yusuke1997/dblp-id-title huggingface dataset:
A database management system for recombinant DNA clones and hosts for use in IBM personal computers
MacPattern: protein pattern searching on the Apple Macintosh
Computer-aided analysis of infrared, circular dichroism and absorption spectra
A browser for expression data
MGraph: graphical models for microarray data analysis
Efficient selection of unique and popular oligos for large EST databases
Normalization of single-cell RNA-seq counts by log(x + 1) or log(1 + x)
IGG: A tool to integrate GeneChips for genetic studies
iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps
TimiRGeN: R/Bioconductor package for time series microRNA-mRNA integration and analysis
Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile
Machine learning empowers phosphoproteome prediction in cancers
A simple method of avoiding the computational problems of the delta method for the end-user of statistical packages
Locality-preserving minimal perfect hashing of k -mers
The effects of probe binding affinity differences on gene expression measurements and how to deal with them
MUFFIN: multi-scale feature fusion for drug-drug interaction prediction
iDNA-ABT: advanced deep learning model for detecting DNA methylation with adaptive features and transductive information maximization
ONETOOL for the analysis of family-based big data
Comment on "network-constrained regularization and variable selection for analysis of genomic data"
info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling
Evolutionary conservation of Ebola virus proteins predicts important functions at residue level
AUC-based biomarker ensemble with an application on gene scores predicting low bone mineral density
PromFD 1.0: a computer program that predicts eukaryotic pol II promoters using strings and IMD matrices
Structural feature-driven pattern analysis for multitarget modulator landscapes
RADIS: analysis of RAD -seq data for interspecific phylogeny
TPpred-ATMV: therapeutic peptide prediction by adaptive multi-view tensor learning model
slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array
FlexLMM: a Nextflow linear mixed model framework for GWAS
A gene-based test of association using canonical correlation analysis
COPYCAT : cophylogenetic analysis tool
PIBASE: a comprehensive database of structurally defined protein interfaces
springD2A: capturing uncertainty in disease-drug association prediction with model integration
Enhanced recognition of protein transmembrane domains with prediction-based structural profiles
A fast fiducial marker tracking model for fully automatic alignment in electron tomography
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Network-based regulatory pathways analysis
PAL: an object-oriented programming library for molecular evolution and phylogenetics
TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds
Visualizing metabolic activity on a genome-wide scale
SteadyCellPhenotype : a web-based tool for the modeling of biological networks with ternary logic
Jane: suggesting journals, finding experts
Seed2LP: seed inference in metabolic networks for reverse ecology applications
Statistical Design of Reverse Dye Microarrays
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
transferGWAS: GWAS of images using deep transfer learning
BioContainers: an open-source and community-driven framework for software standardization
Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm
Logic Forest: an ensemble classifier for discovering logical combinations of binary markers
CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms
Minimum conflict: a divide-and-conquer approach to phylogeny estimation
Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon
ClustalW-MPI: ClustalW analysis using distributed and parallel computing
Effects of choice of DNA sequence model structure on gene identification accuracy
spicyR: spatial analysis of in situ cytometry data in R
NGLview-interactive molecular graphics for Jupyter notebooks
Goldilocks: a tool for identifying genomic regions that are 'just right'
Eagle: multi-locus association mapping on a genome-wide scale made routine
A hierarchical unsupervised growing neural network for clustering gene expression patterns
GRR: graphical representation of relationship errors
Genetic Network Analyzer: qualitative simulation of genetic regulatory networks
Locating probable genes using Fourier transform approach
Local Disordered Region Sampling (LDRS) for ensemble modeling of proteins with experimentally undetermined or low confidence prediction segments
RNAblueprint: flexible multiple target nucleic acid sequence design
Exploring the functional landscape of gene expression: directed search of large microarray compendia
Mapping SNPs to protein sequence and structure data
High-dimensional pharmacogenetic prediction of a continuous trait using machine learning techniques with application to warfarin dose prediction in African Americans
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors
Physical mapping with automatic capture of hybridization data
SplicePlot: a utility for visualizing splicing quantitative trait loci
TeXshade: shading and labeling of multiple sequence alignments using LaTeX2e
KiT: a MATLAB package for kinetochore tracking
LightBBB: computational prediction model of blood-brain-barrier penetration based on LightGBM
Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data
Identifying novel constrained elements by exploiting biased substitution patterns
Small RNAs in angiosperms: sequence characteristics, distribution and generation
DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models
Batch-normalization of cerebellar and medulloblastoma gene expression datasets utilizing empirically defined negative control genes
MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples
A comparative phylogenetic approach for dating whole genome duplication events
SNP discovery using advanced algorithms and neural networks
Characterizing dye bias in microarray experiments
KGVDB: a population-based genomic map of CNVs tagged by SNPs in Koreans
A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription
FuncBase : a resource for quantitative gene function annotation
MeSH Up: effective MeSH text classification for improved document retrieval
Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices
PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs
compcodeR - an R package for benchmarking differential expression methods for RNA-seq data
CIndex: compressed indexes for fast retrieval of FASTQ files
ProbeSelect: selecting differentially expressed probes in transcriptional profile data
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure
A parsimonious tree-grow method for haplotype inference
Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model
Stochastic dynamics of genetic networks: modelling and parameter identification
survex: an R package for explaining machine learning survival models
LaTcOm: a web server for visualizing rare codon clusters in coding sequences
C-InterSecture - a computational tool for interspecies comparison of genome architecture
Protein fold recognition using geometric kernel data fusion
Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index
Deleterious SNP prediction: be mindful of your training data!
Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes
SeqMap: mapping massive amount of oligonucleotides to the genome
Amino acid similarity matrices based on force fields
Organoid model of mammographic density displays a higher frequency of aberrant colony formations with radiation exposure
RVINN: a flexible modeling for inferring dynamic transcriptional and post-transcriptional regulation using physics-informed neural networks
An examination of citation-based impact of the computational biology conferences
Outlier detection for multi-network data
Crypt4GH: a file format standard enabling native access to encrypted data
Genome mining for anti-CRISPR operons using machine learning
Uncover disease genes by maximizing information flow in the phenome-interactome network
Support vector machine approach for protein subcellular localization prediction
Melodia: a Python library for protein structure analysis
Genome wide identification and classification of alternative splicing based on EST data
wEMBOSS: a web interface for EMBOSS
State of the art prediction of HIV-1 protease cleavage sites
Retraction of: Overcoming the inadaptability of sparse group lasso for data with various group structures by stacking
Cross-scale, cross-pathway evaluation using an agent-based non-small cell lung cancer model
HLA predictions from the bronchoalveolar lavage fluid and blood samples of eight COVID-19 patients at the pandemic onset
Integrating proteomic or transcriptomic data into metabolic models using linear bound flux balance analysis
Shouji: a fast and efficient pre-alignment filter for sequence alignment
mCSM-AB2: guiding rational antibody design using graph-based signatures
A statistical approach for inferring the 3D structure of the genome
DNA binding sites: representation and discovery
An algorithm for simultaneous comparison of several sequences
A mixture model approach to the tests of concordance and discordance between two large-scale experiments with two-sample groups
Database for aqueous solubility of nonelectrolytes
Computer graphics as a tool in cytogenetic research and education
ESTminer: a Web interface for mining EST contig and cluster databases
Reconstructing protein networks of epithelial differentiation from histological sections
A span-graph neural model for overlapping entity relation extraction in biomedical texts
SCALCE: boosting sequence compression algorithms using locally consistent encoding
Foldclass and Merizo-search: scalable structural similarity search for single- and multi-domain proteins using geometric learning
Implementations of BLAST for parallel computers
AGC: compact representation of assembled genomes with fast queries and updates
PROLANG: an expandable software in protein chemistry
ABACAS: algorithm-based automatic contiguation of assembled sequences
Classification of ncRNAs using position and size information in deep sequencing data
Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes
PRESM: personalized reference editor for somatic mutation discovery in cancer genomics
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha
A novel approach for clustering proteomics data using Bayesian fast Fourier transform
RawHummus: an R Shiny app for automated raw data quality control in metabolomics
PASSML: combining evolutionary inference and protein secondary structure prediction
AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes
cMapper: gene-centric connectivity mapper for EBI-RDF platform
Matrix algebra routines for the Acorn Archimedes microcomputer: example applications
W2H: WWW interface to the GCG sequence analysis package
Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting
Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank
AluHunter : a database of potentially polymorphic Alu insertions for use in primate phylogeny and population genetics
MDEHT: a multivariate approach for detecting differential expression of microRNA isoform data in RNA-sequencing studies
MetaRank: a rank conversion scheme for comparative analysis of microbial community compositions
PhyloGena - a user-friendly system for automated phylogenetic annotation of unknown sequences
An efficient algorithm for the blocked pattern matching problem
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios
Bayesian models based on test statistics for multiple hypothesis testing problems
Cypiripi: exact genotyping of CYP2D6 using high-throughput sequencing data
MetaboDiff: an R package for differential metabolomic analysis
GenomeScope: fast reference-free genome profiling from short reads
SIGSEQ: a computer program for predicting signal sequence cleavage sites
GoSh: a web-based database for goat and sheep EST sequences
OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets
PAGE: phase-shifted analysis of gene expression
SEBINI: Software Environment for BIological Network Inference
Maximum significance clustering of oligonucleotide microarrays
Database verification studies of SWISS-PROT and GenBank
DeepZF: improved DNA-binding prediction of C2H2-zinc-finger proteins by deep transfer learning
CART variance stabilization and regularization for high-throughput genomic data
Automat and BLAST: comparison of two protein sequence similarity search programs
CausalR: extracting mechanistic sense from genome scale data
Biophysical annotation and representation of CellML models
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
ASSIsT: an automatic SNP scoring tool for in- and outbreeding species
NeuroPedia: neuropeptide database and spectral library
A convolutional neural network and graph convolutional network-based method for predicting the classification of anatomical therapeutic chemicals
PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum
ImpulseDE: detection of differentially expressed genes in time series data using impulse models
MACGT: multi-dimensional automated clustering genotyping tool for analysis of microarray-based mini-sequencing data
A computer system for analysis and integrated description of regulation of the molecular-genetic system of interferon induction and action
MTBindingSim: simulate protein binding to microtubules
FindGeo: a tool for determining metal coordination geometry
Intensity drift removal in LC/MS metabolomics by common variance compensation
Automatic biomarker discovery and enrichment with BRAD
LASSAP, a LArge Scale Sequence compArison Package
popSTR: population-scale detection of STR variants
Prioritizing hypothesis tests for high throughput data
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Identifying functionally informative evolutionary sequence profiles
Biobox: a toolbox for biomolecular modelling
MS1Connect: a mass spectrometry run similarity measure
StonPy: a tool to parse and query collections of SBGN maps in a graph database
Neural networks with circular filters enable data efficient inference of sequence motifs
Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins
Methylartist: tools for visualizing modified bases from nanopore sequence data
unCOVERApp: an interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Mistle: bringing spectral library predictions to metaproteomics with an efficient search index
QuantumClone: clonal assessment of functional mutations in cancer based on a genotype-aware method for clonal reconstruction
Rapid alignment-free phylogenetic identification of metagenomic sequences
QAlign: aligning nanopore reads accurately using current-level modeling
Tricross : using dot-plots in sequence-id space to detect uncataloged intergenic features
LibSBMLSim: a reference implementation of fully functional SBML simulator
CRPMKB: a knowledge base of cancer risk prediction models for systematic comparison and personalized applications
HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer
Protein Refinement: A New Challenge For Casp In Its 10th Anniversary
Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project
HEROD: a human ethnic and regional specific omics database
Integrated Genome Browser App Store
EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction
Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
scWMC: weighted matrix completion-based imputation of scRNA-seq data via prior subspace information
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences
Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data
JESAM: CORBA software components to create and publish EST alignments and clusters
NuST: analysis of the interplay between nucleoid organization and gene expression
MEGADOCK 4.0: an ultra-high-performance protein-protein docking software for heterogeneous supercomputers
Locality-aware pooling enhances protein language model performance across varied applications
The Terabase Search Engine: a large-scale relational database of short-read sequences
GeConT: gene context analysis
NEMO: cancer subtyping by integration of partial multi-omic data
MixingDTA: improved drug-target affinity prediction by extending mixup with guilt-by-association
LRSSL: predict and interpret drug-disease associations based on data integration using sparse subspace learning
IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution
BRISK - research-oriented storage kit for biology-related data
Bio2Rxn: sequence-based enzymatic reaction predictions by a consensus strategy
Unsupervised detection of genes of influence in lung cancer using biological networks
ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats
MCO: towards an ontology and unified vocabulary for a framework-based annotation of microbial growth conditions
Normalization of single-channel DNA array data by principal component analysis
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology
scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization
MULTOVL: fast multiple overlaps of genomic regions
Constructing gene models from accurately predicted exons: an application of dynamic programming
TSPTFBS: a Docker image for trans-species prediction of transcription factor binding sites in plants
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population
Fold recognition by combining profile-profile alignment and support vector machine
A fast, stochastic threading algorithm for proteins
cgmisc: enhanced genome-wide association analyses and visualization
GLIDER: function prediction from GLIDE-based neighborhoods
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective
A novel estimator of the interaction matrix in Graphical Gaussian Model of omics data using the entropy of non-equilibrium systems
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins
Redundancy-weighting the PDB for detailed secondary structure prediction using deep-learning models
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information
Maximal conditional chi-square importance in random forests
SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data
The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework
Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets
Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data
scds: computational annotation of doublets in single-cell RNA sequencing data
Updating the 97% identity threshold for 16S ribosomal RNA OTUs
PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data
A user-oriented web crawler for selectively acquiring online content in e-health research
GC-Profile 2.0: an extended web server for the prediction and visualization of CpG islands
PanGPCR: predictions for multiple targets, repurposing and side effects
A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes
SALIGN: a web server for alignment of multiple protein sequences and structures
SVM based method for predicting HLA-DRB1 * 0401 binding peptides in an antigen sequence
GARSA: genomic analysis resources for sequence annotation
Modeling associations between genetic markers using Bayesian networks
SomaticSignatures: inferring mutational signatures from single-nucleotide variants
DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm
SynBioSS: the synthetic biology modeling suite
Network-guided regression for detecting associations between DNA methylation and gene expression
Exploiting deep transfer learning for the prediction of functional non-coding variants using genomic sequence
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
PROTRIDER: protein abundance outlier detection from mass spectrometry-based proteomics data with a conditional autoencoder
Multi-objective pairwise RNA sequence alignment
Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset
A new method to measure the semantic similarity of GO terms
GuidePro: a multi-source ensemble predictor for prioritizing sgRNAs in CRISPR/Cas9 protein knockouts
Image and volume data rotation with 1- and 3-pass algorithms
A fast and memory efficient MLCS algorithm by character merging for DNA sequences alignment
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences
Scale-space measures for graph topology link protein network architecture to function
Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology
ESTminer: a suite of programs for gene and allele identification
VistaClara: an expression browser plug-in for Cytoscape
PCSB-a program collection for structural biology and biophysical chemistry
A simple method for sizing large fragments of bacterial DNA separated by PFGE
Mutalyzer 2: next generation HGVS nomenclature checker