yusuke1997/dblp-id-title huggingface dataset:
ApaCI, an isoschizomer of BamHI isolated from Acetobacter pasteurianus
DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila
The TissueNet v.2 database: A quantitative view of protein-protein interactions across human tissues
Molecular recognition of B-DNA by Hoechst 33258
DIP: The Database of Interacting Proteins: 2001 update
myExperiment: a repository and social network for the sharing of bioinformatics workflows
PAH Mutation Analysis Consortium Database: a database for disease- producing and other allelic variation at the human PAH locus
A strategy for efficient in vitro translation of cDNAs using the rabbit beta-globin leader sequence
ccmGDB: a database for cancer cell metabolism genes
RPBS: a web resource for structural bioinformatics
PepBuild: a web server for building structure data of peptides/proteins
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response
PRIDB: a protein-RNA interface database
SuperNatural: a searchable database of available natural compounds
Control of 5S RNA transcription in Xenopus somatic cell chromatin: activation with an oocyte extract
SCOP2 prototype: a new approach to protein structure mining
SIFT web server: predicting effects of amino acid substitutions on proteins
DOGMA: a web server for proteome and transcriptome quality assessment
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes
A new rule for analyzing homologous coding sequences in DNA
The nucleotide sequence of a 3.2 kb segment of mitochondrial maxicircle DNA from Crithidia fasciculata containing the gene for cytochrome oxidase subunit III, the N-terminal part of the apocytochrome b gene and a possible frameshift gene; further evidence for the use of unusual initiator triplets in trypanosome mitochondria
Expression Atlas update: from tissues to single cells
Basic peptides enhance protein/DNA interaction in vitro
MAGIA, a web-based tool for miRNA and Genes Integrated Analysis
RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes
TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions
PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem
Specific fluorescent labeling of 7-(aminomethyl)-7-deazaguanosine located in the anticodon of tRNATyr isolated from E. coli mutant
Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data
IMG 4 version of the integrated microbial genomes comparative analysis system
PaLS: filtering common literature, biological terms and pathway information
PROPHECY - a yeast phenome database, update 2006
GONUTS: the Gene Ontology Normal Usage Tracking System
The UCSC Cancer Genomics Browser: update 2015
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment
An asparagine tRNA gene from lupin mitochondria
hPSCreg - the human pluripotent stem cell registry
Rapid DNA fingerprinting using alkaline phosphatase-conjugated oligonucleotides
Dfam: a database of repetitive DNA based on profile hidden Markov models
Mechanism of codon-anticodon interaction in ribosomes. Direct functional evidence that isolated 30S subunits contain two condon- specific binding sites for transfer RNA
GenProBiS: web server for mapping of sequence variants to protein binding sites
GlycoViewer: a tool for visual summary and comparative analysis of the glycome
SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes
An efficient method for matching nucleic acid sequences
miRDB: an online resource for microRNA target prediction and functional annotations
Berkeley PHOG: PhyloFacts orthology group prediction web server
p53 and APC gene mutations: software and databases
PMRD: plant microRNA database
The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics
ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database
dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
xREI: a phylo-grammar visualization webserver
PathExpress: a web-based tool to identify relevant pathways in gene expression data
DBTSS/DBKERO for integrated analysis of transcriptional regulation
dbGuide: a database of functionally validated guide RNAs for genome editing in human and mouse cells
Efficient removal of PCR inhibitors using agarose-embedded DNA preparations
OligoCalc: an online oligonucleotide properties calculator
A web server for performing electronic PCR
BIOSMILE web search: a web application for annotating biomedical entities and relations
Expression Atlas: gene and protein expression across multiple studies and organisms
MTiOpenScreen: a web server for structure-based virtual screening
Characterization and crystallization of the helicase domain of bacteriophage T7 gene 4 protein
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets
A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database
The Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Identification of the in vivo and in vitro origin of transcription in human rDNA
ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins
Integrated databanks access and sequence/structure analysis services at the PBIL
MSDB: a comprehensive, annotated database of microsatellites
ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments
A flexible new computer program for handling DNA sequence data
The RCSB PDB information portal for structural genomics
Characterization of the apolipoprotein B mRNA editing enzyme: no similarity to the proposed mechanism of RNA editing in kinetoplastid protozoa
Plantmetabolomics.org: mass spectrometry-based Arabidopsis metabolomics - database and tools update
UniProt: the Universal Protein knowledgebase
DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues
LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system
InterRNA: a database of base interactions in RNA structures
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations
PlasmID: a centralized repository for plasmid clone information and distribution
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species
Analysis of large nucleic acid dot matrices on small computers
The Zebrafish Information Network: the zebrafish model organism database
Tailing cDNAs with terminal deoxynucleotidyl transferase in RT-PCR assays to identify ribozyme cleavage products
Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory
TCDB: the Transporter Classification Database for membrane transport protein analyses and information
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences
HHMD: the human histone modification database
ZFIN: enhancements and updates to the zebrafish model organism database
The PROSITE database, its status in 1999
MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
BCSearch: fast structural fragment mining over large collections of protein structures
Happy mapping: linkage mapping using a physical analogue of meiosis
WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis
CharProtDB: a database of experimentally characterized protein annotations
Effect of DNA on poly (ADP-ribose) glycohydrolase and the degradation of histone H1-poly (ADP-ribose) complex from HeLa cell nuclei
SwissRegulon: a database of genome-wide annotations of regulatory sites
The nucleotide sequence of 16S rRNA gene from Streptomyces lividans TK21
Sequence specificity of the non-natural pyrido[2, 3-d]pyrimidine nucleoside in triple helix formation
MatrixDB, the extracellular matrix interaction database
PEACE: Parallel Environment for Assembly and Clustering of Gene Expression
SMART 6: recent updates and new developments
Nucleotide sequences of murine intracisternal A-particle gene LTRs have extensive variability within the R region
DESM: portal for microbial knowledge exploration systems
SVMHC: a server for prediction of MHC-binding peptides
Manually curated database of rice proteins
PiSite: a database of protein interaction sites using multiple binding states in the PDB
Nucleotide sequence of the frxB gene in wheat chloroplast DNA
A computer program package for restriction map analysis and manipulation
The nucleotide sequence of pathogenesis-related (PR) 1b protein gene of tobacco
A sequence analysis system encompassing rules for DNA helical distortion
BOMP: a program to predict integral ?barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models
The Sulfolobus database
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes
The Molecular Biology Database Collection: 2004 update
DNA methylation as a regulatory mechanism in rat gamma-crystallin gene expression
GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets
A single nucleotide change in the c-myc internal ribosome entry segment leads to enhanced binding of a group of protein factors
Multiple sequences encoding potential thyroid hormone receptors isolated from mouse skeletal muscle cDNA libraries
Nucleotide sequence of a cDNA coding for the small subunit of human calcium-dependent protease
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences
PIECE 2.0: an update for the plant gene structure comparison and evolution database
Cytidine 5'-diphosphate reductase activity in phytohemagglutinin stimulated human lymphocytes
RecountDB: a database of mapped and count corrected transcribed sequences
Preferential protection of the minor groove of non-operator DNA by lac repressor against methylation by dimethyl sulphate
BodyParts3D: 3D structure database for anatomical concepts
Gene ORGANizer: linking genes to the organs they affect
RefSeq microbial genomes database: new representation and annotation strategy
GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology
Oryza Tag Line , a phenotypic mutant database for the Génoplante rice insertion line library
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts
SAbPred: a structure-based antibody prediction server
SPA: simple web tool to assess statistical significance of DNA patterns
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries
Sequence search on a supercomputer
The Factor VIII Mutation Database on the World Wide Web: the haemophilia A mutation, search, test and resource site. HAMSTeRS update (version 3.0)
FLAN: a web server for influenza virus genome annotation
TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
CA repeat polymorphism in the glucose transporter GLUT 2 gene
The molecular biology computer research resource
pegIT - a web-based design tool for prime editing
ConPlex: a server for the evolutionary conservation analysis of protein complex structures
Collection of mRNA-like non-coding RNAs
Expression of active iron regulatory factor from a full-length human cDNA by in vitro transcription/translation
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks
GRIFFIN: a system for predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model
Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN
SerbGO: searching for the best GO tool
RBPDB: a database of RNA-binding specificities
Plant Reactome: a knowledgebase and resource for comparative pathway analysis
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium
A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines
From ArrayExpress to BioStudies
3D-footprint: a database for the structural analysis of protein-DNA complexes
Chromatin model calculations: Arrays of spherical nu bodies
3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database
M6AREG: m6A-centered regulation of disease development and drug response
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective
SMART: a web-based tool for the study of genetically mobile domains
DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing
FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit
Kinetics of RNA polymerase-promoter complex formation: effects of nonspecific DNA-protein interactions
YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae
A novel method for the isolation of tissue-specific genes
HumanNet v2: human gene networks for disease research
miRBase: annotating high confidence microRNAs using deep sequencing data
MEME: discovering and analyzing DNA and protein sequence motifs
PubMeth: a cancer methylation database combining text-mining and expert annotation
GPCRdb: an information system for G protein-coupled receptors
ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data
IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex
Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs
POGs/PlantRBP: a resource for comparative genomics in plants
SpliceAid-F: a database of human splicing factors and their RNA-binding sites
CFGP 2.0: a versatile web-based platform for supporting comparative and evolutionary genomics of fungi and Oomycetes
CyanoBase: the cyanobacteria genome database update 2010
Characterization of foldback sequences in hamster DNA using electron microsocpy
MolLoc: a web tool for the local structural alignment of molecular surfaces
MEPD: a Medaka gene expression pattern database
BEARR: Batch Extraction and Analysis of cis-Regulatory Regions
Alternative use of chromosome fragmentation sites in the ciliated protozoan Oxytricha nova
HGVbaseG2P: a central genetic association database
Erratum: DisProt 7.0: a major update of the database of disordered proteins
TSpred: a web server for the rational design of temperature-sensitive mutants
HGD: an integrated homologous gene database across multiple species
Editorial: Nucleic Acids Research annual Web Server Issue in 2016
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
The ARTS web server for aligning RNA tertiary structures
Computation of statistical secondary structure of nucleic acids
The role of bacteriophage T7 gene 2 protein in DNA replication
KemaDom: a web server for domain prediction using kernel machine with local context
HMMER web server: 2018 update
DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Characterization of cDNA sequences corresponding to three distinct HMG-1 mRNA species in line CHO Chinese hamster cells and cell cycle expression of the HMG-1 gene
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment
NucMap: a database of genome-wide nucleosome positioning map across species
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans
Strict control of transgene expression in a mouse model for sensitive biological applications based on RMCE compatible ES cells
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB
The IntAct database: efficient access to fine-grained molecular interaction data
Open TG-GATEs: a large-scale toxicogenomics database
Protein structure prediction and analysis using the Robetta server
ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites
Omicseq: a web-based search engine for exploring omics datasets
PopHuman: the human population genomics browser
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
The Genome Database for Rosaceae (GDR): year 10 update
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks
A set of viral DNA decamers enriched in transcription control signals
Rhea, the reaction knowledgebase in 2022
G4Atlas: a comprehensive transcriptome-wide G-quadruplex database
RNApredator: fast accessibility-based prediction of sRNA targets
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics
Minisequencing on oligonucleotide microarrays: comparison of immobilisation chemistries
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures
Targeted resequencing of candidate genes using selector probes
LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine
FeatureScan: revealing property-dependent similarity of nucleotide sequences
Mutational and biochemical analysis of the DNA-entry nuclease EndA from Streptococcus pneumoniae
HUMHOT: a database of human meiotic recombination hot spots
Selectome update: quality control and computational improvements to a database of positive selection
OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions
CompoDynamics: a comprehensive database for characterizing sequence composition dynamics
The nucleotide sequence of phenylalanine tRNA2 of Drosophila melanogaster: four isoacceptors with one basic sequence
INTEDE: interactome of drug-metabolizing enzymes
Tools and data services registry: a community effort to document bioinformatics resources
CADD: predicting the deleteriousness of variants throughout the human genome
Expression Atlas update - a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
Codon usage tabulated from international DNA sequence databases: status for the year 2000
CMGSDB: integrating heterogeneous Caenorhabditis elegans data sources using compositional data mining
Heuristic informational analysis of sequences
An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis
The Transformer database: biotransformation of xenobiotics
The NCBI BioSystems database
Detection of reliable and unexpected protein fold predictions using 3D-Jury
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
The Genome Sequence DataBase (GSDB): improving data quality and data access
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs
COSMIC: the Catalogue Of Somatic Mutations In Cancer
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation
SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers
Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases
BSD: the Biodegradative Strain Database
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives
DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data
RABC: Rheumatoid Arthritis Bioinformatics Center
NaviCell Web Service for network-based data visualization
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins
DNA sequence analysis: a procedure to find homologies among many sequences
DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data
GreeNC 2.0: a comprehensive database of plant long non-coding RNAs
Regulatory Sequence Analysis Tools
iPath3.0: interactive pathways explorer v3
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses
ComPPI: a cellular compartment-specific database for protein-protein interaction network analysis
The EMOTIF database
ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree
2016 update of the PRIDE database and its related tools
Sno/scaRNAbase: a curated database for small nucleolar RNAs and cajal body-specific RNAs
Opal web services for biomedical applications
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis
Significantly higher activity of a cytoplasmic hammerhead ribozyme than a corresponding nuclear counterpart: engineered tRNAs with an extended 3' end can be exported efficiently and specifically to the cytoplasm in mammalian cells
GenMapDB: a database of mapped human BAC clones
IslandViewer update: improved genomic island discovery and visualization
I-COMS: Interprotein-COrrelated Mutations Server
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis
AsiDesigner: exon-based siRNA design server considering alternative splicing
ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins
The ExAC browser: displaying reference data information from over 60 000 exomes
DOOR 2.0: presenting operons and their functions through dynamic and integrated views
PrediSi: prediction of signal peptides and their cleavage positions
PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens
ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium
The effect of H1 histone on the action of DNA-relaxing enzyme
Human Disease Ontology 2018 update: classification, content and workflow expansion
PGDD: a database of gene and genome duplication in plants