yusuke1997/dblp-id-title huggingface dataset:
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data
KEGG for linking genomes to life and the environment
Echo BASE: an integrated post-genomic database for Escherichia coli
Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task?
Isolation and mapping of a polymorphic DNA sequence pMHZ15 on chromosome 10 [D10S17]
The nucleotide sequence of aroG, the gene for 3-deoxy-D- arabinoheptulosonate-7-phosphate synthetase (phe) in Escherichia coli K12
The European Bioinformatics Institute in 2016: Data growth and integration
neXtProt: a knowledge platform for human proteins
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study
Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder
PNRD: a plant non-coding RNA database
Condon usage tabulated from the international DNA sequence databases
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
3dLOGO: a web server for the identification, analysis and use of conserved protein substructures
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Molecular cloning of mouse PSP mRNA
HTCA: a database with an in-depth characterization of the single-cell human transcriptome
PredUs: a web server for predicting protein interfaces using structural neighbors
A RFLP associated with the low-density lipoprotein receptor gene (LDLR)
Molecular cloning of the three base restriction endonuclease R.CviJI from eukaryotic Chlorella virus IL-3A
Ensembl 2020
Nucleotide sequence of human lactoferrin cDNA
CADRE: the Central Aspergillus Data REpository
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining
OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes
Inparanoid: a comprehensive database of eukaryotic orthologs
PlasMapper: a web server for drawing and auto-annotating plasmid maps
PlnTFDB: updated content and new features of the plant transcription factor database
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora -plant interactions
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences
RISE: a database of RNA interactome from sequencing experiments
Binding of integration host factor (IHF) to the ilvGp1 promoter of the ilvGMEDA operon of Escherichia coli K12
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis
DSMNC: a database of somatic mutations in normal cells
T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks
EMAGE mouse embryo spatial gene expression database: 2014 update
DNASU plasmid and PSI: Biology-Materials repositories: resources to accelerate biological research
PlasmoDB: a functional genomic database for malaria parasites
An insulator embedded in the chicken α-globin locus regulates chromatin domain configuration and differential gene expression
FootPrinter3: phylogenetic footprinting in partially alignable sequences
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes
POCO: discovery of regulatory patterns from promoters of oppositely expressed gene sets
StarScan: a web server for scanning small RNA targets from degradome sequencing data
Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements
Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology
Status of the transcription factors database (TFD)
botXminer: mining biomedical literature with a new web-based application
Dr.VIS: a database of human disease-related viral integration sites
Sequencing of oligonucleotide phosphorothioates based on solid- supported desulfurization
Influenza Research Database: An integrated bioinformatics resource for influenza virus research
Protonated polynucleotide structures. 18. Interaction of oligocytidylates with poly (G)
pssRNAMiner: a plant short small RNA regulatory cascade analysis server
Characterization of the barley chloroplast transcription units containing psaA-psaB and psbD-psbC
Hexamminecobalt(III)-induced condensation of calf thymus DNA: circular dichroism and hydration measurements
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes
The GOA database in 2009 - an integrated Gene Ontology Annotation resource
The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples
ViralZone: recent updates to the virus knowledge resource
OryGenesDB 2008 update: database interoperability for functional genomics of rice
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data
ECOD: new developments in the evolutionary classification of domains
Insignia: a DNA signature search web server for diagnostic assay development
VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens
Flexible Structural Neighborhood - a database of protein structural similarities and alignments
PPD v1.0 - an integrated, web-accessible database of experimentally determined protein p K a values
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform
RNABase: an annotated database of RNA structures
Hybridization properties of immobilized nucleic acids
The human interleukin-2 receptor beta-chain gene: genomic organization, promoter analysis and chromosomal assignment
CHOP: visualization of #wobbling' and isolation of highly conserved regions from aligned DNA sequences
PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences
Nucleotide sequence of the 32 kDa-protein gene (antigen 85 A) of Mycobacterium bovis BCG
MMDB: 3D structure data in Entrez
CoV3D: a database of high resolution coronavirus protein structures
Covalent attachment of oligonucleotides to solid supports
SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs
The directory of P450-containing systems in 1996
phiSITE: database of gene regulation in bacteriophages
DistiLD Database: diseases and traits in linkage disequilibrium blocks
LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery
MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins
The 3D rRNA modification maps database: with interactive tools for ribosome analysis
PLASMAP: an interactive computational tool for storage, retrieval and device-independent graphic display of conventional restriction maps
Biocuration of functional annotation at the European nucleotide archive
FNTM: a server for predicting functional networks of tissues in mouse
Genome Variation Map: a worldwide collection of genome variations across multiple species
RNA-related tools on the Bielefeld Bioinformatics Server
The SWISS-MODEL Repository and associated resources
ALFRED: the ALelle FREquency Database. Update
dbCAN3: automated carbohydrate-active enzyme and substrate annotation
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments
Simian rotavirus SA11 segment 11 contains overlapping reading frames
Rotational symmetry in ribonucleotide strand requirements for binding of HIV-1 Tat protein to TAR RNA
Co-packaging of sense and antisense RNAs: a novel strategy for blocking HIV-1 replication
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe
Conformational mutation in human mtDNA detected by direct sequencing of enzymatically amplified DNA
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Transcription Regulatory Regions Database (TRRD): its status in 1999
ISfinder: the reference centre for bacterial insertion sequences
Nucleotide sequence of a cDNA coding for mouse cyclophilin
Reorganizing the protein space at the Universal Protein Resource (UniProt)
Stemformatics: visualize and download curated stem cell data
The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community
The EMBRACE web service collection
The Quest for Orthologs benchmark service and consensus calls in 2020
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans
PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides
ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data
FunShift: a database of function shift analysis on protein subfamilies
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling
AutoSNPdb : an annotated single nucleotide polymorphism database for crop plants
VarFish: comprehensive DNA variant analysis for diagnostics and research
miRU: an automated plant miRNA target prediction server
3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes
VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing
Photocleavage of DNA and photofootprinting of E. coli RNA polymerase bound to promoter DNA by azido-9-acridinylamines
ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry
Haemophilia B (sixth edition): a database of point mutations and short additions and deletions
BIPASS: BioInformatics Pipeline Alternative Splicing Services
Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry
The UCSC Cancer Genomics Browser: update 2013
Theoretical design of antisense genes with statistically increased efficacy
RASS: a web server for RNA alignment in the joint sequence-structure space
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution
H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro
Genew: the Human Gene Nomenclature Database
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs
SOAP-based services provided by the European Bioinformatics Institute
The ASTRAL compendium for protein structure and sequence analysis
The nucleotide sequence of spinach chloroplast methionine elongator tRNA
MitoMiner v3.1, an update on the mitochondrial proteomics database
aCHEdb: the database system for ESTHER, the alpha/beta fold family of proteins and the Cholinesterase gene server
The Peptaibol Database: a database for sequences and structures of naturally occurring peptaibols
The European Bioinformatics Institute in 2017: data coordination and integration
DrugBank 4.0: shedding new light on drug metabolism
The Protein Data Bank: unifying the archive
Fractionation of nucleic acids into single-stranded and double-stranded forms
RsGDB, the Rhodobacter sphaeroides Genome Database
AVPpred: collection and prediction of highly effective antiviral peptides
The SBASE domain sequence library, release 10: domain architecture prediction
LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces
Gene Aging Nexus: a web database and data mining platform for microarray data on aging
NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints
ARED 3.0: the large and diverse AU-rich transcriptome
MvirDB - a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications
The HUGO Gene Nomenclature Database, 2006 updates
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data
LOCnet and LOCtarget: sub-cellular localization for structural genomics targets
T-profiler: scoring the activity of predefined groups of genes using gene expression data
FFPred: an integrated feature-based function prediction server for vertebrate proteomes
Sequence of a Drosophila cDNA encoding a ubiquitin gene fusion to a 52- aa ribosomal protein tail
NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
ProTox: a web server for the in silico prediction of rodent oral toxicity
PoSSuM: a database of similar protein-ligand binding and putative pockets
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters
SIGNOR 2.0, the SIGnaling Network Open Resource 2.0: 2019 update
PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Non-fusion proteins expressed in E. coli: detection by alpha- complementation (blue/white selection)
Functional elements of the ribosomal protein L7a (rpL7a) gene promoter region and their conservation between mammals and birds
BRENDA in 2017: new perspectives and new tools in BRENDA
F-SNP: computationally predicted functional SNPs for disease association studies
S1 sensitive sites in adenovirus DNA
HAMAP in 2013, new developments in the protein family classification and annotation system
Archiving next generation sequencing data
SLAM web server for comparative gene finding and alignment
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements
ParaDB: a tool for paralogy mapping in vertebrate genomes
Comparative and functional analysis of the AP2 promoter indicates that conserved octamer and initiator elements are critical for activity
eggNOG: automated construction and annotation of orthologous groups of genes
The Papillomavirus Episteme: a major update to the papillomavirus sequence database
Site specific enzymatic cleavage of RNA
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures
MoonProt: a database for proteins that are known to moonlight
The guide RNA database (3.0)
RNAct: Protein-RNA interaction predictions for model organisms with supporting experimental data
McKusick's Online Mendelian Inheritance in Man (OMIM®)
ASePCR: alternative splicing electronic RT-PCR in multiple tissues and organs
U-insertion/deletion Edited Sequence Database
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational
ECOdrug: a database connecting drugs and conservation of their targets across species
Bovine Genome Database: integrated tools for genome annotation and discovery
AUGUSTUS: ab initio prediction of alternative transcripts
The GDB human genome data base anno 1993
DisProt 7.0: a major update of the database of disordered proteins
Content of N-6 methyl adenylic acid in heterogeneous nuclear and messenger RNA of HeLa cells
ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)
The immune epitope database (IEDB) 3.0
Enzymatic multiplication of a chemically synthesized DNA fragment
3did: a catalog of domain-based interactions of known three-dimensional structure
SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation
DOMINE: a comprehensive collection of known and predicted domain-domain interactions
WormQTL HD - a web database for linking human disease to natural variation data in C. elegans
Related enhancers in the intron of the beta1 tubulin gene of Drosophila melanogaster are essential for maternal and CNS-specific expression during embryogenesis
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
Dinucleotide repeat polymorphisms at the D8S85, D8S87, and D8S88 loci
Updated MS²PIP web server supports cutting-edge proteomics applications
VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models
Enrichr-KG: bridging enrichment analysis across multiple libraries
IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor VJ and VDJrearrangement analysis
DNAzymeBuilder, a web application for in situ generation of RNA/DNA-cleaving deoxyribozymes
IMG: the integrated microbial genomes database and comparative analysis system
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins
The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research
Phosfinder: a web server for the identification of phosphate-binding sites on protein structures
SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms
GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response
The Comparative Toxicogenomics Database: update 2011
SecReT4: a web-based bacterial type IV secretion system resource
RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes
NCATS Inxight Drugs: a comprehensive and curated portal for translational research
Transmembrane helix: simple or complex
ASEB: a web server for KAT-specific acetylation site prediction
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
SMPDB: The Small Molecule Pathway Database
Web-based access to mouse models of human cancers: the Mouse Tumor Biology (MTB) Database
SPEED2: inferring upstream pathway activity from differential gene expression
RevTrans: multiple alignment of coding DNA from aligned amino acid sequences
The conserved domain database in 2023
TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
The interactions of the separated strands of satellite DNAs with other DNAs: 1. Conditions for associations of the alpha-satellite of the guinea pig with heterologous double-stranded DNAs
BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications
Ring-opened 7-methylguanine residues in DNA are a block to in vitro DNA synthesis
DIANA-miRPath v4.0: expanding target-based miRNA functional analysis in cell-type and tissue contexts
H-DBAS: human-transcriptome database for alternative splicing: update 2010
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows
The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction
Mouse Tumor Biology Database (MTB): enhancements and current status
KLIFS: an overhaul after the first 5 years of supporting kinase research
A comprehensive sequence analysis program for the IBM personal computer
Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts
BGMUT: NCBI dbRBC database of allelic variations of genes encoding antigens of blood group systems
d-Omix: a mixer of generic protein domain analysis tools
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Point mutation analysis of the Xenopus laevis RNA polymerase I core promoter
High-level expression by tissue/cancer-specific promoter with strict specificity using a single-adenoviral vector
NetAligner - a network alignment server to compare complexes, pathways and whole interactomes
Compilation of small RNA sequences
KDBI: Kinetic Data of Bio-molecular Interactions database
Graphic methods to determine the function of nucleic acid sequences
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
DMINDA: an integrated web server for DNA motif identification and analyses
SAM-T08, HMM-based protein structure prediction
Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases
CanPredict: a computational tool for predicting cancer-associated missense mutations
PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm
Resonance assignments of non-exchangeable protons in B type DNA oligomers, an overview
C-->U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica
CPLM 4.0: an updated database with rich annotations for protein lysine modifications
HNADOCK: a nucleic acid docking server for modeling RNA/DNA-RNA/DNA 3D complex structures
The Schizosaccharomyces pombe pla1 gene encodes a poly(A) polymerase and can functionally replace its Saccharomyces cerevisiae homologue
ChemProt-2.0: visual navigation in a disease chemical biology database
zfishbook: connecting you to a world of zebrafish revertible mutants
QUMA: quantification tool for methylation analysis
Complete sequence of rabbit butyrylcholinesterase
Clone DB: an integrated NCBI resource for clone-associated data
NOPdb: Nucleolar Proteome Database - 2008 update
LIGAND database for enzymes, compounds and reactions
BLAST: a more efficient report with usability improvements
PISCES: recent improvements to a PDB sequence culling server
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database
DIMA 2.0 - predicted and known domain interactions
Computer programs used to aid in the selection of DNA hybridization probes
Structural features and restricted expression of a human alpha-tubulin gene
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility
ChemProt: a disease chemical biology database
FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps
5SRNAdb: an information resource for 5S ribosomal RNAs
Sequence of a cDNA coding for human glutathione peroxidase confirms TGA encodes active site selenocysteine
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements
Secondary structure model for the complete simian virus 50 late precursor mRNA
ETOPE: evolutionary test of predicted exons
Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data
PharmaGist: a webserver for ligand-based pharmacophore detection
The mapping of nucleosomes and regulatory protein binding sites at the Saccharomyces cerevisiae MFA2 gene: a high resolution approach
PCRPi - DB: a database of computationally annotated hot spots in protein interfaces