yusuke1997/dblp-id-title huggingface dataset:
MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects
Evaluating single-cell cluster stability using the Jaccard similarity index
iFUSE: integrated fusion gene explorer
Efficient protein structure archiving using ProteStAr
MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data
TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors
ODGI: understanding pangenome graphs
BubbleGun: enumerating bubbles and superbubbles in genome graphs
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
ShereKhan - calculating exchange parameters in relaxation dispersion data from CPMG experiments
Detecting clustering and ordering binding patterns among transcription factors via point process models
Quantitative trait loci identification for brain endophenotypes via new additive model with random networks
DeepPhos: prediction of protein phosphorylation sites with deep learning
Real-time multi-view deconvolution
Specificity control for read alignments using an artificial reference genome-guided false discovery rate
ToxSTAR: drug-induced liver injury prediction tool for the web environment
Topsy-Turvy: integrating a global view into sequence-based PPI prediction
NetPathMiner: R/Bioconductor package for network path mining through gene expression
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures
GO-Elite: a flexible solution for pathway and ontology over-representation
ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions
IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships
SECOST: sequence-conformation-structure database for amino acid residues in proteins
Merging two gene-expression studies via cross-platform normalization
EPS: automated feature selection in case-control studies using extreme pseudo-sampling
MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data
ORI-GENE: gene classification based on the evolutionary tree
WebACT - an online companion for the Artemis Comparison Tool
LipidQuant 1.0: automated data processing in lipid class separation-mass spectrometry quantitative workflows
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
SASpector: analysis of missing genomic regions in draft genomes of prokaryotes
Serial BLAST searching
SbacHTS: Spatial background noise correction for High-Throughput RNAi Screening
A comprehensive protein-centric ID mapping service for molecular data integration
EST-PAGE - managing and analyzing EST data
Mirin: identifying microRNA regulatory modules in protein-protein interaction networks
BayMAP: a Bayesian hierarchical model for the analysis of PAR-CLIP data
VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations
Middle-range clustering of nucleotides in genomes
CEDA: integrating gene expression data with CRISPR-pooled screen data identifies essential genes with higher expression
Multiomix: a cloud-based platform to infer cancer genomic and epigenomic events associated with gene expression modulation
BADASP: predicting functional specificity in protein families using ancestral sequences
A new method for revealing correlated mutations under the structural and functional constraints in proteins
LPmerge: an R package for merging genetic maps by linear programming
Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences
Genome size estimation from long read overlaps
ATHENA: analysis of tumor heterogeneity from spatial omics measurements
Statistics of large-scale sequence searching
Reliable prediction of Drosha processing sites improves microRNA gene prediction
MetaNetter: inference and visualization of high-resolution metabolomic networks
SCHNEL: scalable clustering of high dimensional single-cell data
Structure detection through automated covariance search
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning
LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering
Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks
GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models
SBML2HYB: a Python interface for SBML compatible hybrid modeling
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence
Coding genomes with gapped pattern graph convolutional network
Small compound-based direct cell conversion with combinatorial optimization of pathway regulations
Using DNA microarrays to study gene expression in closely related species
ECCB 2006
FT3D: three-dimensional Fourier analysis on small Unix workstations for electron microscopy and tomographic studies
Powerful fusion: PSI-BLAST and consensus sequences
APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data
Identification of compositionally distinct regions in genomes using the centroid method
Model-based clustering and data transformations for gene expression data
Combining structural analysis of DNA with search routines for the detection of transcription regulatory elements
IGD: high-performance search for large-scale genomic interval datasets
Adaption of the global test idea to proteomics data with missing values
CoP: a database for characterizing co-expressed gene modules with biological information in plants
RNA-d2: a computer program for editing and display of RNA secondary structures
Applying GIFT, a Gene Interactions Finder in Text, to fly literature
A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites
Local RNA structure alignment with incomplete sequence
CLEP: a hybrid data- and knowledge-driven framework for generating patient representations
Predicting relapse prior to transplantation in chronic myeloid leukemia by integrating expert knowledge and expression data
Glycan classification with tree kernels
Biological sequence classification utilizing positive and unlabeled data
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation
A naive Bayes model to predict coupling between seven transmembrane domain receptors, and G-proteins
pWGBSSimla: a profile-based whole-genome bisulfite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions
Message from the ISCB: 2017 ISCB Innovator Award Given to Aviv Regev
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays
The DNA rodent: a portable hand held DNA sequence reader
NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks
TableView: Portable Genomic Data Visualization
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss
Multiple hot-deck imputation for network inference from RNA sequencing data
ITree : a user-driven tool for interactive decision-making with classification trees
ArkDTA: attention regularization guided by non-covalent interactions for explainable drug-target binding affinity prediction
Designing a neural network simulator - the MENS modelling environment for network systems: I
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses
Semantic reclassification of the UMLS concepts
Meta-server for automatic analysis, scoring and ranking of docking models
SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data
Retrieval and on-the-fly alignment of sequence fragments from the HIV database
Deep representation learning for domain adaptable classification of infrared spectral imaging data
V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data
Using fragment lengths from incomplete digestion by multiply cleaving enzymes to map antibody binding sites on a protein
ISIS: interaction sites identified from sequence
An associative analysis of gene expression array data
Reverse-engineering flow-cytometry gating strategies for phenotypic labelling and high-performance cell sorting
vHOG, a multispecies vertebrate ontology of homologous organs groups
Mobyle: a new full web bioinformatics framework
COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data
MARSY: a multitask deep-learning framework for prediction of drug combination synergy scores
Erratum to: An information-theoretic approach for measuring the distance of organ tissue samples using their transcriptomic signatures
Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates
The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis
AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes
BondGraphs.jl: composable energy-based modelling in systems biology
AVPpred-BWR: antiviral peptides prediction via biological words representation
scBSP: a fast and accurate tool for identifying spatially variable features from high-resolution spatial omics data
GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry
Optimized application of penalized regression methods to diverse genomic data
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
Comparison of P-RnaPredict and mfold - algorithms for RNA secondary structure prediction
A segment alignment approach to protein comparison
An evaluation of automated homology modelling methods at low target-template sequence similarity
A simple probabilistic scoring method for protein domain identification
The Protein Imager: a full-featured online molecular viewer interface with server-side HQ-rendering capabilities
EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures
Proteome-level assessment of origin, prevalence and function of leucine-aspartic acid (LD) motifs
Parallel alignment of DNA sequences on the Connection Machine CM-2
The IBM-PC network: a review of the network and associated programs
NMFProfiler: a multi-omics integration method for samples stratified in groups
ResPRE: high-accuracy protein contact prediction by coupling precision matrix with deep residual neural networks
The new protein topology graph library web server
FTEC: a coalescent simulator for modeling faster than exponential growth
GraphCompass: spatial metrics for differential analyses of cell organization across conditions
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
FISH Finder: a high-throughput tool for analyzing FISH images
SCRAM: a pipeline for fast index-free small RNA read alignment and visualization
Swift: primary data analysis for the Illumina Solexa sequencing platform
Predicting class II MHC/peptide multi-level binding with an iterative stepwise discriminant analysis meta-algorithm
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem
Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map
The influence of heterogeneous codon frequencies along sequences on the estimation of molecular adaptation
ARCS: scaffolding genome drafts with linked reads
DeepTraSynergy: drug combinations using multimodal deep learning with transformers
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
COFFEE: an objective function for multiple sequence alignments
DFHiC: a dilated full convolution model to enhance the resolution of Hi-C data
Spatial quantification and classification of skin response following perturbation using organotypic skin cultures
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks
As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets
PROPER: comprehensive power evaluation for differential expression using RNA-seq
PeptideMapper: efficient and versatile amino acid sequence and tag mapping
Predicting thermostability difference between cellular protein orthologs
A case study of high-throughput biological data processing on parallel platforms
A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number
COACH: profile-profile alignment of protein families using hidden Markov models
Immune system simulation online
Database driven test case generation for protein?Cprotein docking
ORBIT: an integrated environment for user-customized bioinformatics tools
EWASex: an efficient R-package to predict sex in epigenome-wide association studies
Alignment of RNA base pairing probability matrices
GeIST: a pipeline for mapping integrated DNA elements
QUBIC2: a novel and robust biclustering algorithm for analyses and interpretation of large-scale RNA-Seq data
NcPath: a novel platform for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways
Hypothesis-driven approach to predict transcriptional units from gene expression data
GenomeTornadoPlot: a novel R package for CNV visualization and focality analysis
Scaffold network generator: a tool for mining molecular structures
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation
PaIntDB: network-based omics integration and visualization using protein-protein interactions in Pseudomonas aeruginosa
BESC knowledgebase public portal
Neural network input representations that produce accurate consensus sequences from DNA fragment assemblies
efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies
Deep learning with multimodal representation for pancancer prognosis prediction
ESCO: single cell expression simulation incorporating gene co-expression
Comments on "On correcting the overestimation of the permutation-based false discovery rate estimator"
Orione, a web-based framework for NGS analysis in microbiology
Characterizing proteolytic cleavage site activity using bio-basis function neural networks
BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences
Advanced pairwise structure alignments of proteins and analysis of conformational changes
ConPlot: web-based application for the visualization of protein contact maps integrated with other data
Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
PrimedRPA: primer design for recombinase polymerase amplification assays
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools
Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface
caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens
HiDi: an efficient reverse engineering schema for large-scale dynamic regulatory network reconstruction using adaptive differentiation
An image-based multi-label human protein subcellular localization predictor ( i Locator) reveals protein mislocalizations in cancer tissues
Triplex: an R/Bioconductor package for identification and visualization of potential intramolecular triplex patterns in DNA sequences
TransformerGO: predicting protein-protein interactions by modelling the attention between sets of gene ontology terms
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data
iRNAD: a computational tool for identifying D modification sites in RNA sequence
SACS-Self-maintaining database of antibody crystal structure information
CParty: hierarchically constrained partition function of RNA pseudoknots
SPRING: a next-generation compressor for FASTQ data
NextPolish: a fast and efficient genome polishing tool for long-read assembly
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields
Common structural patterns in human genes
Guided co-clustering transfer across unpaired and paired single-cell multi-omics data
GSpace: an exact coalescence simulator of recombining genomes under isolation by distance
Designing alternative splicing RNA-seq studies. Beyond generic guidelines
WSsas: a web service for the annotation of functional residues through structural homologues
PathGen: a transitive gene pathway generator
Comparison of side chain interactions performed by structurally equivalent residues in homologous protein structures
Tools4miRs - one place to gather all the tools for miRNA analysis
ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database
Exosomal lncRNAs and cancer: connecting the missing links
nextflu: real-time tracking of seasonal influenza virus evolution in humans
scGAC: a graph attentional architecture for clustering single-cell RNA-seq data
Gene Slider: sequence logo interactive data-visualization for education and research
Parameter estimation using Simulated Annealing for S-system models of biochemical networks
BEL2ABM: agent-based simulation of static models in Biological Expression Language
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins
MotifMap-RNA: a genome-wide map of RBP binding sites
A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients
Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures
MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks
Improving your target-template alignment with MODalign
Prediction of potential disease-associated microRNAs using structural perturbation method
H2GnnDTI: hierarchical heterogeneous graph neural networks for drug-target interaction prediction
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation
SOAP, cleaning multiple alignments from unstable blocks
VISTRAJ: exploring protein conformational space
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models
HIV-1 drug resistance profiling using amino acid sequence space cartography
Automated, image-based quantification of peroxisome characteristics with perox-per-cell
GraphscoreDTA: optimized graph neural network for protein-ligand binding affinity prediction
A probabilistic method for the detection and genotyping of small indels from population-scale sequence data
On correcting the overestimation of the permutation-based false discovery rate estimator
iterClust: a statistical framework for iterative clustering analysis
Protein isoelectric point as a predictor for increased crystallization screening efficiency
Comments on "Bayesian hierarchical error model for analysis of gene expression data"
Accurate prediction of genome-wide RNA secondary structure profile based on extreme gradient boosting
Cooperative sequence clustering and decoding for DNA storage system with fountain codes
<tt>ALLSTAR</tt>: inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes
BioPig: a Hadoop-based analytic toolkit for large-scale sequence data
Predictions of RNA secondary structure by combining homologous sequence information
Network-based multiple locus linkage analysis of expression traits
Protein-to-genome alignment with miniprot
Bio-Ontology and text: bridging the modeling gap
PreDs: a server for predicting dsDNA-binding site on protein molecular surfaces
New strategies to improve minimap2 alignment accuracy
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems
CalcTav - integration of a spreadsheet and Taverna workbench
A novel and versatile computational tool to model translation
Comparative studies of de novo assembly tools for next-generation sequencing technologies
NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph
AntiHIV-Pred: web-resource for in silico prediction of anti-HIV/AIDS activity
PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences
Measuring the wisdom of the crowds in network-based gene function inference
RECSIM and INDSTATS: probabilities of identity in general genealogies
CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks
Gene set analysis for self-contained tests: complex null and specific alternative hypotheses
HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization
YeastMate: neural network-assisted segmentation of mating and budding events in Saccharomyces cerevisiae
Insights into the inner workings of transformer models for protein function prediction
A system for generating transcription regulatory networks with combinatorial control of transcription
IsoTV: processing and visualizing functional features of translated transcript isoforms
Biological impact of missing-value imputation on downstream analyses of gene expression profiles
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer
Streamlined analysis of LINCS L1000 data with the slinky package for R
Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks
pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells
SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data
A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum
NCutYX: a package for clustering analysis of multilayer omics data
Toppar: an interactive browser for viewing association study results
BioArchLinux: community-driven fresh reproducible software repository for life sciences
A computer program for selecting animals for control and experimental groups in biochemical studies
Computational identification of novel chitinase-like proteins in the Drosophila melanogaster genome
Phan3D: design of biological phantoms in 3D electron microscopy
MIG: Multi-Image Genome viewer
Detecting epistatic effects in association studies at a genomic level based on an ensemble approach
Robustness considerations in selecting efficient two-color microarray designs
Reveel: large-scale population genotyping using low-coverage sequencing data
ShiftDetector: detection of shift mutations
Mining gene functional networks to improve mass-spectrometry-based protein identification