yusuke1997/dblp-id-title huggingface dataset:
SPROUTS: a database for the evaluation of protein stability upon point mutation
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
Sequence identity between an inverted repeat family of transposable elements in Drosophila and Caenorhabditis
MADNet: microarray database network web server
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants
PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees
MolAxis: a server for identification of channels in macromolecules
The Path-A metabolic pathway prediction web server
Conformational analysis of oligoarabinonucleotides. An NMR and CD study
A genetic polymorphism within the third poly(A) signal of the DHFR gene alters the polyadenylation pattern of DHFR transcripts in CHL cells
The MetaFMF website: a high quality tool for meta-analysis of FMF
Touring protein fold space with Dali/FSSP
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions
The Ribosomal Database Project (RDP)
Tox21BodyMap: a webtool to map chemical effects on the human body
Stock-based detection of protein oligomeric states in jsPISA
ViroidDB: a database of viroids and viroid-like circular RNAs
RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures
Dinucleotide repeat polymorphisms at the DXS453, DXS454 and DXS458 loci
Ligation-mediated amplification of RNA from murine erythroid cells reveals a novel class of beta globin mRNA with an extended 5'- untranslated region
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
CONREAL web server: identification and visualization of conserved transcription factor binding sites
metaTIGER: a metabolic evolution resource
pKNOT: the protein KNOT web server
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins
RNApathwaysDB - a database of RNA maturation and decay pathways
Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals
PEPPLOT, a protein secondary structure analysis program for the UWGCG sequence analysis software package
mirAct: a web tool for evaluating microRNA activity based on gene expression data
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data
PepServe: a web server for peptide analysis, clustering and visualization
FlyNet: a versatile network prioritization server for the Drosophila community
The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments
DNaseI sensitivity of the rat albumin and alpha-fetoprotein genes
iMKT: the integrative McDonald and Kreitman test
Post-translational control of the MEF2A transcriptional regulatory protein
HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection
The PSIPRED Protein Analysis Workbench: 20 years on
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms
A comparison of the DNA bending activities of the DNA binding proteins CRP and TFIID
GlyTouCan 1.0 - The international glycan structure repository
CEBS - Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data
A versatile in vivo and in vitro eukaryotic expression vector for protein engineering
SynergyFinder 2.0: visual analytics of multi-drug combination synergies
The cell cycle DB: a systems biology approach to cell cycle analysis
Amino acid misincorporation during high-level expression of mouse epidermal growth factor in Escherichia coli
E-RNAi: a web application to design optimized RNAi constructs
DNA sequence-specific adenine alkylation by the novel antitumor drug tallimustine (FCE 24517), a benzoyl nitrogen mustard derivative of distamycin
Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA
DBAli tools: mining the protein structure space
Molecular cloning of mouse cathepsin D
Isolation and mapping of a polymorphic DNA sequence pMCK2 on chromosome 10 [D10S15]
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels
PathoPlant ® : a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation
RTPrimerDB: the portal for real-time PCR primers and probes
MutDB: update on development of tools for the biochemical analysis of genetic variation
UniProt: a worldwide hub of protein knowledge
MassTRIX: mass translator into pathways
gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data
Building protein diagrams on the web with the residue-based diagram editor RbDe
Genomicus: five genome browsers for comparative genomics in eukaryota
DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts
Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation
msRepDB: a comprehensive repetitive sequence database of over 80 000 species
PromoSer: a large-scale mammalian promoter and transcription start site identification service
PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems
ChimerDB 4.0: an updated and expanded database of fusion genes
HOLLYWOOD: a comparative relational database of alternative splicing
Expediting topology data gathering for the TOPDB database
MODOMICS: a database of RNA modification pathways. 2021 update
WoLF PSORT: protein localization predictor
MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data
αCharges: partial atomic charges for AlphaFold structures in high quality
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data
OKCAM: an ontology-based, human-centered knowledgebase for cell adhesion molecules
mGene.web : a web service for accurate computational gene finding
Comparison of IR- and UV-matrix-assisted laser desorption/ionization mass spectrometry of oligodeoxynucleotides
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data
NPIDB: nucleic acid - protein interaction database
The European Nucleotide Archive in 2019
PsRobot: a web-based plant small RNA meta-analysis toolbox
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind
PRED BALB/c : a system for the prediction of peptide binding to H2 d molecules, a haplotype of the BALB/c mouse
SPIKE: a database of highly curated human signaling pathways
TarFisDock: a web server for identifying drug targets with docking approach
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years
HBVdb: a knowledge database for Hepatitis B Virus
VFDB 2019: a comparative pathogenomic platform with an interactive web interface
Identification of the template binding polypeptide in the pea chloroplast transcriptional complex
DGLinker: flexible knowledge-graph prediction of disease-gene associations
TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea
Improving the efficiency of dot-matrix similarity searches through use of an oligomer table
Isolation and mapping of a polymorphic DNA sequence pHBI59 on chromosome 11 [D11S146]
Sequence relationships between single repeat units of highly reiterated African Green monkey DNA
Genenames.org: the HGNC and VGNC resources in 2021
The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites
Rapid searches for complex patterns in biological molecules
LAHEDES: the LAGLIDADG homing endonuclease database and engineering server
The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest
Immune epitope database analysis resource (IEDB-AR)
A novel form of human polymorphism involving the hDHFR-psi 1 pseudogene identifies three RFLPs
Polymerase chain reaction mapping of yeast GAL7 mRNA polyadenylation sites demonstrates that 3' end processing in vitro faithfully reproduces the 3' ends observed in vivo
CpG methylation inhibits proenkephalin gene expression and binding of the transcription factor AP-2
SCOPe: classification of large macromolecular structures in the structural classification of proteins - extended database
GibbsCluster: unsupervised clustering and alignment of peptide sequences
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
Precise location of DNase I cutting sites in the nucleosome core determined by high resolution gel electrophoresis
STarMir: a web server for prediction of microRNA binding sites
GeneFriends: gene co-expression databases and tools for humans and model organisms
GENAS: a database system for nucleic acid sequence analysis
Priority index: database of genetic targets in immune-mediated disease
miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments
The DNA sequence of the gene (rnc) encoding ribonuclease III of Escherichia coli
Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and both the lacI and lacZ gene in transgenic rodents
Xanthusbase after five years expands to become Openmods
INTERFEROME: the database of interferon regulated genes
MBGD: microbial genome database for comparative analysis
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins
COXPRESdb: a database of coexpressed gene networks in mammals
MegaMotifBase: a database of structural motifs in protein families and superfamilies
ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules
O-GLYCBASE: a revised database of O-glycosylated proteins
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
Variation resources at UC Santa Cruz
LncRNADisease: a database for long-non-coding RNA-associated diseases
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
doRiNA: a database of RNA interactions in post-transcriptional regulation
STITCH 3: zooming in on protein-chemical interactions
CSCD2: an integrated interactional database of cancer-specific circular RNAs
Restriction and modification enzymes and their recognition sequences
A new method of representing DNA sequences which combines ease of visual analysis with machine readability
The Prostate Expression Database (PEDB): status and enhancements in 2000
MNDR v2.0: an updated resource of ncRNA-disease associations in mammals
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures
DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database
MHCPEP, a database of MHC-binding peptides: update 1997
The UCSC Genome Browser Database: 2008 update
The RING 2.0 web server for high quality residue interaction networks
GOAL: automated Gene Ontology analysis of expression profiles
RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development
PDA: a pipeline to explore and estimate polymorphism in large DNA databases
The eukaryotic linear motif resource ELM: 10 years and counting
DBTSS: database of transcription start sites, progress report 2008
Signal search analysis: a new method to localize and characterize functionally important DNA sequences
The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes
BioGPS: building your own mash-up of gene annotations and expression profiles
The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics
DNase I sensitivity of ribosomal genes in isolated nucleosome core particles
OryGenesDB: a database for rice reverse genetics
DNMIVD: DNA methylation interactive visualization database
RefSeq and LocusLink: NCBI gene-centered resources
The HGNC Database in 2008: a resource for the human genome
A new polymorphic probe on chromosome 3p: lambda LIB28-77 (D3S169E)
Thionein gene expression in Cd++-variants of the CHO cell: correlation of thionein synthesis rates with translatable mRNA levels during induction, deinduction, and superinduction
Human immunodeficiency virus type 1, human protein interaction database at NCBI
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017
Current status of the Asthma and Allergy Database
PDBe-KB: collaboratively defining the biological context of structural data
MitoDrome: a database of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion
EuPathDB: a portal to eukaryotic pathogen databases
BPS: a database of RNA base-pair structures
MethBank 3.0: a database of DNA methylomes across a variety of species
ppdb: plant promoter database version 3.0
The Histone Database: a comprehensive WWW resource for histones and histone fold-containing proteins
LinkedOmics: analyzing multi-omics data within and across 32 cancer types
Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins
The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction
Hemolytik: a database of experimentally determined hemolytic and non-hemolytic peptides
Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR)
ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection
PomBase 2015: updates to the fission yeast database
Quantification of splice variants using real-time PCR
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
An efficient program to construct restriction maps from experimental data with realistic error levels
pSTIING: a "systems" approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer
iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum
Hitch-hiking from HRAS1 to the WAGR locus with CMGT markers
canSAR: an integrated cancer public translational research and drug discovery resource
The ARKdb: genome databases for farmed and other animals
NPCDR: natural product-based drug combination and its disease-specific molecular regulation
Chemical evidence that chromatin DNA exists as 160 base pair beads interspersed with 40 base pair bridges
CEBS: a comprehensive annotated database of toxicological data
Analysis of proteins binding to the proximal promoter region of the human cytomegalovirus IE-1/2 enhancer/promoter reveals both consensus and aberrant recognition sequences for transcription factors Sp1 and CREB
Complete nucleotide sequence of the gene encoding rat cytochrome c oxidase subunit IV
MusiteDeep: a deep-learning based webserver for protein post-translational modification site prediction and visualization
MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data
denovo-db: a compendium of human de novo variants
CD-Search: protein domain annotations on the fly
MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands
Synthesis of guanosine and its derivatives from 5-amino-1-beta-D- ribofuranosyl-e-imidazolecarboxamide. IV. A new route to guanosine via cyanamide derivative
CyBase: a database of cyclic protein sequences and structures, with applications in protein discovery and engineering
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities
Characterization of a Leishmania donovani gene encoding a protein that closely resembles a type IB topoisomerase
CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra
TFBSbank: a platform to dissect the big data of protein-DNA interaction in human and model species
CeLaVi: an interactive cell lineage visualization tool
FMM: a web server for metabolic pathway reconstruction and comparative analysis
A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae
Ensembl 2016
MNDR v3.0: mammal ncRNA-disease repository with increased coverage and annotation
TcoF-DB: dragon database for human transcription co-factors and transcription factor interacting proteins
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer
NCBI Epigenomics: What's new for 2013
An improved version of the DNA methylation database (MethDB)
Large-scale production of DNA sequencing templates by microtitre format PCR
Darned in 2013: inclusion of model organisms and linking with Wikipedia
The PAH mutation analysis consortium database: update 1996
OrthoDB: the hierarchical catalog of eukaryotic orthologs
MBROLE3: improved functional enrichment of chemical compounds for metabolomics data analysis
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation
BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences
TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome
EMBL Nucleotide Sequence Database in 2006
Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis
LitCovid: an open database of COVID-19 literature
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases
FlyBase: improvements to the bibliography
Escherichia coli promoters: neural networks develop distinct descriptions in learning to search for promoters of different spacing classes
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Next station in microarray data analysis: GEPAS
dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more
DNA sequence of the site-specific recombination function cin of phage P7
NEWT, a new taxonomy portal
METAGENassist: a comprehensive web server for comparative metagenomics
Preparation of polydeoxynucleotides linked to a solid support by coupling CNBr-activated cellulose with 5'-NH2-terminated oligo and poly(pdT)'s
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins
Cloning and structural analyses of hepatitis B virus DNAs, subtype adr
CMAUP: a database of collective molecular activities of useful plants
RECON: a program for prediction of nucleosome formation potential
webPIPSA: a web server for the comparison of protein interaction properties
The online Tabloid Proteome: an annotated database of protein associations
PSORTdb - an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea
REBASE ? restriction enzymes and methylases
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
WikiPathways: capturing the full diversity of pathway knowledge
CENTDIST: discovery of co-associated factors by motif distribution
Database of p53 gene somatic mutations in human tumors and cell lines: updated compilation and future prospects
PASTA 2.0: an improved server for protein aggregation prediction
HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method
SCOP database in 2002: refinements accommodate structural genomics
CancerSplicingQTL: a database for genome-wide identification of splicing QTLs in human cancer
Dinucleotide repeat polymorphism at the human non-histone chromosomal protein HMG14 gene
GRSDB: a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences
Shotgun DNA sequencing using cloned DNase I-generated fragments
LNCipedia 5: towards a reference set of human long non-coding RNAs
Saccharomyces Genome Database: the genomics resource of budding yeast
EpilepsyGene: a genetic resource for genes and mutations related to epilepsy
LenVarDB: database of length-variant protein domains
Estimage: a webserver hub for the computation of methylation age
Saccharomyces cerevisiae exonuclease-1 plays a role in UV resistance that is distinct from nucleotide excision repair
eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity
DSSR-enhanced visualization of nucleic acid structures in Jmol
YLoc - an interpretable web server for predicting subcellular localization
Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C 2 H 2 zinc fingers and engineered zinc finger arrays
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results
Isolation of a deoxycytidylate methyl transferase capable of protecting DNA uniquely against cleavage by endonuclease R.Aqu I (isoschizomer of Ava I)
Megx.net: integrated database resource for marine ecological genomics
WebLab: a data-centric, knowledge-sharing bioinformatic platform
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context
SPD - a web-based secreted protein database
NCIR: a database of non-canonical interactions in known RNA structures
AlloSigMA 2: paving the way to designing allosteric effectors and to exploring allosteric effects of mutations
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants
The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools
The ovalbumin gene-sequence of putative control regions
Biologically-generated primer for PCR: PCR primer of unknown sequence
Orphelia: predicting genes in metagenomic sequencing reads
MEGARes: an antimicrobial resistance database for high throughput sequencing
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies
HepSEQ: International Public Health Repository for Hepatitis B
deepTools: a flexible platform for exploring deep-sequencing data
MHCPEP--a database of MHC-binding peptides: update 1995
yMGV: helping biologists with yeast microarray data mining
SPEER-SERVER: a web server for prediction of protein specificity determining sites
The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community
PGMRA: a web server for (phenotype × genotype) many-to-many relation analysis in GWAS
The ribosomal database project
PertOrg 1.0: a comprehensive resource of multilevel alterations induced in model organisms by in vivo genetic perturbation
The human DEPhOsphorylation database DEPOD: a 2015 update
yMGV: a database for visualization and data mining of published genome-wide yeast expression data