yusuke1997/dblp-id-title huggingface dataset:
A crowd-sourcing approach for the construction of species-specific cell signaling networks
Tolerating some redundancy significantly speeds up clustering of large protein databases
ReconMap: an interactive visualization of human metabolism
vSampler: fast and annotation-based matched variant sampling tool
ISMB 2018 proceedings
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs
Fast Needleman-Wunsch scanning of sequence databanks on a massively parallel computer
Mapping ancestral genomes with massive gene loss: A matrix sandwich problem
Hierarchical graph transformer with contrastive learning for protein function prediction
Extensive complementarity between gene function prediction methods
Molecular principles of human virus protein-protein interactions
schex avoids overplotting for large single-cell RNA-sequencing datasets
Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff
Foveal blur-boosted segmentation of nuclei in histopathology images with shape prior knowledge and probability map constraints
Pv3Rs: Plasmodium vivax relapse, recrudescence, and reinfection statistical genetic inference
Interactive InterPro-based comparisons of proteins in whole genomes
MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context
Highly efficient clustering of long-read transcriptomic data with GeLuster
RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments
Hierarchical optimization for the efficient parametrization of ODE models
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
gEVAL - a web-based browser for evaluating genome assemblies
Discerning static and causal interactions in genome-wide reverse engineering problems
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants
grenepipe: a flexible, scalable and reproducible pipeline to automate variant calling from sequence reads
CASPAR: a hierarchical bayesian approach to predict survival times in cancer from gene expression data
ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU
MaveRegistry: a collaboration platform for multiplexed assays of variant effect
SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments
Bioinorganic motifs: towards functional classification of metalloproteins
Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes
MARAN: Normalizing Micro-array Data
Domain Fishing: a first step in protein comparative modelling
HEGESMA: genome search meta-analysis and heterogeneity testing
MRUniNovo: an efficient tool for de novo peptide sequencing utilizing the hadoop distributed computing framework
Maximization of non-idle enzymes improves the coverage of the estimated maximal in vivo enzyme catalytic rates in Escherichia coli
Agile workflow for interactive analysis of mass cytometry data
GEPIS - quantitative gene expression profiling in normal and cancer tissues
Successful anti-cancer drug targets able to pass FDA review demonstrate the identifiable signature distinct from the signatures of random genes and initially proposed targets
oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor
PACT: a pipeline for analysis of circulating tumor DNA
Bayesian gene set benchmark dose estimation for "omic" responses
Prediction of drug side effects with transductive matrix co-completion
Bases adjacent to mononucleotide repeats show an increased single nucleotide polymorphism frequency in the human genome
SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions
STRIRED: graphical analysis of string repeats
An automated multi-modal graph-based pipeline for mouse genetic discovery
Preferential use of protein domain pairs as interaction mediators: order and transitivity
ukbREST: efficient and streamlined data access for reproducible research in large biobanks
Bayesian variable selection for disease classification using gene expression data
Fixed point characterization of biological networks with complex graph topology
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB
Predicting gene structure changes resulting from genetic variants via exon definition features
MR-Clust: clustering of genetic variants in Mendelian randomization with similar causal estimates
GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling
Structural insight to mutation effects uncover a common allosteric site in class C GPCRs
Weighted analysis of microarray gene expression using maximum-likelihood
CONSEL: for assessing the confidence of phylogenetic tree selection
Pooling mRNA in microarray experiments and its effect on power
Highly specific and accurate selection of siRNAs for high-throughput functional assays
Avoiding C-hacking when evaluating survival distribution predictions with discrimination measures
SVGenes: a library for rendering genomic features in scalable vector graphic format
Compound cis -regulatory elements with both boundary and enhancer sequences in the human genome
POWER_SAGE: comparing statistical tests for SAGE experiments
Identifying trait clusters by linkage profiles: application in genetical genomics
Optimizing static thermodynamic models of transcriptional regulation
DAVID-WS: a stateful web service to facilitate gene/protein list analysis
Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools
Improving data splitting for classification applications in spectrochemical analyses employing a random-mutation Kennard-Stone algorithm approach
DNA microarray data imputation and significance analysis of differential expression
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
ASTRAL-Pro 2: ultrafast species tree reconstruction from multi-copy gene family trees
Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations
HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications
RegScaf: a regression approach to scaffolding
Predicting synthetic lethal interactions using heterogeneous data sources
Tiara: deep learning-based classification system for eukaryotic sequences
andi: Fast and accurate estimation of evolutionary distances between closely related genomes
bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing
isiKnock: in silico knockouts in signaling pathways
WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data
rMSI: an R package for MS imaging data handling and visualization
DisoLipPred: accurate prediction of disordered lipid-binding residues in protein sequences with deep recurrent networks and transfer learning
G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration
Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data
GSEA-InContext: identifying novel and common patterns in expression experiments
Operon prediction without a training set
TnT: a set of libraries for visualizing trees and track-based annotations for the web
Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC)
PoooL: an efficient method for estimating haplotype frequencies from large DNA pools
selectBoost: a general algorithm to enhance the performance of variable selection methods
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data
A novel registration method for long-serial section images of EM with a serial split technique based on unsupervised optical flow network
High efficiency referential genome compression algorithm
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Software patents in Bioinformatics
vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA
HTSvis: a web app for exploratory data analysis and visualization of arrayed high-throughput screens
A web server to locate periodicities in a sequence
On the complexity of haplotyping a microbial community
Individual-level analysis of differential expression of genes and pathways for personalized medicine
Machine learning in computational biology to accelerate high-throughput protein expression
The Tomato Expression Atlas
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing
Knowledge-based computational search for genes associated with the metabolic syndrome
A study of accuracy, precision in oligonucleotide arrays: extracting more signal at large concentrations
NeuCA web server: a neural network-based cell annotation tool with web-app and GUI
Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity
LAMPLINK: detection of statistically significant SNP combinations from GWAS data
Comparison of different melting temperature calculation methods for short DNA sequences
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments
PHD - an automatic mail server for protein secondary structure prediction
A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors
GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion
Inferring disease and gene set associations with rank coherence in networks
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data
LightDock: a new multi-scale approach to protein-protein docking
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
Automated structural classification of lipids by machine learning
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus
Celestial3D: a novel method for 3D visualization of familial data
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
Fast and sensitive mapping of bisulfite-treated sequencing data
MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies
Green listed - a CRISPR screen tool
scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data
scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism
An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data
ConoServer, a database for conopeptide sequences and structures
GENTANGLE: integrated computational design of gene entanglements
Phasing for medical sequencing using rare variants and large haplotype reference panels
Discovery of meaningful associations in genomic data using partial correlation coefficients
A framework for analyzing EEG data using high-dimensional tests
CarbonylDB: a curated data-resource of protein carbonylation sites
PhenoScanner: a database of human genotype-phenotype associations
Towards accurate high-throughput ligand affinity prediction by exploiting structural ensembles, docking metrics and ligand similarity
Domain prediction with probabilistic directional context
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-experts
CFAGO: cross-fusion of network and attributes based on attention mechanism for protein function prediction
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment
PriLive: privacy-preserving real-time filtering for next-generation sequencing
Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013
Electrogenic property of Na+, K(+)-ATPase through computer simulation
Pathway analysis by randomization incorporating structure - PARIS: an update
Sequence-based heuristics for faster annotation of non-coding RNA families
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments
Improving deep learning-based protein distance prediction in CASP14
Clusterdv: a simple density-based clustering method that is robust, general and automatic
Solenoid and non-solenoid protein recognition using stationary wavelet packet transform
SubRecon: ancestral reconstruction of amino acid substitutions along a branch in a phylogeny
LFM-Pro: a tool for detecting significant local structural sites in proteins
hapCon: estimating contamination of ancient genomes by copying from reference haplotypes
Entropy-based consensus clustering for patient stratification
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps
Knowledge-based modeling of peptides at protein interfaces: PiPreD
Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers
A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps
TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees
Wrapping up BLAST and other applications for use on Unix clusters
Mining co-regulated gene profiles for the detection of functional associations in gene expression data
sRNAPrimerDB: comprehensive primer design and search web service for small non-coding RNAs
Proper evaluation of alignment-free network comparison methods
The Fourth Georgia Tech-University of Georgia International Conference in Bioinformatics: in silico Biology, Biological Networks, from Genomics to Epidemiology (November 13-16, 2003, Atlanta, Georgia, USA)
Finding de novo methylated DNA motifs
A simulator for spatially extended kappa models
Fractional populations in multiple gene inheritance
Non-parametric quantification of protein lysate arrays
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on immunohistochemistry images
FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq
Protein-protein interaction site prediction based on conditional random fields
SciRoKo: a new tool for whole genome microsatellite search and investigation
Estimation of fluorescence-tagged RNA numbers from spot intensities
A web application for sample size and power calculation in case-control microbiome studies
LOBSTER: an environment to design bioimage analysis workflows for large and complex fluorescence microscopy data
DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment
SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization
ISMB 2018 PROCEEDINGS PAPERS COMMITTEE
RVP-net: online prediction of real valued accessible surface area of proteins from single sequences
Oasis: online analysis of small RNA deep sequencing data
A structural alignment kernel for protein structures
Prediction of cancer driver genes through network-based moment propagation of mutation scores
Protein-driven inference of miRNA-disease associations
TRES: comparative promoter sequence analysis
Misdetection of frameshifts in SARS-CoV-2 genomes: need for additional harmonisation and efficient monitoring of data workflows
Registration of the expression patterns of Drosophila segmentation genes by two independent methods
Arabidopsis thaliana regulatory element analyzer
RNAshapes: an integrated RNA analysis package based on abstract shapes
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
gplas: a comprehensive tool for plasmid analysis using short-read graphs
TSIS: an R package to infer alternative splicing isoform switches for time-series data
SABmark- a benchmark for sequence alignment that covers the entire known fold space
Protein solubility: sequence based prediction and experimental verification
CLIPreg: constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks
Joint network and node selection for pathway-based genomic data analysis
Robust reconstruction of gene expression profiles from reporter gene data using linear inversion
GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples
End-Epi: an application for inferring phylogenetic and population dynamical processes from molecular sequences
DAMA: a method for computing multiple alignments of protein structures using local structure descriptors
DeepViral: prediction of novel virus-host interactions from protein sequences and infectious disease phenotypes
Evaluating the predictability of conformational switching in RNA
FisHiCal: an R package for iterative FISH-based calibration of Hi-C data
SISEQ: manipulation of multiple sequence and large database files for common platforms
ZEAL: protein structure alignment based on shape similarity
Application and evaluation of automated semantic annotation of gene expression experiments
ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays
Comparison of tRNA sequences
MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor
Optimizing amino acid groupings for GPCR classification
A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz)
Practical dynamic de Bruijn graphs
A parsimonious threshold-independent protein feature selection method through the area under receiver operating characteristic curve
PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets
Assembly reconciliation
DNA Features Viewer: a sequence annotation formatting and plotting library for Python
METAbolomics data Balancing with Over-sampling Algorithms (META-BOA): an online resource for addressing class imbalance
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program
HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials
Large-scale machine learning for metagenomics sequence classification
A program to optimize DNA sequences for protein expression
DrivR-Base: a feature extraction toolkit for variant effect prediction model construction
PHANOTATE: a novel approach to gene identification in phage genomes
Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data
Biased hosting of intronic microRNA genes
FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci
PhyloBLAST: facilitating phylogenetic analysis of BLAST results
DiProGB: the dinucleotide properties genome browser
BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis
Efficient learning of microbial genotype-phenotype association rules
ChAMP: updated methylation analysis pipeline for Illumina BeadChips
scBGEDA: deep single-cell clustering analysis via a dual denoising autoencoder with bipartite graph ensemble clustering
neoepiscope improves neoepitope prediction with multivariant phasing
An efficient parallel algorithm for accelerating computational protein design
SOMM4mC: a second-order Markov model for DNA N4-methylcytosine site prediction in six species
An exhaustive tree-searching algorithm for high-resolution computer- assisted nucleotide sequence analysis
Oncopacket: integration of cancer research data using GA4GH phenopackets
Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences
An efficient strategy for extensive integration of diverse biological data for protein function prediction
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks
Identifiability of isoform deconvolution from junction arrays and RNA-Seq
BRAT-nova: fast and accurate mapping of bisulfite-treated reads
Parallelization of the MAFFT multiple sequence alignment program
Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression
Halcyon: an accurate basecaller exploiting an encoder-decoder model with monotonic attention
Estimates for different stages of HIV/AIDS disease
Over-optimism in bioinformatics: an illustration
Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus
yMap: an automated method to map yeast variants to protein modifications and functional regions
The structural bioinformatics library: modeling in biomolecular science and beyond
A global approach for contig construction
SPRITE: improving spatial gene expression imputation with gene and cell networks
fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood
ProteomeCommons.org JAF: reference information and tools for proteomics
A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2
Novel pathway compendium analysis elucidates mechanism of pro-angiogenic synthetic small molecule
Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications
MRSD: a web server for Metabolic Route Search and Design
Finding associated variants in genome-wide association studies on multiple traits
The scalable variant call representation: enabling genetic analysis beyond one million genomes
Protein structure alignment by deterministic annealing
The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding
HiC-TE: a computational pipeline for Hi-C data analysis to study the role of repeat family interactions in the genome 3D organization
Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks)
SWORD - a highly efficient protein database search
Detecting functional modules in the yeast protein-protein interaction network
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs
Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery
A novel method for large tree visualization
<tt> scNODE </tt>: generative model for temporal single cell transcriptomic data prediction