yusuke1997/dblp-id-title huggingface dataset:
ArrayPipe: a flexible processing pipeline for microarray data
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
Glycosciences.DB: an annotated data collection linking glycomics and proteomics data (2018 update)
nCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands
BacWGSTdb, a database for genotyping and source tracking bacterial pathogens
MatrixDB: integration of new data with a focus on glycosaminoglycan interactions
The ModFOLD4 server for the quality assessment of 3D protein models
EVOG: a database for evolutionary analysis of overlapping genes
miRTargetLink 2.0 - interactive miRNA target gene and target pathway networks
The BaMM web server for de-novo motif discovery and regulatory sequence analysis
CVTree: a phylogenetic tree reconstruction tool based on whole genomes
Measurements of the effects that coding for a protein has on a DNA sequence and their use for finding genes
Expression Atlas update - an integrated database of gene and protein expression in humans, animals and plants
SALAD database: a motif-based database of protein annotations for plant comparative genomics
Unusual features of transcribed and translated regions of the histone H4 gene family of Tetrahymena thermophila
YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research
SulfAtlas, the sulfatase database: state of the art and new developments
CAPS- DB : a structural classification of helix-capping motifs
Genome surveyor 2.0: cis- regulatory analysis in Drosophila
The PRINTS protein fingerprint database in its fifth year
crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays
Characterization of a factor that can prevent random transcription of cloned rDNA and its probable relationship to poly(ADP-ribose) polymerase
Glycoconjugate Data Bank: Structures - an annotated glycan structure database and N -glycan primary structure verification service
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database
Electrophoresis for genotyping: temporal thermal gradient gel electrophoresis for profiling of oligonucleotide dissociation
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
KinaseMD: kinase mutations and drug response database
QuickSNP : an automated web server for selection of tagSNPs
qPhos: a database of protein phosphorylation dynamics in humans
Sequence rearrangement and duplication of double stranded fibronectin cDNA probably occurring during cDNA synthesis by AMV reverse transcriptase and Escherichia coli DNA polymerase I
Oligonucleotides containing fluorescent 2'-deoxyisoinosine: solid-phase synthesis and duplex stability
The BioStudies database - one stop shop for all data supporting a life sciences study
SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions
INDI - integrated nanobody database for immunoinformatics
DrugCombDB: a comprehensive database of drug combinations toward the discovery of combinatorial therapy
STITCH: interaction networks of chemicals and proteins
NAR Breakthrough Article: DIDA: A curated and annotated digenic diseases database
OncoDB.HCC: an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci
A novel assay of 8-oxo-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase (8-oxo-dGTPase) activity in cultured cells and its use for evaluation of cadmium(II) inhibition of this activity
Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage
DDPC: Dragon Database of Genes associated with Prostate Cancer
Caged RNA: photo-control of a ribozyme reaction
The Zebrafish Information Network: new support for non-coding genes, richer Gene Ontology annotations and the Alliance of Genome Resources
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation
DNase I cleavage of adenoviral nucleoprotein
LigAdvisor: a versatile and user-friendly web-platform for drug design
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center
NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes
Generating non-overlapping displays of nucleic acid secondary structure
InnateDB: systems biology of innate immunity and beyond - recent updates and continuing curation
BRIO: a web server for RNA sequence and structure motif scan
CORUM: the comprehensive resource of mammalian protein complexes
RFLP mapping of thymidine kinase mutants places D17S4 proximal to the human TK1 locus
CPred: a web server for predicting viable circular permutations in proteins
FluGenome: a web tool for genotyping influenza A virus
PlanMine 3.0 - improvements to a mineable resource of flatworm biology and biodiversity
LSD: a leaf senescence database
Indian genetic disease database
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes
Srp2, an SR protein family member of fission yeast: in vivo characterization of its modular domains
ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria
miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs
IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank
Peptiderive server: derive peptide inhibitors from protein-protein interactions
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics
The MG-RAST metagenomics database and portal in 2015
The IntAct molecular interaction database in 2012
OGEE: an online gene essentiality database
Nuclear RNA transcripts from Drosophila melanogaster ribosomal RNA genes containing introns
Studies of the transcription of viral genome in adenovirus 5 transformed cells
A series of PDB-related databanks for everyday needs
trEST, trGEN and Hits: access to databases of predicted protein sequences
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
Data, information, knowledge and principle: back to metabolism in KEGG
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
NAPS: Network Analysis of Protein Structures
The Mouse Genome Database (MGD): integration nexus for the laboratory mouse
PhaSepDB: a database of liquid-liquid phase separation related proteins
EK3D: an E . coli K antigen 3-dimensional structure database
Homologous genes for mouse 4.5S hybRNA are found in all eukaryotes and their low molecular weight RNA transcripts intermolecularly hybridize with eukaryotic 18S ribosomal RNAs
7-Deazapurine containing DNA: efficiency of c7GdTP, c7AdTP and c7IdTP incorporation during PCR-amplification and protection from endodeoxyribonuclease hydrolysis
The nucleotide sequences of two tRNA genes from Campylobacter jejuni
miRNEST database: an integrative approach in microRNA search and annotation
Sys-BodyFluid: a systematical database for human body fluid proteome research
CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators
DBASS3 and DBASS5: databases of aberrant 3′- and 5′-splice sites
Cleavage of DNA.RNA hybrids by type II restriction enzymes
GenDiS: Genomic Distribution of protein structural domain Superfamilies
Expansion of the Gene Ontology knowledgebase and resources
VirHostNet 2.0: surfing on the web of virus/host molecular interactions data
tsRFun: a comprehensive platform for decoding human tsRNA expression, functions and prognostic value by high-throughput small RNA-Seq and CLIP-Seq data
RiceFREND: a platform for retrieving coexpressed gene networks in rice
DIALIGN at GOBICS - multiple sequence alignment using various sources of external information
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL
ModFOLD8: accurate global and local quality estimates for 3D protein models
HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons
Isolation and analysis of chick homeobox cDNA clones
SoyNet: a database of co-functional networks for soybean Glycine max
The Universal Protein Resource (UniProt): an expanding universe of protein information
AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana
MMMDB: Mouse Multiple Tissue Metabolome Database
4D Xpress : a database for cross-species expression pattern comparisons
Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences
The factor VIII Structure and Mutation Resource Site: HAMSTeRS version 4
PubChem BioAssay: 2017 update
SitesBase: a database for structure-based protein-ligand binding site comparisons
Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis
scMethBank: a database for single-cell whole genome DNA methylation maps
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
Developments in CORG: a gene-centric comparative genomics resource
OlfactionBase: a repository to explore odors, odorants, olfactory receptors and odorant-receptor interactions
In vitro selection supports the view of a kinetic control of antisense RNA-mediated inhibition of gene expression in mammalian cells
VARIDT 2.0: structural variability of drug transporter
HeLa DNA polymerase alpha activity in vitro: specific stimulation by a non-enzymic protein factor
GenePlexus: a web-server for gene discovery using network-based machine learning
O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins
MutS binding protects heteroduplex DNA from exonuclease digestion in vitro: a simple method for detecting mutations
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
GIS: a comprehensive source for protein structure similarities
ForestTreeDB: a database dedicated to the mining of tree transcriptomes
DDBJ new system and service refactoring
CuGenDBv2: an updated database for cucurbit genomics
IMGT® databases, related tools and web resources through three main axes of research and development
Human cardiac myosin heavy chain genes and their linkage in the genome
PGSB PlantsDB: updates to the database framework for comparative plant genome research
WormBase 2007
ProteoSign: an end-user online differential proteomics statistical analysis platform
Variants of the Xenopus laevis ribosomal transcription factor xUBF are developmentally regulated by differential splicing
SMART: recent updates, new developments and status in 2020
Xenbase: expansion and updates of the Xenopus model organism database
Improvements to CluSTr: the database of SWISS-PROT+TrEMBL protein clusters
HOX Pro DB: the functional genomics of hox ensembles
GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes
The European Bioinformatics Institute (EBI) databases
PIE: an online prediction system for protein-protein interactions from text
PhaSepDB in 2022: annotating phase separation-related proteins with droplet states, co-phase separation partners and other experimental information
A highly polymorphic region 3' to the human type II collagen gene
Remediation of the protein data bank archive
Argonaute - a database for gene regulation by mammalian microRNAs
CAMPR4: a database of natural and synthetic antimicrobial peptides
Heterogeneity in the 3'-portion of Papilionaceae 5S rRNAs. The primary structure of alfalfa 5S rRNA
Characterization of the effects of Escherichia coli replication terminator protein (Tus) on transcription reveals dynamic nature of the tus block to transcription complex progression
eggNOG v4.0: nested orthology inference across 3686 organisms
SEanalysis: a web tool for super-enhancer associated regulatory analysis
MassNet: a functional annotation service for protein mass spectrometry data
Noncoding regulatory RNAs database
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
SIRW: a web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches
Update of the Diatom EST Database: a new tool for digital transcriptomics
Dinucleotide repeat polymorphisms at the D5S107, D5S108, D5S111, D5S117 and D5S118 loci
Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli
MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa
euL1db: the European database of L1HS retrotransposon insertions in humans
SBCDDB: Sleeping Beauty Cancer Driver Database for gene discovery in mouse models of human cancers
Rfam 11.0: 10 years of RNA families
RNADisease v4.0: an updated resource of RNA-associated diseases, providing RNA-disease analysis, enrichment and prediction
The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information
Mendel, a database of nomenclature for sequenced plant genes
GeSeq - versatile and accurate annotation of organelle genomes
NCBI Reference Sequence Project: update and current status
DNannotator: annotation software tool kit for regional genomic sequences
ReMap 2020: a database of regulatory regions from an integrative analysis of Human and Arabidopsis DNA-binding sequencing experiments
ImmCluster: an ensemble resource for immunology cell type clustering and annotations in normal and cancerous tissues
RGD v2.0: a major update of the ruminant functional and evolutionary genomics database
DIANA-microT 2023: including predicted targets of virally encoded miRNAs
SDM - a server for predicting effects of mutations on protein stability and malfunction
RFLPs associated with pMC1, an anonymous single copy clone from the short arm of chromosome 19 [HGM8 assignment no. D19S14]
Conformation and structural fluctuations of a 218 nucleotides long rRNA fragment: 4-thiouridine as an intrinsic photolabelling probe
PIGSPro: prediction of immunoGlobulin structures v2
SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus , B. anthracis and B. thuringiensis )
RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
MyHits: a new interactive resource for protein annotation and domain identification
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs
mirEX: a platform for comparative exploration of plant pri-miRNA expression data
ENCODE data at the ENCODE portal
PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation
CleanEST: a database of cleansed EST libraries
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
Nucleotide sequences of 16S rRNA encoding genes from halophilic archaea Halococcus morrhuae NRC16008 and Haloferax mediterranei ATCC33500
Gramene 2018: unifying comparative genomics and pathway resources for plant research
Signature, a web server for taxonomic characterization of sequence samples using signature genes
The Pfam Protein Families Database
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Breaking-Cas - interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes
DRASTIC - INSIGHTS: querying information in a plant gene expression database
REDfly: the transcriptional regulatory element database for Drosophila
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal
HRaP: database of occurrence of HomoRepeats and patterns in proteomes
The HuGeMap Database: interconnection and visualization of human genome maps
Origin and direction of replication of the bacteriocinogenic plasmid Clo DF13
The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments
Xenbase: a Xenopus biology and genomics resource
Tissue specific sequence motifs in the enhancer of the leukaemogenic mouseretrovirus SL3-3
Monte Carlo simulations of peptide-membrane interactions with the MCPep web server
JSNP: a database of common gene variations in the Japanese population
CC+: a relational database of coiled-coil structures
CoinFold: a web server for protein contact prediction and contact-assisted protein folding
Localization of an RNA binding element of the iron responsive element binding protein within a proteolytic fragment containing iron coordination ligands
Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana
Group specific sequences and conserved secondary structures at the 3' end of HCV genome and its implication for viral replication
SCOR: a Structural Classification of RNA database
Glucose repression of lactose/galactose metabolism in Kluyveromyces lactis is determined by the concentration of the transcriptional activator LAC9 (K1GAL4) [corrected] [published erratum appears in Nucleic Acids Res 1993 Feb 25;21(4): 1054]
PLAN2L: a web tool for integrated text mining and literature-based bioentity relation extraction
Induced formation of covalent bonds between nucleoprotein components. V. UV or bisulfite induced polynucleotide-protein crosslinkage in bacteriophage MS2
DOMINO: a database of domain-peptide interactions
Structure of the Saccharomyces cerevisiae gene encoding tRNAIle (IAU)
CanGEM: mining gene copy number changes in cancer
Pfam: The protein families database in 2021
LMSD: LIPID MAPS structure database
DrLLPS: a data resource of liquid?liquid phase separation in eukaryotes
MRS: a fast and compact retrieval system for biological data
FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum
DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation
The Molecular Biology Database Collection: 2006 update
The 2010 Nucleic Acids Research Database Issue and online Database Collection: a community of data resources
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis
The Homeodomain Resource: a prototype database for a large protein family
Enzymatic and antisense effects of a specific anti-Ki-ras ribozyme in vitro and in cell culture
Genenames.org: the HGNC and VGNC resources in 2019
Ramped field inversion gel electrophoresis: a cautionary note
GWAS Atlas: an updated knowledgebase integrating more curated associations in plants and animals
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data
The Ensembl genome database project
Gramene database in 2010: updates and extensions
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures
A highly conserved SOX6 double binding site mediates SOX6 gene downregulation in erythroid cells
AMOD: a morpholino oligonucleotide selection tool
TMPad: an integrated structural database for helix-packing folds in transmembrane proteins
Interspersed repetitive sequence (IRS)-PCR amplification of pulsed- field gel fractionated DNA to derive markers from the incontinentia pigmenti 1 (IP1) locus
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding
IntScore: a web tool for confidence scoring of biological interactions
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins
PCGA: a comprehensive web server for phenotype-cell-gene association analysis
A polymorphic locus, D10S5, at 10q21.1
The Gene Ontology project in 2008
A new efficient gene disruption cassette for repeated use in budding yeast
Struct2Net: a web service to predict protein-protein interactions using a structure-based approach
SATPdb: a database of structurally annotated therapeutic peptides
ANISEED 2015: a digital framework for the comparative developmental biology of ascidians
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation
MarkUs: a server to navigate sequence-structure-function space
High resolution psoralen mapping reveals an altered DNA helical structure in the SV40 regulatory region
Improvements in the protein identifier cross-reference service
The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome
Spliceosome Database: a tool for tracking components of the spliceosome
The Reactome Pathway Knowledgebase
NCBI GEO: archive for high-throughput functional genomic data
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt
ProteomicsDB
RNAdb 2.0 - an expanded database of mammalian non-coding RNAs
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
Cancer3D: understanding cancer mutations through protein structures
Promoters of Mycoplasma capricolum ribosomal RNA operons: identical activities but different regulation in homologous and heterologous cells
DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels
Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species
Compilation of human mtDNA control region sequences
QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes
KEGG as a reference resource for gene and protein annotation
MODOMICS: a database of RNA modification pathways, update 2008
DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions
MAVL/StickWRLD for protein: visualizing protein sequence families to detect non-consensus features
Pulsed-field electrophoresis indicates larger-than-expected sizes for mycoplasma genomes
ProCarbDB: a database of carbohydrate-binding proteins
One-step affinity purification protocol for human telomerase
DNA Data Bank of Japan
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
INGA 2.0: improving protein function prediction for the dark proteome