yusuke1997/dblp-id-title huggingface dataset:
DockIT: a tool for interactive molecular docking and molecular complex construction
Parameterized complexity analysis in computational biology
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
The RNA shapes studio
scMCs: a framework for single-cell multi-omics data integration and multiple clusterings
MADE4: an R package for multivariate analysis of gene expression data
PUGSVM: a caBIG TM analytical tool for multiclass gene selection and predictive classification
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling
MASISH: a database for gene expression in maize seeds
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
The OGCleaner: filtering false-positive homology clusters
Analysing gene expressions with GRANK
InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets
APTANI2: update of aptamer selection through sequence-structure analysis
Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME
I-PV: a CIRCOS module for interactive protein sequence visualization
CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors
ELISA assay optimization using hyperbolic regression
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks
Highly consistent patterns for inherited human diseases at the molecular level
PlateDesigner: a web-based application for the design of microplate experiments
PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering
goCluster integrates statistical analysis and functional interpretation of microarray expression data
repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects
SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data
Graphlet-based measures are suitable for biological network comparison
mOWL: Python library for machine learning with biomedical ontologies
Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis
Small molecule generation via disentangled representation learning
DecentTree: scalable Neighbour-Joining for the genomic era
Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API
MotifHyades: expectation maximization for de novo DNA motif pair discovery on paired sequences
TMCrys: predict propensity of success for transmembrane protein crystallization
The power of word-frequency-based alignment-free functions: a comprehensive large-scale experimental analysis
On an efficient parallelization of exhaustive sequence comparison algorithms on message passing architectures
Annotating high-impact 5′untranslated region variants with the UTRannotator
ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
Predictive and interpretable models via the stacked elastic net
ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencing
Transcript mapping with high-density oligonucleotide tiling arrays
wQFM: highly accurate genome-scale species tree estimation from weighted quartets
A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures
apTreeshape: statistical analysis of phylogenetic tree shape
emMAW: computing minimal absent words in external memory
PLMaddon: a power-law module for the Matlab TM SBToolbox
BTR: a bioinformatics tool recommendation system
Detection of rare disease variants in extended pedigrees using RVS
jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data
Detection of significantly differentially methylated regions in targeted bisulfite sequencing data
Complex discovery from weighted PPI networks
A complete graph-based approach with multi-task learning for predicting synergistic drug combinations
Identification of chemogenomic features from drug-target interaction networks using interpretable classifiers
High dimensional classification with combined adaptive sparse PLS and logistic regression
OPM: Orientations of Proteins in Membranes database
RNAcommender: genome-wide recommendation of RNA-protein interactions
Ligand-induced changes in the binding sites of proteins
Faster computation of exact RNA shape probabilities
Reproducible and flexible simulation experiments with ML-Rules and SESSL
A brief history of genome research and bioinformatics in France
Single-cell RNA-seq interpretations using evolutionary multiobjective ensemble pruning
Corrigendum to: Single-sample landscape entropy reveals the imminent phase transition during disease progression
Detection of compositional constraints in nucleic acid sequences using neural networks
VECTOR-PC: a flexible tool for the design, display and retrieval of information regarding to cloning vectors
Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles
Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization
VSClust: feature-based variance-sensitive clustering of omics data
PiNGO: a Cytoscape plugin to find candidate genes in biological networks
Collateral missing value imputation: a new robust missing value estimation algorithm for microarray data
HATK: HLA analysis toolkit
RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach
Using evolutionary Expectation Maximization to estimate indel rates
A structure-based method for protein sequence alignment
Accelerating in silico saturation mutagenesis using compressed sensing
An efficient randomized algorithm for contact-based NMR backbone resonance assignment
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA)
Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications
The UK Human Genome Mapping Project online computing service
KRAB ZNF explorer - the online tool for the exploration of the transcriptomic profiles of KRAB-ZNF factors in The Cancer Genome Atlas
Spatial transcriptomics deconvolution methods generalize well to spatial chromatin accessibility data
De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding
Matrix factorization-based data fusion for the prediction of lncRNA-disease associations
mspack: efficient lossless and lossy mass spectrometry data compression
ChemGAPP: a tool for chemical genomics analysis and phenotypic profiling
NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data
Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
INTREPID - INformation-theoretic TREe traversal for Protein functional site IDentification
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
RIP: the regulatory interaction predictor - a machine learning-based approach for predicting target genes of transcription factors
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins
Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit
A general near-exact k-mer counting method with low memory consumption enables de novo assembly of 106× human sequence data in 2.7 hours
Model selection in Bayesian segmentation of multiple DNA alignments
geneAttribution: trait agnostic identification of candidate genes associated with noncoding variation
Combined prediction of Tat and Sec signal peptides with hidden Markov models
A Spatial Omnibus Test (SPOT) for Spatial Proteomic Data
Efficient selective screening of haplotype tag SNPs
CINNA: an R/CRAN package to decipher Central Informative Nodes in Network Analysis
Application of latent semantic analysis to protein remote homology detection
A probabilistic algorithm for interactive huge genome comparison
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates
Galaxy Helm chart: a standardized method for deploying production Galaxy servers
PathFinder: Bayesian inference of clone migration histories in cancer
SynBa: improved estimation of drug combination synergies with uncertainty quantification
iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators
Pro54DB: a database for experimentally verified sigma-54 promoters
ShinyArchR.UiO: user-friendly, integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR
PCMA: fast and accurate multiple sequence alignment based on profile consistency
SMaSH: a benchmarking toolkit for human genome variant calling
Binning_refiner: improving genome bins through the combination of different binning programs
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action
Analysis of single amino acid variations in singlet hot spots of protein-protein interfaces
Exploiting and assessing multi-source data for supervised biomedical named entity recognition
A System for Information Management in BioMedical Studies - SIMBioMS
Computer program for prediction of the optimal and suboptimal secondary structures of long RNA molecules
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
Multiple association analysis via simulated annealing (MASSA)
Cordova: Web-based management of genetic variation data
AttentionPert: accurately modeling multiplexed genetic perturbations with multi-scale effects
Estimating population diversity with CatchAll
A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
ZooDDD: a cross-species database for digital differential display analysis
The Rényi divergence enables accurate and precise cluster analysis for localization microscopy
RNAget: an API to securely retrieve RNA quantifications
VISSA: a program to visualize structural features from structure sequence alignment
KADAIF: an anomaly detection method for complex microbiome data
GeneNetTools: tests for Gaussian graphical models with shrinkage
MrBayes on a Graphics Processing Unit
iMRM: a platform for simultaneously identifying multiple kinds of RNA modifications
Validating clustering for gene expression data
beadarray: R classes and methods for Illumina bead-based data
Predict drug permeability to blood-brain-barrier from clinical phenotypes: drug side effects and drug indications
Isoform-level quantification for single-cell RNA sequencing
Doelan: a solution for quality control monitoring of microarray production
Qualimap: evaluating next-generation sequencing alignment data
A signal-noise model for significance analysis of ChIP-seq with negative control
DaliLite workbench for protein structure comparison
Scalable inference of cell differentiation networks in gene therapy clonal tracking studies of haematopoiesis
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
TPWshiny: an interactive R/Shiny app to explore cell line transcriptional responses to anti-cancer drugs
TSAFinder: exhaustive tumor-specific antigen detection with RNAseq
Harmonization of gene/protein annotations: towards a gold standard MEDLINE
Integrated software for probabilistic identification of microorganisms
The topology of data: opportunities for cancer research
Personalized regression enables sample-specific pan-cancer analysis
Modeling positional effects of regulatory sequences with spline transformations increases prediction accuracy of deep neural networks
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
Characterization of the SOS meta-regulon in the human gut microbiome
KIMGENS: a novel method to estimate kinship in organisms with mixed haploid diploid genetic systems robust to population structure
SimService: a lightweight library for building simulation services in Python
DCSE, an interactive tool for sequence alignment and secondary structure research
Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae
V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers
R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression
SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing
Intelligent client for integrating bioinformatics services
ColocQuiaL: a QTL-GWAS colocalization pipeline
piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
A Drug-Side Effect Context-Sensitive Network approach for drug target prediction
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations
A data-adaptive Bayesian regression approach for polygenic risk prediction
EnDecon: cell type deconvolution of spatially resolved transcriptomics data via ensemble learning
A novel method for mining highly imbalanced high-throughput screening data in PubChem
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions
OCSANA: optimal combinations of interventions from network analysis
ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface
VirtualCytometry: a webserver for evaluating immune cell differentiation using single-cell RNA sequencing data
Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes
ProteinLIPs: a web server for identifying highly polar and poorly packed interfaces in proteins
A latent unknown clustering integrating multi-omics data (LUCID) with phenotypic traits
Filtering duplicate reads from 454 pyrosequencing data
AS-EAST: a functional annotation tool for putative proteins encoded by alternatively spliced transcripts
SCExecute: custom cell barcode-stratified analyses of scRNA-seq data
An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes
Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
Sliding MinPD: building evolutionary networks of serial samples via an automated recombination detection approach
Construction of reliable protein-protein interaction networks with a new interaction generality measure
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce
Gossamer - a resource-efficient de novo assembler
Don't use a cannon to kill the ... miRNA mosquito
A novel method for predicting activity of cis-regulatory modules, based on a diverse training set
Peptide sequencing program
USAGE: a web-based approach towards the analysis of SAGE data
ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality
Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression
Unsupervised embedding of single-cell Hi-C data
MAINE: a web tool for multi-omics feature selection and rule-based data exploration
MetaMapR: pathway independent metabolomic network analysis incorporating unknowns
Analyzing taxonomic classification using extensible Markov models
Cross-lingual semantic annotation of biomedical literature: experiments in Spanish and English
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types
A Bayesian approach for structure learning in oscillating regulatory networks
Computation of DNA structural variability - a new predictor of DNA regulatory regions
LC-IMS-MS Feature Finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets
TPepPro: a deep learning model for predicting peptide-protein interactions
A decision-theoretic approach to the evaluation of machine learning algorithms in computational drug discovery
CoverM: read alignment statistics for metagenomics
New phylogenetic venues opened by a novel implementation of the DNAml algorithm
Refget: standardized access to reference sequences
A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
Correction to: Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
MTTFsite: cross-cell type TF binding site prediction by using multi-task learning
Examining DNA breathing with pyDNA-EPBD
Normalization of two-channel microarray experiments: a semiparametric approach
Search for structural similarity in proteins
CPSP-web-tools: a server for 3D lattice protein studies
Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data
WhichCyp: prediction of cytochromes P450 inhibition
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
The bioinformatics wealth of nations
COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases
HELM: searching for helix motifs within protein sequences
Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals
EpiGEN: an epistasis simulation pipeline
A case study in genome-level fragment assembly
Testing association of a pathway with survival using gene expression data
Cross-species prediction of essential genes in insects
Quantitative trait prediction based on genetic marker-array data, a simulation study
CySBML: a Cytoscape plugin for SBML
Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner
NucliTrack: an integrated nuclei tracking application
DNAid: a Macintosh full screen editor featuring a built-in regular expression interpreter for the search of specific patterns in biological sequences using finite state automata
LUCY2: an interactive DNA sequence quality trimming and vector removal tool
The Graphical Query Language: a tool for analysis of gene expression time-courses
AltAVisT: Comparing alternative multiple sequence alignments
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions
pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies
On the feasibility of dynamical analysis of network models of biochemical regulation
APDB: a web server to evaluate the accuracy of sequence alignments using structural information
Tumor purity quantification by clonal DNA methylation signatures
iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing
ProFET: Feature engineering captures high-level protein functions
svviz: a read viewer for validating structural variants
Optimal selection of suitable templates in protein interface prediction
Group and sparse group partial least square approaches applied in genomics context
Evaluation of hierarchical models for integrative genomic analyses
Identifying progressive imaging genetic patterns via multi-task sparse canonical correlation analysis: a longitudinal study of the ADNI cohort
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models
Biologically valid linear factor models of gene expression
pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm
A program for the graphic representation and manipulation of DNA sequences
Quick and simple: quality control of microarray data
Nebulosa recovers single-cell gene expression signals by kernel density estimation
MRBAYES: Bayesian inference of phylogenetic trees
DIAMOD: display and modeling of DNA bending
Higher classification sensitivity of short metagenomic reads with CLARK- S
GECO-linear visualization for comparative genomics
Copying nodes versus editing links: the source of the difference between genetic regulatory networks and the WWW
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO)
The Encyclopedia of Proteome Dynamics: the KinoViewer
Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays
DWE: Discriminating Word Enumerator
Optimal simultaneous superpositioning of multiple structures with missing data
Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines
ggseqlogo: a versatile R package for drawing sequence logos
Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome
Molecular approaches to genome analysis: a strategy for the construction of ordered overlapping clone libraries
HiCBricks: building blocks for efficient handling of large Hi-C datasets
NerLTR-DTA: drug-target binding affinity prediction based on neighbor relationship and learning to rank
FRED 2: an immunoinformatics framework for Python
GEOfetch: a command-line tool for downloading data and standardized metadata from GEO and SRA
Exploiting the kernel trick to correlate fragment ions for peptide identification via tandem mass spectrometry
Molecular-level protein semantic learning via structure-aware coarse-grained language modeling
A periodicity analysis of transmembrane helices
EUCLID: automatic classification of proteins in functional classes by their database annotations
FunFrame: functional gene ecological analysis pipeline
Motif discovery and motif finding from genome-mapped DNase footprint data
CMAP: contig mapping and analysis package, a relational database for chromosome reconstruction
PhenoPro: a novel toolkit for assisting in the diagnosis of Mendelian disease
CoMM-S2: a collaborative mixed model using summary statistics in transcriptome-wide association studies
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data