from temporal measurements
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes
Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network
Fulcrum: condensing redundant reads from high-throughput sequencing studies
Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
Genome structures embossed by oligonucleotide-stickiness
BEAM web server: a tool for structural RNA motif discovery
NGSEP3: accurate variant calling across species and sequencing protocols
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
PLAID: ultrafast single-sample gene set enrichment scoring
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments
GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence
ProteoWizard: open source software for rapid proteomics tools development
Multi-platform segmentation for joint detection of copy number variants
Local coherence in genetic interaction patterns reveals prevalent functional versatility
RVAgene: generative modeling of gene expression time series data
FMCA-DTI: a fragment-oriented method based on a multihead cross attention mechanism to improve drug-target interaction prediction
Allele-specific expression analysis methods for high-density SNP microarray data
Association screening of common and rare genetic variants by penalized regression
Extracting three-way gene interactions from microarray data
fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets
PanExplorer: a web-based tool for exploratory analysis and visualization of bacterial pan-genomes
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities
Insights into polypharmacology from drug-domain associations
FBA: feature barcoding analysis for single cell RNA-Seq
Systematic identification of biochemical networks in cancer cells by functional pathway inference analysis
BMC3C: binning metagenomic contigs using codon usage, sequence composition and read coverage
Getting 'ϕψχal' with proteins: minimum message length inference of joint distributions of backbone and sidechain dihedral angles
ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations
Arcadia: a visualization tool for metabolic pathways
A rank-based statistical test for measuring synergistic effects between two gene sets
Meta-analytic principal component analysis in integrative omics application
A new method to predict the consensus secondary structure of a set of unaligned RNA sequences
A program for the application of the radial distribution function to cluster analysis in cell biology
Parallelization of MAFFT for large-scale multiple sequence alignments
PlantMiRNAPred : efficient classification of real and pseudo plant pre-miRNAs
VIPER: an advanced software package to support high-throughput LC-MS peptide identification
Memory-efficient, accelerated protein interaction inference with blocked, multi-GPU D-SCRIPT
Integrative analysis of multi-omics data for discovering low-frequency variants associated with low-density lipoprotein cholesterol levels
Bacnet: a user-friendly platform for building multi-omics websites
Large-scale inference of population structure in presence of missingness using PCA
PROTEUS: a suite of programs for prediction of structural features of proteins using an Apple IIe
BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration
UMA and MABP domains throw light on receptor endocytosis and selection of endosomal cargoes
A graph kernel approach for alignment-free domain-peptide interaction prediction with an application to human SH3 domains
Automated management of gene discovery projects
A method for finding consensus breakpoints in the cancer genome from copy number data
Ontodog: a web-based ontology community view generation tool
QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time
Structure-aware protein-protein interaction site prediction using deep graph convolutional network
IsoCor: correcting MS data in isotope labeling experiments
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes
De no vo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads
SLPred: a multi-view subcellular localization prediction tool for multi-location human proteins
GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data
TIP: protein backtranslation aided by genetic algorithms
Seq-InSite: sequence supersedes structure for protein interaction site prediction
Inferring gene regulatory networks from time series data using the minimum description length principle
Nonparametric methods for identifying differentially expressed genes in microarray data
VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data
Mutation-Simulator: fine-grained simulation of random mutations in any genome
Liquid-chromatography retention order prediction for metabolite identification
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
MULTICOMP: a program for preparing sequence data for phylogenetic analysis
An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus
FORESST: fold recognition from secondary structure predictions of proteins
Module-based prediction approach for robust inter-study predictions in microarray data
GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML
Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure
BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data
LPM: a latent probit model to characterize the relationship among complex traits using summary statistics from multiple GWASs and functional annotations
PEtab.jl: advancing the efficiency and utility of dynamic modelling
pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS
tPatternHunter: gapped, fast and sensitive translated homology search
Metab2MeSH: annotating compounds with medical subject headings
Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein-protein interactions
Computational refinement of post-translational modifications predicted from tandem mass spectrometry
learnMSA2: deep protein multiple alignments with large language and hidden Markov models
Noise reduction in genome-wide perturbation screens using linear mixed-effect models
MEDS and PocR are novel domains with a predicted role in sensing simple hydrocarbon derivatives in prokaryotic signal transduction systems
Algorithms for alignment of mass spectrometry proteomic data
tcsBU: a tool to extend TCS network layout and visualization
An EXCEL template for calculation of enzyme kinetic parameters by non-linear regression
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Novel Clustering Algorithm for Microarray Expression Data in A Truncated SVD Space
EPI-peptide designer: a tool for designing peptide ligand libraries based on epitope-paratope interactions
BugView: a browser for comparing genomes
Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion
Enrichment or depletion of a GO category within a class of genes: which test?