yusuke1997/dblp-id-title huggingface dataset:
SUPERFAMILY 1.75 including a domain-centric gene ontology method
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database
LnCompare: gene set feature analysis for human long non-coding RNAs
The web server of IBM's Bioinformatics and Pattern Discovery group
ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins
Rosetta FlexPepDock web server - high resolution modeling of peptide-protein interactions
UniPathway: a resource for the exploration and annotation of metabolic pathways
ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes
COACH-D: improved protein-ligand binding sites prediction with refined ligand-binding poses through molecular docking
The InterPro Database, 2003 brings increased coverage and new features
EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species
SELEX and missing phosphate contact analyses reveal flexibility within the AP-2[alpha] protein: DNA binding complex
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information
TSEA-DB: a trait?tissue association map for human complex traits and diseases
CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
Transcription Regulatory Regions Database (TRRD): its status in 2000
The PeptideAtlas project
isomiRdb: microRNA expression at isoform resolution
RegulonDB: a database on transcriptional regulation in Escherichia coli
PrismNet: predicting protein-RNA interaction using in vivo RNA structural information
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs
BYKdb: the Bacterial protein tYrosine Kinase database
Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium
GRAND: a database of gene regulatory network models across human conditions
GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates
Updates in Rhea - a manually curated resource of biochemical reactions
PigGIS: Pig Genomic Informatics System
pathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis
VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds
Investigation of activation of phosphate groups in mono- and oligonucleotides with mesitoyl chloride
Molecular cloning of the complete Epstein-Barr virus genome as a set of overlapping restriction endonuclease fragments
TransmiR v2.0: an updated transcription factor-microRNA regulation database
GTOP: a database of protein structures predicted from genome sequences
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements
SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)
JVirGel: calculation of virtual two-dimensional protein gels
DDMut: predicting effects of mutations on protein stability using deep learning
systemsDock: a web server for network pharmacology-based prediction and analysis
STRING 7 - recent developments in the integration and prediction of protein interactions
ASD v2.0: updated content and novel features focusing on allosteric regulation
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms
MMDB and VAST+: tracking structural similarities between macromolecular complexes
The SBASE protein domain library, release 9.0: an online resource for protein domain identification
GEPAS, a web-based tool for microarray data analysis and interpretation
FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles
pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
The human type I collagen mutation database
REBASE - enzymes and genes for DNA restriction and modification
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants
NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data
HGTree: database of horizontally transferred genes determined by tree reconciliation
Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
EBI metagenomics in 2016 - an expanding and evolving resource for the analysis and archiving of metagenomic data
Kinact: a computational approach for predicting activating missense mutations in protein kinases
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential
BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles
A software tool-box for analysis of regulatory RNA elements
A computer program for translating DNA sequences into protein
arrayMap 2014: an updated cancer genome resource
The Immune Epitope Database 2.0
OMIM.org: leveraging knowledge across phenotype-gene relationships
SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis
RHdb: the Radiation Hybrid database
ToxoDB: accessing the Toxoplasma gondii genome
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling
BioModels: expanding horizons to include more modelling approaches and formats
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
TcSNP: a database of genetic variation in Trypanosoma cruzi
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
The pepATTRACT web server for blind, large-scale peptide-protein docking
MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments
The translational termination signal database
Determinants of half-site spacing preferences that distinguish AP-1 and ATF/CREB bZIP domains
Mutagenicity and pausing of HIV reverse transcriptase during HIV plus- strand DNA synthesis
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges
Isolation of specific messenger RNA by adsorption of polysomes to matrix-bound antibody
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
Database Resources of the National Genomics Data Center in 2020
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex
The Homeodomain Resource: 2003 update
TropGeneDB, the multi-tropical crop information system updated and extended
Quantitative estimation of the contribution of pyrrolcarboxamide groups of the antibiotic distamycin A into specificity of its binding to DNA AT pairs
Rad51p and Rad54p, but not Rad52p, elevate gene repair in Saccharomyces cerevisiae directed by modified single-stranded oligonucleotide vectors
TriTrypDB: a functional genomic resource for the Trypanosomatidae
dutA RNA functions as an untranslatable RNA in the development of Dictyostelium discoideum
SUPFAM - a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes
MITOMAP: an update on the status of the human mitochondrial genome database
GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
Evolutionary changes in the higher order structure of the ribosomal 5S RNA
Companion: a web server for annotation and analysis of parasite genomes
DrugCentral: online drug compendium
FireDB: a compendium of biological and pharmacologically relevant ligands
PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
Web Services at the European Bioinformatics Institute
x BASE2: a comprehensive resource for comparative bacterial genomics
Screening of phage display immunoglobulin libraries by anti-M13 ELISA and whole phage PCR
WormBase: a cross-species database for comparative genomics
INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information
Nonrepetitive DNA transcription in normal and regenerating rat liver
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures
Superimposé: a 3D structural superposition server
AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative
sRNAtoolbox: an integrated collection of small RNA research tools
Formylatable methionine transfer RNA from Mycoplasma: purification and comparison of partial nucleotide sequences with those of other prokaryotic initiator tRNAs
RatMap - rat genome tools and data
The SWISS-PROT protein sequence data bank and its supplement TrEMBL
GenePath: from mutations to genetic networks and back
Evolutionarily conserved and functionally important residues in the I- CeuI homing endonuclease
Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks
TCRmodel: high resolution modeling of T cell receptors from sequence
MetaCrop: a detailed database of crop plant metabolism
Ensembl 2011
A computer program for comparative analysis of nucleic acid sequences
TeamTat: a collaborative text annotation tool
RFLPs revealed by cosmid 131 [HGM9 no. D17S78]
The European Genome-phenome Archive in 2021
YM500v3: a database for small RNA sequencing in human cancer research
Gamma thalassemia resulting from the deletion of a gamma-globin gene
Kincore: a web resource for structural classification of protein kinases and their inhibitors
LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
CCTOP: a Consensus Constrained TOPology prediction web server
Long range RNA-RNA interactions in the 30 S ribosomal subunit of E. coli
piRBase: integrating piRNA annotation in all aspects
ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments
Mapping the path of the nascent peptide chain through the 23S RNA in the 50S ribosomal subunit
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
TcruziDB: an integrated Trypanosoma cruzi genome resource
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs
COPS - a novel workbench for explorations in fold space
RNAdb - a comprehensive mammalian noncoding RNA database
Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource
Efficient methods for attachment of thiol specific probes to the 3'- ends of synthetic oligodeoxyribonucleotides
CE-MC: a multiple protein structure alignment server
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
ProSAS: a database for analyzing alternative splicing in the context of protein structures
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
Megx.net - database resources for marine ecological genomics
The NRSub database: update 1997
IntAct: an open source molecular interaction database
miRiadne: a web tool for consistent integration of miRNA nomenclature
Codon preference and its use in identifying protein coding regions in long DNA sequences
SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genes
BioGRID: a general repository for interaction datasets
Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli
BASys: a web server for automated bacterial genome annotation
FastML: a web server for probabilistic reconstruction of ancestral sequences
PHASTEST: faster than PHASTER, better than PHAST
Complete nucleotide sequence of the fumarase gene (citG) of Bacillus subtilis 168
GENEVIEW and the DNACE data bus: computational tools for analysis, display and exchange of genetic information
Increased coverage of protein families with the Blocks Database servers
NOREVA: normalization and evaluation of MS-based metabolomics data
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
EXProt: a database for proteins with an experimentally verified function
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
Computer assisted microdensitometric analysis of footprinting autoradiographic DATA
PairsDB atlas of protein sequence space
Europe PMC: a full-text literature database for the life sciences and platform for innovation
The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses
MeMo: a web tool for prediction of protein methylation modifications
Predictome: a database of putative functional links between proteins
DDBJ with new system and face
dreamBase: DNA modification, RNA regulation and protein binding of expressed pseudogenes in human health and disease
Preparation and hybridization properties of oligonucleotides containing 1-alpha-D-arabinofuranosylthymine
PID: the Pathway Interaction Database
Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases
Pattern recognition in nucleic acid sequences. II. An efficient method for finding locally stable secondary structures
STAB: a spatio-temporal cell atlas of the human brain
Pharmit: interactive exploration of chemical space
Transterm: a database to aid the analysis of regulatory sequences in mRNAs
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals
HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot
SCR: novel human suppressors of cdc2/cdc13 mutants of Schizosaccharomyces pombe harbour motifs for RNA binding proteins
MachiBase: a Drosophila melanogaster 5'-end mRNA transcription database
FLUXestimator: a webserver for predicting metabolic flux and variations using transcriptomics data
Purification of histone messenger ribonucleoprotein particles from HeLa cell S-phase polysomes. Characterization of associated proteins
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family
Mutational analysis of the contribution of sequence motifs within the IgH enhancer to tissue specific transcriptional activation
Site-specific inhibition of EcoRI restriction/modification enzymes by a DNA triple helix
CDD: specific functional annotation with the Conserved Domain Database
A simple computer program for calculating, modifying and drawing circular restriction maps
UgMicroSat db : database for mining microsatellites from unigenes
Nucleotide sequence of the genetically labile repeated elements 5' to the origin of mouse rRNA transcription
The EBI search engine: EBI search as a service - making biological data accessible for all
STACK: Sequence Tag Alignment and Consensus Knowledgebase
Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis
FireDock: a web server for fast interaction refinement in molecular docking
ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species
SNPedia: a wiki supporting personal genome annotation, interpretation and analysis
BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles
PLOTREP: a web tool for defragmentation and visual analysis of dispersed genomic repeats
MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer
GOBASE: an organelle genome database
MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes
MemPype: a pipeline for the annotation of eukaryotic membrane proteins
MiCroKit 3.0: an integrated database of midbody, centrosome and kinetochore
GLIDA: GPCR-ligand database for chemical genomic drug discovery
The Arabidopsis SeedGenes Project
Dominant negative mutator mutations in the mutL gene of Escherichia coli
ECgene: an alternative splicing database update
MASI: microbiota - active substance interactions database
CAVE: a cloud-based platform for analysis and visualization of metabolic pathways
WIWS: a protein structure bioinformatics Web service collection
BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization
CDD: conserved domains and protein three-dimensional structure
MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases
Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases
GeneTrail 3: advanced high-throughput enrichment analysis
MITOMAP: a human mitochondrial genome database--1998 update
NONCODE v3.0: integrative annotation of long noncoding RNAs
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute
dictyBase 2013: integrating multiple Dictyostelid species
The Mouse SAGE Site: database of public mouse SAGE libraries
Cloning and characterisation of the rad9 DNA repair gene from Schizosaccharomyces pombe
circMine: a comprehensive database to integrate, analyze and visualize human disease-related circRNA transcriptome
Collection of published 5S and 5.8S ribosomal RNA sequences
HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns
Computer-aided prediction of RNA secondary structures
DNAmoreDB, a database of DNAzymes
Plant Reactome: a resource for plant pathways and comparative analysis
InBase, the New England Biolabs Intein Database
Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding
pKNOT v.2: the protein KNOT web server
ENDEAVOUR update: a web resource for gene prioritization in multiple species
ASTRAL compendium enhancements
firestar - prediction of functionally important residues using structural templates and alignment reliability
The FunFOLD2 server for the prediction of protein-ligand interactions
STITCH 2: an interaction network database for small molecules and proteins
ODB: a database for operon organizations, 2011 update
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface
MHCPred: a server for quantitative prediction of peptide-MHC binding
The ERPIN server: an interface to profile-based RNA motif identification
CFGP: a web-based, comparative fungal genomics platform
Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides
GPCRdb in 2021: integrating GPCR sequence, structure and function
The DNA (cytosine-5) methyltransferases
TB database: an integrated platform for tuberculosis research
DAnCER: Disease-Annotated Chromatin Epigenetics Resource
PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
PopHumanScan: the online catalog of human genome adaptation
VLDP web server: a powerful geometric tool for analysing protein structures in their environment
Spritz: a server for the prediction of intrinsically disordered regions in protein sequences using kernel machines
RASMOT-3D PRO: a 3D motif search webserver
The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks
The Stanford Microarray Database accommodates additional microarray platforms and data formats
NucleaRDB: information system for nuclear receptors
CAMP: Collection of sequences and structures of antimicrobial peptides
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs
Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
Transfer RNA methyltransferases from yellow lupin seeds: purification and properties
The TissueNet database of human tissue protein-protein interactions
BioSamples database: an updated sample metadata hub
PANNZER2: a rapid functional annotation web server
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3? end sequencing
Defining the sequence recognized with BmFTZ-F1, a sequence specific DNA binding factor in the silkworm, Bombyx mori, as revealed by direct sequencing of bound oligonucleotides and gel mobility shift competition analysis
Writing DNA with GenoCAD TM
Gene2Oligo: oligonucleotide design for in vitro gene synthesis
The Protein Ontology: a structured representation of protein forms and complexes
LIGAND: database of chemical compounds and reactions in biological pathways
Prediction of oligodeoxyribonucleotides eluting salt conditions on anion exchange column
SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures
Exposome-Explorer: a manually-curated database on biomarkers of exposure to dietary and environmental factors
The ENZYME data bank in 1995
Human M1 subunit of ribonucleotide reductase: cDNA sequence and expression in stimulated lymphocytes
GermSAGE: a comprehensive SAGE database for transcript discovery on male germ cell development
Prophage Hunter: an integrative hunting tool for active prophages
GenomicKB: a knowledge graph for the human genome
MBROLE 2.0 - functional enrichment of chemical compounds
Intron splicing: a conserved internal signal in introns of Drosophila pre-mRNAs
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information
SIMAP - structuring the network of protein similarities
The REFOLD database: a tool for the optimization of protein expression and refolding
CPGAVAS2, an integrated plastome sequence annotator and analyzer
Target-Pathogen: a structural bioinformatic approach to prioritize drug targets in pathogens
DBETH: A Database of Bacterial Exotoxins for Human
Polymorphism detected by multiple RENS in the human coagulation factor II (F2) gene
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation
Database Resources of the BIG Data Center in 2018
G-language genome analysis environment with REST and SOAP web service interfaces