yusuke1997/dblp-id-title huggingface dataset:
Application of machine learning techniques to tuberculosis drug resistance analysis
miniTUBA: medical inference by network integration of temporal data using Bayesian analysis
Metriculator: quality assessment for mass spectrometry-based proteomics
Oligonucleotide arrays: information from replication and spatial structure
Characterizing protein-DNA binding event subtypes in ChIP-exo data
FastHPOCR: pragmatic, fast, and accurate concept recognition using the human phenotype ontology
ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity
ReliableGenome: annotation of genomic regions with high/low variant calling concordance
The EVcouplings Python framework for coevolutionary sequence analysis
Efficient genome ancestry inference in complex pedigrees with inbreeding
A Bayesian framework for combining gene predictions
MMseqs2 desktop and local web server app for fast, interactive sequence searches
Characterizing gene sets with FuncAssociate
miREval 2.0: a web tool for simple microRNA prediction in genome sequences
GenRGenS: software for generating random genomic sequences and structures
A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis
A program for computer-aided analyses of ecological field data
A platform-independent graphical user interface for SEQSEE and XALIGN
Kernel-based hierarchical structural component models for pathway analysis
ViruClust: direct comparison of SARS-CoV-2 genomes and genetic variants in space and time
Optimization of cDNA-AFLP experiments using genomic sequence data
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology
ADAPTIVE: leArning DAta-dePendenT, concIse molecular VEctors for fast, accurate metabolite identification from tandem mass spectra
Entrezpy: a Python library to dynamically interact with the NCBI Entrez databases
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase
Optimal transport improves cell-cell similarity inference in single-cell omics data
NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
The NRGTEN Python package: an extensible toolkit for coarse-grained normal mode analysis of proteins, nucleic acids, small molecules and their complexes
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy
BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny
An accurate and powerful method for copy number variation detection
Predicting protein functions with message passing algorithms
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
Effect of pooling samples on the efficiency of comparative studies using microarrays
Confidence measures for protein fold recognition
Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns
Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets
A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
PolarMorphism enables discovery of shared genetic variants across multiple traits from GWAS summary statistics
A hybrid approach to extract protein-protein interactions
GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
Novel organelle-targeting signals in viral proteins
Nemo: an evolutionary and population genetics programming framework
Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data
An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing
ROBIN: a tool for genome rearrangement of block-interchanges
Nucleotide sequence statistical analysis of pauses in RNA elongation by Escherichia coli RNA polymerase
CRiSP: accurate structure prediction of disulfide-rich peptides with cystine-specific sequence alignment and machine learning
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR
ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets
Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution
Mapping multiple co-sequenced T-DNA integration sites within the Arabidopsis genome
Fast metabolite identification with Input Output Kernel Regression
wft4galaxy: a workflow testing tool for galaxy
DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy
Solubility-Weighted Index: fast and accurate prediction of protein solubility
Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen
DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences
Vorolign - fast structural alignment using Voronoi contacts
Topology and prediction of RNA pseudoknots
Local versus global biological network alignment
GoFigure: Automated Gene OntologyTM annotation
NOODAI: a webserver for network-oriented multi-omics data analysis and integration pipeline
Sequence analysis of GerM and SpoVS, uncharacterized bacterial "sporulation" proteins with widespread phylogenetic distribution
Multi-species comparative mapping in silico using the COMPASS strategy
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments
Paired-end RAD-seq for de novo assembly and marker design without available reference
Deuteration distribution estimation with improved sequence coverage for HX/MS experiments
pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
Tree and rate estimation by local evaluation of heterochronous nucleotide data
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies
ADZE: a rarefaction approach for counting alleles private to combinations of populations
Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbrück fluctuation analysis
Statistical mechanical simulation of polymeric DNA melting with MELTSIM
phangorn: phylogenetic analysis in R
Machine Boss: rapid prototyping of bioinformatic automata
Standard virtual biological parts: a repository of modular modeling components for synthetic biology
Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP)
PyPanda: a Python package for gene regulatory network reconstruction
DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications
MR4Cancer: a web server prioritizing master regulators for cancer
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments
Prediction of recursive convex hull class assignments for protein residues
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells
An adaptive direction-assisted test for microbiome compositional data
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach
ProSynAR: a reference aware read merger
aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants
An extensive list of genes that produce alternative transcripts in the mouse
cerebroViz: an R package for anatomical visualization of spatiotemporal brain data
ChronQC: a quality control monitoring system for clinical next generation sequencing
A demonstration of pharmacokinetics and physiological modelling using a microcomputer for data capture and analysis
IsotopicLabelling: an R package for the analysis of MS isotopic patterns of labelled analytes
Rapid identification of non-human sequences in high-throughput sequencing datasets
The use of semiparametric mixed models to analyze PamChip ® peptide array data: an application to an oncology experiment
Comparison of probabilistic combination methods for protein secondary structure prediction
Using information theory to search for co-evolving residues in proteins
RACER: Rapid and accurate correction of errors in reads
Biologically informed variational autoencoders allow predictive modeling of genetic and drug-induced perturbations
The UAB Proteomics Database
Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R
pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes
CeCaFLUX: the first web server for standardized and visual instationary 13C metabolic flux analysis
shinyseg: a web application for flexible cosegregation and sensitivity analysis
An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments
SPARKI: a tool for the statistical analysis of pathogen identification results
Probabilistic nucleotide assembling method for sequencing by hybridization
Learning Rule-based Models of Biological Process from Gene Expression Time Profiles Using Gene Ontology
A novel pattern recognition algorithm to classify membrane protein unfolding pathways with high-throughput single-molecule force spectroscopy
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer
LexExp: a system for automatically expanding concept lexicons for noisy biomedical texts
Predicting the pathogenicity of missense variants using features derived from AlphaFold2
Integrative survival analysis of breast cancer with gene expression and DNA methylation data
Wavelet change-point prediction of transmembrane proteins
Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes
Cancer progression models and fitness landscapes: a many-to-many relationship
MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information
HTML5 PivotViewer: high-throughput visualization and querying of image data on the web
A Bayesian framework for high-throughput T cell receptor pairing
DIG - a system for gene annotation and functional discovery
The Jalview Java alignment editor
pedigreejs: a web-based graphical pedigree editor
An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
ISMB 2012 Committee
An HMM-based algorithm for evaluating rates of receptor-ligand binding kinetics from thermal fluctuation data
Integrative annotation scores of variants for impact on RNA binding protein activities
Modeling biological systems using Dynetica-a simulator of dynamic networks
K-Fold: a tool for the prediction of the protein folding kinetic order and rate
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes
Genome-wide multimediator analyses using the generalized Berk-Jones statistics with the composite test
Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization
Metavir: a web server dedicated to virome analysis
Interpreting peptide mass spectra by VEMS
comoRbidity: an R package for the systematic analysis of disease comorbidities
2020 ISCB Innovatory Award: Xiaole Shirley Liu
An ontology driven architecture for derived representations of macromolecular structure
Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression
METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking
TEPIC 2 - an extended framework for transcription factor binding prediction and integrative epigenomic analysis
Modelling cellular systems with PySCeS
The strength of intron donor splice sites in human genes displays a bell-shaped pattern
Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data
Automatic recognition of conceptualization zones in scientific articles and two life science applications
Effect of the mutation rate and background size on the quality of pathogen identification
TractaViewer: a genome-wide tool for preliminary assessment of therapeutic target druggability
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data
Question answering systems in biology and medicine - the time is now
A learned score function improves the power of mass spectrometry database search
IcyTree: rapid browser-based visualization for phylogenetic trees and networks
Predicting mechanism of action of cellular perturbations with pathway activity signatures
mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes
Normalization of microarray data using a spatial mixed model analysis which includes splines
TERMINUS - Telomeric End-Read Mining IN Unassembled Sequences
freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers
A novel significance score for gene selection and ranking
D-MANOVA: fast distance-based multivariate analysis of variance for large-scale microbiome association studies
Improvements on bicriteria pairwise sequence alignment: algorithms and applications
In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention
COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge
Ballast: Blast post-processing based on locally conserved segments
Reaction Decoder Tool (RDT): extracting features from chemical reactions
Predicting protein residue-residue contacts using deep networks and boosting
Bayesian experts in exploring reaction kinetics of transcription circuits
QCGWAS: A flexible R package for automated quality control of genome-wide association results
CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes
SimPhospho: a software tool enabling confident phosphosite assignment
Granger-causal testing for irregularly sampled time series with application to nitrogen signalling in Arabidopsis
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Quantifying uncertainty in genotype calls
SAMSON: a software package for the biopolymer primary structure analysis
Jflow: a workflow management system for web applications
BioNet: an R-Package for the functional analysis of biological networks
MicroRazerS: rapid alignment of small RNA reads
Hostile: accurate decontamination of microbial host sequences
Biochemical systems analysis of genome-wide expression data
Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Single-sequence and profile-based prediction of RNA solvent accessibility using dilated convolutional neural network
Predicting the effects of SNPs on transcription factor binding affinity
Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates
PhylArray: phylogenetic probe design algorithm for microarray
Exact algorithms for haplotype assembly from whole-genome sequence data
SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
Complexity reduction of biochemical rate expressions
Fitchi: haplotype genealogy graphs based on the Fitch algorithm
An optimization framework for network annotation
Approximate Variance-stabilizing Transformations for Gene-expression Microarray Data
Fast Sequence Clustering Using A Suffix Array Algorithm
DomainSieve: a protein domain-based screen that led to the identification of dam -associated genes with potential link to DNA maintenance
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks
Reconstructing the Temporal Ordering of Biological Samples Using Microarray Data
OCAP: an open comprehensive analysis pipeline for iTRAQ
Comparative analysis and unification of domain-domain interaction networks
InterPepScore: a deep learning score for improving the FlexPepDock refinement protocol
Graphlet Laplacians for topology-function and topology-disease relationships
Searching DNA databases for similarities to DNA sequences: when is a match significant?
TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
Protein domain decomposition using a graph-theoretic approach
Reconstructing viral haplotypes using long reads
Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci
Efficiently counting all orbits of graphlets of any order in a graph using autogenerated equations
FuncISH: learning a functional representation of neural ISH images
Reconstructing biological networks using conditional correlation analysis
FunMap: functional mapping of complex traits
A penalized linear mixed model with generalized method of moments estimators for complex phenotype prediction
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference
Pinnacle : a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
Characterizing rate limiting steps in transcription from RNA production times in live cells
gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing
EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data
A new computer program for nematode identification
OrgNet: orientation-gnostic protein stability assessment using convolutional neural networks
Partially non-homogeneous dynamic Bayesian networks based on Bayesian regression models with partitioned design matrices
Pairwise alignment incorporating dipeptide covariation
TaggerOne: joint named entity recognition and normalization with semi-Markov Models
PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
Efficient multivariate analysis algorithms for longitudinal genome-wide association studies
SimkaMin: fast and resource frugal de novo comparative metagenomics
QGene 4.0, an extensible Java QTL-analysis platform
Prediction of gene co-expression from chromatin contacts with graph attention network
Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design
Correction to: "Retraction of: DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency"
Protein fold recognition based on multi-view modeling
Alignment of multiple DNA and protein sequence data
A parallel computational framework for ultra-large-scale sequence clustering analysis
Peptide length-based prediction of peptide-MHC class II binding
The Synergizer service for translating gene, protein and other biological identifiers
Estimation of restriction maps with known site order using a generalized linear model [published erratum appears in Comput Appl Biosci 1993 Apr;9(2): 242]
TSGDB: a database system for tumor suppressor genes
MIGS - a simple graphics utility program
Statistical prediction of protein-chemical interactions based on chemical structure and mass spectrometry data
A new cis -acting regulatory element driving gene expression in the zebrafish pineal gland
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
METACLUSTER - an R package for context-specific expression analysis of metabolic gene clusters
Promoter analysis and prediction in the human genome using sequence-based deep learning models
Driving multiple pulsed field electrophoresis devices from one personal computer
ATHENA: the analysis tool for heritable and environmental network associations
PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data
PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy
Computer-based learning of cooperativity and allostery
Spaced seeds improve k -mer-based metagenomic classification
UglyTrees: a browser-based multispecies coalescent tree visualizer
GrandPrix: scaling up the Bayesian GPLVM for single-cell data
Gene clustering by Latent Semantic Indexing of MEDLINE abstracts
Moderated effect size and P -value combinations for microarray meta-analyses
A mixture model-based strategy for selecting sets of genes in multiclass response microarray experiments
A geometric invariant-based framework for the analysis of protein conformational space
Missing value estimation methods for DNA methylation data
Tersect: a set theoretical utility for exploring sequence variant data
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes
Enhancing statistical power in temporal biomarker discovery through representative shapelet mining
A gene-phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach
Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
HIV classification using the coalescent theory
A scalable moment-closure approximation for large-scale biochemical reaction networks
PARIS: a proteomic analysis and resources indexation system
Bayesian multitask learning for medicine recommendation based on online patient reviews
MGPLI: exploring multigranular representations for protein-ligand interaction prediction
SBML export interface for the systems biology toolbox for MATLAB
Standardization and denoising algorithms for mass spectra to classify whole-organism bacterial specimens
An iterative algorithm for converting a class II MHC binding motif into a quantitative predictive model
Identification of Context-Dependent Motifs by Contrasting ChIP Binding Data
Influenza classification from short reads with VAPOR facilitates robust mapping pipelines and zoonotic strain detection for routine surveillance applications
CoGenT++: an extensive and extensible data environment for computational genomics
Multivariate analysis of variance test for gene set analysis
IntelliGenes : a novel machine learning pipeline for biomarker discovery and predictive analysis using multi-genomic profiles
YODA: selecting signature oligonucleotides
<tt>MAGScoT</tt>: a fast, lightweight and accurate bin-refinement tool
MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization
GROMACS molecule & liquid database
CpG Transformer for imputation of single-cell methylomes
structureViz: linking Cytoscape and UCSF Chimera
COPRED: prediction of fold, GO molecular function and functional residues at the domain level
Branch-recombinant Gaussian processes for analysis of perturbations in biological time series
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data
RankViaContact: ranking and visualization of amino acid contacts