yusuke1997/dblp-id-title huggingface dataset:
The restriction enzyme BanI is inhibited by dcm-methylation of the GGCGCm5C site
PhosphoBase: a database of phosphorylation sites
Prothymosin alpha modulates the interaction of histone H1 with chromatin
SmedGD: the Schmidtea mediterranea genome database
NPDock: a web server for protein-nucleic acid docking
ProbeLynx: a tool for updating the association of microarray probes to genes
Purification to apparent homogeneity and partial amino acid sequence of rat liver O6-alkylguanine-DNA-alkyltransferase
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
DNA Data Bank of Japan dealing with large-scale data submission
Editorial: the 20th annual Nucleic Acids Research Web Server Issue 2022
The Ensembl COVID-19 resource: ongoing integration of public SARS-CoV-2 data
miRGator v2.0 : an integrated system for functional investigation of microRNAs
IGRhCellID: integrated genomic resources of human cell lines for identification
Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes
FIMM, a database of functional molecular immunology
DOUTfinder - identification of distant domain outliers using subsignificant sequence similarity
ViralORFeome: an integrated database to generate a versatile collection of viral ORFs
AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics
Pharos: Collating protein information to shed light on the druggable genome
Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases
BanI dimorphic site in the third intron of the human apolipoprotein AI gene (Apo A1)
Servers for sequence-structure relationship analysis and prediction
dictyBase update 2011: web 2.0 functionality and the initial steps towards a genome portal for the Amoebozoa
Chemical Entities of Biological Interest: an update
A computer program for the management of small cosmid banks
Apple II software for M13 shotgun DNA sequencing
COSMIC: exploring the world's knowledge of somatic mutations in human cancer
DBTMEE: a database of transcriptome in mouse early embryos
Protein folds and families: sequence and structure alignments
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services
The RNAmute web server for the mutational analysis of RNA secondary structures
TrSDB: a proteome database of transcription factors
Polyethylene glycol derivatives of base and sequence specific DNA ligands: DNA interaction and application for base specific separation of DNA fragments by gel electrophoresis
dictyBase, the model organism database for Dictyostelium discoideum
P2CS: updates of the prokaryotic two-component systems database
ProtoNet 4.0: A hierarchical classification of one million protein sequences
incaRNAfbinv: a web server for the fragment-based design of RNA sequences
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors
Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence
RepeatsDB: a database of tandem repeat protein structures
LigASite - a database of biologically relevant binding sites in proteins with known apo -structures
GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA
A novel nuclear receptor superfamily member in Xenopus that associates with RXR, and shares extensive sequence similarity to the mammalian vitamin D3 receptor
GrainGenes, the genome database for small-grain crops
M1CR0B1AL1Z3R - a user-friendly web server for the analysis of large-scale microbial genomics data
GEOexplorer: a webserver for gene expression analysis and visualisation
PLMItRNA, a database for mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
PROTCOM: searchable database of protein complexes enhanced with domain-domain structures
SDR: a database of predicted specificity-determining residues in proteins
Nucleotide sequence of the promoter region of the gene encoding chicken calbindin D28K
MaizeGDB, the community database for maize genetics and genomics
MaGenDB: a functional genomics hub for Malvaceae plants
FunSimMat update: new features for exploring functional similarity
CellWhere: graphical display of interaction networks organized on subcellular localizations
ExPASy: the proteomics server for in-depth protein knowledge and analysis
webPSN v2.0: a webserver to infer fingerprints of structural communication in biomacromolecules
AmyPro: a database of proteins with validated amyloidogenic regions
SBSPKS: structure based sequence analysis of polyketide synthases
The GDB Human Genome Database Anno 1997
Radioimmunoassays for the modified nucleosides N[9-(beta-D- ribofuranosyl)purin-6-ylcarbamoyl]-L-threonine and 2- methylthioadenosine
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
BioSamples database: FAIRer samples metadata to accelerate research data management
Low resolution models of self-assembled histone fibers from X-ray diffraction studies
MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations
The TRANSFAC system on gene expression regulation
GWIPS-viz: development of a ribo-seq genome browser
Butyrate selectively activates the metallothionein gene in teratocarcinoma cells and induces hypersensitivity to metal induction
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences
PLMItRNA, a database for higher plant mitochondrial tRNAs and tRNA genes
NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data
eSLDB: eukaryotic subcellular localization database
BioBIKE: A Web-based, programmable, integrated biological knowledge base
SSRome: an integrated database and pipelines for exploring microsatellites in all organisms
Splicing of a human endogenous retrovirus to a novel phospholipase A2 related gene
Isolation and mapping of a polymorphic DNA sequence pYNZ156 on chromosome 10 [D10S18]
Open Targets Platform: supporting systematic drug-target identification and prioritisation
SARSA: a web tool for structural alignment of RNA using a structural alphabet
The use of s-2-cyanoethyl phosphorothioate in the preparation of oligo 5'-deoxy-5'-thiothymidylates
SITEHOUND-web: a server for ligand binding site identification in protein structures
DDBJ in collaboration with mass-sequencing teams on annotation
The Molecular Biology Database Collection: 2003 update
RNA Bricks - a database of RNA 3D motifs and their interactions
mVOC: a database of microbial volatiles
PlantProm: a database of plant promoter sequences
The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice
VFDB 2022: a general classification scheme for bacterial virulence factors
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees
Transcription of the viral genome in cell lines transformed by simian virus 40. I. Mapping of virus-specific nuclear RNAs
MALISAM: a database of structurally analogous motifs in proteins
Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes
JASPAR 2020: update of the open-access database of transcription factor binding profiles
SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping
NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data
SNP2TFBS - a database of regulatory SNPs affecting predicted transcription factor binding site affinity
ProPortal: a resource for integrated systems biology of Prochlorococcus and its phage
CRISP-view: a database of functional genetic screens spanning multiple phenotypes
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
The Yeast Resource Center Public Data Repository
GENIES: gene network inference engine based on supervised analysis
Determination of methylation specificity of DsaV methyltransferase by a simple biochemical method
Database resources of the national center for biotechnology information
An anonymous genomic clone that detects a frequent RFLP adjacent to the D4S10 (G8) marker and Huntington's disease
Cloning and nucleotide sequence of the gene encoding yeast ribosomal protein YS25
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
The SALAMI protein structure search server
sORFs.org: a repository of small ORFs identified by ribosome profiling
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis
PASSer: fast and accurate prediction of protein allosteric sites
IGDB.NSCLC: integrated genomic database of non-small cell lung cancer
Cloning of two distinct copies of human phosphoribosylpyrophosphate synthetase cDNA
POPSCOMP: an automated interaction analysis of biomolecular complexes
ProteomicsDB: toward a FAIR open-source resource for life-science research
RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling
MutDB services: interactive structural analysis of mutation data
The Transporter Classification Database (TCDB): recent advances
The UCSC Archaeal Genome Browser: 2012 update
TIGRFAMs: a protein family resource for the functional identification of proteins
KEGG for integration and interpretation of large-scale molecular data sets
Plasma Proteome Database as a resource for proteomics research: 2014 update
GPCRdb in 2018: adding GPCR structure models and ligands
IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
ProTeus: identifying signatures in protein termini
TassDB: a database of alternative tandem splice sites
Improvements to a program for DNA analysis: a procedure to find homologies among many sequences
SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates
DisProt: intrinsic protein disorder annotation in 2020
SURFACE: a database of protein surface regions for functional annotation
StreptomeDB: a resource for natural compounds isolated from Streptomyces species
AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca
TOM: a web-based integrated approach for identification of candidate disease genes
Cell-type specific multiprotein complex formation over the c-fos serum response element in vivo: ternary complex formation is not required for the induction of c-fos
Detecting selection in immunoglobulin sequences
Molecular cloning of human interleukin 2 cDNA and its expression in E. coli
DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways
Data growth and its impact on the SCOP database: new developments
MINER: software for phylogenetic motif identification
A complete nucleolin cDNA sequence from Xenopus laevis
InterEvol database: exploring the structure and evolution of protein complex interfaces
CB-Dock2: improved protein-ligand blind docking by integrating cavity detection, docking and homologous template fitting
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans
StreptomeDB 3.0: an updated compendium of streptomycetes natural products
PlantGSAD: a comprehensive gene set annotation database for plant species
Different TBP-associated factors are required for mediating the stimulation of transcription in vitro by the acidic transactivator GAL- VP16 and the two nonacidic activation functions of the estrogen receptor
Nucleotide sequence encoding the membrane protein of the IBV strain 6/82
The UniProt-GO Annotation database in 2011
The InterPro protein families and domains database: 20 years on
Greglist: a database listing potential G-quadruplex regulated genes
The uRNA database
The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome
PGG .MHC: toward understanding the diversity of major histocompatibility complexes in human populations
Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1
Software and database for the analysis of mutations in the human FBN1 gene
DNA repair and sequence context affect 1O2-induced mutagenesis in bacteria
Detecting distant homology with Meta-BASIC
Assembly: a resource for assembled genomes at NCBI
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation
The BioGRID Interaction Database: 2008 update
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database
PhytoPath: an integrative resource for plant pathogen genomics
T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations
WDDD: Worm Developmental Dynamics Database
The specificity of in vitro chromatin transcription
The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata
NRSAS: Nuclear Receptor Structure Analysis Servers
SEPPA: a computational server for spatial epitope prediction of protein antigens
Bovine Genome Database: new annotation tools for a new reference genome
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data
MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks
Expression Profiler: next generation - an online platform for analysis of microarray data
The Saccharomyces Genome Database Variant Viewer
ILM: a web server for predicting RNA secondary structures with pseudoknots
MICdb: database of prokaryotic microsatellites
CATANA: an online modelling environment for proteins and nucleic acid nanostructures
The PEDANT genome database in 2005
The COG database: a tool for genome-scale analysis of protein functions and evolution
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning
dbCAN: a web resource for automated carbohydrate-active enzyme annotation
KEA3: improved kinase enrichment analysis via data integration
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations
MitoProteome: mitochondrial protein sequence database and annotation system
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
antiSMASH 3.0 - a comprehensive resource for the genome mining of biosynthetic gene clusters
T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research
PolyA_DB: a database for mammalian mRNA polyadenylation
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis
MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry
Reactome: a database of reactions, pathways and biological processes
AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors
LitSense: making sense of biomedical literature at sentence level
Chemical and enzymatic properties of bridging 5'-S-phosphorothioester linkages in DNA
Self-splicing group I introns in eukaryotic viruses
SAVoR: a server for sequencing annotation and visualization of RNA structures
The BioGRID interaction database: 2015 update
compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes
BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits
The CATH classification revisited - architectures reviewed and new ways to characterize structural divergence in superfamilies
VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA
SEVA 2.0: an update of the Standard European Vector Architecture for de-/re-construction of bacterial functionalities
TCMID: traditional Chinese medicine integrative database for herb molecular mechanism analysis
IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature
YPL.db: the Yeast Protein Localization database
PINT: Protein-protein Interactions Thermodynamic Database
ExPheWas: a platform for cis -Mendelian randomization and gene-based association scans
Compilation of 5S rRNA and 5S rRNA gene sequences
Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server
GeneSeqer add PlantGDB: gene structure prediction in plant genomes
Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
MODOMICS: a database of RNA modification pathways
The c-myc protein represses the lambda 5 and TdT initiators
miRSwitch: detecting microRNA arm shift and switch events
WikiPathways: connecting communities
STCDB: Signal Transduction Classification Database
Comparison of the sequence organization of related retrovirus-like multigene families in three evolutionarily distant rodent genomes
PlantCARE, a plant cis-acting regulatory element database
JAFA: a protein function annotation meta-server
Genes and proteins of Escherichia coli (GenProtEc)
Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes
Some simple computational methods to improve the folding of large RNAs
The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit
PatchSearch: a web server for off-target protein identification
IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids
PCR using a thermostable polymerase with 3' to 5' exonuclease activity generates blunt products suitable for direct cloning
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
RNApdbee 2.0: multifunctional tool for RNA structure annotation
VNTRDB: a bacterial variable number tandem repeat locus database
Changes in methylation pattern of albumin and alpha-fetoprotein genes in developing rat liver and neoplasia
The SWISS-PROT protein sequence data bank, recent developments
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
DDBJ dealing with mass data produced by the second generation sequencer
BAGEL2: mining for bacteriocins in genomic data
SuperSweet - a resource on natural and artificial sweetening agents
The KMDB/MutationView: a mutation database for human disease genes
The SUPERFAMILY 1.75 database in 2014: a doubling of data
MHCPEP, a database of MHC-binding peptides: update 1996
Complementation of the xeroderma pigmentosum DNA repair synthesis defect with Escherichia coli UvrABC proteins in a cell-free system
PCFamily: a web server for searching homologous protein complexes
RJunBase: a database of RNA splice junctions in human normal and cancerous tissues
The IntAct molecular interaction database in 2010
HC Forum®: a web site based on an international human cytogenetic database
Affinity adsorbents consisting of nucleic acids immobilized via bisoxirane activated polysaccharides
Ongoing and future developments at the Universal Protein Resource
Synthesis and properties of mirror-image DNA
BSubLoc: database of protein subcellular localization
PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis
Isolation and mapping of a polymorphic DNA sequence pTHH54 on chromosome 10 [D10S13]
CATH FunFHMMer web server: protein functional annotations using functional family assignments
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes
Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA
The signal recognition particle database (SRPDB)
The Human PAX6 Mutation Database
The Genome Sequence DataBase
The existence of eukaryotic ribonucleoprotein consensus sequence-type RNA-binding proteins in a prokaryote, Synechococcus 6301
MetaRef: a pan-genomic database for comparative and community microbial genomics
MultitaskProtDB: a database of multitasking proteins
VDJbase: an adaptive immune receptor genotype and haplotype database
The importance of a single G in the hairpin loop of the iron responsive element (IRE) in ferritin mRNA for structure: an NMR spectroscopy study
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse
MitBASE: a comprehensive and integrated mitochondrial DNA database
AthaMap web tools for database-assisted identification of combinatorial cis -regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana
ViRBase: a resource for virus-host ncRNA-associated interactions
Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases
MMsINC: a large-scale chemoinformatics database
Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences
Specific and cooperative binding of E. coli single-stranded DNA binding protein to mRNA
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections
GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
Genenames.org: the HGNC resources in 2023
Conserved sequences in both coding and 5' flanking regions of mammalian opal suppressor tRNA genes
Mechnetor: a web server for exploring protein mechanism and the functional context of genetic variants
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update
Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
Fragnostic: walking through protein structure space
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling