yusuke1997/dblp-id-title huggingface dataset:
Finding optimal interaction interface alignments between biological complexes
hicGAN infers super resolution Hi-C data with generative adversarial networks
SPLICE, a computer program for automated extraction of information from GenBank sequence entries
FWER and FDR control when testing multiple mediators
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study
MolTrans: Molecular Interaction Transformer for drug-target interaction prediction
Efficient storage and regression computation for population-scale genome sequencing studies
Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays
BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
VIS-O-BAC: exploratory visualization of functional genome studies from bacteria
Building multiple alignments from pairwise alignments
Modified SIMPSON O ( n 3 ) algorithm for the full sibship reconstruction problem
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction
Comparison of sequence masking algorithms and the detection of biased protein sequence regions
NvMap: automated analysis of NMR chemical shift perturbation data
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies
Quantification of transcription noise's impact on cell fate commitment with digital resolutions
MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures
A robust approach for identifying differentially abundant features in metagenomic samples
FASTSP: linear time calculation of alignment accuracy
Probabilistic count matrix factorization for single cell expression data analysis
scME: a dual-modality factor model for single-cell multiomics embedding
Miso: an R package for multiple isotope labeling assisted metabolomics data analysis
A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases
A duplication growth model of gene expression networks
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
Hierarchical and multi-resolution representation of protein flexibility
High-sensitivity pattern discovery in large, paired multiomic datasets
Bedtk: finding interval overlap with implicit interval tree
DNAMAT: an efficient graphic matrix sequence homology algorithm and its application to structural analysis
Picasso: generating a covering set of protein family profiles
PathwayConnector: finding complementary pathways to enhance functional analysis
PhD: a web database application for phenotype data management
CNVineta: a data mining tool for large case-control copy number variation datasets
propy: a tool to generate various modes of Chou's PseAAC
Improving the reuse of computational models through version control
Genome-scale regression analysis reveals a linear relationship for promoters and enhancers after combinatorial drug treatment
T-Pile - a package for thermodynamic calculations for biomolecules
Predicting in vitro drug sensitivity using Random Forests
qValue - a program to calculate comparative measures of genomic reorganisation from cytogenetic and/or linkage information
Detecting Gene Ontology misannotations using taxon-specific rate ratio comparisons
DECOMP - from interpreting Mass Spectrometry peaks to solving the Money Changing Problem
Quantification of cell behaviors and computational modeling show that cell directional behaviors drive zebrafish pectoral fin morphogenesis
SIGN: similarity identification in gene expression
Pathway-based approach using hierarchical components of collapsed rare variants
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation
EGene: a configurable pipeline generation system for automated sequence analysis
SEK: sparsity exploiting k -mer-based estimation of bacterial community composition
Automatic design of gene-specific sequence tags for genome-wide functional studies
Genome-scale de novo assembly using ALGA
Finding motifs from all sequences with and without binding sites
Comparison of genomic DNA sequences: solved and unsolved problems
DECO: decompose heterogeneous population cohorts for patient stratification and discovery of sample biomarkers using omic data profiling
SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations
Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning
Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling
MPF-BML: a standalone GUI-based package for maximum entropy model inference
Circular genome visualization and exploration using CGView
A support vector machine-based method for predicting the propensity of a protein to be soluble or to form inclusion body on overexpression in Escherichia coli
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes
De-correlating expression in gene-set analysis
Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors
Fast stochastic algorithm for simulating evolutionary population dynamics
Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling
STAR: ultrafast universal RNA-seq aligner
DNA Compass: a secure, client-side site for navigating personal genetic information
Boosting proportional hazards models using smoothing splines, with applications to high-dimensional microarray data
Steer'n'Detect: fast 2D template detection with accurate orientation estimation
LICORN: learning cooperative regulation networks from gene expression data
DiffNetFDR: differential network analysis with false discovery rate control
MindTheGap: integrated detection and assembly of short and long insertions
Abundance estimation and differential testing on strain level in metagenomics data
The DOMON domains are involved in heme and sugar recognition
Partition: a surjective mapping approach for dimensionality reduction
Efficient merging of genome profile alignments
What are the baselines for protein fold recognition?
IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data
A machine-learning-based alternative to phylogenetic bootstrap
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Evaluating the performance of microarray segmentation algorithms
ACNE: a summarization method to estimate allele-specific copy numbers for Affymetrix SNP arrays
Statistical model-based testing to evaluate the recurrence of genomic aberrations
The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding
Inferring pathways from gene lists using a literature-derived network of biological relationships
A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks
Fast numerical optimization for genome sequencing data in population biobanks
MFCompress: a compression tool for FASTA and multi-FASTA data
MSAViewer: interactive JavaScript visualization of multiple sequence alignments
TriPoly: haplotype estimation for polyploids using sequencing data of related individuals
actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions
edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test
Profiles from structure based sequence alignment of porins can identify ß stranded integral membrane proteins
D 3 M: detection of differential distributions of methylation levels
SVScore: an impact prediction tool for structural variation
WATCLUST: a tool for improving the design of drugs based on protein-water interactions
The Virtual Fly Brain browser and query interface
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
FREGAT: an R package for region-based association analysis
Real-time mapping of nanopore raw signals
EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models
A novel SCCA approach via truncated ℓ1-norm and truncated group lasso for brain imaging genetics
Assessing association between protein truncating variants and quantitative traits
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments
PreP: gene expression data pre-processing
PRANC: ML species tree estimation from the ranked gene trees under coalescence
myTAI: evolutionary transcriptomics with R
BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
plasmidSPAdes: assembling plasmids from whole genome sequencing data
dAPE: a web server to detect homorepeats and follow their evolution
The Ark: a customizable web-based data management tool for health and medical research
Materials methods: a Macintosh hypercard stack for laboratory protocols
Differential methylation values in differential methylation analysis
ISPyB: an information management system for synchrotron macromolecular crystallography
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment
Sorting the nuclear proteome
Use of AAScatterPlot tool for monitoring the evolution of the hemagglutinin cleavage site in H9 avian influenza viruses
CORAL: aligning conserved core regions across domain families
An improved FORTRAN 77 recombinant DNA database management system with graphic extensions in GKS
A latent variable model for chemogenomic profiling
RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss
Topology-function conservation in protein-protein interaction networks
General framework for developing and evaluating database scoring algorithms using the TANDEM search engine
COMBAT-TB-NeoDB: fostering tuberculosis research through integrative analysis using graph database technologies
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues
Uniform integration of genome mapping data using intersection graphs
Formalization of mouse embryo anatomy
Conservation analysis of small RNA genes in Escherichia coli
A phylogenetic Gibbs sampler that yields centroid solutions for cis -regulatory site prediction
PERFILS: a program for the quantitative treatment of footprinting data
Scoring of predicted GRK2 phosphorylation sites in Nedd4-2
TranSyT , an innovative framework for identifying transport systems
Exact Bayesian inference for phylogenetic birth-death models
A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values)
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches
Bioinformatics analyses of circular dichroism protein reference databases
SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits
polyPK: an R package for pharmacokinetic analysis of multi-component drugs using a metabolomics approach
MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins
Computation and application of tissue-specific gene set weights
Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics
Predicting cancer drug response using parallel heterogeneous graph convolutional networks with neighborhood interactions
Anatomical entity mention recognition at literature scale
Reference-based compression of short-read sequences using path encoding
Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family
Detection of circular permutations within protein structures using CE-CP
Analysing high-throughput sequencing data in Python with HTSeq 2.0
Automated mapping of large-scale chromatin structure in ENCODE
ScGOclust: leveraging gene ontology to find functionally analogous cell types between distant species
COOL - a VAX program for finding COmmon OLigomers in nucleic acid sequences. Thyroid hormone receptor sequences used as an example
Motif identification neural design for rapid and sensitive protein family search
CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes
Considering dependence among genes and markers for false discovery control in eQTL mapping
SANA NetGO: a combinatorial approach to using Gene Ontology (GO) terms to score network alignments
Automated bond order assignment as an optimization problem
MSeasy: unsupervised and untargeted GC-MS data processing
Empirical determination of effective gap penalties for sequence comparison
scDoc: correcting drop-out events in single-cell RNA-seq data
Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA
PCOAT: positional correlation analysis using multiple methods
FigSearch: a figure legend indexing and classification system
BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads
Tumor classification by partial least squares using microarray gene expression data
A predictive model for identifying mini-regulatory modules in the mouse genome
Quantification of biases in predictions of protein stability changes upon mutations
A framework for identifying dysregulated chromatin regulators as master regulators in human cancer
sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications
A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins
cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions
Twelve C2H2 zinc-finger genes on human chromosome 19 can be each translated into the same type of protein after frameshifts
SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes
In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma
Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function
ART: a next-generation sequencing read simulator
A novel meta-analysis method exploiting consistency of high-throughput experiments
TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models
ADVANCE and ADAM: two algorithms for the analysis of global similarity between homologous informational sequences
Automatic classification of single-molecule force spectroscopy traces from heterogeneous samples
DeepS: a web server for image optical sectioning and super resolution microscopy based on a deep learning framework
Anisotropic network model: systematic evaluation and a new web interface
SPMM: estimating infection duration of multivariant HIV-1 infections
Bayesian nonparametrics in protein remote homology search
Algorithms for variable length Markov chain modeling
Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping
MEvA-X: a hybrid multiobjective evolutionary tool using an XGBoost classifier for biomarkers discovery on biomedical datasets
Dante: genotyping of known complex and expanded short tandem repeats
Kablammo: an interactive, web-based BLAST results visualizer
Identifying genes from up-down properties of microarray expression series
Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs
A high-resolution map of the human small non-coding transcriptome
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
Dicodon-based measures for modeling gene expression
CONSTRUCT: an algorithmic tool for identifying functional or structurally important regions in protein tertiary structure
A consensus program for molecular sequences
Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data
Prediction of Indel flanking regions in protein sequences using a variable-order Markov model
Compositional analysis of microbiome data using the linear decomposition model (LDM)
biMM: efficient estimation of genetic variances and covariances for cohorts with high-dimensional phenotype measurements
JAMI: fast computation of conditional mutual information for ceRNA network analysis
GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers
PPDMs - a resource for mapping small molecule bioactivities from ChEMBL to Pfam-A protein domains
ISMB/ECCB 2019 PROCEEDINGS PAPERS COMMITTEE
DULoc: quantitatively unmixing protein subcellular location patterns in immunofluorescence images based on deep learning features
ontoCAT: an R package for ontology traversal and search
HPOFiller: identifying missing protein-phenotype associations by graph convolutional network
Accurate estimation of microbial sequence diversity with Distanced
CD-HIT: accelerated for clustering the next-generation sequencing data
CellSort: a support vector machine tool for optimizing fluorescence-activated cell sorting and reducing experimental effort
Statistical challenges associated with detecting copy number variations with next-generation sequencing
CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis
poreTally: run and publish de novo nanopore assembler benchmarks
FullMeSH: improving large-scale MeSH indexing with full text
Prediction of RNA secondary structure based on helical regions distribution
Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants
Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
Separation of nearly identical repeats in shotgun assemblies using defined nucleotide positions, DNPs
Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles
varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data
Phosphomatics: interactive interrogation of substrate-kinase networks in global phosphoproteomics datasets
iMembrane: homology-based membrane-insertion of proteins
Joint haplotype phasing and genotype calling of multiple individuals using haplotype informative reads
ERC analysis: web-based inference of gene function via evolutionary rate covariation
RAPID detection of gene-gene interactions in genome-wide association studies
Investigating extended regulatory regions of genomic DNA sequences
OSIRIS: a tool for retrieving literature about sequence variants
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis
Intervention in context-sensitive probabilistic Boolean networks
proTF: a comprehensive data and phylogenomics resource for prokaryotic transcription factors
The domain-server: direct prediction of protein domain-homologies from BLAST search
A graph neural network approach for molecule carcinogenicity prediction
Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript
Perfect phylogeny haplotyper: haplotype inferral using a tree model
Avoiding model selection bias in small-sample genomic datasets
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
PatternHunter: faster and more sensitive homology search
Syntons, metabolons and interactons: an exact graph-theoretical approach for exploring neighbourhood between genomic and functional data
THEA: ontology-driven analysis of microarray data
Identifying HLA supertypes by learning distance functions
A scalable method for integration and functional analysis of multiple microarray datasets
Quantitative Quality Control in Microarray Experiments and the Application in Data Filtering, Normalization and False Positive Rate Prediction
Bayesian GWAS with Structured and Non-Local Priors
Cytoscape 2.8: new features for data integration and network visualization
A graphical method for reducing and relating models in systems biology
Gos: a declarative library for interactive genomics visualization in Python
Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data
Frequency-domain analysis of biomolecular sequences
DeepIsoFun: a deep domain adaptation approach to predict isoform functions
Clustered alignments of gene-expression time series data
Methods for labeling error detection in microarrays based on the effect of data perturbation on the regression model
Using interpretable deep learning to model cancer dependencies
Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum
Hummingbird: efficient performance prediction for executing genomic applications in the cloud
1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions
TimeCycle: topology inspired method for the detection of cycling transcripts in circadian time-series data
Correlated mutations select misfolded from properly folded proteins
HyperGraphs.jl: representing higher-order relationships in Julia
Tmod: toolbox of motif discovery
Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer
Discovering well-ordered folding patterns in nucleotide sequences
Annotare - a tool for annotating high-throughput biomedical investigations and resulting data
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization
The early days of bioinformatics publishing
Bias in the estimation of false discovery rate in microarray studies
Surface-based multimodal protein-ligand binding affinity prediction
Predicting alpha-helix and beta-strand segments of globular proteins
Median and small parsimony problems on RNA trees
Context-dependent DNA recognition code for C 2 H 2 zinc-finger transcription factors
Optimizing data integration improves gene regulatory network inference in Arabidopsis thaliana
Inferring gene ontologies from pairwise similarity data
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
High-speed and high-ratio referential genome compression
Driver gene mutations based clustering of tumors: methods and applications
Using neighborhood cohesiveness to infer interactions between protein domains
Correcting for gene-specific dye bias in DNA microarrays using the method of maximum likelihood
Precise prediction of hotspot residues in protein-RNA complexes using graph attention networks and pretrained protein language models
scTPA: a web tool for single-cell transcriptome analysis of pathway activation signatures
ipaPy2: Integrated Probabilistic Annotation (IPA) 2.0 - an improved Bayesian-based method for the annotation of LC-MS/MS untargeted metabolomics data