yusuke1997/dblp-id-title huggingface dataset:
Density parameter estimation for finding clusters of homologous proteins - tracing actinobacterial pathogenicity lifestyles
Optimized multilayer perceptrons for molecular classification and diagnosis using genomic data
BiCoN: network-constrained biclustering of patients and omics data
BiNGO : a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions
Mammalian genome evolution is governed by multiple pacemakers
BioCommons: a robust java library for RNA structural bioinformatics
Cdc45: the missing RecJ ortholog in eukaryotes?
FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors
MEMBPLUGIN: studying membrane complexity in VMD
A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)
MUCIDS: an operative C environment for acquisition and processing of polarized-light scattered from biological specimens
Extendable words in nucleotide sequences
Restriction map construction using a 'complete sentences compatibility' algorithm
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles
LoopIng: a template-based tool for predicting the structure of protein loops
Interactive visualization and analysis of morphological skeletons of brain vasculature networks with VessMorphoVis
NURBS: a database of experimental and predicted nuclear receptor binding sites of mouse
TeraPCA: a fast and scalable software package to study genetic variation in tera-scale genotypes
Truncated branch and bound achieves efficient constraint-based genetic design
Unipept web services for metaproteomics analysis
Simulating complex traits influenced by genes with fuzzy-valued effects in pedigreed populations
Bayesian variable selection for the analysis of microarray data with censored outcomes
SELANSI: a toolbox for simulation of stochastic gene regulatory networks
Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability
Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models
NetSHy: network summarization via a hybrid approach leveraging topological properties
An integrated approach to reduce the impact of minor allele frequency and linkage disequilibrium on variable importance measures for genome-wide data
A comprehensive graph neural network method for predicting triplet motifs in disease-drug-gene interactions
Using convex hulls to extract interaction interfaces from known structures
ORE identifies extreme expression effects enriched for rare variants
DensiTree: making sense of sets of phylogenetic trees
HaDeX: an R package and web-server for analysis of data from hydrogen-deuterium exchange mass spectrometry experiments
Comments on 'Bayesian variable selection for disease classification using gene expression data'
SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments
Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
ProtVista: visualization of protein sequence annotations
sAOP: linking chemical stressors to adverse outcomes pathway networks
Visualization and Phospholipid Identification (VaLID): online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass
Global dynamics of biological systems from time-resolved omics experiments
TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts
Federated Random Forests can improve local performance of predictive models for various healthcare applications
PANACEA: network-based methods for pharmacotherapy prioritization in personalized oncology
Modular analysis of the probabilistic genetic interaction network
diXa: a data infrastructure for chemical safety assessment
Automatic analysis of DNA microarray images using mathematical morphology
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
WALT: fast and accurate read mapping for bisulfite sequencing
Sequence alignment kernel for recognition of promoter regions
PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations
Suffix-tree analyser (STAN): looking for nucleotidic and peptidic patterns in chromosomes
Corrigendum to: LipidQuant 1.0: automated data processing in lipid class separation-mass spectrometry quantitative workflows
Simple decision rules for classifying human cancers from gene expression profiles
ResPAN: a powerful batch correction model for scRNA-seq data through residual adversarial networks
excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies
Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites
CellAnn: a comprehensive, super-fast, and user-friendly single-cell annotation web server
Obtaining better quality final clustering by merging a collection of clusterings
Enhanced Waddington landscape model with cell-cell communication can explain molecular mechanisms of self-organization
NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction
Comparative analysis of algorithms for next-generation sequencing read alignment
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT
Inferring the paths of somatic evolution in cancer
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Estimating the number and assignment of clock models in analyses of multigene datasets
Genome-scale strain designs based on regulatory minimal cut sets
Image-based surrogate biomarkers for molecular subtypes of colorectal cancer
IMEx: Imperfect Microsatellite Extractor
GPDBN: deep bilinear network integrating both genomic data and pathological images for breast cancer prognosis prediction
EXTREME: an online EM algorithm for motif discovery
Structure motif discovery and mining the PDB
PHACTS, a computational approach to classifying the lifestyle of phages
A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data
STAR/mmCIF: An ontology for macromolecular structure
ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data
Fast and efficient QTL mapper for thousands of molecular phenotypes
BioBlend.objects: metacomputing with Galaxy
ISMB/ECCB 2019 Proceedings
MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk
Clustering of proximal sequence space for the identification of protein families
HDX-Viewer: interactive 3D visualization of hydrogen-deuterium exchange data
High-dimensional causal mediation analysis by partial sum statistic and sample splitting strategy in imaging genetics application
e-Driver: a novel method to identify protein regions driving cancer
Scoring hidden Markov models
Rectified factor networks for biclustering of omics data
Identifying differentially expressed subnetworks with MMG
Scaffolding pre-assembled contigs using SSPACE
OGRE: Overlap Graph-based metagenomic Read clustEring
EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data
Identification of trans -acting siRNAs and their regulatory cascades in grapevine
Rapid screening and detection of inter-type viral recombinants using phylo-k-mers
Efficient inference of local ancestry
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli
Mapping genes for calcium signaling and their associated human genetic disorders
Differential expression in SAGE: accounting for normal between-library variation
MICAlign: a sequence-to-structure alignment tool integrating multiple sources of information in conditional random fields
Data structures and compression algorithms for genomic sequence data
A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data
BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
Efficient approximations of RNA kinetics landscape using non-redundant sampling
crisscrosslinkeR: identification and visualization of protein-RNA and protein-protein interactions from crosslinking mass spectrometry
Optimal design of gene knockout experiments for gene regulatory network inference
MulBlast 1.0: a multiple alignment of BLAST output to boost protein sequence similarity analysis
Mapmerge: merge genomic maps
Limits of homology detection by pairwise sequence comparison
BioWish: a molecular biology command extension to Tcl/Tk
BP4RNAseq: a babysitter package for retrospective and newly generated RNA-seq data analyses using both alignment-based and alignment-free quantification method
A supervised Bayesian factor model for the identification of multi-omics signatures
How accurately can we control the FDR in analyzing microarray data?
The tspair package for finding top scoring pair classifiers in R
ntHash2: recursive spaced seed hashing for nucleotide sequences
MAC5: Bayesian inference of phylogenetic trees from DNA sequences incorporating gaps
A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions
CMMS-GCL: cross-modality metabolic stability prediction with graph contrastive learning
VeloViz: RNA velocity-informed embeddings for visualizing cellular trajectories
Conditional asymptotic inference for the kernel association test
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms
BioSynther: a customized biosynthetic potential explorer
Identifying simultaneous rearrangements in cancer genomes
DeepCoVDR: deep transfer learning with graph transformer and cross-attention for predicting COVID-19 drug response
Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway
Steady-state expression of self-regulated genes
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks
PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data
SPiD: a subtilis protein interaction database
Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data
Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference
isomiRID: a framework to identify microRNA isoforms
Updates to the RMAP short-read mapping software
Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance
Hidden Markov models for detecting remote protein homologies
Sircah: a tool for the detection and visualization of alternative transcripts
Real-time demultiplexing Nanopore barcoded sequencing data with npBarcode
Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data
MuCor: mutation aggregation and correlation
ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images
SESAME (SEquence Sorter & AMplicon Explorer): genotyping based on high-throughput multiplex amplicon sequencing
Identification of transcription factor binding sites from ChIP-seq data at high resolution
The evolution of contact prediction: evidence that contact selection in statistical contact prediction is changing
Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning
MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data
Isoform function prediction based on bi-random walks on a heterogeneous network
Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples
A relational schema for both array-based and SAGE gene expression experiments
Bayesian modelling of time series data (BayModTS) - a FAIR workflow to process sparse and highly variable data
Sequential Monte Carlo multiple testing
DNMAD: web-based diagnosis and normalization for microarray data
LITTLE KEVIN: a program for the estimation of protein homology by analysing the amino acid compositions and sequences
CSB.DB: a comprehensive systems-biology database
Reply to "Comment on causality and pathway search in microarray time series experiment"
Pseudoknots in RNA folding landscapes
Accuracy improvement for identifying translation initiation sites in microbial genomes
Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences
AI-augmented physics-based docking for antibody-antigen complex prediction
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles
An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
Flapjack - graphical genotype visualization
BERTMHC: improved MHC-peptide class II interaction prediction with transformer and multiple instance learning
CancerTrialMatch: a computational resource for the management of biomarker-based clinical trials at a community cancer center
Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment
Floria: fast and accurate strain haplotyping in metagenomes
ConceptDrift: leveraging spatial, temporal and semantic evolution of biomedical concepts for hypothesis generation
CALDERA: finding all significant de Bruijn subgraphs for bacterial GWAS
Applications of beta-mixture models in bioinformatics
The Amordad database engine for metagenomics
A Bayesian approach to reconstructing genetic regulatory networks with hidden factors
The GNAT library for local and remote gene mention normalization
Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly
DDN: a caBIG ® analytical tool for differential network analysis
SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
A comparison of rule-based and centroid single-sample multiclass predictors for transcriptomic classification
Creating protein models from electron-density maps using particle-filtering methods
Identifying bacterial genes and endosymbiont DNA with Glimmer
Assigning duplication events to relative temporal scales in genome-wide studies
Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach
Geometricus represents protein structures as shape-mers derived from moment invariants
Adversarial generation of gene expression data
Brain Predictability toolbox: a Python library for neuroimaging-based machine learning
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites
gmcoda: Graphical model for multiple compositional vectors in microbiome studies
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
deepDR: a network-based deep learning approach to in silico drug repositioning
Fast computation of neighbor seeds
ASAFE: ancestry-specific allele frequency estimation
A powerful and flexible weighted distance-based method incorporating interactions between DNA methylation and environmental factors on health outcomes
SigMat: a classification scheme for gene signature matching
TRACTOR, a program to locate subclones in a nucleotide sequence using only one sequencing reaction
A space-efficient algorithm for aligning large genomic sequences
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
Assemblytics: a web analytics tool for the detection of variants from an assembly
Predicting multicellular function through multi-layer tissue networks
Improving cross-study prediction through addon batch effect adjustment or addon normalization
Basic program to assess the extent and pattern of agreement between two procedures
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy
COBrA: a bio-ontology editor
M-ZDOCK: a grid-based approach for C n symmetric multimer docking
MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets
Power Analysis for Genetic Association Test (PAGEANT) provides insights to challenges for rare variant association studies
Erratum to: abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Linear effects models of signaling pathways from combinatorial perturbation data
Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants
Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network
A Boolean network model of the FA/BRCA pathway
AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency
Computer program for the equations describing the steady state of enzyme reactions
GENIUS II: a high-throughput database system for linking ORFs in complete genomes to known protein three-dimensional structures
CODEX: COunterfactual Deep learning for the in silico EXploration of cancer cell line perturbations
Optimal Gene Filtering for Single-Cell data (OGFSC) - a gene filtering algorithm for single-cell RNA-seq data
Clann: investigating phylogenetic information through supertree analyses
SwiftLink: parallel MCMC linkage analysis using multicore CPU and GPU
TsImpute: an accurate two-step imputation method for single-cell RNA-seq data
Allerdictor: fast allergen prediction using text classification techniques
Multi-modal contrastive learning of subcellular organization using DICE
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis
GDISC: a web portal for integrative analysis of gene-drug interaction for survival in cancer
A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data
OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding
Cell++ - simulating biochemical pathways
Multiscale DNA partitioning: statistical evidence for segments
Vaa3D-x for cross-platform teravoxel-scale immersive exploration of multidimensional image data
Creating reusable tools from scripts: the Galaxy Tool Factory
Phenonaut: multiomics data integration for phenotypic space exploration
A Zoom-Focus algorithm (ZFA) to locate the optimal testing region for rare variant association tests
rh_tsp_map 3.0: end-to-end radiation hybrid mapping with improved speed and quality control
MinSet: a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database
INTERCAAT: identifying interface residues between macromolecules
A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags
How and when should interactome-derived clusters be used to predict functional modules and protein function?
Structurexplor: a platform for the exploration of structural features of RNA secondary structures
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models
CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data
Predicting protein functions using positive-unlabeled ranking with ontology-based priors
Efficient estimation of pairwise distances between genomes
Predicting loop conformational ensembles
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
Analyse This...Or: Intelligent Help for The Rest of Us
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation
Revealing aperiodic aspects of solenoid proteins from sequence information
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
Discovering personalized driver mutation profiles of single samples in cancer by network control strategy
POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties
Enhancements and modifications of primer design program Primer3
Multilevel support vector regression analysis to identify condition-specific regulatory networks
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
aCLImatise: automated generation of tool definitions for bioinformatics workflows
Impact of protein conformational diversity on AlphaFold predictions
Network-based analysis of omics data: the LEAN method
Identification of GPI anchor attachment signals by a Kohonen self-organizing map
'Hybrid Protein Model' for optimally defining 3D protein structure fragments
Exploring genome characteristics and sequence quality without a reference
BEDTools: a flexible suite of utilities for comparing genomic features
Protein-Sol: a web tool for predicting protein solubility from sequence
A multivariate regression approach to association analysis of a quantitative trait network
MAP-O-MAT: internet-based linkage mapping
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays
JSBML 1.0: providing a smorgasbord of options to encode systems biology models
Convergence of the proteomic pattern in cancer
Bayesian detection of non-sinusoidal periodic patterns in circadian expression data
An optimized algorithm for flux estimation from isotopomer distribution in glucose metabolites
A wavelet-based method to exploit epigenomic language in the regulatory region
Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
QuickGO: a web-based tool for Gene Ontology searching
RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics
The PRALINE database: protein and Rna humAn singLe nucleotIde variaNts in condEnsates
Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep
DIANA-mirPath: Integrating human and mouse microRNAs in pathways
Measuring phylogenetic signal between categorical traits and phylogenies
MetTailor: dynamic block summary and intensity normalization for robust analysis of mass spectrometry data in metabolomics
Functional Gene Networks: R/Bioc package to generate and analyse gene networks derived from functional enrichment and clustering
Structural systems identification of genetic regulatory networks
SRG extractor: a skinny reference genome approach for reduced-representation sequencing
RedoxDB - a curated database for experimentally verified protein oxidative modification
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A