yusuke1997/dblp-id-title huggingface dataset:
Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - Application to H5N1 spread in the Mekong region
H(O)TA: estimation of DNA methylation and hydroxylation levels and efficiencies from time course data
SCANGRAPH: a program for digitization of graphs using an image scanner
PathText: a text mining integrator for biological pathway visualizations
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction
CASA: a server for the critical assessment of protein sequence alignment accuracy
RaNA-Seq: interactive RNA-Seq analysis from FASTQ files to functional analysis
Locating alignments with k differences for nucleotide and amino acid sequences
antaRNA: ant colony-based RNA sequence design
MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets
New evaluation measures for multifactor dimensionality reduction classifiers in gene-gene interaction analysis
PathCNN: interpretable convolutional neural networks for survival prediction and pathway analysis applied to glioblastoma
Positive multistate protein design
Accounting for epistatic interactions improves the functional analysis of protein structures
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment
Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling
MemBlob database and server for identifying transmembrane regions using cryo-EM maps
SnoReport: computational identification of snoRNAs with unknown targets
Structure-based prediction of transcription factor binding specificity using an integrative energy function
SARGE: a tool for creation of putative genetic networks
fastGapFill: efficient gap filling in metabolic networks
Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models
Identification of functional CNV region networks using a CNV-gene mapping algorithm in a genome-wide scale
Solving and analyzing side-chain positioning problems using linear and integer programming
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Optimal alignments in linear space
Fold-recognition detects an error in the Protein Data Bank
Syntactic pattern analysis of 5'-splice site sequences of mRNA precursors in higher eukaryote genes
Design tools for MPRA experiments
Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes
Identifying the topology of protein complexes from affinity purification assays
footprintDB: a database of transcription factors with annotated cis elements and binding interfaces
WAT3R: recovery of T-cell receptor variable regions from 3′ single-cell RNA-sequencing
What handedness and angles between helices has the studied three-helical protein domain?
What time is it? Deep learning approaches for circadian rhythms
MichelaNglo: sculpting protein views on web pages without coding
PESDserv: a server for high-throughput comparison of protein binding site surfaces
Lineage-based identification of cellular states and expression programs
GraphADT: empowering interpretable predictions of acute dermal toxicity with multi-view graph pooling and structure remapping
STAM: simple Transmembrane Alignment Method
Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
BioCCP.jl: collecting coupons in combinatorial biotechnology
PyGenePlexus: a Python package for gene discovery using network-based machine learning
Towards the in silico identification of class II restricted T-cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction
PEASE: predicting B-cell epitopes utilizing antibody sequence
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations
Protein graphics: historical development, future directions and microcomputer applications
Flashzoi: an enhanced Borzoi for accelerated genomic analysis
CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles
htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets
GRaSP: a graph-based residue neighborhood strategy to predict binding sites
PathExt: a general framework for path-based mining of omics-integrated biological networks
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database
Ridom TraceEdit: a DNA trace editor and viewer
Assessing the need for sequence-based normalization in tiling microarray experiments
ELOPER: elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly
Microindel detection in short-read sequence data
Chromatin network markers of leukemia
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors
Reporting bias when using real data sets to analyze classification performance
ARAX: a graph-based modular reasoning tool for translational biomedicine
Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases
Noise-cancelling repeat finder: uncovering tandem repeats in error-prone long-read sequencing data
Protein-ligand binding affinity prediction exploiting sequence constituent homology
The GlycomeAtlas tool for visualizing and querying glycome data
RED: the analysis, management and dissemination of expressed sequence tags
FastDup: a scalable duplicate marking tool using speculation-and-test mechanism
Identification of novel families of membrane proteins from the model plant Arabidopsis thaliana
e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures
Fuento: functional enrichment for bioinformatics
EpiTOP - a proteochemometric tool for MHC class II binding prediction
MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms
ProMAT: protein microarray analysis tool
DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for human next-generation sequencing data
The MaSuRCA genome assembler
Simulating domain architecture evolution
Error filtering, pair assembly and error correction for next-generation sequencing reads
eXPatGen: Generating Dynamic Expression Patterns for the Systematic Evaluation of Analytical Methods
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery
Figeno: multi-region genomic figures with long-read support
PEDL+: protein-centered relation extraction from PubMed at your fingertip
µ-ANT: semantic microaggregation-based anonymization tool
Semi-supervised network inference using simulated gene expression dynamics
Nucleosome formation potential of exons, introns, and Alu repeats
CAMML with the Integration of Marker Proteins (ChIMP)
Using chemical organization theory for model checking
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information
IBIS version 3: an OSF/Motif-based interface for IBIS - integrated biological imaging system
FrameDP: sensitive peptide detection on noisy matured sequences
FitMultiCell: simulating and parameterizing computational models of multi-scale and multi-cellular processes
FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes
BacTregulators: a database of transcriptional regulators in bacteria and archaea
BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model
Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads
Active site prediction using evolutionary and structural information
Read-based phasing of related individuals
An easy and efficient approach for testing identifiability
Pepitope: epitope mapping from affinity-selected peptides
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy
Classification of Multiple Cancer Types by Multicategory Support Vector Machines Using Gene Expression Data
GeneContent: software for whole-genome phylogenetic analysis
Predicting the oxidation state of cysteines by multiple sequence alignment
Special issue containing a selection of papers presented at the 1st International Conference on Bioinformatics of Genome Regulation and Structure. BGRS '98. Novosibirsk, Altai Mountains, Russia. 24-31 August 1998
GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop
Evolink: a phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multispecies data
Penalized estimation of haplotype frequencies
Predicting CTCF-mediated chromatin loops using CTCF-MP
Identification of differentially expressed gene modules in heterogeneous diseases
Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment
BEN: a novel domain in chromatin factors and DNA viral proteins
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects
Striped Smith-Waterman speeds database searches six times over other SIMD implementations
gKaKs: the pipeline for genome-level Ka/Ks calculation
Optimizing representations for integrative structural modeling using Bayesian model selection
Tcbf: a novel user-friendly tool for pan-3D genome analysis of topologically associating domain in eukaryotic organisms
Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information
Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology
CloudBurst: highly sensitive read mapping with MapReduce
A graph-based approach to diploid genome assembly
Metabolic pathways in three dimensions
Generating synthetic genotypes using diffusion models
RBSDesigner : software for designing synthetic ribosome binding sites that yields a desired level of protein expression
VisFeature: a stand-alone program for visualizing and analyzing statistical features of biological sequences
METATOOL: for studying metabolic networks
RNAdetect: efficient computational detection of novel non-coding RNAs
De novo computational prediction of non-coding RNA genes in prokaryotic genomes
CROTON: an automated and variant-aware deep learning framework for predicting CRISPR/Cas9 editing outcomes
A semiparametric approach for marker gene selection based on gene expression data
GALGO: an R package for multivariate variable selection using genetic algorithms
Performance assessment of copy number microarray platforms using a spike-in experiment
A method for learning a sparse classifier in the presence of missing data for high-dimensional biological datasets
Ontological analysis of gene expression data: current tools, limitations, and open problems
Fast zero-inflated negative binomial mixed modeling approach for analyzing longitudinal metagenomics data
Predicting protein secondary structure by cascade-correlation neural networks
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays
Artificial neural network for prediction of antigenic activity for a major conformational epitope in the hepatitis C virus NS3 protein
MethPanel: a parallel pipeline and interactive analysis tool for multiplex bisulphite PCR sequencing to assess DNA methylation biomarker panels for disease detection
MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
EMBOPRO--an automatically generated protein sequence database
Transcriptogramer: an R/Bioconductor package for transcriptional analysis based on protein-protein interaction
PAVOOC: designing CRISPR sgRNAs using 3D protein structures and functional domain annotations
A new interactive protein sequence alignment program and comparison of its results with widely used algorithms
CEBS object model for systems biology data, SysBio-OM
SinNLRR: a robust subspace clustering method for cell type detection by non-negative and low-rank representation
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis
MHCSeqNet2 - improved peptide-class I MHC binding prediction for alleles with low data
Interactive and graphic coupling between multiple alignments, secondary structure predictions and motif/pattern scanning into proteins
i6mA-Caps: a CapsuleNet-based framework for identifying DNA N6-methyladenine sites
Unbiased pangenome graphs
Enhancing the rate of scaffold discovery with diversity-oriented prioritization
DeepBlueR: large-scale epigenomic analysis in R
GPA-Tree: statistical approach for functional-annotation-tree-guided prioritization of GWAS results
Web-based design and evaluation of T-cell vaccine candidates
CAPITO - a web server-based analysis and plotting tool for circular dichroism data
Identifiers.org: Compact Identifier services in the cloud
Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1
Inferring gene regulatory network via fusing gene expression image and RNA-seq data
Bayesian integration of networks without gold standards
PREDA : an R-package to identify regional variations in genomic data
Crossfinder-assisted mapping of protein crosslinks formed by site-specifically incorporated crosslinkers
TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain
FunNet: an integrative tool for exploring transcriptional interactions
Drug-target interaction prediction through domain-tuned network-based inference
SylArray: a web server for automated detection of miRNA effects from expression data
FunGeCo: a web-based tool for estimation of functional potential of bacterial genomes and microbiomes using gene context information
RETRACTED: Analysis and prediction of β-turn types using multinomial logistic regression and artificial neural network
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
A dotplot program for the Atari ST, for the analysis of DNA and protein sequences
A mixture model for determining SARS-Cov-2 variant composition in pooled samples
YAHA: fast and flexible long-read alignment with optimal breakpoint detection
A survey of BWT variants for string collections
MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks
Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
An ontology for bioinformatics applications
Chembench: a cheminformatics workbench
Differential network analysis by simultaneously considering changes in gene interactions and gene expression
Efficient large-scale sequence comparison by locality-sensitive hashing
Genome-scale prediction of moonlighting proteins using diverse protein association information
Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data
DeepCellEss: cell line-specific essential protein prediction with attention-based interpretable deep learning
Robust relationship inference in genome-wide association studies
netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling
Tandem repeats over the edit distance
Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures
agplus: a rapid and flexible tool for aggregation plots
Functional stoichiometric analysis of metabolic networks
Semiotes: a semantics for sharing
FANMOD: a tool for fast network motif detection
FastMotif: spectral sequence motif discovery
WAVES: a web application for versatile enhanced bioinformatic services
KODAMA: an R package for knowledge discovery and data mining
Point-group symmetry detection in three-dimensional charge density of biomolecules
CRONOS: the cross-reference navigation server
Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes
AGILE: an assembled genome mining pipeline
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony
MSCquartets 1.0: quartet methods for species trees and networks under the multispecies coalescent model in R
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs
DextMP: deep dive into text for predicting moonlighting proteins
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
Phables: from fragmented assemblies to high-quality bacteriophage genomes
FUSION : a family-level integration approach for robust differential analysis of small non-coding RNAs
VARAN-GIE: curation of genomic interval sets
PARC: ultrafast and accurate clustering of phenotypic data of millions of single cells
Computational network analysis of the anatomical and genetic organizations in the mouse brain
Model-based clustering of multi-tissue gene expression data
The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank
Discovery of disease- and drug-specific pathways through community structures of a literature network
Stepwise detection of recombination breakpoints in sequence alignments
Synthetic-to-real: instance segmentation of clinical cluster cells with unlabeled synthetic training
Unbiased classification of spatial strategies in the Barnes maze
Estimating error models for whole genome sequencing using mixtures of Dirichlet-multinomial distributions
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments
A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data
Ryūtō: improved multi-sample transcript assembly for differential transcript expression analysis and more
EDCNN: identification of genome-wide RNA-binding proteins using evolutionary deep convolutional neural network
Automated diagnosis of LC-MS/MS performance
Tabhu: tools for antibody humanization
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequences
XQTav: an XQuery processor for Taverna environment
The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data
RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments
Discovering combinatorial interactions in survival data
Statistical detection of chromosomal homology using shared-gene density alone
Bacterial GRAS domain proteins throw new light on gibberellic acid response mechanisms
Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices
IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
Simulating haplotype blocks in the human genome
Scalable preprocessing for sparse scRNA-seq data exploiting prior knowledge
scDetect: a rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer
AlphaMate: a program for optimizing selection, maintenance of diversity and mate allocation in breeding programs
How significant is a protein structure similarity with TM-score = 0.5?
Knowledge enhanced LSTM for coreference resolution on biomedical texts
Gene function prediction from synthetic lethality networks via ranking on demand
MR.RGM: an R package for fitting Bayesian multivariate bidirectional Mendelian randomization networks
Multivariate multi-way analysis of multi-source data
Boolean approach to signalling pathway modelling in HGF-induced keratinocyte migration
m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human
Enhancement of beta-sheet assembly by cooperative hydrogen bonds potential
Utilizing RNA-Seq data for de novo coexpression network inference
Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions
Targeted metabolomics analyses for brain tumor margin assessment during surgery
Predicting functional regulatory polymorphisms
raxtax : a k -mer-based non-Bayesian taxonomic classifier
QSCOP - SCOP quantified by structural relationships
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data
Uncovering complementary sets of variants for predicting quantitative phenotypes
Prediction of human-Bacillus anthracis protein-protein interactions using multi-layer neural network
DisEnrich: database of enriched regions in human dark proteome
Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors
ESTAP-an automated system for the analysis of EST data
XFINGER: a tool for searching and visualising protein fingerprints and patterns
Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study
ACDtool: a web-server for the generic analysis of large data sets of counts
PIP: a database of potential intron polymorphism markers
Automated machine learning for genome wide association studies
PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings
Statistics of protein library construction
Powerful molecule generation with simple ConvNet
Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs
A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling
Bayesian models for the analysis of genetic structure when populations are correlated
A dynamic wavelet-based algorithm for pre-processing tandem mass spectrometry data
PecanPy: a fast, efficient and parallelized Python implementation of node2vec
ACTG: novel peptide mapping onto gene models
Constructing prediction models from expression profiles for large scale lncRNA-miRNA interaction profiling
The ties problem resulting from counting-based error estimators and its impact on gene selection algorithms
An Adjustable-threshold Algorithm for the Identification of Objects in Three-dimensional Images
OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics
TOPAL 2.0: improved detection of mosaic sequences within multiple alignments
FlowDock: Geometric flow matching for generative protein-ligand docking and affinity prediction
NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data
Cell shape characterization, alignment, and comparison using FlowShape
bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files
AutoDock Bias: improving binding mode prediction and virtual screening using known protein-ligand interactions
Empirical Bayes screening of many p-values with applications to microarray studies
An analysis of gene-finding programs for Neurospora crassa
fconv: format conversion, manipulation and feature computation of molecular data