yusuke1997/dblp-id-title huggingface dataset:
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins
CellCircuits: a database of protein network models
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects
Translesion synthesis by yeast DNA polymerase from templates containing lesions of ultraviolet radiation and acetylaminofluorene
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool
DriverDBv2: a database for human cancer driver gene research
BIONET: national computer resource for molecular biology
Activities at the Universal Protein Resource (UniProt)
ConsensusPathDB 2022: molecular interactions update as a resource for network biology
EuroPhenome and EMPReSS: online mouse phenotyping resource
RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts
Recognition of a cytosine base lesion by a human damage-specific DNA binding protein
CoffeeProt: an online tool for correlation and functional enrichment of systems genetics data
COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses
Cloning of a new mouse foetal beta-globin mRNA sequence
PepSite: prediction of peptide-binding sites from protein surfaces
ADReCS-Target: target profiles for aiding drug safety research and application
CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens
CMDB: the comprehensive population genome variation database of China
Disease Ontology: a backbone for disease semantic integration
A negative regulating element controlling transcription of the gene encoding acyl-CoA oxidase in Saccharomyces cerevisiae
KERIS: kaleidoscope of gene responses to inflammation between species
The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform
The Pathogen-Host Interactions database (PHI-base): additions and future developments
atabase resources of the National Center for Biotechnology Information: update
pKM101 is an IS46-promoted deletion of R46
HMDB 3.0 - The Human Metabolome Database in 2013
The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion
Compilation of sequences of tRNA genes
Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase
Studies on the function of two adjacent N6, N6-dimethyladenosines near the 3' end of 16S ribosomal RNA of Escherichia coli. IV. The effect of the methylgroups on ribosomal subunit interaction
Fragment Finder: a web-based software to identify similar three-dimensional structural motif
SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties
Integr8 and Genome Reviews: integrated views of complete genomes and proteomes
LNCediting: a database for functional effects of RNA editing in lncRNAs
The Diamond STING server
e-LEA3D: a computational-aided drug design web server
EcoGene 3.0
A compilation of molecular biology web servers: 2006 update on the Bioinformatics Links Directory
The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes
Transcriptional regulation of plasminogen activator inhibitor type-1 mRNA in Hep G2 cells by epidermal growth factor
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
The PROSITE dictionary of sites and patterns in proteins, its current status
SEdb 2.0: a comprehensive super-enhancer database of human and mouse
3DGenBench: a web-server to benchmark computational models for 3D Genomics
DBCP: a web server for disulfide bonding connectivity pattern prediction without the prior knowledge of the bonding state of cysteines
Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003
Metagrowth: a new resource for the building of metabolic hypotheses in microbiology
MEME SUITE: tools for motif discovery and searching
PlantTribes: a gene and gene family resource for comparative genomics in plants
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments
BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells
Update for users of the Cornell sequence analysis package
EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases
ConTra v2: a tool to identify transcription factor binding sites across species, update 2011
IAnimal: a cross-species omics knowledgebase for animals
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
CandidaDB: a genome database for Candida albicans pathogenomics
MVIP: multi-omics portal of viral infection
Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15
CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens
UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
DNA is a co-factor for its own replication in Xenopus egg extracts
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB
SNPsyn: detection and exploration of SNP-SNP interactions
CReSCENT: CanceR Single Cell ExpressioN Toolkit
PMDBase: a database for studying microsatellite DNA and marker development in plants
USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques
HomozygosityMapper - an interactive approach to homozygosity mapping
LGA: a method for finding 3D similarities in protein structures
siRecords: a database of mammalian RNAi experiments and efficacies
Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
Pancan-meQTL: a database to systematically evaluate the effects of genetic variants on methylation in human cancer
Transcriptional analyses of the Bacillus licheniformis penP gene
ResponseNet v.3: revealing signaling and regulatory pathways connecting your proteins and genes across human tissues
Efficient use of accessibility in microRNA target prediction
enrichMiR predicts functionally relevant microRNAs based on target collections
Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms
A Protein Classification Benchmark collection for machine learning
New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC
SDBASE: a consortium of native and modelled disulphide bonds in proteins
Nucleotide sequence of crystal protein gene isolated from B. thuringiensis subspecies entomocidus 60.5 coding for a toxin highly active against Spodoptera species
The VK genes on human chromosome 22 are located at 22q11
The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery
SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis
Dali/FSSP classification of three-dimensional protein folds
Update of the Human MitBASE database
PACRAT: a database and analysis system for archaeal and bacterial intergenic sequence features
ChimerDB - a knowledgebase for fusion sequences
TOPS: an enhanced database of protein structural topology
DBJ in the stream of various biological data
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
PSCDB: a database for protein structural change upon ligand binding
Synthesis and application of charge-modified dye-labeled dideoxynucleoside-5'-triphosphates to ?direct-load? DNA sequencing
Sequence dependent electrophoretic mobilities and melting temperatures for A-T containing oligodeoxyribonucleotides
PLSDB: advancing a comprehensive database of bacterial plasmids
MetaRanker 2.0: a web server for prioritization of genetic variation data
Europe PMC in 2020
Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates
Transcription Regulatory Regions Database (TRRD): its status in 2002
DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture
The mobility minima in pulsed-field capillary electrophoresis of large DNA
DOP-vector PCR: a method for rapid isolation and sequencing of insert termini from PAC clones
Non-redundant patent sequence databases with value-added annotations at two levels
An RNasin-resistant ribonuclease selective for interleukin 2 mRNA
Aminoacyl-tRNA synthetases database
OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins
Genes and proteins of Escherichia coli K-12 (GenProtEC)
Olelo: a web application for intuitive exploration of biomedical literature
IDEAL in 2014 illustrates interaction networks composed of intrinsically disordered proteins and their binding partners
The BioGRID interaction database: 2013 update
Snap: an integrated SNP annotation platform
Human calcitonin gene regulation by helix-loop-helix recognition sequences
VarMod: modelling the functional effects of non-synonymous variants
Chlamydomonas reinhardtii telomere repeats form unstable structures involving guanine-guanine base pairs
PreBI: prediction of biological interfaces of proteins in crystals
Nucleotide sequence of a novel diverged human homeobox gene encodes a DNA binding protein
UniProt: the Universal Protein Knowledgebase in 2023
MACiE: exploring the diversity of biochemical reactions
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain
HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts
PhylomeDB: a database for genome-wide collections of gene phylogenies
GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models
1H NMR study of an ethidium dimer poly(dA-dT) complex: evidence of a transition between bis and monointercalation
The DifferentialNet database of differential protein-protein interactions in human tissues
Transcriptional and posttranscriptional control of immunoglobulin mRNA production during B lymphocyte development
m6AVar: a database of functional variants involved in m6A modification
DaReUS-Loop: a web server to model multiple loops in homology models
The Database of Macromolecular Motions: new features added at the decade mark
ThYme: a database for thioester-active enzymes
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans
HotSpot Wizard: a web server for identification of hot spots in protein engineering
Savant Genome Browser 2: visualization and analysis for population-scale genomics
QGRS-H Predictor: a web server for predicting homologous quadruplex forming G-rich sequence motifs in nucleotide sequences
The human U1 snRNA promoter and enhancer do not direct synthesis of messenger RNA
Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides
SIMAP: the similarity matrix of proteins
PHASTER: a better, faster version of the PHAST phage search tool
CTGA: the database for genetic disorders in Arab populations
OPTIC: orthologous and paralogous transcripts in clades
SuperLooper - a prediction server for the modeling of loops in globular and membrane proteins
Isolation of two cDNAs encoding zinc finger proteins which bind to the alpha 1-antitrypsin promoter and to the major histocompatibility complex class I enhancer
The detection of DNA-binding proteins by protein blotting
ProLint: a web-based framework for the automated data analysis and visualization of lipid-protein interactions
miRViz: a novel webserver application to visualize and interpret microRNA datasets
Ensembl 2004
NLProt: extracting protein names and sequences from papers
Sharing of worldwide distributed carbohydrate-related digital resources: online connection of the Bacterial Carbohydrate Structure DataBase and GLYCOSCIENCES.de
ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
EMDataBank.org: unified data resource for CryoEM
BioMagResBank
DroPNet: a web portal for integrated analysis of Drosophila protein-protein interaction networks
BusyBee Web: towards comprehensive and differential composition-based metagenomic binning
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology
The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology
fpocket: online tools for protein ensemble pocket detection and tracking
Graphic display of nucleic acid structure by a microcomputer
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database
PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology
GlycomeDB - a unified database for carbohydrate structures
GCView: the genomic context viewer for protein homology searches
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences
Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species
Recognition of GT mismatches by Vsr mismatch endonuclease
SIEGE: Smoking Induced Epithelial Gene Expression Database
FlyBase: a Drosophila database. The FlyBase consortium
SCOP: a structural classification of proteins database
TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks
QuasiMotiFinder: protein annotation by searching for evolutionarily conserved motif-like patterns
The MEME Suite
Reaction kinetics of some important site-specific endonucleases
TransportDB: a relational database of cellular membrane transport systems
Two dimensional single-strand conformation polymorphism analysis: a useful tool for the detection of mutations in long DNA fragments
A suite of web-based programs to search for transcriptional regulatory motifs
OrCGDB: a database of genes involved in oral cancer
EBI metagenomics - a new resource for the analysis and archiving of metagenomic data
TREND-DB - a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation
A PanorOmic view of personal cancer genomes
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
A functional splice site in the 5' untranslated region of a zein gene
DrugScore PPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions
5'-flanking sequence of mouse glutathione S-transferase Ya gene
Topoisomer gel retardation: detection of anti-Z-DNA antibodies bound to Z-DNA within supercoiled DNA minicircles
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities
webPRC: the Profile Comparer for alignment-based searching of public domain databases
PvuII polymorphic site upstream to the human ApoCIII gene
CovalentDock Cloud: a web server for automated covalent docking
Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards
Updates on the web-based VIOLIN vaccine database and analysis system
Expansion of the 16S and 23S ribosomal RNA mutation databases (16SMDB and 23SMDB)
The nucleotide sequence of pathogenesis-related (PR) 1c protein gene of tobacco
SPRING: a tool for the analysis of genome rearrangement using reversals and block-interchanges
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences
UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
MutM, a protein that prevents G.C----T.A transversions, is formamidopyrimidine-DNA glycosylase
ICARUS, an interactive web server for single cell RNA-seq analysis
NCBI Bookshelf: books and documents in life sciences and health care
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures
SwissDock, a protein-small molecule docking web service based on EADock DSS
Virgil database for rich links (1999 update)
KEGG: integrating viruses and cellular organisms
sfkit: a web-based toolkit for secure and federated genomic analysis
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
Yeast viral RNA polymerase is a transcriptase
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions
Effective - a database of predicted secreted bacterial proteins
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration
A rapid one-tube genomic DNA extraction process for PCR and RAPD analyses
HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses
WEB-THERMODYN: sequence analysis software for profiling DNA helical stability
Polymorphix: a sequence polymorphism database
PMG: online generation of high-quality molecular pictures and storyboarded animations
BacDive in 2019: bacterial phenotypic data for High-throughput biodiversity analysis
The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
An enhanced MITOMAP with a global mtDNA mutational phylogeny
COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information
Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-, NMT and PTS1
ChEBI: a database and ontology for chemical entities of biological interest
RhesusBase: a knowledgebase for the monkey research community
Beta-amyloid gene dosage in Alzheimer's disease
CASTp: Computed Atlas of Surface Topography of proteins
ZINCPharmer: pharmacophore search of the ZINC database
ChiTaRS 2.1 - an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts
BioMet Toolbox: genome-wide analysis of metabolism
PmiREN2.0: from data annotation to functional exploration of plant microRNAs
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses
PSEUDOVIEWER2: visualization of RNA pseudoknots of any type
DoRiNA 2.0 - upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence
A method to locate protein coding sequences in DNA of prokaryotic systems
Dcode.org anthology of comparative genomic tools
Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA fMet selection on the ribosomal P-site in Escherichia coli
DiProDB: a database for dinucleotide properties
Proksee: in-depth characterization and visualization of bacterial genomes
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes
MODBASE, a database of annotated comparative protein structure models, and associated resources
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network
SETTER: web server for RNA structure comparison
A database of immunoglobulins with integrated tools: DIGIT
DDBJ working on evaluation and classification of bacterial genes in INSDC
VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data
TreeDet: a web server to explore sequence space
Transfection of mitochondria: strategy towards a gene therapy of mitochondrial DNA diseases
Updates to the RNA mapping database (RMDB), version 2
P1 nuclease defines a subpopulation of active SV40 chromatin - a new nuclease hypersensitivity assay
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
OREST: the online resource for EST analysis
Cyber-T web server: differential analysis of high-throughput data
The mouse Gene Expression Database (GXD): 2021 update
GenomeFLTR: filtering reads made easy
AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species
APPRIS: selecting functionally important isoforms
A comparative study of the interaction of 5, 10, 15, 20-tetrakis (N- methylpyridinium-4-yl)porphyrin and its zinc complex with DNA using fluorescence spectroscopy and topoisomerisation
Chloroplast genes transferred to the nuclear plant genome have adjusted to nuclear base composition and codon usage
The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins
The Genome Portal of the Department of Energy Joint Genome Institute
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
DIMA 3.0: Domain Interaction Map
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences
TMPDB: a database of experimentally-characterized transmembrane topologies
Electronic access to mouse tumor data: the Mouse Tumor Biology Database (MTB) project
The nucleotide sequence of bacteriophage T5 DNA at the region between early and late genes
The secondary structure of oocyte and somatic 5S ribosomal RNAs of the fish Misgurnus fossilis L. from nuclease hydrolyses and chemical modification data
DrugVirus.info 2.0: an integrative data portal for broad-spectrum antivirals (BSA) and BSA-containing drug combinations (BCCs)
DeepFun: a deep learning sequence-based model to decipher non-coding variant effect in a tissue- and cell type-specific manner
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns
HvrBase: compilation of mtDNA control region sequences from primates
Initiation of plasmid R1 replication in vitro is independent of transcription by host RNA polymerase
The nucleotide sequence of spinach chloroplast tryptophan transfer RNA
YASS: enhancing the sensitivity of DNA similarity search
mSignatureDB: a database for deciphering mutational signatures in human cancers
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
PhenoM: a database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae
Influenza sequence and epitope database
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
Human metallothionein-specific riboprobes
The hepatitis C sequence database in Los Alamos
AIDA: ab initio domain assembly server
PCRTiler: automated design of tiled and specific PCR primer pairs
HERVd: database of human endogenous retroviruses
iProX in 2021: connecting proteomics data sharing with big data