yusuke1997/dblp-id-title huggingface dataset:
PDBe: Protein Data Bank in Europe
PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures
TreeFam v9: a new website, more species and orthology-on-the-fly
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways
Database on the structure of large ribosomal subunit RNA
eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications
EMDataBank unified data resource for 3DEM
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database
GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics
coliSNP database server mapping nsSNPs on protein structures
The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics
ChimerDB 2.0 - a knowledgebase for fusion genes updated
GRBase, a database linking information on proteins involved in gene regulation
Pathview Web: user friendly pathway visualization and data integration
A lysine-rich protein functions as an H1 histone in Dictyostelium discoideum chromatin
metaMicrobesOnline: phylogenomic analysis of microbial communities
Pol3Base: a resource for decoding the interactome, expression, evolution, epitranscriptome and disease variations of Pol III-transcribed ncRNAs
The expression of the amyloid precursor protein (APP) is regulated by two GC-elements in the promoter
NeuroPred: a tool to predict cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides
iProClass: an integrated, comprehensive and annotated protein classification database
1H and 31P NMR data of protected deoxycytidylyl-deoxyribonucleoside phosphates
HoPaCI-DB: host- Pseudomonas and Coxiella interaction database
Genenames.org: the HGNC resources in 2013
PHOSIDA 2011: the posttranslational modification database
miR2Disease: a manually curated database for microRNA deregulation in human disease
ChEA3: transcription factor enrichment analysis by orthogonal omics integration
PELE web server: atomistic study of biomolecular systems at your fingertips
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
Updates of the HbVar database of human hemoglobin variants and thalassemia mutations
An efficient string matching algorithm with k differences for nucleotide and amino acid sequences
Tetranucleotide repeat polymorphism at the human aromatase cytochrome P- 450 gene (CYP19)
Torque: topology-free querying of protein interaction networks
WebCSEA: web-based cell-type-specific enrichment analysis of genes
SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace
AmtDB: a database of ancient human mitochondrial genomes
A study of the dimer formation of Rous sarcoma virus RNA and of its effect on viral protein synthesis in vitro
The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group
EpiDenovo: a platform for linking regulatory de novo mutations to developmental epigenetics and diseases
OGRe: a relational database for comparative analysis of mitochondrial genomes
DrugCentral 2018: an update
i -GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study
CARGO: a web portal to integrate customized biological information
HUSCH: an integrated single-cell transcriptome atlas for human tissue gene expression visualization and analyses
KEGG: new perspectives on genomes, pathways, diseases and drugs
omIns: a web resource for domain insertions in known protein structures
Integrating protein annotation resources through the Distributed Annotation System
RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions
FATCAT: a web server for flexible structure comparison and structure similarity searching
sigma factor mutations affecting the sequence-selective interaction of RNA polymerase with -10 region single-stranded DNA
The International Nucleotide Sequence Database Collaboration
Inferred Biomolecular Interaction Server - a web server to analyze and predict protein interacting partners and binding sites
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
GeneSilico protein structure prediction meta-server
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
EPD in 2020: enhanced data visualization and extension to ncRNA promoters
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs. Update 2002
Human AGEs: an interactive spatio-temporal visualization and database of human archeogenomics
OMIM.org: Online Mendelian Inheritance in Man (OMIM ® ), an online catalog of human genes and genetic disorders
Alkemio: association of chemicals with biomedical topics by text and data mining
Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data and new query tools
Collection of small subunit (16S- and 16S-like) ribosomal RNA structures
p300/CBP is required for transcriptional induction by interleukin-4 and interacts with Stat6
NAFlex: a web server for the study of nucleic acid flexibility
The TIGR Maize Database
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research
Autorepressor properties of the pi-initiation protein encoded by plasmid R6K
Aging Atlas: a multi-omics database for aging biology
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes
The Telomerase Database
DAtA: Database of Arabidopsis thaliana Annotation
UCNEbase - a database of ultraconserved non-coding elements and genomic regulatory blocks
PSICA: a fast and accurate web service for protein model quality analysis
Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995)
SuperTarget and Matador: resources for exploring drug-target relationships
Chemical method for DNA sequence determination from the 5'-extremity on PCR amplified fragments
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model
The RDP (Ribosomal Database Project)
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations
AthaMap web tools for the analysis and identification of co-regulated genes
ClanTox: a classifier of short animal toxins
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases
Nucleotide sequence of mouse genomic DNA coding for a brain specific small RNA
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease
bioNMF: a web-based tool for nonnegative matrix factorization in biology
tatDB: a database of Ago1-mediated targets of transfer RNA fragments
GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs
High efficiency transformation of E. coli by high voltage electroporation
World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide
Completion of the nucleotide sequence of the central region of Tn5 confirms the presence of three resistance genes
pdbFun: mass selection and fast comparison of annotated PDB residues
tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species
mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud
The jPOST environment: an integrated proteomics data repository and database
NCBI GEO: archive for functional genomics data sets - update
The Generation Challenge Programme comparative plant stress-responsive gene catalogue
Meningococcus genome informatics platform: a system for analyzing multilocus sequence typing data
The androgen receptor gene mutations database
RosettaBackrub - a web server for flexible backbone protein structure modeling and design
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets
LOCATE: a mouse protein subcellular localization database
GENESIS, a knowledge-based genetic engineering simulation system for representation of genetic data and experiment planning
Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite
TransmiR: a transcription factor-microRNA regulation database
huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
PlantDHS: a database for DNase I hypersensitive sites in plants
GBshape: a genome browser database for DNA shape annotations
BTW: a web server for Boltzmann time warping of gene expression time series
Conformational characteristics of the trinucleoside diphosphate xyloA2'- 5'xyloA2'-5'xyloA. A nuclear magnetic resonance and CD study
CoPAP: Coevolution of Presence-Absence Patterns
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites
OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines
m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome
FunSimMat: a comprehensive functional similarity database
Genes for tRNAIle and tRNAAla in the spacer between the 16S and 23S rRNA genes of a blue-green alga: strong homology to chloroplast tRNA genes and tRNA genes of the E. coli rrnD gene cluster
The PredictProtein server
TFClass: an expandable hierarchical classification of human transcription factors
Use of statistical criteria for screening potential homologies in nucleic acid sequences
The current state of Subti Wiki, the database for the model organism Bacillus subtilis
PINT: Pathways INtegration Tool
FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments
The UCSC Genome Browser database: extensions and updates 2013
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics
MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities
Databases and software for the analysis of mutations in the human p53 gene, the human hprt gene and the lacZ gene in transgenic rodents
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum)
Structural insights into cis element recognition of non-polyadenylated RNAs by the Nab3-RRM
scAPAatlas: an atlas of alternative polyadenylation across cell types in human and mouse
Current status and new features of the Consensus Coding Sequence database
TISIGNER.com: web services for improving recombinant protein production
MetaboAnalyst 2.0 - a comprehensive server for metabolomic data analysis
ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms
MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III
SCPortalen: human and mouse single-cell centric database
SEA: a super-enhancer archive
Automatic construction of restriction site maps
Tsetse fly rDNA: an analysis of structure and sequence
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm
Validation of an in vitro RNA processing system for CT/CGRP precursor mRNA
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome
A nuclear Nicotiana DNA sequence homologous to the 5' half of tRNATyr may have derived from reverse transcription of a pre-tRNA splicing intermediate
EndoNet: an information resource about endocrine networks
Transcriptional repression by the human bZIP factor E4BP4: definition of a minimal repression domain
Improved deoxyribozymes for synthesis of covalently branched DNA and RNA
TRIPLES: a database of gene function in Saccharomyces cerevisiae
Isolation of cloned Moloney murine leukemia virus reverse transcriptase lacking ribonuclease H activity
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function
On the mechanism of preferential incorporation of dAMP at abasic sites in translesional DNA synthesis. Role of proofreading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site
VISDB: a manually curated database of viral integration sites in the human genome
dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation
Detection of single-base mutations by reaction of DNA heteroduplexes with a water-soluble carbodiimide followed by primer extension: application to products from the polymerase chain reaction
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics
TropGENE-DB, a multi-tropical crop information system
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants
SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes
EMPIAR: the Electron Microscopy Public Image Archive
Double-stranded cucumovirus associated RNA 5: which sequence variations may be detected by optical melting and temperature-gradient gel electrophoresis?
Laminin database: a tool to retrieve high-throughput and curated data for studies on laminins
MolMovDB: analysis and visualization of conformational change and structural flexibility
PROMISE: a database of information on prosthetic centres and metal ions in protein active sites
MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits
OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences
A general DNA analysis program for the Hewlett-Packard Model 86/87 microcomputer
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees
Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles
SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns
ORFeus: detection of distant homology using sequence profiles and predicted secondary structure
LIGAND: chemical database of enzyme reactions
Complete nucleotide sequence of a hepatitis E virus isolated from the Xinjiang epidemic (1986-1988) of China
Minimotif Miner 4: a million peptide minimotifs and counting
Cyber infrastructure for Fusarium : three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
DRIMust: a web server for discovering rank imbalanced motifs using suffix trees
MotifViz: an analysis and visualization tool for motif discovery
Functional analysis of the regulatory region of polyoma mutant F9-1 DNA
DRYGIN: a database of quantitative genetic interaction networks in yeast
SuperPain - a resource on pain-relieving compounds targeting ion channels
tmRDB (tmRNA database)
PaccMann: a web service for interpretable anticancer compound sensitivity prediction
FlyBase: genes and gene models
Subti Wiki - a comprehensive community resource for the model organism Bacillus subtilis
DNA analysis servers: plot.it, bend.it, model.it and IS
BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser
MetaBase - the wiki-database of biological databases
LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation
MirGeneDB 2.0: the metazoan microRNA complement
BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics
mirConnX: condition-specific mRNA-microRNA network integrator
EcoRI RFLP at the creatine kinase-brain type gene locus (CKBB, chromosome 14)
SplicePort - An interactive splice-site analysis tool
JPred4: a protein secondary structure prediction server
Cyclical regulation of the insulin-like growth factor binding protein 3 gene in response to 1α, 25-dihydroxyvitamin D 3
Histone Sequence Database: new histone fold family members
The European Nucleotide Archive in 2022
AnnoLnc2: the one-stop portal to systematically annotate novel lncRNAs for human and mouse
OMPdb: a database of β-barrel outer membrane proteins from Gram-negative bacteria
The Ribonuclease P Database
TADB 2.0: an updated database of bacterial type II toxin-antitoxin loci
New challenges in gene expression data analysis and the extended GEPAS
TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species
A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures
Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee
T3DB: the toxic exposome database
A non-curved chicken lysozyme 5' matrix attachment site is 3' followed by a strongly curved DNA sequence
MODOMICS: a database of RNA modification pathways. 2017 update
READ: RIKEN Expression Array Database
PyIgClassify: a database of antibody CDR structural classifications
MultiPhyl: a high-throughput phylogenomics webserver using distributed computing
iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families
PlantTFDB: a comprehensive plant transcription factor database
VOLPES: an interactive web-based tool for visualizing and comparing physicochemical properties of biological sequences
GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery
RDfolder: a web server for prediction of RNA secondary structure
AtMAD: Arabidopsis thaliana multi-omics association database
ProMateus - an open research approach to protein-binding sites analysis
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome
Compilation of DNA sequences of Escherichia coli (update 1993)
Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34, snR35 and snR36
CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803
Rfam: updates to the RNA families database
ASD: a comprehensive database of allosteric proteins and modulators
The IMGT/HLA database
A program for reading DNA sequence gels using a small computer equipped with a graphics tablet
Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells
Nucleotide sequence of transfer RNA genes from the linear mitochondrial DNA of the yeast Williopsis mrakii and Pichia pijperi
Database resources of the National Center for Biotechnology Information
ccPDB: compilation and creation of data sets from Protein Data Bank
KOSMOS: a universal morph server for nucleic acids, proteins and their complexes
pyDockSAXS: protein-protein complex structure by SAXS and computational docking
BACTOME - a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates
The translational signal database, TransTerm, is now a relational database
DrugComb update: a more comprehensive drug sensitivity data repository and analysis portal
DNATCO: assignment of DNA conformers at dnatco.org
Length and structural effect of signal peptides derived from Bacillus subtilis alpha-amylase on secretion of Escherichia coli beta-lactamase in B. subtilis cells
The EBI enzyme portal
SIMAP - the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information
Probability of coding of a DNA sequence: an algorithm to predict translated reading frames from their thermodynamic characteristics
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database
Infectivity and complete nucleotide sequence of the genome of a South African isolate of maize streak virus
Media Dive : the expert-curated cultivation media database
Cassettes of the Streptoalloteichus hindustanus ble gene for transformation of lower and higher eukaryotes to phleomycin resistance
The UCSC cancer genomics browser: update 2011
3'-Terminal sequence of wheat mitochondrial 18S ribosomal RNA: further evidence of a eubacterial evolutionary origin
Java Protein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure
Change of the higher order structure of DNA induced by the complexation with intercalating synthetic polymer, as is visualized by fluorescence microscopy
Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy
PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis
MoMA-LigPath: a web server to simulate protein-ligand unbinding
CorGen - measuring and generating long-range correlations for DNA sequence analysis
MGD: the Mouse Genome Database
CORUM: the comprehensive resource of mammalian protein complexes - 2009
SchistoDB: a Schistosoma mansoni genome resource
CMNPD: a comprehensive marine natural products database towards facilitating drug discovery from the ocean
Nucleotide sequence of tryptophan tRNA from Bacillus subtilis
CSAR-web: a web server of contig scaffolding using algebraic rearrangements
VaDE: a manually curated database of reproducible associations between various traits and human genomic polymorphisms
PredyFlexy: flexibility and local structure prediction from sequence
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
The EcoCyc Database
GENCODE 2021
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates
Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases
Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
SNPServer: a real-time SNP discovery tool
A convenient procedure for the synthesis of oligodeoxyribonucleotide affinity columns for the isolation of mRNA
lncRNAdb: a reference database for long noncoding RNAs
PROMALS3D web server for accurate multiple protein sequence and structure alignments
MIPModDB: a central resource for the superfamily of major intrinsic proteins
Sequence and base modifications of two phenylalanine-tRNAs from Thermus thermophilus HB8
JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands