yusuke1997/dblp-id-title huggingface dataset:
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs
Generation of sequence-based data for pedigree-segregating Mendelian or Complex traits
Gene expression analysis on biochemical networks using the Potts spin model
Bifurcation discovery tool
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
SIBER: systematic identification of bimodally expressed genes using RNAseq data
HapCol: accurate and memory-efficient haplotype assembly from long reads
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data
Predictive rule inference for epistatic interaction detection in genome-wide association studies
Prediction of translation initiation site for microbial genomes with TriTISA
SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences
MArray: analysing single, replicated or reversed microarray experiments
The protein structure code: what is its present status?
ISMB/ECCB 2021 proceedings
Lep-Anchor: automated construction of linkage map anchored haploid genomes
Prediction of protease substrates using sequence and structure features
Cascade detection for the extraction of localized sequence features; specificity results for HIV-1 protease and structure-function results for the Schellman loop
Objectively judging the quality of a protein structure from a Ramachandran plot
Recognizing translation initiation sites of eukaryotic genes based on the cooperatively scanning model
lgpr: an interpretable non-parametric method for inferring covariate effects from longitudinal data
Hierarchical HotNet: identifying hierarchies of altered subnetworks
dbSNO: a database of cysteine S -nitrosylation
MUTbase: maintenance and analysis of distributed mutation databases
Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data
PepCrawler: a fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors
Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors
A statistical framework for protein quantitation in bottom-up MS-based proteomics
Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer
Protein data representation and query using optimized data decomposition
Classification using functional data analysis for temporal gene expression data
fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps
Human microRNAs co-silence in well-separated groups and have different predicted essentialities
BioNorm: deep learning-based event normalization for the curation of reaction databases
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses
Faster exact Markovian probability functions for motif occurrences: a DFA-only approach
MMAP: a cloud computing platform for mining the maximum accuracy of predicting phenotypes from genotypes
Bit-parallel sequence-to-graph alignment
Mining genetic epidemiology data with Bayesian networks I: Bayesian networks and example application (plasma apoE levels)
An efficient TOF-SIMS image analysis with spatial correlation and alternating non-negativity-constrained least squares
Functional data analysis for computational biology
Geometric epitope and paratope prediction
Network-based comparison of temporal gene expression patterns
FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation
MacFrag: segmenting large-scale molecules to obtain diverse fragments with high qualities
A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations
Accurate and efficient gene function prediction using a multi-bacterial network
Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
MRMPROBS suite for metabolomics using large-scale MRM assays
MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes
LexicHash: sequence similarity estimation via lexicographic comparison of hashes
Automated programming for bioinformatics algorithm deployment
The complexities of genome analysis, the Retroid agent perspective
Picky: oligo microarray design for large genomes
netReg: network-regularized linear models for biological association studies
Tracking and curating putative SARS-CoV-2 recombinants with RIVET
Cis -regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana
ODNBase-a web database for antisense oligonucleotide effectiveness studies
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses
A statistical model for HIV-1 sequence classification using the subtype analyser (STAR)
CATHER: a novel threading algorithm with predicted contacts
Multiple sequence alignment by a pairwise algorithm
FTSite: high accuracy detection of ligand binding sites on unbound protein structures
Panache: a web browser-based viewer for linearized pangenomes
Clearcut: a fast implementation of relaxed neighbor joining
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm
MUGBAS: a species free gene-based programme suite for post-GWAS analysis
Optimally discriminative subnetwork markers predict response to chemotherapy
NucPred - Predicting nuclear localization of proteins
CyAnno : a semi-automated approach for cell type annotation of mass cytometry datasets
Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold
A highly accurate statistical approach for the prediction of transmembrane beta-barrels
Phenoclustering: online mining of cross-species phenotypes
CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
A curriculum for bioinformatics: the time is ripe
A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations
The Binding Database: data management and interface design
A numerical method for allocating microbial isolates to strain types when characterized by typing methods that are not 100% reproducible
OnTheFly: a tool for automated document-based text annotation, data linking and network generation
ClusterSignificance: a bioconductor package facilitating statistical analysis of class cluster separations in dimensionality reduced data
EMBL sequence submission system--an object-oriented approach to developing interactive data collection systems through the WWW
A network of networks approach for modeling interconnected brain tissue-specific networks
The super-n-motifs model: a novel alignment-free approach for representing and comparing RNA secondary structures
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy
Algorithms and software for support of gene identification experiments
RBPSponge: genome-wide identification of lncRNAs that sponge RBPs
TVNViewer: An interactive visualization tool for exploring networks that change over time or space
An Ergatis-based prokaryotic genome annotation web server
The Feature-Viewer: a visualization tool for positional annotations on a sequence
Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data
pipesnake : generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci
A concanavalin A-like lectin domain in the CHS1/LYST protein, shared by members of the BEACH family
BioCIDER: a Contextualisation InDEx for biological Resources discovery
CW-NET for multitype cell detection and classification in bone marrow examination and mitotic figure examination
HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations
deepSimDEF: deep neural embeddings of gene products and gene ontology terms for functional analysis of genes
A DNA shape-based regulatory score improves position-weight matrix-based recognition of transcription factor binding sites
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
Heterogeneous graph embedding model for predicting interactions between TF and target gene
GAT: a simulation framework for testing the association of genomic intervals
MFEprimer: multiple factor evaluation of the specificity of PCR primers
HSMotifDiscover: identification of motifs in sequences composed of non-single-letter elements
Kalman filtering for disease-state estimation from microarray data
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings
Quantitating tissue specificity of human genes to facilitate biomarker discovery
FastBMD: an online tool for rapid benchmark dose-response analysis of transcriptomics data
Generalized correlation measure using count statistics for gene expression data with ordered samples
Identification and function of FAR protein family genes from a transcriptome analysis of Aphelenchoides besseyi
Network module-based model in the differential expression analysis for RNA-seq
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling
Consensus label propagation with graph convolutional networks for single-cell RNA sequencing cell type annotation
SED-ED, a workflow editor for computational biology experiments written in SED-ML
Rnalib: a Python library for custom transcriptomics analyses
ipyrad: Interactive assembly and analysis of RADseq datasets
CytoSEED: a Cytoscape plugin for viewing, manipulating and analyzing metabolic models created by the Model SEED
Evaluating the molecule-based prediction of clinical drug responses in cancer
cloudrna SP Ades : isoform assembly using bulk barcoded RNA sequencing data
cit: hypothesis testing software for mediation analysis in genomic applications
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins
A procedure to statistically evaluate agreement of differential expression for cross-species genomics
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
AIDS in Ireland: the reporting delay distribution and the implementation of integral equation models
OrthoInspector 2.0: Software and database updates
Finding long tandem repeats in long noisy reads
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes
Gene finding for the helical cytokines
Bi-dimensional scaling map (BDS-Map): an approach for building large genetic maps
DelPhiPKa web server: predicting p K a of proteins, RNAs and DNAs
Reactome diagram viewer: data structures and strategies to boost performance
Supervised prediction of drug-target interactions using bipartite local models
Integration and visualization of host-pathogen data related to infectious diseases
MEGA2: molecular evolutionary genetics analysis software
DNase II is a member of the phospholipase D superfamily
EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database
Bloader - a batch loader application for MIAMExpress
Exploratory analysis of multiple sequence alignments using phylogenies
Analysis of nanopore data using hidden Markov models
Swarm v3: towards tera-scale amplicon clustering
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins
ANAGEL: a personal computer program for evaluating DNA fragment lengths from distances migrated in an agarose gel
Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data
Simultaneous clustering of multiview biomedical data using manifold optimization
SimiTri-visualizing similarity relationships for groups of sequences
In silico Biochemical Reaction Network Analysis (IBRENA): a package for simulation and analysis of reaction networks
TandTRAQ : an open-source tool for integrated protein identification and quantitation
Model-based Bayesian clustering (MBBC)
PowQ: a user-friendly package for the design of variance component multipoint linkage analysis studies
Graphics of RNA secondary structure; towards an object-oriented algorithm [published erratum appears in Comput Appl Biosci 1987 Sep 3(3): 277]
The role of indirect connections in gene networks in predicting function
GHap: an R package for genome-wide haplotyping
Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model
MUSA: a parameter free algorithm for the identification of biologically significant motifs
Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach
Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants
Evaluating phylogenetic footprinting for human-rodent comparisons
TGSA: protein-protein association-based twin graph neural networks for drug response prediction with similarity augmentation
COBALT: constraint-based alignment tool for multiple protein sequences
PDBImages: a command-line tool for automated macromolecular structure visualization
A genetic programming approach for Burkholderia Pseudomallei diagnostic pattern discovery
Alignment-free estimation of nucleotide diversity
In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon
OSLay: optimal syntenic layout of unfinished assemblies
Semiconductor sequencing: how many flows do you need?
The value of prior knowledge in machine learning of complex network systems
MERRIN: MEtabolic regulation rule INference from time series data
ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation
DA 1.0: parameter estimation of biological pathways using data assimilation approach
EnImpute: imputing dropout events in single-cell RNA-sequencing data via ensemble learning
A strategy for building neuroanatomy ontologies
An integrated system for studying residue coevolution in proteins
RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures
RAISS: robust and accurate imputation from summary statistics
GLAD: GLycan Array Dashboard, a visual analytics tool for glycan microarrays
metGWAS 1.0: an R workflow for network-driven over-representation analysis between independent metabolomic and meta-genome-wide association studies
Transfer learning for biomedical named entity recognition with neural networks
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG
Nonlinear dimension reduction and clustering by Minimum Curvilinearity unfold neuropathic pain and tissue embryological classes
MMOSurv: meta-learning for few-shot survival analysis with multi-omics data
EWF: simulating exact paths of the Wright-Fisher diffusion
The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
SHOGUN: a modular, accurate and scalable framework for microbiome quantification
JDotter: a Java interface to multiple dotplots generated by dotter
False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing
Decompositions of large-scale biological systems based on dynamical properties
JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures
KmerStream: streaming algorithms for k -mer abundance estimation
HaploPainter: a tool for drawing pedigrees with complex haplotypes
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
Integrating multiomics and prior knowledge: a study of the Graphnet penalty impact
PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors
Automated analysis of giant unilamellar vesicles using circular Hough transformation
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
Rapid similarity search of proteins using alignments of domain arrangements
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data
Detection of cell-type-specific differentially methylated regions in epigenome-wide association studies
ABlooper: fast accurate antibody CDR loop structure prediction with accuracy estimation
DUI: the drug use insights web server
Virtual exploration of early stage atherosclerosis
Statistical interpretation of machine learning-based feature importance scores for biomarker discovery
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data
Peptriever: a Bi-Encoder approach for large-scale protein-peptide binding search
Communication between the PC and laboratory instruments
Genome scale enzyme-metabolite and drug-target interaction predictions using the signature molecular descriptor
A didactic computer simulation of the environmental impact of a pollution discharge
An evaluation of some statistics packages for the BBC microcomputer
Feature-based 3D motif filtering for ribosomal RNA
DIANA-EST: a statistical analysis
pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data
A hierarchical approach to aligning collinear regions of genomes
Detection and removal of spatial bias in multiwell assays
On the limitations of automated restriction mapping
Design and application of a knowledge network for automatic prioritization of drug mechanisms
Rapid membrane protein topology prediction
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery
SpliceRover: interpretable convolutional neural networks for improved splice site prediction
Carbon-fate maps for metabolic reactions
Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs
VISDA: an open-source caBIG TM analytical tool for data clustering and beyond
A novel method for comparing topological models of protein structures enhanced with ligand information
AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function
CDvist: a webserver for identification and visualization of conserved domains in protein sequences
Non-negative Independent Factor Analysis disentangles discrete and continuous sources of variation in scRNA-seq data
Madeline 2.0 PDE: a new program for local and web-based pedigree drawing
Efficient primer design algorithms
A count-based model for delineating cell-cell interactions in spatial transcriptomics data
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning
STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data
Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design
PgRC: pseudogenome-based read compressor
Enhanced homology searching through genome reading frame predetermination
Patterns of amino acid conservation in human and animal immunodeficiency viruses
FBA-SimVis: interactive visualization of constraint-based metabolic models
Response to 'Comments on "MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets"'
Inferring perturbation profiles of cancer samples
ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution
Identifying multiple alignment regions satisfying simple formulas and patterns
CRISPRon/off: CRISPR/Cas9 on- and off-target gRNA design
CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools
nucleR: a package for non-parametric nucleosome positioning
ccNetViz: a WebGL-based JavaScript library for visualization of large networks
A general framework for powerful confounder adjustment in omics association studies
Computing exact P -values for DNA motifs
AEMDA: inferring miRNA-disease associations based on deep autoencoder
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB
Ultra-fast FFT protein docking on graphics processors
Structural profiles of human miRNA families from pairwise clustering
Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
The Annotator's Assistant: an expert system for direct submission of genetic sequence data
A general UNIX interface for biocomputing and network information retrieval software
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA
miES: predicting the essentiality of miRNAs with machine learning and sequence features
Bioinformatics in the human interactome project
RONN: the bio-basis function neural network technique applied to the detection of natively disordered regions in proteins
QuantProReloaded: quantitative analysis of microspot immunoassays
A framework for installable external tools in Skyline
ncRNAppi - a tool for identifying disease-related miRNA and siRNA targeting pathways
GenSSI: a software toolbox for structural identifiability analysis of biological models
Efficient discovery of conserved patterns using a pattern graph
Pooled library tissue tags for EST-based gene discovery
Publication-ready single nucleotide polymorphism visualization with snipit
In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power
Machine learning annotation of human branchpoints
Modeling community-wide molecular networks of multicellular systems
Genetic association testing using the GENESIS R/Bioconductor package
GeneANOVA-gene expression analysis of variance
Correction to: Topological analysis as a tool for detection of abnormalities in protein-protein interaction data
Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts
3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs
Two applications to facilitate the viewing of database search result files on the Macintosh
Multi-population GWA mapping via multi-task regularized regression
A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm
GBPM: GRID-based pharmacophore model: concept and application studies to protein-protein recognition
Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach
AutoDock CrankPep: combining folding and docking to predict protein-peptide complexes
DBDIpy: a Python library for processing of untargeted datasets from real-time plasma ionization mass spectrometry
Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes
A novel strategy for microarray quality control using Bayesian networks
Tree2GD: a phylogenomic method to detect large-scale gene duplication events
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
Resolving abbreviations to their senses in Medline
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
xQTL workbench: a scalable web environment for multi-level QTL analysis