yusuke1997/dblp-id-title huggingface dataset:
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
WMSA: a novel method for multiple sequence alignment of DNA sequences
FastSK: fast sequence analysis with gapped string kernels
RANKPROP: a web server for protein remote homology detection
Statistical methods to infer cooperative binding among transcription factors in Saccharomyces cerevisiae
Disease gene prediction with privileged information and heteroscedastic dropout
DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences
Asymptotically optimal minimizers schemes
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data
metID: an R package for automatable compound annotation for LC-MS-based data
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment
A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana
Genotyping of single nucleotide polymorphism using model-based clustering
Quantitative analysis of the selective pressure exerted on homologous proteins
Pseudoalignment tools as an efficient alternative to detect repeated transposable elements in scRNAseq data
A more efficient search strategy for aging genes based on connectivity
GoFish finds genes with combinations of Gene Ontology attributes
A character separation index suitable for binary data containing equivocal responses
Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data
BioERP: biomedical heterogeneous network-based self-supervised representation learning approach for entity relationship predictions
An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes
CytoGEDEVO - global alignment of biological networks with Cytoscape
SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein-protein binding affinity
Multiple flexible structure alignment using partial order graphs
LapTrack: linear assignment particle tracking with tunable metrics
Graph2MDA: a multi-modal variational graph embedding model for predicting microbe-drug associations
Positional candidate gene selection from livestock EST databases using Gene Ontology
PC2P: parameter-free network-based prediction of protein complexes
Extraction of data deposition statements from the literature: a method for automatically tracking research results
Large-scale dynamic gene regulatory network inference combining differential equation models with local dynamic Bayesian network analysis
Proteus: a web-based, context-specific modelling tool for molecular networks
GeneMachine: gene prediction and sequence annotation
RiboMaker: computational design of conformation-based riboregulation
omicsPrint: detection of data linkage errors in multiple omics studies
Comment on 'Hayai-Annotation Plants: an ultrafast and comprehensive functional gene annotation system in plants': the importance of taking the GO graph structure into account
Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds
Integrated analysis of copy number alterations and gene expression: a bivariate assessment of equally directed abnormalities
Sequence similarity scores and the inference of structure-function relationships
PEATH: single-individual haplotyping by a probabilistic evolutionary algorithm with toggling
HaploVar: an R package for defining local haplotype variants for trait association and trait prediction analyses
GSCALite: a web server for gene set cancer analysis
A handy database for culture collections worldwide: CCINFO-PC
InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm
A simple shape characteristic of protein-protein recognition
An algorithm for designing minimal microbial communities with desired metabolic capacities
Application of a simple likelihood ratio approximant to protein sequence classification
Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
imputomics: web server and R package for missing values imputation in metabolomics data
Robustly interrogating machine learning-based scoring functions: what are they learning?
Predicting the functional consequences of cancer-associated amino acid substitutions
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees
Generating interacting protein sequences using domain-to-domain translation
OMPPM: online multiple palindrome pattern matching
An integrated system for high throughput TaqManTM based SNP genotyping
Random distance dependent attachment as a model for neural network generation in the Caenorhabditis elegans
A database for management of gene expression data in situ
The ancestral KH peptide at the root of a domain family with three different folds
AgentCell: a digital single-cell assay for bacterial chemotaxis
incaRNAfbinv 2.0: a webserver and software with motif control for fragment-based design of RNAs
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
A generic motif discovery algorithm for sequential data
Flexible design of multiple metagenomics classification pipelines with UGENE
ssbio: a Python framework for structural systems biology
MOODS: fast search for position weight matrix matches in DNA sequences
Profile hidden Markov models
Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform
Prediction of protein solvent accessibility using fuzzy k-nearest neighbor method
NetworkTrail - a web service for identifying and visualizing deregulated subnetworks
13CFLUX2 - high-performance software suite for 13 C-metabolic flux analysis
An integrated structure- and system-based framework to identify new targets of metabolites and known drugs
Switching regulatory models of cellular stress response
Borrowing strength: a likelihood ratio test for related sparse signals
SYSBIONS: nested sampling for systems biology
EVpedia: a community web portal for extracellular vesicles research
LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins
MFAML: a standard data structure for representing and exchanging metabolic flux models
Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
DeepSig: deep learning improves signal peptide detection in proteins
Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction
Gene co-expression network topology provides a framework for molecular characterization of cellular state
Tracker: continuous HMMER and BLAST searching
A motif of a microbial starch-binding domain found in human genethonin
iDNA4mC: identifying DNA N4-methylcytosine sites based on nucleotide chemical properties
Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data
Localized motif discovery in gene regulatory sequences
MAGNA: Maximizing Accuracy in Global Network Alignment
Improving flux predictions by integrating data from multiple strains
cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling
Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd -trees
TargetDB: a database of peptides targeting proteins to subcellular locations
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
SNPselector: a web tool for selecting SNPs for genetic association studies
Predicting Nash equilibria for microbial metabolic interactions
PlasCAT: Plasmid Cloud Assembly Tool
SylvX: a viewer for phylogenetic tree reconciliations
TranspoScope: interactive visualization of retrotransposon insertions
Tumor origin detection with tissue-specific miRNA and DNA methylation markers
The interwinding nature of protein-protein interfaces and its implication for protein complex formation
RuleBender: a visual interface for rule-based modeling
getDNB: identifying dynamic network biomarkers of hepatocellular carcinoma from time-varying gene regulations utilizing graph embedding techniques for anomaly detection
Comparative gene marker selection suite
Figbird: a probabilistic method for filling gaps in genome assemblies
HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees
A distributed environment for physical map construction
A new algorithm for detecting low-complexity regions in protein sequences
Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking
Association mapping in biomedical time series via statistically significant shapelet mining
Identification of cell-type-specific marker genes from co-expression patterns in tissue samples
MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data
DeuteRater: a tool for quantifying peptide isotope precision and kinetic proteomics
CFinder: locating cliques and overlapping modules in biological networks
Protein motif by computer: the perfect Greek key jellyroll designer
TITINdb - a computational tool to assess titin's role as a disease gene
LevioSAM: fast lift-over of variant-aware reference alignments
DySC: software for greedy clustering of 16S rRNA reads
SENSE: Siamese neural network for sequence embedding and alignment-free comparison
Proteins without 3D structure: definition, detection and beyond
Mapping physiological states from microarray expression measurements
parMATT: parallel multiple alignment of protein 3D-structures with translations and twists for distributed-memory systems
Algorithms for determining the fate of sites and domain boundaries in computer simulations of recombinant DNA procedures
rMSIproc: an R package for mass spectrometry imaging data processing
Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!
MetAssign: probabilistic annotation of metabolites from LC-MS data using a Bayesian clustering approach
CGHnormaliter: a Bioconductor package for normalization of array CGH data with many CNAs
TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data
SomVarIUS: somatic variant identification from unpaired tissue samples
Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
PCA disjoint models for multiclass cancer analysis using gene expression data
High-resolution spatial normalization for microarrays containing embedded technical replicates
CellLine , a stochastic cell lineage simulator
Phylogenetically enhanced statistical tools for RNA structure prediction
SCORER 2.0: an algorithm for distinguishing parallel dimeric and trimeric coiled-coil sequences
Cell line name recognition in support of the identification of synthetic lethality in cancer from text
Clustering by soft-constraint affinity propagation: applications to gene-expression data
RseqFlow: workflows for RNA-Seq data analysis
Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures
Finding correct protein-protein docking models using ProQDock
Ratio statistics of gene expression levels and applications to microarray data analysis
An effective framework for reconstructing gene regulatory networks from genetical genomics data
About the use of protein models
RILogo: visualizing RNA-RNA interactions
Estimating dynamic models for gene regulation networks
A fast and sensitive multiple sequence alignment algorithm
Computer simulation of the cellular arrangement using physical model in early cleavage of the nematode Caenorhabditis elegans
Modeling of signal-response cascades using decision tree analysis
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer
Assessment of significance of conditionally independent GWAS signals
Optimal gap-affine alignment in O ( s ) space
CaFE: a tool for binding affinity prediction using end-point free energy methods
VarB: a variation browsing and analysis tool for variants derived from next-generation sequencing data
ELViS: an R package for estimating copy number levels of viral genomic segments at base-resolution
DIMERBOW: exploring possible GPCR dimer interfaces
DeepHIT: a deep learning framework for prediction of hERG-induced cardiotoxicity
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts
BioDynaMo: a modular platform for high-performance agent-based simulation
AmplificationTimeR: an R package for timing sequential amplification events
Efficient whole-genome association mapping using local phylogenies for unphased genotype data
Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data
Identification of OBO nonalignments and its implications for OBO enrichment
Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation
ADaCGH2: parallelized analysis of (big) CNA data
Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs
Flexibility of the genetic code with respect to DNA structure
Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations
Ribbon: intuitive visualization for complex genomic variation
CoCo: a web application to display, store and curate ChIP-on-chip data integrated with diverse types of gene expression data
Exact model-free function inference using uniform marginal counts for null population
PaRSnIP: sequence-based protein solubility prediction using gradient boosting machine
Phylogenetics, likelihood, evolution and complexity
RabbitQC: high-speed scalable quality control for sequencing data
OmicsEV: a tool for comprehensive quality evaluation of omics data tables
High-dimension to high-dimension screening for detecting genome-wide epigenetic and noncoding RNA regulators of gene expression
Discriminatory power of RNA family models
GSP: a web-based platform for designing genome-specific primers in polyploids
GenePro: a cytoscape plug-in for advanced visualization and analysis of interaction networks
Identification and quantification of disease-related gene clusters
Systems biology model repository for macrophage pathway simulation
MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics
Knowledge transfer from macro-world to micro-world: enhancing 3D Cryo-ET classification through fine-tuning video-based deep models
A-Cell: graphical user interface for the construction of biochemical reaction models
GARFIELD-NGS: Genomic vARiants FIltering by dEep Learning moDels in NGS
Constructing small genome graphs via string compression
Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model
SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Evolutionary design principles and functional characteristics based on kingdom-specific network motifs
MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequences
Erratum: sample size determination for the false discovery rate
Towards clinically more relevant dissection of patient heterogeneity via survival-based Bayesian clustering
2019 Outstanding Contributions to ISCB Awarded to Barb Bryant
MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities
TOM: enhancement and extension of a tool suite for in silico approaches to multigenic hereditary disorders
Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation
Deciphering high-order structures in spatial transcriptomes with graph-guided Tucker decomposition
ORCAN - a web-based meta-server for real-time detection and functional annotation of orthologs
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction
A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data
SRS - an indexing and retrieval tool for flat file data libraries
Data mining of sequences and 3D structures of allergenic proteins
ModView, visualization of multiple protein sequences and structures
Parallelized calculation of permutation tests
ATLIGATOR: editing protein interactions with an atlas-based approach
An integrative clustering and modeling algorithm for dynamical gene expression data
ggkegg : analysis and visualization of KEGG data utilizing the grammar of graphics
Revealing differences in gene network inference algorithms on the network level by ensemble methods
Reviewer-coerced citation: case report, update on journal policy and suggestions for future prevention
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
Precision and recall estimates for two-hybrid screens
AllergenFP: allergenicity prediction by descriptor fingerprints
Quantitative method for the assignment of hinge and shear mechanism in protein domain movements
DeepNano-blitz: a fast base caller for MinION nanopore sequencers
RDAVIDWebService: a versatile R interface to DAVID
Efficient remote homology detection using local structure
METAINTER: meta-analysis of multiple regression models in genome-wide association studies
Prediction of lncRNA-disease associations based on inductive matrix completion
Feature weighted models to address lineage dependency in drug-resistance prediction from Mycobacterium tuberculosis genome sequences
CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure
Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming
A heuristic approach for detecting RNA H-type pseudoknots
delta rho-Web, an online tool to assess composition similarity of individual nucleic acid sequences
The revival of the Gini importance?
Predicting residue-residue contacts using random forest models
Global stabilizing control of large-scale biomolecular regulatory networks
TiFoSi: an efficient tool for mechanobiology simulations of epithelia
NinimHMDA: neural integration of neighborhood information on a multiplex heterogeneous network for multiple types of human Microbe-Disease association
A probabilistic method for identifying start codons in bacterial genomes
Identification and quantification of metabolites in 1 H NMR spectra by Bayesian model selection
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline
UPDtool: a tool for detection of iso- and heterodisomy in parent-child trios using SNP microarrays
3Dee: a database of protein structural domains
Prediction of Ras-effector interactions using position energy matrices
SVJedi-graph: improving the genotyping of close and overlapping structural variants with long reads using a variation graph
DOSE-L1000: unveiling the intricate landscape of compound-induced transcriptional changes
HyperGen: compact and efficient genome sketching using hyperdimensional vectors
LIBRA: LIgand Binding site Recognition Application
Predicting accurate contacts in thousands of Pfam domain families using PconsC3
PERF: an exhaustive algorithm for ultra-fast and efficient identification of microsatellites from large DNA sequences
PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive
EPIK: precise and scalable evolutionary placement with informative k -mers
Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase
APPRIS principal isoforms and MANE Select transcripts define reference splice variants
DUDes: a top-down taxonomic profiler for metagenomics
FLASH: fast length adjustment of short reads to improve genome assemblies
Nimbus: a design-driven analyses suite for amplicon-based NGS data
SNPlice: variants that modulate Intron retention from RNA-sequencing data
METAMOD: software for steady-state modelling and control analysis of metabolic pathways on the BBC microcomputer
A compact, flexible and cheap system for acquiring sequence data from autoradiograms with a digitizer and transferring it to an arbitrary host computer
STAR: an integrated solution to management and visualization of sequencing data
A quantitative model for oxygen uptake and release in a family of hemeproteins
Towards Computer Aided Design (CAD) of Useful Microorganisms
SaRAD: a Simple and Robust Abbreviation Dictionary
ACTIVA : realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders
Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants
Probabilities of spurious connections in gene networks: application to expression time series
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca
EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions
The bio-objects project. Part I: the object data model core elements
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations
Biocellion : accelerating computer simulation of multicellular biological system models
RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset
Improving dynamic predictions with ensembles of observable models
DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data
Analysis of dose-response effects on gene expression data with comparison of two microarray platforms
PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation
Bayesian learning of biological pathways on genomic data assimilation
Conserved RNA secondary structures in viral genomes: a survey
A hierarchical model for incomplete alignments in phylogenetic inference
AQUA-DUCT: a ligands tracking tool
MBRole: enrichment analysis of metabolomic data
ABSP: an automated R tool to efficiently analyze region-specific CpG methylation from bisulfite sequencing PCR
uHAF: a unified hierarchical annotation framework for cell type standardization and harmonization
rMETL: sensitive mobile element insertion detection with long read realignment
A lock-and-key model for protein-protein interactions
Natively unstructured regions in proteins identified from contact predictions
MedScan, a natural language processing engine for MEDLINE abstracts
Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq
Benchmarking of 4C-seq pipelines based on real and simulated data
TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization
Serial SimCoal: A population genetics model for data from multiple populations and points in time
NAM: association studies in multiple populations
Clustering by common friends finds locally significant proteins mediating modules
Friend, an integrated analytical front-end application for bioinformatics
SBML2TikZ: supporting the SBML render extension in LaTeX