yusuke1997/dblp-id-title huggingface dataset:
Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing
Aligning optical maps to de Bruijn graphs
Smoothing waves in array CGH tumor profiles
Two-group comparisons of zero-inflated intensity values: the choice of test statistic matters
GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data
The GeneAround GO viewer
Imputing dropouts for single-cell RNA sequencing based on multi-objective optimization
Proline: an efficient and user-friendly software suite for large-scale proteomics
DataRemix: a universal data transformation for optimal inference from gene expression datasets
Deriving quantitative conclusions from microarray expression data
A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits
PPaxe: easy extraction of protein occurrence and interactions from the scientific literature
A path recorder algorithm for Multiple Longest Common Subsequences (MLCS) problems
Comparing Petri net-based models of biological systems using Holmes
spacodiR: structuring of phylogenetic diversity in ecological communities
Exploring spatially adjacent TFBS-clustered regions with Hi-C data
PredAcc: prediction of solvent accessibility
Corrigendum: EuGene: maximizing synthetic gene design for heterologous expression
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes
Yale Image Finder (YIF): a new search engine for retrieving biomedical images
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments
P 2 BAT: a massive parallel implementation of PBAT for genome-wide association studies in R
RaPID-Query for fast identity by descent search and genealogical analysis
Improved design and analysis of CRISPR knockout screens
Identifying small interfering RNA loci from high-throughput sequencing data
MIPSIM: similarity analysis of molecular interaction potentials
Codetta: predicting the genetic code from nucleotide sequence
iBioProVis: interactive visualization and analysis of compound bioactivity space
RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidy
An APN model for Arrhythmic beat classification
Multifaceted protein-protein interaction prediction based on Siamese residual RCNN
Predicting the optimal growth temperatures of prokaryotes using only genome derived features
MAT2: manifold alignment of single-cell transcriptomes with cell triplets
CoLiDe: Combinatorial Library Design tool for probing protein sequence space
A framework for high-throughput sequence alignment using real processing-in-memory systems
Identifying small-effect genetic associations overlooked by the conventional fixed-effect model in a large-scale meta-analysis of coronary artery disease
gcExplorer: interactive exploration of gene clusters
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics
PingPongPro: a tool for the detection of piRNA-mediated transposon-silencing in small RNA-Seq data
MIO: microRNA target analysis system for immuno-oncology
Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph
Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans
Enhancing biomedical relation extraction with directionality
Robust genetic model-based SNP-set association test using CauchyGM
A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data
DNAlive: a tool for the physical analysis of DNA at the genomic scale
IntronDB: a database for eukaryotic intron features
An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays
Modeling DNA methylation dynamics with approaches from phylogenetics
Toward the estimation of the absolute quality of individual protein structure models
MADS+: discovery of differential splicing events from Affymetrix exon junction array data
Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks
YASARA View - molecular graphics for all devices - from smartphones to workstations
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels
Analyzing large scale genomic data on the cloud with Sparkhit
miRcode: a map of putative microRNA target sites in the long non-coding transcriptome
Chado Controller: advanced annotation management with a community annotation system
Novel algorithms and the benefits of comparative validation
Supervised feature selection in mass spectrometry-based proteomic profiling by blockwise boosting
flowPeaks: a fast unsupervised clustering for flow cytometry data via K -means and density peak finding
Creating views on integrated multidomain data
Ondex Web: web-based visualization and exploration of heterogeneous biological networks
DamageProfiler: fast damage pattern calculation for ancient DNA
Empirical estimation of the reliability of ribosomal RNA alignments
A web-based three-dimensional protein retrieval system by matching visual similarity
Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows
Prediction of 3D neighbours of molecular surface patches in proteins by artificial neural networks
Discriminating early- and late-stage cancers using multiple kernel learning on gene sets
FlexServ: an integrated tool for the analysis of protein flexibility
Integrative data semantics through a model-enabled data stewardship
A microprocessor-based control unit for Plasmodium falciparum culture apparatus
MAISTAS: a tool for automatic structural evaluation of alternative splicing products
LarvaTagger: manual and automatic tagging of Drosophila larval behaviour
The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool
Improved sensitivity of profile searches through the use of sequence weights and gap excision
Determining the subcellular location of new proteins from microscope images using local features
Biomarker discovery in MALDI-TOF serum protein profiles using discrete wavelet transformation
Automated genome sequence analysis and annotation
Minimap2: pairwise alignment for nucleotide sequences
FUS: a system to simulate conformational changes in biological macromolecules
ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions
PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy
High-complexity regions in mammalian genomes are enriched for developmental genes
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure
VCF-kit: assorted utilities for the variant call format
A genomic random interval model for statistical analysis of genomic lesion data
FarFetch - an Internet-based sequence entry server
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Nanopore decoding with speed and versatility for data storage
iAlign: a method for the structural comparison of protein-protein interfaces
The fuzzy polynucleotide space: basic properties
Multi-project and Multi-profile joint Non-negative Matrix Factorization for cancer omic datasets
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding
Predicting and understanding transcription factor interactions based on sequence level determinants of combinatorial control
Pangenome graph layout by Path-Guided Stochastic Gradient Descent
GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks
PyLiger: scalable single-cell multi-omic data integration in Python
Analysis of mixed lipid extracts using 1H NMR spectra
Coevolution-based prediction of protein-protein interactions in polyketide biosynthetic assembly lines
Extending gene ontology with gene association networks
PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures
CroP - Coordinated Panel visualization for biological networks analysis
Comparative annotation of viral genomes with non-conserved gene structure
Infernal 1.0: inference of RNA alignments
Co-expression networks: graph properties and topological comparisons
Resolving diverse protein-DNA footprints from exonuclease-based ChIP experiments
Integration of molecular network data reconstructs Gene Ontology
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
ProPred: prediction of HLA-DR binding sites
BioABACUS: a database of abbreviations and acronyms in biotechnology and computer science
IMpRH Server: an RH mapping server available on the Web
Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS
Ct3d: tracking microglia motility in 3D using a novel cosegmentation approach
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB
Identifying structural variants using linked-read sequencing data
ASDB: a resource for probing protein functions with small molecules
Predicting protein contact map using evolutionary and physical constraints by integer programming
POPSIM: a general population simulation program
Rknots: topological analysis of knotted biopolymers with R
Multiresolution correction of GC bias and application to identification of copy number alterations
A Blind and Independent Benchmark Study for Detecting Differentially Methylated Regions in Plants
Circular RNAs are depleted of polymorphisms at microRNA binding sites
The DISOPRED server for the prediction of protein disorder
A pairwise strategy for imputing predictive features when combining multiple datasets
About the need to make computational models of biological macromolecules available and discoverable
Large-scale inference of competing endogenous RNA networks with sparse partial correlation
VINYL: Variant prIoritizatioN bY survivaL analysis
Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA
Quantifying the relevance of different mediators in the human immune cell network
A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f 4-statistics
Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
Using local alignment to enhance single-cell bisulfite sequencing data efficiency
ColocML: machine learning quantifies co-localization between mass spectrometry images
HiCube: interactive visualization of multiscale and multimodal Hi-C and 3D genome data
BrainImageR: spatiotemporal gene set analysis referencing the human brain
TTA Lynx: a web-based service for analysis of actinomycete genes containing rare TTA codon
On expert curation and scalability: UniProtKB/Swiss-Prot as a case study
Use of keyword hierarchies to interpret gene expression patterns
PIR: a new resource for bioinformatics
PySCeSToolbox: a collection of metabolic pathway analysis tools
MAD: a suite of tools for microarray data management and processing
Inference of clonal selection in cancer populations using single-cell sequencing data
DeepSinse: deep learning-based detection of single molecules
CHORAL: a differential geometry approach to the prediction of the cores of protein structures
Information-theoretic evaluation of predicted ontological annotations
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser
McSplicer: a probabilistic model for estimating splice site usage from RNA-seq data
Characterizing spatial distributions of astrocytes in the mammalian retina
MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data
FastSpar: rapid and scalable correlation estimation for compositional data
Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates
oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA
NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks
ipDMR: identification of differentially methylated regions with interval P-values
Causal analysis approaches in Ingenuity Pathway Analysis
MetaBCC-LR: metagenomics binning by coverage and composition for long reads
SiTaR: a novel tool for transcription factor binding site prediction
Discovering disease-genes by topological features in human protein-protein interaction network
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data
Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling
A co-module approach for elucidating drug-disease associations and revealing their molecular basis
CellClassifier: supervised learning of cellular phenotypes
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID)
STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
Classifying and segmenting microscopy images with deep multiple instance learning
BINOCh: binding inference from nucleosome occupancy changes
Meffil: efficient normalization and analysis of very large DNA methylation datasets
BLogo: a tool for visualization of bias in biological sequences
MageComet - web application for harmonizing existing large-scale experiment descriptions
FRODOCK 2.0: fast protein-protein docking server
TURNIP: tracking unresolved nucleotide polymorphisms in large hard-to-assemble regions of repetitive DNA sequence
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments
NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics
Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition
Analysis of dynamics trajectories of DNA and DNA-drug complexes
Recovering key biological constituents through sparse representation of gene expression
Discriminating the reaction types of plant type III polyketide synthases
GeneRAGE: a robust algorithm for sequence clustering and domain detection
CCIBP: a comprehensive cosmetic ingredients bioinformatics platform
SampleExplorer: using language models to discover relevant transcriptome data
Cellware-a multi-algorithmic software for computational systems biology
simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics
RAxML-Light: a tool for computing terabyte phylogenies
Detecting regulatory gene-environment interactions with unmeasured environmental factors
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks
RASER: reads aligner for SNPs and editing sites of RNA
GeneTUKit: a software for document-level gene normalization
BALL-rapid software prototyping in computational molecular biology
RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data
Network analyses in systems pharmacology
Phyx: phylogenetic tools for unix
ADAPTSITE: detecting natural selection at single amino acid sites
FunctanSNP: an R package for functional analysis of dense SNP data (with interactions)
Recognition of small molecule-RNA binding sites using RNA sequence and structure
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining
A more precise characterization of chaperonin substrates
Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III
On the complexity measures of genetic sequences
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes
The language of RNA: a formal grammar that includes pseudoknots
ProRule: a new database containing functional and structural information on PROSITE profiles
MOVICS: an R package for multi-omics integration and visualization in cancer subtyping
Locality-sensitive hashing for the edit distance
Tribus: semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic data
Integrating transcription factor binding site information with gene expression datasets
PDBench: evaluating computational methods for protein-sequence design
'COV'COP' allows to detect CNVs responsible for inherited diseases among amplicons sequencing data
Fuse: multiple network alignment via data fusion
A dynamic programming algorithm for identification of triplex-forming sequences
RamiGO: an R/Bioconductor package providing an AmiGO Visualize interface
HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data
MPIDB: the microbial protein interaction database
PATMAT: a searching and extraction program for sequence, pattern and block queries and databases
CryoTEN: efficiently enhancing cryo-EM density maps using transformers
The Predictive Toxicology Challenge 2000-2001
A low-complexity add-on score for protein remote homology search with COMER
Discriminant analysis of promoter regions in Escherichia coli sequences
An algorithm for the identification of similar oligopeptides between amino acid sequences
Improved predictions by Pcons.net using multiple templates
PyEvoCell: an LLM-augmented single-cell trajectory analysis dashboard
Graph-regularized dual Lasso for robust eQTL mapping
WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms
Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data
SIGNAL SCAN 3.0: new database and program features
Learned protein embeddings for machine learning
KCOSS: an ultra-fast k-mer counter for assembled genome analysis
FPC: a system for building contigs from restriction fingerprinted clones
Iterative Cluster Analysis of Protein Interaction Data
Succinct dynamic de Bruijn graphs
PlantSat: a specialized database for plant satellite repeats
Intervention in a family of Boolean networks
Insane in the vembrane: filtering and transforming VCF/BCF files
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
Joint detection of germline and somatic copy number events in matched tumor-normal sample pairs
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C
Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic
ENANO: Encoder for NANOpore FASTQ files
The ACPYPE web server for small-molecule MD topology generation
Visualization of nucleic acid sequence structural information
RING: networking interacting residues, evolutionary information and energetics in protein structures
Characterization of disordered proteins with ENSEMBLE
The utility of different representations of protein sequence for predicting functional class
Irys Extract
Mixture models for assessing differential expression in complex tissues using microarray data
Prediction of disulfide connectivity in proteins
Benchmarking fold detection by DaliLite v.5
Visualizing profile-profile alignment: pairwise HMM logos
New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics
MASQOT-GUI: spot quality assessment for the two-channel microarray platform
Determination of sets of covariating gene expression using graph analysis on pairwise expression ratios
Voro3D: 3D Voronoi tessellations applied to protein structures
MC-Fit: using Monte-Carlo methods to get accurate confidence limits on enzyme parameters
InterMap3D: predicting and visualizing co-evolving protein residues
SoS Notebook: an interactive multi-language data analysis environment
Coral: a web-based visual analysis tool for creating and characterizing cohorts
Natural sequence code representations for compression and rapid searching of human-genome style databases
A permissive secondary structure-guided superposition tool for clustering of protein fragments toward protein structure prediction via fragment assembly
Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing
CTree : comparison of clusters between phylogenetic trees made easy
A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes
ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Customized de novo mutation detection for any variant calling pipeline: SynthDNM
Semi-supervised learning via penalized mixture model with application to microarray sample classification
Phenopolis: an open platform for harmonization and analysis of genetic and phenotypic data
Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold
TopoICE-R: 3D visualization modeling the topology of DNA recombination
Prediction of mutation effects using a deep temporal convolutional network
MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences
STatistical Inference Relief (STIR) feature selection
TarPmiR: a new approach for microRNA target site prediction
A fast layout algorithm for protein interaction networks
Multiple network-constrained regressions expand insights into influenza vaccination responses
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees
Network-based analysis of genotype-phenotype correlations between different inheritance modes
CLUSTAL V: improved software for multiple sequence alignment
SOAPMetaS: profiling large metagenome datasets efficiently on distributed clusters
Large-scale extraction of gene interactions from full-text literature using DeepDive
Validation of alternative methods of data normalization in gene co-expression studies
A Lasso regression model for the construction of microRNA-target regulatory networks
SPACER: identification of cis -regulatory elements with non-contiguous critical residues
IntegratedMap: a Web interface for integrating genetic map data
A method for integrative structure determination of protein-protein complexes
A span-based joint model for extracting entities and relations of bacteria biotopes
Detecting the impact of sequencing errors on SAGE data
Improved performance on high-dimensional survival data by application of Survival-SVM
mzMD: visualization-oriented MS data storage and retrieval
A linear programming model for protein inference problem in shotgun proteomics
PDBML: the representation of archival macromolecular structure data in XML
GASS: identifying enzyme active sites with genetic algorithms
Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies
qTeller: a tool for comparative multi-genomic gene expression analysis
Human structural proteome-wide characterization of Cyclosporine A targets
Quantifying circular RNA expression from RNA-seq data using model-based framework
Spathial: an R package for the evolutionary analysis of biological data
Enrichment of oligonucleotide sets with transcription control signals. III: DNA from non-mammalian vertebrates