yusuke1997/dblp-id-title huggingface dataset:
ncDR: a comprehensive resource of non-coding RNAs involved in drug resistance
Non-linear regression models to estimate the size of DNA fragments
Rapid match-searching for gene silencing assessment
Prediction of protein subcellular locations using fuzzy k -NN method
epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology
SAIGEgds - an efficient statistical tool for large-scale PheWAS with mixed models
Inverse modeling using multi-block PLS to determine the environmental conditions that provide optimal cellular function
PE-Assembler: de novo assembler using short paired-end reads
PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences
miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry-mass spectrometry
Benchmarking and integration of methods for deconvoluting spatial transcriptomic data
StructureProfiler: an all-in-one tool for 3D protein structure profiling
Polyester : simulating RNA-seq datasets with differential transcript expression
TFBSTools: an R/bioconductor package for transcription factor binding site analysis
A program for predicting significant RNA secondary structures
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments
Tools for visually exploring biological networks
Projected t-SNE for batch correction
Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold
BioOptimizer: a Bayesian scoring function approach to motif discovery
Efficient filtering methods for clustering cDNAs with spliced sequence alignment
BamHash: a checksum program for verifying the integrity of sequence data
MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
The Sulfinator: predicting tyrosine sulfation sites in protein sequences
InterProScan - an integration platform for the signature-recognition methods in InterPro
BioCaster in 2021: automatic disease outbreaks detection from global news media
Visual exploration of large metabolic models
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data
Higher-order molecular organization as a source of biological function
Identifying duplicate content using statistically improbable phrases
Multimodal network diffusion predicts future disease-gene-chemical associations
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug-target affinities
LdCompare: rapid computation of single- and multiple-marker r 2 and genetic coverage
Kpax3: Bayesian bi-clustering of large sequence datasets
Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism
Gene set enrichment analysis using linear models and diagnostics
Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function
Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
alpha-Helix region prediction with stochastic rule learning
AUGIST: inferring species trees while accommodating gene tree uncertainty
atSNP: transcription factor binding affinity testing for regulatory SNP detection
Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone
A novel bi-level meta-analysis approach: applied to biological pathway analysis
The JWS online simulation database
OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks
CoMSA: compression of protein multiple sequence alignment files
EpitopeVec: linear epitope prediction using deep protein sequence embeddings
ANTIGEN: protein surface residue prediction
DictyMOLD - a Dictyostelium discoideum genome browser database
Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns
mspire: mass spectrometry proteomics in Ruby
ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets
Capturing expert knowledge with argumentation: a case study in bioinformatics
Sisyphus and prediction of protein structure
OxfordGrid: a web interface for pairwise comparative map views
DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results
DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method
Iterative attack-and-defend framework for improving TCR-epitope binding prediction models
TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information
HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
Viewing cancer genes from co-evolving gene modules
Antisense transcription is coupled to nucleosome occupancy in sense promoters
WebAllergen: a web server for predicting allergenic proteins
Analyzing biological network parameters with CentiScaPe
TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits
MOSGA: Modular Open-Source Genome Annotator
Supervised biological network alignment with graph neural networks
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities
MCS2: minimal coordinated supports for fast enumeration of minimal cut sets in metabolic networks
Seeding with minimized subsequence
Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
Free molecular biological software available from the EMBL file server
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms
Protein classification using modified n-grams and skip-grams
Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data
A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data
NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures
CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
PAVIS: a tool for Peak Annotation and Visualization
Alignments of DNA and protein sequences containing frameshift errors
NegGOA: negative GO annotations selection using ontology structure
MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles
CATH-ddG: towards robust mutation effect prediction on protein-protein interactions out of CATH homologous superfamily
GOplot: an R package for visually combining expression data with functional analysis
RadCon: phylogenetic tree comparison and consensus
Calculation of the molecular weight of proteins from electrophoretic and gel exclusion chromatographic experiments
Cross-study validation for the assessment of prediction algorithms
Revisiting the negative example sampling problem for predicting protein-protein interactions
SQID-XLink: implementation of an intensity-incorporated algorithm for cross-linked peptide identification
Advances to Bayesian network inference for generating causal networks from observational biological data
Expression of Concern: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking
Global modeling of transcriptional responses in interaction networks
PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids
Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters
Tertiary structure-based prediction of conformational B-cell epitopes through B factors
BraneMF: integration of biological networks for functional analysis of proteins
PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation
A qualitative ecological model to support mariculture pond water quality management
ESyPred3D: Prediction of proteins 3D structures
Ranking models of transmembrane β -barrel proteins using Z-coordinate predictions
Comparative conservation analysis of the human mitotic phosphoproteome
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys
Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes
Prioritizing genes for systematic variant effect mapping
Database of evidence for precision oncology portal
Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry
gMCS: fast computation of genetic minimal cut sets in large networks
Modeling immune system control of atherogenesis
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases
IsoRankN: spectral methods for global alignment of multiple protein networks
SitePainter: a tool for exploring biogeographical patterns
Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide
ReDiT: Repeat Discrepancy Tagger-a shotgun assembly finishing aid
Estimation of errors introduced by confocal imaging into the data on segmentation gene expression in Drosophila
MetaFam: a unified classification of protein families. I. Overview and statistics
Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG
Identification of feedback loops in neural networks based on multi-step Granger causality
miComplete: weighted quality evaluation of assembled microbial genomes
dittoSeq: universal user-friendly single-cell and bulk RNA sequencing visualization toolkit
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
iBAG: integrative Bayesian analysis of high-dimensional multiplatform genomics data
NOA: a cytoscape plugin for network ontology analysis
MBV: a method to solve sample mislabeling and detect technical bias in large combined genotype and sequencing assay datasets
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC
Interactive, multiscale navigation of large and complicated biological networks
Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
E-CELL: software environment for whole-cell simulation
Protein residues determining interaction specificity in paralogous families
Bayesian weighted Mendelian randomization for causal inference based on summary statistics
Comparison of statistical algorithms for daily syndromic surveillance aberration detection
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data
Semi-blind sparse affine spectral unmixing of autofluorescence-contaminated micrographs
BiORSEO: a bi-objective method to predict RNA secondary structures with pseudoknots using RNA 3D modules
PRESS: PRotEin S-Sulfenylation server
BioXSD: the common data-exchange format for everyday bioinformatics web services
ptairMS: real-time processing and analysis of PTR-TOF-MS data for biomarker discovery in exhaled breath
Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes
Graph-based analysis and visualization of experimental results with ONDEX
Length bias correction for RNA-seq data in gene set analyses
Design and implementation of a qualitative simulation model of lambda phage infection
BoolNet - an R package for generation, reconstruction and analysis of Boolean networks
Haptools: a toolkit for admixture and haplotype analysis
SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments
ARCS: an aggregated related column scoring scheme for aligned sequences
Detecting gene-environment interactions from multiple continuous traits
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system
Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
Phyutility: a phyloinformatics tool for trees, alignments and molecular data
Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
Correction to: Python interfaces for the Smoldyn simulator
A new fourier transform approach for protein coding measure based on the format of the Z curve
Lemon: a framework for rapidly mining structural information from the Protein Data Bank
PREFMD: a web server for protein structure refinement via molecular dynamics simulations
Computer simulation of selection in a hypothetical crop species
Steady-state modelling of metabolic pathways: a guide for the prospective simulator
The anisotropic network model web server at 2015 (ANM 2.0)
twas_sim, a Python-based tool for simulation and power analysis of transcriptome-wide association analysis
CGPE: an integrated online server for Cancer Gene and Pathway Exploration
Peptide Finder: mapping measured molecular masses to peptides and proteins
A multi-stage approach to clustering and imputation of gene expression profiles
VisRD--visual recombination detection
jmodeltest .org: selection of nucleotide substitution models on the cloud
GenomePixelizer-a visualization program for comparative genomics within and between species
otargen : GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr
Issues in developing integrated genomic databases and application to the human X chromosome
Harnessing deep learning for proteome-scale detection of amyloid signaling motifs
DLocalMotif: a discriminative approach for discovering local motifs in protein sequences
A method for probing the mutational landscape of amyloid structure
primirTSS: an R package for identifying cell-specific microRNA transcription start sites
Efficient sampling for Bayesian inference of conjunctive Bayesian networks
A new JAVA interface implementation of THESIAS: testing haplotype effects in association studies
MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray datasets
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association
Imaging, quantification and visualization of spatio-temporal patterning in mESC colonies under different culture conditions
RECKONER: read error corrector based on KMC
Maximum likelihood estimation of locus-specific mutation rates in Y-chromosome short tandem repeats
bdvis: visualizing biodiversity data in R
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
Searching for amino acid sequence motifs among enzymes: the Enzyme- Reaction Database
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming
Mitigating the adverse impact of batch effects in sample pattern detection
Evaluating putative chimeric sequences from PCR-amplified products
Efficient haplotype matching between a query and a panel for genealogical search
Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions
PANPROVA: pangenomic prokaryotic evolution of full assemblies
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures
Phi-psi conformational pattern clustering of protein amino acid residues using the potential function method
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
VoDEx: a Python library for time annotation and management of volumetric functional imaging data
Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE
Evaporative cooling feature selection for genotypic data involving interactions
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing
EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types
A method of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry
Prediction of therapeutic microRNA based on the human metabolic network
ConfID: an analytical method for conformational characterization of small molecules using molecular dynamics trajectories
HAlign: Fast multiple similar DNA/RNA sequence alignment based on the centre star strategy
Strain-GeMS: optimized subspecies identification from microbiome data based on accurate variant modeling
FluPhenotype - a one-stop platform for early warnings of the influenza A virus
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB
Modeling polypharmacy side effects with graph convolutional networks
Gene ranking and biomarker discovery under correlation
PBAP: a pipeline for file processing and quality control of pedigree data with dense genetic markers
SigTools: exploratory visualization for genomic signals
DIVE: a data intensive visualization engine
2HAPI: A Microarray Data Analysis System
D-VASim: an interactive virtual laboratory environment for the simulation and analysis of genetic circuits
ADPredict: ADP-ribosylation site prediction based on physicochemical and structural descriptors
Genetic code symmetry and efficient design of GC-constrained coding sequences
A novel signaling pathway impact analysis
DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model
TMBB-DB: a transmembrane β-barrel proteome database
Properties and identification of human protein drug targets
MISTRAL: a tool for energy-based multiple structural alignment of proteins
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
Joint detection of copy number variations in parent-offspring trios
Bio-Object, a stochastic simulator for post-transcriptional regulation
Detecting clusters of different geometrical shapes in microarray gene expression data
maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines
Phylocomposer and phylodirector: analysis and visualization of transducer indel models
Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis
HippDB: a database of readily targeted helical protein-protein interactions
Representations of lipid nanoparticles using large language models for transfection efficiency prediction
Extended connectivity interaction features: improving binding affinity prediction through chemical description
hCoCena: horizontal integration and analysis of transcriptomics datasets
diffuStats: an R package to compute diffusion-based scores on biological networks
Sequence-based Gaussian network model for protein dynamics
Lap computers in the laboratory
PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition
Modelling cancer progression using Mutual Hazard Networks
METAREP: JCVI metagenomics reports - an open source tool for high-performance comparative metagenomics
fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
BGT: efficient and flexible genotype query across many samples
wgd - simple command line tools for the analysis of ancient whole-genome duplications
Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data
Predicting reliable regions in protein sequence alignments
Scalable sequence database search using partitioned aggregated Bloom comb trees
HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data
Artificial intelligence methods for theory representation and hypothesis formation
The new biological literature
Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments
Simulating systems genetics data with SysGenSIM
Position dependencies in transcription factor binding sites
Mainzelliste SecureEpiLinker (MainSEL): privacy-preserving record linkage using secure multi-party computation
deconvSeq: deconvolution of cell mixture distribution in sequencing data
Integrating sequence, expression and interaction data to determine condition-specific miRNA regulation
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes
BioTextQuest+: a knowledge integration platform for literature mining and concept discovery
Novel approach for parallelizing pairwise comparison problems as applied to detecting segments identical by decent in whole-genome data
Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins
BNFinder2: Faster Bayesian network learning and Bayesian classification
MicroRNA modules prefer to bind weak and unconventional target sites
Self-organizing and self-correcting classifications of biological data
MTide: an integrated tool for the identification of miRNA-target interaction in plants
Flexbar 3.0 - SIMD and multicore parallelization
tasiRNAdb: a database of ta-siRNA regulatory pathways
Defining the clonality of peripheral T cell lymphomas using RNA-seq
diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals
Better bioinformatics through usability analysis
Alignment-free local structural search by writhe decomposition
COGENT: evaluating the consistency of gene co-expression networks
Text mining meets workflow: linking U-Compare with Taverna
R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data
Arrayplot for visualization and normalization of cDNA microarray data
Sequence alignment visualization in HTML5 without Java
A tree-based approach for motif discovery and sequence classification
Computational prediction of species-specific malonylation sites via enhanced characteristic strategy
Proteoform identification and quantification based on alignment graphs
Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes
HTSeq - a Python framework to work with high-throughput sequencing data
DTMiner: identification of potential disease targets through biomedical literature mining
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks
BioDownloader: bioinformatics downloads and updates in a few clicks
VSTH: a user-friendly web server for structure-based virtual screening on Tianhe-2
IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes
From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures
MFR-DTA: a multi-functional and robust model for predicting drug-target binding affinity and region
DSK: k -mer counting with very low memory usage