yusuke1997/dblp-id-title huggingface dataset:
The alpha/beta fold family of proteins database and the cholinesterase gene server ESTHER
FAF-Drugs: free ADME/tox filtering of compound collections
Nucleotide sequence and deduced amino acid sequence of Escherichia coli pyruvate oxidase, a lipid-activated flavoprotein
SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients
Ensembl 2007
OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes
The BioExtract Server: a web-based bioinformatic workflow platform
Assembly of overlapping DNA sequences by a program written in BASIC for 64K CP/M and MS-DOS IBM-compatible microcomputers
Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans
Phosphorylated protamines. I. Binding stoichiometry and thermal stability of complexes in DNA
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker
Quantitative analysis of specific labelled RNA'S using DNA covalently linked to diazobenzyloxymethyl-paper
The UCSC Genome Browser Database: update 2009
KBDOCK 2013: a spatial classification of 3D protein domain family interactions
E-MSD: improving data deposition and structure quality
PSC: protein surface classification
dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes
CnidBase: The Cnidarian Evolutionary Genomics Database
The presence of terminal deoxynucleotidyl transferase in the N-methyl-N- nitrosourea induced leukaemia in BDF1 mice and its effect on the accuracy of the DNA polymerases
Sequencing and expression of the rne gene of Escherichia coli
liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies
NGL Viewer: a web application for molecular visualization
The University of Minnesota Pathway Prediction System: multi-level prediction and visualization
RECODE 2003
RiceGAAS: an automated annotation system and database for rice genome sequence
GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing
ArrayExpress - a public repository for microarray gene expression data at the EBI
Nuclear magnetic resonance studies on yeast tRNAPhe. II. Assignment of the iminoproton resonances of the anticodon and T stem by means of nuclear Overhauser effect experiments at 500 MHz
InterPred: a webtool to predict chemical autofluorescence and luminescence interference
Database on the structure of small ribosomal subunit RNA
Premature termination of RNA polymerase II mediated transcription of a seed protein gene in Schizosaccharomyces pombe
2StrucCompare: a webserver for visualizing small but noteworthy differences between protein tertiary structures through interrogation of the secondary structure content
TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction
A novel and simple methodology to generate subtracted cDNA libraries
Synthesis of DNA fragments containing 5, 6-dihydrothymine, a major product of thymine gamma radiolysis
SL2: an interactive webtool for modeling of missing segments in proteins
ANISEED 2019: 4D exploration of genetic data for an extended range of tunicates
PBEQ-Solver for online visualization of electrostatic potential of biomolecules
Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods
CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology
Alkali-labile structures linked to the 5' ends of Bacillus subtilis short DNA chains
HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies
PRED-GPCR: GPCR recognition and family classification server
HMMER web server: interactive sequence similarity searching
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Sequence of the 5' end of the developmentally regulated rat P450 PB1 (P450IIC6) gene
The Sequence Read Archive
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions
I-TASSER server: new development for protein structure and function predictions
The Vienna RNA Websuite
FlyBase 2.0: the next generation
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents
SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data
Photoaffinity polyamines: sequence-specific interactions with DNA
A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage lambda
Pathbase: a database of mutant mouse pathology
HomozygosityMapper2012 - bridging the gap between homozygosity mapping and deep sequencing
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing
HCMDB: the human cancer metastasis database
NCBI GEO: archive for functional genomics data sets - 10 years on
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands
The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
Mouse Tumor Biology Database (MTB): status update and future directions
The molecular cloning of the ovine gamma-interferon cDNA using the polymerase chain reaction
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction
Nucleotide sequence of the Zymomonas mobilis alcohol dehydrogenase II gene
DrugMAP: molecular atlas and pharma-information of all drugs
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets
Two initiation sites for adenovirus 5.5S RNA
Rat uroporphyrinogen decarboxylase cDNA: nucleotide sequence and comparison to human uroporphyrinogen decarboxylase
Quantitative hybridization-arrest of mRNA in Xenopus oocytes using single-stranded complementary DNA or oligonucleotide probes
LNCipedia: a database for annotated human lncRNA transcript sequences and structures
Interaction of a limited set of proteins with different mRNAs and protection of 5'-caps against pyrophosphatase digestion in initiation complexes
The glucocorticoid receptor resource
Cloning, nucleotide sequence, and expression of the HincII restriction- modification system
A partial characterization of DNA fragments protected from nuclease degradation in histone depleted metaphase chromosomes of the Chinese hamster
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection
GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
FlyBase: genomes by the dozen
PASS2 version 4: An update to the database of structure-based sequence alignments of structural domain superfamilies
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA
ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences
Measurement of steady-state kinetic parameters for DNA unwinding by the bacteriophage T4 Dda helicase: use of peptide nucleic acids to trap single-stranded DNA products of helicase reactions
The ITS2 Database III - sequences and structures for phylogeny
iMODS: internal coordinates normal mode analysis server
PhyloCloud: an online platform for making sense of phylogenomic data
MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification
The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System - a one-stop gateway to online bioinformatics databases and software tools
ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism
CPLA 1.0: an integrated database of protein lysine acetylation
DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides
AlloMAPS: allosteric mutation analysis and polymorphism of signaling database
Amino Acid Interaction (INTAA) web server
HotPoint: hot spot prediction server for protein interfaces
The human hnRNP-M proteins: structure and relation with early heat shock-induced splicing arrest and chromosome mapping
ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another
Oestradiol-receptor complexes in subnuclear fractions of rat uterine tissue
PHI-base: the pathogen?host interactions database
POSA: a user-driven, interactive multiple protein structure alignment server
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
NEMBASE: a resource for parasitic nematode ESTs
SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks
The Centre for Modeling Human Disease Gene Trap resource
Developmental regulation of transcription factor AP-2 during Xenopus laevis embryogenesis
The Mouse Genome Database (MGD): mouse biology and model systems
BloodExpress: a database of gene expression in mouse haematopoiesis
Calculating the expected frequencies of potential secondary structure in nucleic acids as a function of stem length, loop size, base composition and nearest-neighbor frequencies
Ensembl 2002: accommodating comparative genomics
PipeAlign: a new toolkit for protein family analysis
The Microbe browser for comparative genomics
InParanoid 6: eukaryotic ortholog clusters with inparalogs
PceRBase: a database of plant competing endogenous RNA
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems
The international glycan repository GlyTouCan version 3.0
AutDB: a gene reference resource for autism research
An update of the DEF database of protein fold class predictions
RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction
The Androgen Receptor Gene Mutations Database
A rapid and sensitive assay for the detection of DNA fragmentation during early phases of apoptosis
Butylanilinouracil: a selective inhibitor of HeLa cell DNA synthesis and HeLa cell DNA polymerase alpha
miRTarBase: a database curates experimentally validated microRNA-target interactions
ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins
RMVar: an updated database of functional variants involved in RNA modifications
Mapping of a Physarum chromosomal origin of replication tightly linked to a developmentally-regulated profilin gene
PRince: a web server for structural and physicochemical analysis of Protein-RNA interface
An integrated software system for microcomputer management of recombinant DNA data
Protein annotation and modelling servers at University College London
The nucleotide sequence of a delayed early gene (31K) of frog virus 3
DNA sequence analysis on the IBM-PC
Axeldb: a Xenopus laevis database focusing on gene expression
Gene3D: Extensive prediction of globular domains in proteins
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
Influence of promoter potency on the transcriptional effects of YY1, SRF and Msx-1 in transient transfection analysis
The telomeric GGGTTA repeats of Trypanosoma brucei contain the hypermodified base J in both strands
InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data
The SYSTERS Protein Family Database in 2005
MitoP2, an integrated database on mitochondrial proteins in yeast and man
PoMaMo - a comprehensive database for potato genome data
CAMP R3 : a database on sequences, structures and signatures of antimicrobial peptides
MaizeGDB's new data types, resources and activities
The RNA helicase database
SCLD: a stem cell lineage database for the annotation of cell types and developmental lineages
gutMDisorder v2.0: a comprehensive database for dysbiosis of gut microbiota in phenotypes and interventions
Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines
GenColors-based comparative genome databases for small eukaryotic genomes
TOPDB: topology data bank of transmembrane proteins
The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies
Deletion analysis of the CAP-cAMP binding site of the Escherichia coli lactose promoter
An updated version of NPIDB includes new classifications of DNA-protein complexes and their families
GOBASE - a database of organelle and bacterial genome information
The UCSC genome browser database: update 2007
The Rice Annotation Project Database (RAP-DB): 2008 update
ABC portal: a single-cell database and web server for blood cells
Identification of nuclear factor delta EF1 and its binding site essential for lens-specific activity of the delta 1-crystallin enhancer
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible
CRSD: a comprehensive web server for composite regulatory signature discovery
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies
BRepertoire: a user-friendly web server for analysing antibody repertoire data
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods
PubCrawler: keeping up comfortably with PubMed and GenBank
mirTrans: a resource of transcriptional regulation on microRNAs for human cell lines
Human Ageing Genomic Resources: new and updated databases
UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity
LOMETS2: improved meta-threading server for fold-recognition and structure-based function annotation for distant-homology proteins
RACE : Remote Analysis Computation for gene Expression data
GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data
tRNAviz: explore and visualize tRNA sequence features
MTR-Viewer: identifying regions within genes under purifying selection
Terminal labeling and addition of homopolymer tracts to duplex DNA fragments by terminal deoxynucleotidyl transferase
Motif Enrichment Tool
KLIFS: a structural kinase-ligand interaction database
VARIDT 1.0: variability of drug transporter database
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more
The EMBL Nucleotide Sequence Database
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
PlantGSEA: a gene set enrichment analysis toolkit for plant community
CircadiOmics: circadian omic web portal
DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies
PosMed: ranking genes and bioresources based on Semantic Web Association Study
WormQTL - public archive and analysis web portal for natural variation data in Caenorhabditis spp
SSEP: secondary structural elements of proteins
ChemMine tools: an online service for analyzing and clustering small molecules
The Drosophila PROS-29 gene is a new member of the PROS-gene family
Increased level of prolactin gene sequences in bromodeoxyuridine treated GH cells
DBD: a transcription factor prediction database
Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
BIOZON: a hub of heterogeneous biological data
PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
The Comparative Toxicogenomics Database: update 2017
Molecular Probe Data Base: a database on synthetic oligonucleotides
Removal of RNase activity from DNase by affinity chromatography on agarose coupled aminophenylphosphoryl-uridine-2' (3')-phosphate
Protegen: a web-based protective antigen database and analysis system
HMDB: the Human Metabolome Database
BacDive - the Bacterial Diversity Metadatabase
Stability of G, A triple helices
CyBase: a database of cyclic protein sequence and structure
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
Updates in Rhea - an expert curated resource of biochemical reactions
The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge
SUBA: the Arabidopsis Subcellular Database
The RNA modification database, RNAMDB: 2011 update
SubtiList: the reference database for the Bacillus subtilis genome
GELYSIS: Pascal-implemented analysis of one-dimensional electrophoresis gels
QA-RecombineIt: a server for quality assessment and recombination of protein models
ODB: a database of operons accumulating known operons across multiple genomes
MRPrimerW: a tool for rapid design of valid high-quality primers for multiple target qPCR experiments
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline
PubChem BioAssay: 2014 update
GeneHub-GEPIS: digital expression profiling for normal and cancer tissues based on an integrated gene database
PrankWeb: a web server for ligand binding site prediction and visualization
A comprehensive set of sequence analysis programs for the VAX
sgTarget: a target selection resource for structural genomics
Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies
enviPath - The environmental contaminant biotransformation pathway resource
Analysis of the occurrence of promoter-sites in DNA
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes
The HIV positive selection mutation database
Cooperative binding of fluorescein-labeled clupeine by DNA
ThermoMutDB: a thermodynamic database for missense mutations
DNA Data Bank of Japan at work on genome sequence data
miRNet - dissecting miRNA-target interactions and functional associations through network-based visual analysis
MouseBook: an integrated portal of mouse resources
minepath.org: a free interactive pathway analysis web server
A sensitive, single-tube assay to measure the enzymatic activities of influenza RNA polymerase and other poly(A) polymerases: application to kinetic and inhibitor analysis
Sequence of the mitochondrial oli2 gene coding for subunit 6 of the mitochondrial ATPase complex in different strains of Saccharomyces
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
Anthranilate synthase component II from Hansenula polymorpha
Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelixAla variants
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association
PathBLAST: a tool for alignment of protein interaction networks
BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands
The PROSITE database
RaftProt: mammalian lipid raft proteome database
Hembase: browser and genome portal for hematology and erythroid biology
ENCODE whole-genome data in the UCSC genome browser (2011 update)
GlobPlot: exploring protein sequences for globularity and disorder
miRBase: from microRNA sequences to function
The Encyclopedia of Proteome Dynamics: a big data ecosystem for (prote)omics
fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies
SuperNatural 3.0 - a database of natural products and natural product-based derivatives
The COG database: new developments in phylogenetic classification of proteins from complete genomes
GeneGenie: optimized oligomer design for directed evolution
AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures
YM500: a small RNA sequencing (smRNA-seq) database for microRNA research
DoBISCUIT: a database of secondary metabolite biosynthetic gene clusters
An archaebacterial RNA polymerase binding site and transcription initiation of the hisA gene in Methanococcus vannielii
Drosophila Cu-Zn superoxide dismutase cDNA sequence
HMMER web server: 2015 update
The TRIPLES database: a community resource for yeast molecular biology
PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants
The diagonal-traverse homology search algorithm for locating similarities between two sequences
EcoliWiki: a wiki-based community resource for Escherichia coli
MiST: a microbial signal transduction database
CDD: a conserved domain database for interactive domain family analysis
xiSPEC: web-based visualization, analysis and sharing of proteomics data
ARDB - Antibiotic Resistance Genes Database
NLSdb: database of nuclear localization signals
A fast and convenient way to produce single stranded DNA from a phagemid
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021
EMGLib: the Enhanced Microbial Genomes Library (update 2000)
EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis
MINT: the Molecular INTeraction database
The p120ctn-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides
Use of RNase H and primer extension to analyze RNA splicing
Nucleotide sequence of the gene ompA coding the outer membrane protein II of Escherichia coli K-12
SIMAP - a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters
Rtools: a web server for various secondary structural analyses on single RNA sequences
IPD - the Immuno Polymorphism Database
DBD--taxonomically broad transcription factor predictions: new content and functionality
A rapid, small scale method for characterization of plasmid insertions in the Dictyostelium genome
Computer programs for the analysis and the management of DNA sequences
The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters
The CtBP binding domain in the adenovirus E1A protein controls CR1- dependent transactivation
Cloning and sequencing of the rat Oct-1 POU box
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications
Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment
canSAR: update to the cancer translational research and drug discovery knowledgebase
An accelerated algorithm for calculating the secondary structure of single stranded RNAs
High efficiency, long-term clinical expression of cottontail rabbit papillomavirus (CRPV) DNA in rabbit skin following particle-mediated DNA transfer
Nucleotide sequence of a mouse testis poly(A) binding protein cDNA
Sensitive detection of RNAs in single cells by flow cytometry [published erratum appears in Nucleic Acids Res 1992 Oct 25;20(20): 5518]
P 3 DB: a plant protein phosphorylation database
FINDbase: a relational database recording frequencies of genetic defects leading to inherited disorders worldwide