yusuke1997/dblp-id-title huggingface dataset:
A combinatorial approach to the peptide feature matching problem for label-free quantification
Capturing dynamic relevance in Boolean networks using graph theoretical measures
Mauve Assembly Metrics
Nucleosomal DNA property database
rbioapi: user-friendly R interface to biologic web services' API
B2G-FAR, a species-centered GO annotation repository
MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers
Optimal production of biological documentation: the JAM format
d-PBWT: dynamic positional Burrows-Wheeler transform
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia
ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data
Tree-structured algorithm for long weak motif discovery
Factor graph analysis of live cell-imaging data reveals mechanisms of cell fate decisions
MOLGENIS Armadillo: a lightweight server for federated analysis using DataSHIELD
NetComm: a network analysis tool based on communicability
Combenefit: an interactive platform for the analysis and visualization of drug combinations
Generalized Venn diagrams: a new method of visualizing complex genetic set relations
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development
Learning gene network structure from time laps cell imaging in RNAi Knock downs
StrateGene: object-oriented programming in molecular biology
Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model
RVboost: RNA-seq variants prioritization using a boosting method
Filtering and inference for stochastic oscillators with distributed delays
VarGen: an R package for disease-associated variant discovery and annotation
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics
Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA
Evaluation and integration of 49 genome-wide experiments and the prediction of previously unknown obesity-related genes
Assortative mixing in Protein Contact Networks and protein folding kinetics
Identifying time-lagged gene clusters using gene expression data
ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation
Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects
LIMES: a tool for comparing species partition
Parasitologist-level classification of apicomplexan parasites and host cell with deep cycle transfer learning (DCTL)
A bio-inspired computing model for ovarian carcinoma classification and oncogene detection
fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data
Prediction and early diagnosis of complex diseases by edge-network
Sampling and summarizing transmission trees with multi-strain infections
Fast and accurate prediction of protein side-chain conformations
A variant selection framework for genome graphs
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks
Client-Server environment for high-performance gene expression data analysis
An efficient Monte Carlo approach to assessing statistical significance in genomic studies
Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design
ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data
Insights into performance evaluation of compound-protein interaction prediction methods
UniRef: comprehensive and non-redundant UniProt reference clusters
Bosque: integrated phylogenetic analysis software
AnnotSV: an integrated tool for structural variations annotation
Investigation of an expert systems approach to bacterial identification
Predicting tumor purity from methylation microarray data
MutDB: annotating human variation with functionally relevant data
A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes
COSIFER: a Python package for the consensus inference of molecular interaction networks
Random forest based similarity learning for single cell RNA sequencing data
MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data
A fast DNA sequence handling program for Apple II computer in BASIC and 6502 assembler
SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties
Prophet, a web-based tool for class prediction using microarray data
Computing heart rate variability using spectral analysis techniques: HRVUAB, a ready-to-use program
CBNplot : Bayesian network plots for enrichment analysis
LSTrAP-Kingdom: an automated pipeline to generate annotated gene expression atlases for kingdoms of life
KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels
Mocafe: a comprehensive Python library for simulating cancer development with Phase Field Models
NGS++: a library for rapid prototyping of epigenomics software tools
Recording waveforms with the ACORN BBC microcomputer
SEPON, a Selection and Evaluation Pipeline for OligoNucleotides based on ESTs with a non-target T m algorithm for reducing cross-hybridization in microarray gene expression experiments
R.JIVE for exploration of multi-source molecular data
Determination of genomic copy number alteration emphasizing a restriction site-based strategy of genome re-sequencing
LDAP: a web server for lncRNA-disease association prediction
QRank: a novel quantile regression tool for eQTL discovery
TOPDOM: database of domains and motifs with conservative location in transmembrane proteins
Detection of multi-dimensional co-exclusion patterns in microbial communities
Sebida: a database for the functional and evolutionary analysis of genes with sex-biased expression
A performance enhanced PSI-BLAST based on hybrid alignment
2DProts: database of family-wide protein secondary structure diagrams
Variational Bayes for high-dimensional proportional hazards models with applications within gene expression
MeltDB: a software platform for the analysis and integration of metabolomics experiment data
dbInDel: a database of enhancer-associated insertion and deletion variants by analysis of H3K27ac ChIP-Seq
MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification
Composite Kernel Association Test (CKAT) for SNP-set joint assessment of genotype and genotype-by-treatment interaction in Pharmacogenetics studies
False discovery rate, sensitivity and sample size for microarray studies
Uncovering antibody cross-reaction dynamics in influenza A infections
Biomedical image augmentation using Augmentor
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics
EpiGraph: an open-source platform to quantify epithelial organization
Hardware acceleration of genomics data analysis: challenges and opportunities
An investigation of the epidemiology of neuroblastoma in children under the age of 15 years in England, Scotland and Wales
Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling
An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System
The Connectivity Structure, Giant Strong Component and Centrality of Metabolic Networks
Robust and ultrafast fiducial marker correspondence in electron tomography by a two-stage algorithm considering local constraints
ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions
A new haplotype block detection method for dense genome sequencing data based on interval graph modeling of clusters of highly correlated SNPs
GeneValidator: identify problems with protein-coding gene predictions
CNpare: matching DNA copy number profiles
Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques
The use of various properties of amino acids in color and monochrome dot-matrix analyses for protein homologies
Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency
Derivative processes for modelling metabolic fluxes
A framework for oligonucleotide microarray preprocessing
MIRA: mutual information-based reporter algorithm for metabolic networks
Metagenome SNP calling via read-colored de Bruijn graphs
MACA: marker-based automatic cell-type annotation for single-cell expression data
DBAli: a database of protein structure alignments
Probe-level measurement error improves accuracy in detecting differential gene expression
MIPS bacterial genomes functional annotation benchmark dataset
Array-based genotyping in S.cerevisiae using semi-supervised clustering
REDfly: a Regulatory Element Database for Drosophila
Transformations for the compression of FASTQ quality scores of next-generation sequencing data
A multi-step approach to time series analysis and gene expression clustering
High-throughput analysis of epistasis in genome-wide association studies with BiForce
ZipHiC: a novel Bayesian framework to identify enriched interactions and experimental biases in Hi-C data
Graph-based peak alignment algorithms for multiple liquid chromatography-mass spectrometry datasets
AnnTools: a comprehensive and versatile annotation toolkit for genomic variants
FUNKI: interactive functional footprint-based analysis of omics data
Identifying biologically relevant differences between metagenomic communities
Search and clustering orders of magnitude faster than BLAST
Investigating the dynamic behavior of biochemical networks using model families
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations
Clustering of samples with a tree-shaped dependence structure, with an application to microscopic time lapse imaging
The properties of protein family space depend on experimental design
A Bayesian group sparse multi-task regression model for imaging genetics
konnect2prot: a web application to explore the protein properties in a functional protein-protein interaction network
SCPD: a promoter database of the yeast Saccharomyces cerevisiae
Comparing expression profiles of genes with similar promoter regions
Adaptive reference-free compression of sequence quality scores
Identification of protein complexes from co-immunoprecipitation data
Accurate estimation of short read mapping quality for next-generation genome sequencing
M3Drop: dropout-based feature selection for scRNASeq
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs)
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
Mean curvature as a major determinant of ß-sheet propensity
Re-analysis and meta-analysis of summary statistics from gene-environment interaction studies
Estimating abundances of retroviral insertion sites from DNA fragment length data
Drug-Protein interaction prediction by correcting the effect of incomplete information in heterogeneous information
Desktop prediction/analysis of mass spectrometric data in proteomic projects by using massXpert
CTDquerier: a bioconductor R package for Comparative Toxicogenomics DatabaseTM data extraction, visualization and enrichment of environmental and toxicological studies
Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated
Agos - a universal web tool for GW Argonaute-binding domain prediction
Cross-validation under separate sampling: strong bias and how to correct it
HitPickV2: a web server to predict targets of chemical compounds
Bayesian structural equation modeling in multiple omics data with application to circadian genes
Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps
Multistructural hot spot characterization with FTProd
Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs
pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models
Identification of transcription factors for drug-associated gene modules and biomedical implications
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)
Health assistant: answering your questions anytime from biomedical literature
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing
refineD: improved protein structure refinement using machine learning based restrained relaxation
Bayesian search of functionally divergent protein subgroups and their function specific residues
FastSCODE: an accelerated SCODE algorithm for inferring gene regulatory networks on manycore processors
Linear modes of gene expression determined by independent component analysis
HCS - hierarchical algorithm for simulation of omics datasets
scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS
Identifying differentially expressed genes using false discovery rate controlling procedures
Correction to: For antibody sequence generative modeling, mixture models may be all you need
GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis
Fast grid layout algorithm for biological networks with sweep calculation
CommWalker: correctly evaluating modules in molecular networks in light of annotation bias
PIP-DB: the Protein Isoelectric Point database
The wisdom of the commons: ensemble tree classifiers for prostate cancer prognosis
TMpro web server and web service: transmembrane helix prediction through amino acid property analysis
Pedigree-drawing with R and graphviz
SnoopCGH: software for visualizing comparative genomic hybridization data
ReactomeGSA: new features to simplify public data reuse
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
Finding flexible patterns in a text: an application to three-dimensional molecular matching
Predicting MHC-peptide binding affinity by differential boundary tree
Genetic algorithm for shift-uncertainty correction in 1-D NMR-based metabolite identifications and quantifications
Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census
Fold recognition by scoring protein maps using the congruence coefficient
Wright-Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy
A semantic analysis of the annotations of the human genome
Design of optimal labeling patterns for optical genome mapping via information theory
GeneView: multi-language human gene mapping library with a graphical user interface
Computer-assisted mathematical analysis of sigmoid biological events
LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis
Literature-based priors for gene regulatory networks
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model
ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation
Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
A boosting approach for motif modeling using ChIP-chip data
Extending ontologies by finding siblings using set expansion techniques
CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
PdbMotif--a tool for the automatic identification and display of motifs in protein structures
swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution
ASSIST: a fast versatile local structural comparison tool
CatReNet: interactive analysis of (auto-) catalytic reaction networks
A rapid access motif database (RAMdb) with a search algorithm for the retrieval patterns in nucleic acids or protein databanks
RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data
GenAlyzer: interactive visualization of sequence similarities between entire genomes
skandiver: a divergence-based analysis tool for identifying intercellular mobile genetic elements
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data
Uniformly curated signaling pathways reveal tissue-specific cross-talks and support drug target discovery
SNPper: retrieval and analysis of human SNPs
ProQ3D: improved model quality assessments using deep learning
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
Conserved and differential gene interactions in dynamical biological systems
Local modeling of global interactome networks
Evaluation of efficiency prediction algorithms and development of ensemble model for CRISPR/Cas9 gRNA selection
GeneNetwork: an interactive tool for reconstruction of genetic networks using microarray data
Discovering comorbid diseases using an inter-disease interactivity network based on biobank-scale PheWAS data
Computer programs for the rapid determination of enzyme kinetics on MS- DOS compatible microcomputers
HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation
Genome-scale analysis of interaction dynamics reveals organization of biological networks
KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology
Improving the prediction of protein-nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images
A graph-theoretic modeling on GO space for biological interpretation of gene clusters
GPSDB: a new database for synonyms expansion of gene and protein names
hPDI: a database of experimental human protein-DNA interactions
QVALITY: non-parametric estimation of q -values and posterior error probabilities
Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data
GenePath: a system for automated construction of genetic networks from mutant data
The SSEA server for protein secondary structure alignment
QuASAR: quantitative allele-specific analysis of reads
PoDCall: positive droplet calling and normalization of droplet digital PCR DNA methylation data
eQTL Explorer: integrated mining of combined genetic linkage and expression experiments
The choice of optimal distance measure in genome-wide datasets
GWAsimulator: a rapid whole-genome simulation program
Exact global alignment using A* with chaining seed heuristic and match pruning
NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks
Unbiased and error-detecting combinatorial pooling experiments with balanced constant-weight Gray codes for consecutive positives detection
Improving sequence-based fold recognition by using 3D model quality assessment
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures
Thermodynamics of RNA structures by Wang-Landau sampling
IBS: an illustrator for the presentation and visualization of biological sequences
GLYCO: a tool to quantify glycan shielding of glycosylated proteins
Response to the comment on 'protein-protein binding affinity prediction from amino acid sequence'
Degrees of differential gene expression: detecting biologically significant expression differences and estimating their magnitudes
Three sets of Macintosh AppleScripts for the automatic submission of sequence data to the internet BLAST server
A program for drawing evolutionary trees
Enzyme promiscuity prediction using hierarchy-informed multi-label classification
RNANet: an automatically built dual-source dataset integrating homologous sequences and RNA structures
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
WindowMasker: window-based masker for sequenced genomes
RECAP reveals the true statistical significance of ChIP-seq peak calls
A simple tool for drawing proteolytic peptide maps
UC2 search: using unique connectivity of uncharged compounds for metabolite annotation by database searching in mass spectrometry-based metabolomics
Principal metabolic flux mode analysis
Whisper: read sorting allows robust mapping of DNA sequencing data
Molecular signatures database (MSigDB) 3.0
Covariance adjustment of survival curves based on Cox's proportional hazards regression model
Knockoff boosted tree for model-free variable selection
Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping
Global optimization-based inference of chemogenomic features from drug-target interactions
Structural basis for triplet repeat disorders: a computational analysis
Analyzing gene perturbation screens with nested effects models in R and bioconductor
Cryfa: a secure encryption tool for genomic data
SMILE: mutual information learning for integration of single-cell omics data
Secure multiparty computation for privacy-preserving drug discovery
Rapid 3D protein structure database searching using information retrieval techniques
SCARAP: scalable cross-species comparative genomics of prokaryotes
A sequential Monte Carlo EM approach to the transcription factor binding site identification problem
Automated analysis of time-lapse fluorescence microscopy images: from live cell images to intracellular foci
Computer simulation of tRNA secondary structure folding
Analysis of recursive gene selection approaches from microarray data
Reactome Pengine: a web-logic API to the Homo sapiens reactome
Missing-value estimation using linear and non-linear regression with Bayesian gene selection
Cloud-based interactive analytics for terabytes of genomic variants data
PCCA: a program for phylogenetic canonical correlation analysis
DREME: motif discovery in transcription factor ChIP-seq data
POSBIOTM-NER: a trainable biomedical named-entity recognition system
An empirical Bayes approach to inferring large-scale gene association networks
Predicting clone genotypes from tumor bulk sequencing of multiple samples
A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals
Estimating the significance of sequence order in protein secondary structure and prediction
OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs
GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts
Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus
FX: an RNA-Seq analysis tool on the cloud
NAIL-Network Analysis Interface for Linking HMMER results
Feature selection and transduction for prediction of molecular bioactivity for drug design
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
Prototypes of elementary functional loops unravel evolutionary connections between protein functions
TogoID: an exploratory ID converter to bridge biological datasets