yusuke1997/dblp-id-title huggingface dataset:
IMGT, the international ImMunoGeneTics information system ®
DOMMINO: a database of macromolecular interactions
The Lipase Engineering Database: a navigation and analysis tool for protein families
AHMII: Agent to Help Microbial Information Integration
Quantitative characterization of the interaction between purified human estrogen receptor and DNA using fluorescence anisotropy
The Structure-Function Linkage Database
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways
IXDB, an X chromosome integrated database (update)
TiProD: the Tissue-specific Promoter Database
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
IBWS: IST Bioinformatics Web Services
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis
DDBJ progress report: a new submission system for leading to a correct annotation
ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
DePIE: Designing Primers for Protein Interaction Experiments
RTPrimerDB: the real-time PCR primer and probe database, major update 2006
probeBase - an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016
Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2)
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
HmtVar: a new resource for human mitochondrial variations and pathogenicity data
TRANSFAC ® and its module TRANSCompel ® : transcriptional gene regulation in eukaryotes
PubServer: literature searches by homology
VADAR: a web server for quantitative evaluation of protein structure quality
The Arabidopsis Information Resource (TAIR): gene structure and function annotation
A circular dichroism study of the structure of Penicillium chrysogenum mycovirus
RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli
PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning
DSP: a protein shape string and its profile prediction server
EndoNet: an information resource about regulatory networks of cell-to-cell communication
InterMine: extensive web services for modern biology
L1Base: from functional annotation to prediction of active LINE-1 elements
STRING: a database of predicted functional associations between proteins
Physical interference between escherichia coli RNA polymerase molecules transcribing in tandem enhances abortive synthesis and misincorporation
BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'- G(G/T)GC(A/C)C-3'
SCOPe: Structural Classification of Proteins - extended, integrating SCOP and ASTRAL data and classification of new structures
miRmap web: comprehensive microRNA target prediction online
KGB: a single buffer for all restriction endonucleases
The National Center for Biotechnology Information's Protein Clusters Database
COMAP: a comigrating analysis program for estimating the relationship of adenoviruses on the genome level
PhaSePro: the database of proteins driving liquid?liquid phase separation
Expression Atlas update: gene and protein expression in multiple species
The Pancreatic Expression database: 2011 update
Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning
Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
miRDB: an online database for prediction of functional microRNA targets
TCRD and Pharos 2021: mining the human proteome for disease biology
A system in mouse liver for the repair of O6-methylguanine lesions in methylated DNA
SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments
Transcription of the 'non-transcribed' spacer of Drosophila melanogaster rDNA
Characterization of a protein binding sequence in the promoter region of the 16S rRNA gene of the spinach chloroplast genome
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
Nuclear factor-I and activator protein-2 bind in a mutually exclusive way to overlapping promoter sequences and trans-activate the human growth hormone gene
Plasmo GEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites
A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae
Nucleotide sequence of the ilvB multivalent attenuator region of Escherichia coli K12
MFEprimer-3.0: quality control for PCR primers
The Database of Genomic Variants: a curated collection of structural variation in the human genome
Two forms of transcription factor TFIIIC in extracts from HeLa cells
CalFitter: a web server for analysis of protein thermal denaturation data
SyntDB: defining orthologues of human long noncoding RNAs across primates
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features
The phosphate clamp: a small and independent motif for nucleic acid backbone recognition
RiceWiki: a wiki-based database for community curation of rice genes
GenoList: an integrated environment for comparative analysis of microbial genomes
PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites
Constructing DNA by polymerase recombination
ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation
Gene3D: expanding the utility of domain assignments
SMART: identification and annotation of domains from signalling and extracellular protein sequences
Content discovery and retrieval services at the European Nucleotide Archive
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
GenDecoder: genetic code prediction for metazoan mitochondria
The PSSH database of alignments between protein sequences and tertiary structures
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks
SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations
BiForce Toolbox: powerful high-throughput computational analysis of gene-gene interactions in genome-wide association studies
GREAT: a web portal for Genome Regulatory Architecture Tools
Molecular cloning of a cDNA of a camptothecin-resistant human DNA topoisomerase I and identification of mutation sites
IntAct - open source resource for molecular interaction data
Automated preparation of DNA sequences for publication
antiSMASH 4.0 - improvements in chemistry prediction and gene cluster boundary identification
miROrtho: computational survey of microRNA genes
Doc2Hpo: a web application for efficient and accurate HPO concept curation
RY repeats are conserved in the 5'-flanking regions of legume seed- protein genes
GDA, a web-based tool for Genomics and Drugs integrated analysis
TMBETA-NET: discrimination and prediction of membrane spanning ß-strands in outer membrane proteins
LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system
DNA containing the base analogue 2-aminoadenine: preparation, use as hybridization probes and cleavage by restriction endonucleases
LinkProt: a database collecting information about biological links
GPCR-SSFE 2.0 - a fragment-based molecular modeling web tool for Class A G-protein coupled receptors
Interruption of a human nuclear sequence homologous to mitochondrial DNA by a member of the KpnI 1.8 kb family
Compilation of tRNA sequences and sequences of tRNA genes
REBASE--restriction enzymes and methylases
SeMPI: a genome-based secondary metabolite prediction and identification web server
SDM: a server for predicting effects of mutations on protein stability
In vitro DNA dependent synthesis of globin RNA sequences from erythroleukemic cell chromatin
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants
Isolation of cDNA clones using yeast artificial chromosome probes
The SWISS-PROT protein sequence data bank and its new supplement TREMBL
Structure and expression of the gene coding for the alpha-subunit of DNA-dependent RNA polymerase from the chloroplast genome of Zea mays
PeroxiBase: a database with new tools for peroxidase family classification
mirnaQC: a webserver for comparative quality control of miRNA-seq data
GSA-SNP: a general approach for gene set analysis of polymorphisms
MRPrimerV: a database of PCR primers for RNA virus detection
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
The EMBL-EBI search and sequence analysis tools APIs in 2019
The transcription termination region between two convergently- transcribed photoregulated operons in the maize plastid chromosome contains rps14, trnR (UCU) and a putative trnfM pseudogene
MODBASE, a database of annotated comparative protein structure models and associated resources
Sfold web server for statistical folding and rational design of nucleic acids
EMMA - mouse mutant resources for the international scientific community
SABIO-RK: an updated resource for manually curated biochemical reaction kinetics
The microRNA.org resource: targets and expression
The viroid and viroid-like RNA database
Primer-dependent synthesis by poliovirus RNA-dependent RNA polymerase (3Dpol)
Super Natural II - a database of natural products
CovalentInDB: a comprehensive database facilitating the discovery of covalent inhibitors
DigSee: disease gene search engine with evidence sentences (version cancer)
BioMe: biologically relevant metals
COLORADO3D, a web server for the visual analysis of protein structures
Aquaculture Molecular Breeding Platform (AMBP): a comprehensive web server for genotype imputation and genetic analysis in aquaculture
Nuclear Receptor Signaling Atlas (www.nursa.org): hyperlinking the nuclear receptor signaling community
DDGun: an untrained predictor of protein stability changes upon amino acid variants
scAPAdb: a comprehensive database of alternative polyadenylation at single-cell resolution
MoonProt 2.0: an expansion and update of the moonlighting proteins database
NIASGBdb: NIAS Genebank databases for genetic resources and plant disease information
5' Terminal noncoding sequence heterogeneity in reovirus mRNA
UniProt: the universal protein knowledgebase
The Molecular Biology Database Collection: 2007 update
SANSparallel: interactive homology search against Uniprot
NBBC: a non-B DNA burden explorer in cancer
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
DINAMelt web server for nucleic acid melting prediction
Major oxidative products of cytosine, 5-hydroxycytosine and 5- hydroxyuracil, exhibit sequence context-dependent mispairing in vitro
Cap ribose methylation of c-mos mRNA stimulates translation and oocyte maturation in Xenopus laevis
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules
The Protein Data Bank and structural genomics
iMOT: an interactive package for the selection of spatially interacting motifs
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY
Integrated interactions database: tissue-specific view of the human and model organism interactomes
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
TarO: a target optimisation system for structural biology
Sequence and properties of the message encoding Tetrahymena hv1, a highly evolutionarily conserved histone H2A variant that is associated with active genes
Protein-chemical evidence for the signal sequence of the pro-ompA protein
Direct calculation of the sizes of DNA fragments separated by gel electrophoresis using programmes written for a pocket calculator
Heterogeneity of interferon mRNA species from Sendai virus-induced human lymphoblastoid (Namalva) cells and Newcastle disease virus- induced murine fibroblastoid (L) cells
CKAAPs DB: a Conserved Key Amino Acid Positions DataBase
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures
Intrastrand cross-links are not formed in the reaction between transplatin and native DNA: relation with the clinical inefficiency of transplatin
VKCDB: voltage-gated K + channel database updated and upgraded
Animal-eRNAdb: a comprehensive animal enhancer RNA database
The Mitochondrial Protein Import Machinery of Plants (MPIMP) database
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
Conserved unique peptide patterns (CUPP) online platform: peptide-based functional annotation of carbohydrate active enzymes
Human Protein Reference Database - 2009 update
Gene Expression Atlas update - a value-added database of microarray and sequencing-based functional genomics experiments
META-PP: single interface to crucial prediction servers
SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design
Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues
GeNMR: a web server for rapid NMR-based protein structure determination
RNALocate: a resource for RNA subcellular localizations
The Organelle Genome Database Project (GOBASE)
DNA traffic - a new database for systems biology of DNA dynamics during the cell life
VectorBase: a home for invertebrate vectors of human pathogens
MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins
Analysis of two human pre-ribosomal factors, bystin and hTsr1, highlights differences in evolution of ribosome biogenesis between yeast and mammals
Template-directed photoligation of oligodeoxyribonucleotides via 4- thiothymidine
NAR Breakthrough Article: dbMAE: the database of autosomal monoallelic expression
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
Nucleotide sequences of the chloroplast psbA and trnH genes from cotton Gossypium hirsutum
The ends of a large RNA molecule are necessarily close
Voronoia: analyzing packing in protein structures
SCANMOT: searching for similar sequences using a simultaneous scan of multiple sequence motifs
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
The human Pat1b protein: a novel mRNA deadenylation factor identified by a new immunoprecipitation technique
SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny
DSMM: a Database of Simulated Molecular Motions
Cloning of bovine growth hormone gene and its expression in bacteria
The XRCC2 DNA repair gene from human and mouse encodes a novel member of the recA/RAD51 family
Oviz-Bio: a web-based platform for interactive cancer genomics data visualization
The chromosome 2 breakpoint in Burkitt lymphoma Ly66 lies between VK and JK
Preselector.uni-jena.de: optimize your cloning - a resource for identifying restriction enzymes for preselection reactions
The MPI Bioinformatics Toolkit for protein sequence analysis
ICB database: the gyrB database for identification and classification of bacteria
Software and database for the analysis of mutations in the VHL gene
geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data
Geneshot: search engine for ranking genes from arbitrary text queries
InSatDb: a microsatellite database of fully sequenced insect genomes
QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database
Heterology of mitochondrial DNA from mammals detected by electron microscopic heteroduplex analyses
Chromosome-bound mitotic factors: release by endonucleases
RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis
StemMapper: a curated gene expression database for stem cell lineage analysis
SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences
PDBselect 1992-2009 and PDBfilter-select
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints
iCSDB: an integrated database of CRISPR screens
BRENDA, the enzyme information system in 2011
Regional assignment of Y-linked DNA probes by deletion mapping and their homology with X-chromosome and autosomal sequences
TC3A: The Cancer 3′ UTR Atlas
SGMD: the Soybean Genomics and Microarray Database
CR-EST: a resource for crop ESTs
VirusMentha: a new resource for virus-host protein interactions
The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
ASGS: an alternative splicing graph web service
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser
Voronoia4RNA - a database of atomic packing densities of RNA structures and their complexes
Reverse crosstalk of TGFβ and PPARβ/δ signaling identified by transcriptional profiling
The Molecular Biology Database Collection: an online compilation of relevant database resources
The MTX package of computer programmes for the comparison of sequences of nucleotides and amino acid residues
REBASE: restriction enzymes and methyltransferases
MonarchBase: the monarch butterfly genome database
Site specific endonuclease from Fusobacterium nucleatum
CandidaDB: a multi-genome database for Candida species and related Saccharomycotina
EcoCyc: a comprehensive database resource for Escherichia coli
MeT-DB: a database of transcriptome methylation in mammalian cells
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
Specific termination of in vitro transcription by calf thymus RNA polymerase III
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
SDAP: database and computational tools for allergenic proteins
Ensembl's 10th year
DMAPS: a database of multiple alignments for protein structures
Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins
MobiDB: intrinsically disordered proteins in 2021
PaeExo IX: a unique deoxyribonuclease from Pseudomonas aeruginosa active in the presence of EDTA
Software and database for the analysis of mutations in the human LDL receptor gene
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data
deepBase: a database for deeply annotating and mining deep sequencing data
Overlapping of MINK and CHRNE gene loci in the course of mammalian evolution
Silencer binding proteins function on multiple cis-elements in the glutathione transferase P gene
The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching
Variable transfer of Y-specific sequences in XX males
SCENERY: a web application for (causal) network reconstruction from cytometry data
SCOP: a Structural Classification of Proteins database
A high throughput screening for rarely transcribed differentially expressed genes
MAK, a computational tool kit for automated MITE analysis
Reactome: a knowledgebase of biological pathways
The GENETPIG database: a tool for comparative mapping in pig (Sus scrofa)
Spermine inhibition of the 2, 5-diaziridinyl-1, 4-benzoquinone (DZQ) crosslinking reaction with DNA duplexes containing poly(purine). poly(pyrimidine) tracts
Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes
In situ hybridization with oligonucleotides: a simplified method to detect Drosophila transcripts
GWAS Central: a comprehensive resource for the discovery and comparison of genotype and phenotype data from genome-wide association studies
DIAL: a web-based server for the automatic identification of structural domains in proteins
Transcription of single base oligonucleotides by ribonucleic acid- directed deoxyribonucleic acid polymerase
The different intron 2 species excised in vivo from the E2A premRNA of adenovirus-2: an approach to analyse alternative splicing
In vitro cleavage of double- and single-stranded DNA by plasmid RSF1010- encoded mobilization proteins
Nucleotide sequence of a mouse tRNALeu gene
A human T24 Ha-ras cassette suitable for expression studies in eukaryotic cells
NeuroPID: a classifier of neuropeptide precursors
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates
COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
Footprinting, circular dichroism and UV melting studies on neomycin B binding to the packaging region of human immunodeficiency virus type-1 RNA
PRINTS and PRINTS-S shed light on protein ancestry
PhosPhAt : a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor
The Gene Ontology resource: enriching a GOld mine
Database of mutations within the adenovirus 5 E1A oncogene
MatrisomeDB: the ECM-protein knowledge database
YIDB: the Yeast Intron DataBase
Homology in accessory proteins of replicative polymerases--E. coli to humans
Ribocentre: a database of ribozymes
SH2db, an information system for the SH2 domain
MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS
Database resources of the National Center for Biotechnology Information: 2002 update
Databases and software for the analysis of mutations in the human p53 gene, human hprt gene and both the lacI and lacZ gene in transgenic rodents
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
DiANNA: a web server for disulfide connectivity prediction
CleanEx: new data extraction and merging tools based on MeSH term annotation
The MAR databases: development and implementation of databases specific for marine metagenomics
Distinct subfamilies of primate L1Gg retroposons, with some elements carrying tandem repeats in the 5' region
CrossLink: visualization and exploration of sequence relationships between (micro) RNAs
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models
The SWISS-MODEL Repository - new features and functionality
CCancer: a bird's eye view on gene lists reported in cancer-related studies
Interaction of the nuclear protein CBF1 with the kappaB site of the IL- 6 gene promoter
Sequence of a tRNAGly from Streptomyces coelicolor
Developmentally-regulated packaging of mitochondrial DNA by the HMG-box protein mtTFA during Xenopus oogenesis
EVAcon: a protein contact prediction evaluation service
The European Small Subunit Ribosomal RNA database
Implementation of GenePattern within the Stanford Microarray Database
FlyBase: updates to the Drosophila melanogaster knowledge base
iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2
Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families
Pathguide: a Pathway Resource List
SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes
JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles