yusuke1997/dblp-id-title huggingface dataset:
Network inference using steady-state data and Goldbeter-koshland kinetics
Heterogeneity detector: finding heterogeneous positions in Phred/Phrap assemblies
wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants
A cautionary tale on using imputation methods for inference in matched-pairs design
libRoadRunner: a high performance SBML simulation and analysis library
Template-free detection of macromolecular complexes in cryo electron tomograms
Smoothing profiles with sliding windows: better to wear a hat!
Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
INTERALIGN: interactive alignment editor for distantly related protein sequences
epiTCR: a highly sensitive predictor for TCR-peptide binding
Structural genomics of histone tail recognition
Faster and more accurate graphical model identification of tandem mass spectra using trellises
On searching for the active sites in proteins and peptide hormones
Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation
A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
PeptideLocator: prediction of bioactive peptides in protein sequences
ImageJ-MATLAB: a bidirectional framework for scientific image analysis interoperability
SecureMA: protecting participant privacy in genetic association meta-analysis
PyFDAP: automated analysis of fluorescence decay after photoconversion (FDAP) experiments
CANA v1.0.0: efficient quantification of canalization in automata networks
MolClass: a web portal to interrogate diverse small molecule screen datasets with different computational models
Correction to: plotsr: visualizing structural similarities and rearrangements between multiple genomes
CLUEY enables knowledge-guided clustering and cell type detection from single-cell omics data
Protein homology detection using string alignment kernels
Calculation of accurate interatomic contact surface areas for the quantitative analysis of non-bonded molecular interactions
PascalX: a Python library for GWAS gene and pathway enrichment tests
BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm
An RNA conformational shift in recent H5N1 influenza A viruses
Brain: biomedical knowledge manipulation
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
Comment on 'Protein isoelectric point as a predictor for increased crystallization screening efficiency'
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images
A computational system to select candidate genes for complex human traits
BioContext: an integrated text mining system for large-scale extraction and contextualization of biomolecular events
GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development
MAGIC Tool: integrated microarray data analysis
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences
Precise inference of copy number alterations in tumor samples from SNP arrays
ADAPT: a database of affymetrix probesets and transcripts
MutCombinator: identification of mutated peptides allowing combinatorial mutations using nucleotide-based graph search
GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts
METHCOMP: a special purpose compression platform for DNA methylation data
Detailing regulatory networks through large scale data integration
AQUa: an adaptive framework for compression of sequencing quality scores with random access functionality
findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies
TIMSCONVERT: a workflow to convert trapped ion mobility data to open data formats
Synthetic Biology: challenges ahead
LabArray: real-time imaging and analytical tool for microarrays
gVolante for standardizing completeness assessment of genome and transcriptome assemblies
CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform
Reference genome assessment from a population scale perspective: an accurate profile of variability and noise
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files
WWW access to the SYSTERS protein sequence cluster set
A high-performance computing toolset for relatedness and principal component analysis of SNP data
EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits
DanteR: an extensible R-based tool for quantitative analysis of -omics data
ImaGEO: integrative gene expression meta-analysis from GEO database
An integer programming formulation to identify the sparse network architecture governing differentiation of embryonic stem cells
TAPPA: topological analysis of pathway phenotype association
Panta rhei (QAlign2): an open graphical environment for sequence analysis
Full-length isoform constructor (FLIC) - a tool for isoform discovery based on long reads
Block searches on VAX and Alpha computer systems
Gene Time E chi pression Warper: a tool for alignment, template matching and visualization of gene expression time series
The SWIB and the MDM2 domains are homologous and share a common fold
CAPRI: efficient inference of cancer progression models from cross-sectional data
destiny : diffusion maps for large-scale single-cell data in R
ARIA: automated NOE assignment and NMR structure calculation
Rcupcake: an R package for querying and analyzing biomedical data through the BD2K PIC-SURE RESTful API
MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data
New quality measure for SNP array based CNV detection
RCandy: an R package for visualizing homologous recombinations in bacterial genomes
anexVis: visual analytics framework for analysis of RNA expression
A statistical framework for power calculations in ChIP-seq experiments
Identifying target sites for cooperatively binding factors
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction
How threshold behaviour affects the use of subgraphs for network comparison
Conformational model for binding site recognition by the E.coli MetJ transcription factor
GeneOrder: comparing the order of genes in small genomes
Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping
Visualization of near-optimal sequence alignments
Computational prediction and characterization of cell-type-specific and shared binding sites
MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments
tranSMART-XNAT Connector tranSMART-XNAT connector - image selection based on clinical phenotypes and genetic profiles
PICMI: mapping point mutations on genomes
GBZ file format for pangenome graphs
A large quantity of novel human antisense transcripts detected by LongSAGE
Correlating multiple SNPs and multiple disease phenotypes: penalized non-linear canonical correlation analysis
Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data
HAL: a hierarchical format for storing and analyzing multiple genome alignments
Mutadelic: mutation analysis using description logic inferencing capabilities
Reconstruction of strings past
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data
TFInfer: a tool for probabilistic inference of transcription factor activities
teff : estimation of Treatment EFFects on transcriptomic data using causal random forest
affy - analysis of Affymetrix GeneChip data at the probe level
Query-driven module discovery in microarray data
An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life
Application of clinical text data for phenome-wide association studies (PheWASs)
CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching
Sequence-based prediction of protein crystallization, purification and production propensity
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments
Optimizing substitution matrices by separating score distributions
No means 'No': a non-improper modeling approach, with embedded speculative context
Noise-Transfer2Clean: denoising cryo-EM images based on noise modeling and transfer
Discovering graphical Granger causality using the truncating lasso penalty
YAMACS: a graphical interface for GROMACS
Improving SNP discovery by base alignment quality
ccSVM: correcting Support Vector Machines for confounding factors in biological data classification
Fully unsupervised deep mode of action learning for phenotyping high-content cellular images
Frame: detection of genomic sequencing errors
Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region
PyLink: a PyMOL plugin to identify links
This is GlycoQL
LogoBar: bar graph visualization of protein logos with gaps
CNAmet: an R package for integrating copy number, methylation and expression data
Metabolite and reaction inference based on enzyme specificities
State and parameter estimation of the heat shock response system using Kalman and particle filters
An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification
protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
pKPDB: a protein data bank extension database of pKa and pI theoretical values
Using flowViz to visualize flow cytometry data
Pseudo-periodic partitions of biological sequences
PAnnBuilder: an R package for assembling proteomic annotation data
Module networks revisited: computational assessment and prioritization of model predictions
Controlling the joint local false discovery rate is more powerful than meta-analysis methods in joint analysis of summary statistics from multiple genome-wide association studies
Bayesian assignment of gene ontology terms to gene expression experiments
Integrating ARC grid middleware with Taverna workflows
plotsr: visualizing structural similarities and rearrangements between multiple genomes
Automatic extraction of gene/protein biological functions from biomedical text
Regulatory annotation of genomic intervals based on tissue-specific expression QTLs
ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications
Message-passing algorithms for the prediction of protein domain interactions from protein-protein interaction data
SquiggleKit: a toolkit for manipulating nanopore signal data
Efficient inference for sparse latent variable models of transcriptional regulation
DAPPLE: a pipeline for the homology-based prediction of phosphorylation sites
BBKNN: fast batch alignment of single cell transcriptomes
Software for the analysis of DNA sequence elements of transcription
PLRS: a flexible tool for the joint analysis of DNA copy number and mRNA expression data
SimRVSequences: an R package to simulate genetic sequence data for pedigrees
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly
A geometric algorithm to find small but highly similar 3D substructures in proteins
scOrange - a tool for hands-on training of concepts from single-cell data analytics
Optimal water networks in protein cavities with GAsol and 3D-RISM
Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations
POOL server: machine learning application for functional site prediction in proteins
SWGTS - a platform for stream-based host DNA depletion
Matt: Unix tools for alternative splicing analysis
BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID
modPhEA: model organism Phenotype Enrichment Analysis of eukaryotic gene sets
Accurate prediction of enzyme mutant activity based on a multibody statistical potential
An integrated approach for automating validation of extracted ion chromatographic peaks
MIRAGAA - a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
MIRUReader: MIRU-VNTR typing directly from long sequencing reads
RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments
Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans
Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph
CuBlock: a cross-platform normalization method for gene-expression microarrays
ACID: a database for microarray clone information
BioText Search Engine: beyond abstract search
Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways
Management, presentation and interpretation of genome scans using GSCANDB
AOP4EUpest: mapping of pesticides in adverse outcome pathways using a text mining tool
Mat_peptide: comprehensive annotation of mature peptides from polyproteins in five virus families
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction
Ontology for immunogenetics: the IMGT-ONTOLOGY
Gene selection: a Bayesian variable selection approach
Applications of fractal geometry to biology
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes
Modified variational Bayes EM estimation of hidden Markov tree model of cell lineages
Syotti: scalable bait design for DNA enrichment
SANA: simulated annealing far outperforms many other search algorithms for biological network alignment
SUBAcon: a consensus algorithm for unifying the subcellular localization data of the Arabidopsis proteome
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction
ngsLD: evaluating linkage disequilibrium using genotype likelihoods
esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis
TRScore: a 3D RepVGG-based scoring method for ranking protein docking models
Rgb: a scriptable genome browser for R
Correcting the loss of cell-cycle synchrony in clustering analysis of microarray data using weights
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
ParGenes: a tool for massively parallel model selection and phylogenetic tree inference on thousands of genes
Non-linear Normalization and Background Correction in One-channel CDNA Microarray Studies
Refined elasticity sampling for Monte Carlo-based identification of stabilizing network patterns
MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads
Accomplishments and challenges in literature data mining for biology
TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes
Exploring genome architecture through GOV: a WWW-based gene order visualizer
Bayesian integrated functional analysis of microarray data
Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning
Gene selection using a two-level hierarchical Bayesian model
Reference-free cell mixture adjustments in analysis of DNA methylation data
VIRUSBreakend: Viral Integration Recognition Using Single Breakends
Response to comments on "Bayesian Hierarchical Error Model for Analysis of Gene Expression Data"
Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data
PyWGCNA: a Python package for weighted gene co-expression network analysis
GUUGle: a utility for fast exact matching under RNA complementary rules including G-U base pairing
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes
targetHub: a programmable interface for miRNA-gene interactions
Robust partial reference-free cell composition estimation from tissue expression
Classification of RNA structure change by 'gazing' at experimental data
Assembling draft genomes using contiBAIT
BMDExpress 2: enhanced transcriptomic dose-response analysis workflow
Predicting functionally important residues from sequence conservation
Compound image segmentation of published biomedical figures
Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis
Designing and executing scientific workflows with a programmable integrator
<tt>pyaging</tt> : a Python-based compendium of GPU-optimized aging clocks
FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences
Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification
NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data
Can ODE gene regulatory models neglect time lag or measurement scaling?
A visual environment for the manipulation and integration of JAVA beans
BioPAX support in CellDesigner
Exploiting ontology graph for predicting sparsely annotated gene function
ddbRNA: detection of conserved secondary structures in multiple alignments
MPSA: integrated system for multiple protein sequence analysis with client/server capabilities
Fusion-Bloom: fusion detection in assembled transcriptomes
Document-level biomedical relation extraction via hierarchical tree graph and relation segmentation module
Identifying interactions in omics data for clinical biomarker discovery using symbolic regression
Integration of gene interaction information into a reweighted Lasso-Cox model for accurate survival prediction
iLoops: a protein-protein interaction prediction server based on structural features
MetAssimulo 2.0: a web app for simulating realistic 1D and 2D metabolomic 1H NMR spectra
ESPERANTO: a GLP-field sEmi-SuPERvised toxicogenomics metadAta curatioN TOol
A rapid retrieval tool for operating on large, flat archive files
LncRNA-ID: Long non-coding RNA IDentification using balanced random forests
ODORactor: a web server for deciphering olfactory coding
Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes
Learning and Imputation for Mass-spec Bias Reduction (LIMBR)
A unifying kinetic framework for modeling oxidoreductase-catalyzed reactions
Reducing storage requirements for biological sequence comparison
Structural distinctions of fast and slow bacterial luciferases revealed by phylogenetic analysis
An exact solution for the segment-to-segment multiple sequence alignment problem
Deconvolving molecular signatures of interactions between microbial colonies
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
READemption - a tool for the computational analysis of deep-sequencing-based transcriptome data
Identification of optimal classification functions for biological sample and state discrimination from metabolic profiling data
Improved inference of tandem domain duplications
Hierarchical multi-label prediction of gene function
DPTF: a database of poplar transcription factors
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier
Training for bioinformatics and computational biology
SECLAF: a webserver and deep neural network design tool for hierarchical biological sequence classification
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
Disease gene prioritization with quantum walks
SODA: multi-locus species delimitation using quartet frequencies
FRED - a framework for T-cell epitope detection
CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs
IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis
Detecting periodic patterns in biological sequences
Correlating patterns in alignments of polymorphic sequences with experimental assays
EnrichrBot: Twitter bot tracking tweets about human genes
SAMStat: monitoring biases in next generation sequencing data
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing
Vocabulon: a dictionary model approach for reconstruction and localization of transcription factor binding sites
A statistical framework for combining and interpreting proteomic datasets
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity
ESTviewer: a web interface for visualizing mouse, rat, cattle, pig and chicken conserved ESTs in human genes and human alternatively spliced variants
mirPLS: a partial linear structure identifier method for cancer subtyping using microRNAs
MetaHD: a multivariate meta-analysis model for metabolomics data
An Internet linkage and mutation database for the complex phenotype asthma
TRAL: tandem repeat annotation library
A comparison of sequence and structure protein domain families as a basis for structural genomics
The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants
Integrative chromatin domain annotation through graph embedding of Hi-C data
Precise modelling and interpretation of bioactivities of ligands targeting G protein-coupled receptors
Correlations between predicted protein disorder and post-translational modifications in plants
MethPrimer: designing primers for methylation PCRs
bollito: a flexible pipeline for comprehensive single-cell RNA-seq analyses
Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters
DLAB: deep learning methods for structure-based virtual screening of antibodies
Network-guided search for genetic heterogeneity between gene pairs
propeller: testing for differences in cell type proportions in single cell data
Strategies to improve the performance of rare variant association studies by optimizing the selection of controls
RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation
SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions
Defining 3D residue environment in protein structures using SCORPION and FORMIGA
Evaluation and comparison of gene clustering methods in microarray analysis
SCEPTRANS: an online tool for analyzing periodic transcription in yeast
GlycoStore: a database of retention properties for glycan analysis
A novel method for accurate one-dimensional protein structure prediction based on fragment matching
Family pairwise search with embedded motif models
Differential regulation enrichment analysis via the integration of transcriptional regulatory network and gene expression data
BioRuby: bioinformatics software for the Ruby programming language
FROGS: Find, Rapidly, OTUs with Galaxy Solution
Trans-species learning of cellular signaling systems with bimodal deep belief networks
Alerting users to relevant new entries in the GenBank DNA sequence database
Recovering time-varying networks from single-cell data