yusuke1997/dblp-id-title huggingface dataset:
The prediction of vertebrate promoter regions using differential hexamer frequency analysis
BioShell - a package of tools for structural biology computations
An automated comparative analysis of 17 complete microbial genomes
GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank
A multi-scenario genome-wide medical population genetics simulation framework
MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences
HotSpot3D web server: an integrated resource for mutation analysis in protein 3D structures
Memdock: an α-helical membrane protein docking algorithm
DoRes within CellMissy: dose-response analysis on cell migration and related data
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals
Improving signal peptide prediction accuracy by simulated neural network
MOBI: a web server to define and visualize structural mobility in NMR protein ensembles
Support vector machine classification and validation of cancer tissue samples using microarray expression data
Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
Exploring drug space with ChemMaps.com
Family genome browser: visualizing genomes with pedigree information
ANAQUIN: a software toolkit for the analysis of spike-in controls for next generation sequencing
HumanMSD and MouseMSD: generating genetic maps for human and murine microsatellite markers
Presenting and sharing clinical data using the eTRIKS Standards Master Tree for tranSMART
SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures
CoxMKF: a knockoff filter for high-dimensional mediation analysis with a survival outcome in epigenetic studies
3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations
New models of atherosclerosis and multi-drug therapeutic interventions
ScanGEO: parallel mining of high-throughput gene expression data
MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants
sefOri: selecting the best-engineered sequence features to predict DNA replication origins
An algorithm for automated layout of process description maps drawn in SBGN
A congruence index for testing topological similarity between trees
Genomes as documents of evolutionary history: a probabilistic macrosynteny model for the reconstruction of ancestral genomes
Rapid T-cell receptor interaction grouping with ting
GPro: generative AI-empowered toolkit for promoter design
PopIns: population-scale detection of novel sequence insertions
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression
Mosclust: a software library for discovering significant structures in bio-molecular data
Fully interpretable deep learning model of transcriptional control
scMatch: a single-cell gene expression profile annotation tool using reference datasets
crosshap: R package for local haplotype visualization for trait association analysis
Improved centroids estimation for the nearest shrunken centroid classifier
Dependence network modeling for biomarker identification
Directed indices for exploring gene expression data
Data-based filtering for replicated high-throughput transcriptome sequencing experiments
SiteComp: a server for ligand binding site analysis in protein structures
Automated manipulation of systems biology models using libSBML within Taverna workflows
Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics
An approach to infer putative disease-specific mechanisms using neighboring gene networks
A joint method for marker-free alignment of tilt series in electron tomography
CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations
A multimodal deep learning framework for predicting drug-drug interaction events
Mayday-a microarray data analysis workbench
InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses
Rose: generating sequence families
Monte Carlo simulation program for ecosystems
Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements
Detection of PCR chimeras in adaptive immune receptor repertoire sequences
Graph attention network for link prediction of gene regulations from single-cell RNA-sequencing data
LabxDB: versatile databases for genomic sequencing and lab management
Context-aware learning for cancer cell nucleus recognition in pathology images
Optimal timepoint sampling in high-throughput gene expression experiments
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes
synergy: a Python library for calculating, analyzing and visualizing drug combination synergy
NetSolP: predicting protein solubility in Escherichia coli using language models
Analysis of a Gibbs sampler method for model-based clustering of gene expression data
SANTA domain: a novel conserved protein module in Eukaryota with potential involvement in chromatin regulation
microRPM: a microRNA prediction model based only on plant small RNA sequencing data
Non-local residue-residue contacts in proteins are more conserved than local ones
Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures
SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses
Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids
A profile hidden Markov model for signal peptides generated by HMMER
Grimon: graphical interface to visualize multi-omics networks
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
De novo clustering of large long-read transcriptome datasets with isONclust3
Mixed graphical models for integrative causal analysis with application to chronic lung disease diagnosis and prognosis
PoLoBag: Polynomial Lasso Bagging for signed gene regulatory network inference from expression data
Accurate prediction of RNA nucleotide interactions with backbone k -tree model
NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data
A2Sign: Agnostic Algorithms for Signatures - a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution
SimSon: simple contrastive learning of SMILES for molecular property prediction
ModBase: A database of comparative protein structure models
MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins
Cloud-native distributed genomic pileup operations
Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data
RNAplex: a fast tool for RNA-RNA interaction search
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome
Parallelized prediction error estimation for evaluation of high-dimensional models
DeFries-Fulker multiple regression analysis of sibship QTL data: a SAS® macro
A user-friendly Hypercard interface for human linkage analysis
An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios
The interfacial character of antibody paratopes: analysis of antibody-antigen structures
Light-weight integration of molecular biological databases
BRAGI: linking and visualization of database information in a 3D viewer and modeling tool
The IDSM mass spectrometry extension: searching mass spectra using SPARQL
SpA: web-accessible spectratype analysis: data management, statistical analysis and visualization
A set of programs for analysis of kinetic and equilibrium data
Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
HiXCorr : a portable high-speed X Corr engine for high-resolution tandem mass spectrometry
HTqPCR : high-throughput analysis and visualization of quantitative real-time PCR data in R
Identification of microRNA activity by Targets' Reverse EXpression
TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes
Darwin v. 2.0: an interpreted computer language for the biosciences
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
PLEXY: efficient target prediction for box C/D snoRNAs
iDINGO - integrative differential network analysis in genomics with Shiny application
WebSTAR3D: a web server for RNA 3D structural alignment
massDatabase: utilities for the operation of the public compound and pathway database
Bayesian parameter estimation for biochemical reaction networks using region-based adaptive parallel tempering
hts-nim: scripting high-performance genomic analyses
SNPtoGO: characterizing SNPs by enriched GO terms
Reliable gene signatures for microarray classification: assessment of stability and performance
Mining HIV Dynamics Using Independent Component Analysis
RightField: embedding ontology annotation in spreadsheets
Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
KeggExp: a web server for visual integration of KEGG pathways and expression profile data
Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors
BELB: a biomedical entity linking benchmark
Multiview: a software package for multiview pattern recognition methods
JIGSAW: integration of multiple sources of evidence for gene prediction
Assessing the biological significance of primary structure consensus patterns using sequence databanks. I. Heat-shock and glucocorticoid control elements in eukaryotic promoters
Relating periodicity of nucleosome organization and gene regulation
Unsupervised multiple kernel learning for heterogeneous data integration
New KEGG pathway-based interpretable features for classifying ageing-related mouse proteins
Dynamical modeling and multi-experiment fitting with PottersWheel
New Normalization Methods for CDNA Microarray Data
matchRanges: generating null hypothesis genomic ranges via covariate-matched sampling
Genexp-a genetic network simulation environment
Learning HMMs for nucleotide sequences from amino acid alignments
Fast and accurate approximate inference of transcript expression from RNA-seq data
Robustness analysis of the E.coli chemosensory system to perturbations in chemoattractant concentrations
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
essaMEM: finding maximal exact matches using enhanced sparse suffix arrays
SC 2 ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data
Accurate cell segmentation in microscopy images using membrane patterns
Assessing phylogenetic motif models for predicting transcription factor binding sites
Bayesian sparse hidden components analysis for transcription regulation networks
Integrating genome-scale metabolic modelling and transfer learning for human gene regulatory network reconstruction
MD DaVis: interactive data visualization of protein molecular dynamics
msa: an R package for multiple sequence alignment
GAMMA: a tool for the rapid identification, classification and annotation of translated gene matches from sequencing data
VEGA: variational segmentation for copy number detection
CaLMPhosKAN: prediction of general phosphorylation sites in proteins via fusion of codon aware embeddings with amino acid aware embeddings and wavelet-based Kolmogorov-Arnold network
The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana
Rediscover: an R package to identify mutually exclusive mutations
Detecting high-scoring local alignments in pangenome graphs
Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction
Population length variability and nucleoid numbers in Escherichia coli
SeQuiLa: an elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals
Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome
aphid: an R package for analysis with profile hidden Markov models
Efficient computation of contributional diversity metrics from microbiome data with FuncDiv
Node similarity-based graph convolution for link prediction in biological networks
A Turing test for artificial expression data
Optimal enhancement of immune response
mpwR: an R package for comparing performance of mass spectrometry-based proteomic workflows
A Gibbs sampler for the identification of gene expression and network connectivity consistency
Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions
A Status Report on Mage
CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors
Selection of optimal DNA oligos for gene expression arrays
Modeling genome coverage in single-cell sequencing
checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes
TA-RNN: an attention-based time-aware recurrent neural network architecture for electronic health records
Meta, Metan and Cyber Servers
MEANS: python package for Moment Expansion Approximation, iNference and Simulation
Multistage attention-based extraction and fusion of protein sequence and structural features for protein function prediction
A fast adaptive algorithm for computing whole-genome homology maps
Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection
DeepMAsED: evaluating the quality of metagenomic assemblies
DESHARKY: automatic design of metabolic pathways for optimal cell growth
MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions
De novo drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment
GeneCodeq: quality score compression and improved genotyping using a Bayesian framework
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks
PARSEC: PAtteRn SEarch and Contextualization
Network-adjusted Kendall's Tau Measure for Feature Screening with Application to High-dimensional Survival Genomic Data
Phylogenetic tree-based microbiome association test
Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis
A collaborative database of inbred mouse strain characteristics
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells
CloudASM: an ultra-efficient cloud-based pipeline for mapping allele-specific DNA methylation
Discriminative motif analysis of high-throughput dataset
LCE: a link-based cluster ensemble method for improved gene expression data analysis
Map2mod - a server for evaluation of crystallographic models and their agreement with electron density maps
snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics
Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
URec: a system for unrooted reconciliation
ProtBuD: a database of biological unit structures of protein families and superfamilies
Combining probabilistic alignments with read pair information improves accuracy of split-alignments
Learning string similarity measures for gene/protein name dictionary look-up using logistic regression
An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files
VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects
A method to infer positive selection from marker dynamics in an asexual population
Do you do text?
Adversarial dense graph convolutional networks for single-cell classification
GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content
SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing
STCRpy: a software suite for T-cell receptor structure parsing, interaction profiling, and machine learning dataset preparation
DrForna: visualization of cotranscriptional folding
Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites
UTGB toolkit for personalized genome browsers
Brewery: deep learning and deeper profiles for the prediction of 1D protein structure annotations
ASAP: analysis of peptide composition
Integrative analysis identifies co-dependent gene expression regulation of BRG1 and CHD7 at distal regulatory sites in embryonic stem cells
RNAStructViz: graphical base pairing analysis
DNAdesign: feature-aware in silico design of synthetic DNA through mutation
CGAT: computational genomics analysis toolkit
DPAM-AI: a domain parser for AlphaFold models powered by artificial intelligence
Simulated maximum likelihood method for estimating kinetic rates in gene expression
Deep centroid: a general deep cascade classifier for biomedical omics data classification
A dynamic programing approach to integrate gene expression data and network information for pathway model generation
Epigenetic priors for identifying active transcription factor binding sites
The genetic data environment an expandable GUI for multiple sequence analysis
CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity
Correlation between gene expression profiles and protein-protein interactions within and across genomes
Conveyor: a workflow engine for bioinformatic analyses
Topological analysis as a tool for detection of abnormalities in protein-protein interaction data
Maximum likelihood of phylogenetic networks
BiVisu: software tool for bicluster detection and visualization
Object-oriented developmental environment for image-analysis applications: implementation for 2D gel electrophoretogram analysis
FASPAD: fast signaling pathway detection
IgSimulator: a versatile immunosequencing simulator
Leveraging heterogeneous network embedding for metabolic pathway prediction
The GMOD Drupal Bioinformatic Server Framework
Characterizing molecular adaptation: a hierarchical approach to assess the selective influence of amino acid properties
HyperPhS: a pharmacophore-guided multimodal representation framework for metabolic stability prediction through contrastive hypergraph learning
Functional characterization of co-phosphorylation networks
Phylogenetic reconstruction from non-genomic data
LLR: a latent low-rank approach to colocalizing genetic risk variants in multiple GWAS
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination
TurboTree: a fast algorithm for minimal trees
Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification
Retroviral promoters in the human genome
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data
Deriving transcriptional programs and functional processes from gene expression databases
FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction
StochKit2: software for discrete stochastic simulation of biochemical systems with events
SDEAP: a splice graph based differential transcript expression analysis tool for population data
AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics
EDEN: evolutionary dynamics within environments
High-throughput minor histocompatibility antigen prediction
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients
A hierarchical Bayesian model for flexible module discovery in three-way time-series data
A hidden-line algorithm for graphical reconstruction of serially sectioned objects
Correction to: Multi-omic integration by machine learning (MIMaL)
Reconstructing the architecture of the ancestral amniote genome
Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives
GeneRecon - a coalescent based tool for fine-scale association mapping
Identification of hierarchical chromatin domains
ABWGAT: anchor-based whole genome analysis tool
Critical Assessment of Microarray Data Analysis: the 2001 challenge
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework
SMARTS: the social media-based addiction recovery and intervention targeting server
CONNECTOR, fitting and clustering of longitudinal data to reveal a new risk stratification system
Automatic semantic classification of scientific literature according to the hallmarks of cancer
Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species
Semi-supervised data-integrated feature importance enhances performance and interpretability of biological classification tasks
TrioVis: a visualization approach for filtering genomic variants of parent-child trios
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
Look4TRs: a de novo tool for detecting simple tandem repeats using self-supervised hidden Markov models
Fast filtering for RNA homology search
DeepMirTar: a deep-learning approach for predicting human miRNA targets
SAWTED: Structure Assignment With Text Description-Enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons
AXZ viewer: a web application to visualize unprocessed AFM-IR data
XGBLC: an improved survival prediction model based on XGBoost
Multiscale model of the different modes of cancer cell invasion
A Macintosh Hypercard stack for calculation of thermodynamically- corrected buffer recipes
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
Correction of image distortion in large-field ssEM stitching by an unsupervised intermediate-space solving network
ECMarker: interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages
Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction
Pheno4J: a gene to phenotype graph database
Characterizing leader sequences of CRISPR loci
Sigmoni: classification of nanopore signal with a compressed pangenome index
Evolutionary footprint of coevolving positions in genes
DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family
SimMLST: simulation of multi-locus sequence typing data under a neutral model
MyMiner: a web application for computer-assisted biocuration and text annotation
A systematic approach to dynamic programming in bioinformatics
AdvISER-PYRO: Amplicon Identification using SparsE Representation of PYROsequencing signal
Computing linkage disequilibrium aware genome embeddings using autoencoders
HiTRACE: high-throughput robust analysis for capillary electrophoresis
TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials