yusuke1997/dblp-id-title huggingface dataset:
SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment
g:Profiler - interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)
SuperPose: a simple server for sophisticated structural superposition
ProKware: integrated software for presenting protein structural properties in protein tertiary structures
INVHOGEN: a database of homologous invertebrate genes
Protinfo PPC: A web server for atomic level prediction of protein complexes
Vir-Mir db: prediction of viral microRNA candidate hairpins
The RCSB Protein Data Bank: redesigned web site and web services
ImmuCo: a database of gene co-expression in immune cells
Unusual properties of two branched RNA's with circular and linear components
FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid-liquid phase separation and aggregation of proteins
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome
The KEGG resource for deciphering the genome
GreenPhylDB v2.0: comparative and functional genomics in plants
RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps
The ENZYME database in 2000
The 2021 Nucleic Acids Research database issue and the online molecular biology database collection
A statistical method for correlating tRNA sequence with amino acid specificity
Expression of Drosophila heat shock genes is regulated in Rat-cells
DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
An overview of the PubChem BioAssay resource
Sequence harmony: detecting functional specificity from alignments
BTSS, DataBase of Transcriptional Start Sites: progress report 2004
WikiPathways: building research communities on biological pathways
The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics and prediction
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
hiPathDB: a human-integrated pathway database with facile visualization
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis
Expression and function of the homeodomain-containing protein Hex in thyroid cells
The Protist Ribosomal Reference database (PR 2 ): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities
Protein frustratometer: a tool to localize energetic frustration in protein molecules
GEL - a computer tool for DNA sequencing projects
Formation of extrachromosomal circular DNA in HeLa cells by nonhomologous recombination
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins
LDLR Database (second edition): new additions to the database and the software, and results of the first molecular analysis
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts
BarleyBase - an expression profiling database for plant genomics
QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences
Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing
The location of the globin mRNA sequence within its 16S precursor
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study
PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished)
The IMB Jena Image Library of Biological Macromolecules: 2002 update
The non-coding RNAs as riboregulators
SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks
HLungDB: an integrated database of human lung cancer research
MITOPRED: a web server for the prediction of mitochondrial proteins
HOX Pro: a specialized database for clusters and networks of homeobox genes
A macrocyclic bis-acridine shifts the equilibrium from duplexes towards DNA hairpins
PLACE: a database of plant cis-acting regulatory DNA elements
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects
ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures
PDBe-KB: a community-driven resource for structural and functional annotations
P 3 DB 3.0: From plant phosphorylation sites to protein networks
idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach
CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells
Alternative 5' exons either provide or deny an initiator methionine codon to the same alpha-tubulin coding region
HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis
Object oriented Transcription Factors Database (ooTFD)
tRFtarget: a database for transfer RNA-derived fragment targets
ncFANs: a web server for functional annotation of long non-coding RNAs
Phosphorylation of a chloroplast RNA-binding protein changes its affinity to RNA
GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003, update
HIT: linking herbal active ingredients to targets
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution
MedlineRanker: flexible ranking of biomedical literature
Lnc2Cancer v2.0: updated database of experimentally supported long non-coding RNAs in human cancers
An efficient method for finding repeats in molecular sequences
MEROPS : the database of proteolytic enzymes, their substrates and inhibitors
Primer3Plus, an enhanced web interface to Primer3
T-RMSD: a web server for automated fine-grained protein structural classification
SEARCHGTr: a program for analysis of glycosyltransferases involved in glycosylation of secondary metabolites
Ensembl 2018
Computer selection of oligonucleotide probes from amino acid sequences for use in gene library screening
UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs
The Blocks database--a system for protein classification
The microRNA Registry
GO PaD: the Gene Ontology Partition Database
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases
HIV N-linked glycosylation site analyzer and its further usage in anchored alignment
Update on activities at the Universal Protein Resource (UniProt) in 2013
AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses
PIG - the pathogen interaction gateway
Ensembl 2023
Analysis of NADH dehydrogenase proteins, ATPase subunit 9, cytochrome b, and ribosomal protein L14 encoded in the mitochondrial DNA of Paramecium
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects
Fido-SNP: the first webserver for scoring the impact of single nucleotide variants in the dog genome
SwissBioisostere: a database of molecular replacements for ligand design
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
Satellite II DNA of human lymphocytes: tandem repeats of a simple sequenceelement
Genetic and biochemical analysis of the fission yeast ribonucleoprotein particle containing a homolog of Srp54p
VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors
Analysis of the terminator region after the deoCABD operon of Escherichia coli K-12 using a new class of single copy number operon-fusion vectors
MPW: the Metabolic Pathways Database
Personal access to sequence databases on personal computers
Mechanism of dioxin action: receptor-enhancer interactions in intact cells
The Stanford Tissue Microarray Database
The DT40 web site: sampling and connecting the genes of a B cell line
The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995
UTRdb 2.0: a comprehensive, expert curated catalog of eukaryotic mRNAs untranslated regions
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update
VThunter: a database for single-cell screening of virus target cells in the animal kingdom
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale
The European Bioinformatics Institute (EMBL-EBI) in 2021
dbPTM: an information repository of protein post-translational modification
CARNA - alignment of RNA structure ensembles
Fast optimal alignment
Antisense display - a method for functional gene screening: evaluation in a cell-free system and isolation of angiogenesis-related genes
GeneTide - Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases
HEDD: Human Enhancer Disease Database
AmyloGraph: a comprehensive database of amyloid-amyloid interactions
PRODORIC2: the bacterial gene regulation database in 2018
PROTAC-DB 2.0: an updated database of PROTACs
SPAR: small RNA-seq portal for analysis of sequencing experiments
DichroMatch: a website for similarity searching of circular dichroism spectra
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression
The nucleotide sequence of an untranslated but conserved domain at the 3' end of the avian sarcoma virus genome
MBIS - an integrated system for the retrieval and analyses of sequence data from nucleic acids and proteins
Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools
3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR
AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts
BTKbase, mutation database for X-linked agammaglobulinemia (XLA)
Photochemical properties of Yt base in aqueous solution
dnaMATE: a consensus melting temperature prediction server for short DNA sequences
jPREdictor: a versatile tool for the prediction of cis -regulatory elements
TOPCONS: consensus prediction of membrane protein topology
Study of DNA films by the CD, X-ray and polarization microscopy techniques
MULTAN: a program to align multiple DNA sequences
The European Variation Archive: a FAIR resource of genomic variation for all species
PIQMIe: a web server for semi-quantitative proteomics data management and analysis
Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts
Noncoding RNAs database (ncRNAdb)
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes
CancerImmunityQTL: a database to systematically evaluate the impact of genetic variants on immune infiltration in human cancer
Dali server update
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes
Inferring the regulatory network behind a gene expression experiment
An update on PUG-REST: RESTful interface for programmatic access to PubChem
HGBASE: a database of SNPs and other variations in and around human genes
The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database
b2bTools: online predictions for protein biophysical features and their conservation
LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species
Immune epitope database analysis resource
Chick pro alpha 2 (I) collagen gene: exon location and coding potential for the prepropeptide
Human pro alpha 1(I) collagen: cDNA sequence for the C-propeptide domain
The Ontology Lookup Service: bigger and better
WebProAnalyst: an interactive tool for analysis of quantitative structure-activity relationships in protein families
The POU-domain factor Brn-3.0 recognizes characteristic sites in the herpes simplex virus genome
EpiAlignment: alignment with both DNA sequence and epigenomic data
ProtozoaDB: dynamic visualization and exploration of protozoan genomes
GeneWeaver: a web-based system for integrative functional genomics
CAMP: a useful resource for research on antimicrobial peptides
H++: a server for estimating p K a s and adding missing hydrogens to macromolecules
PGG.Han: the Han Chinese genome database and analysis platform
EG: a database of essential genes
Promoter analysis of the phosphoenolpyruvate carboxylase gene of Escherichia coli
ISSD Version 2.0: taxonomic range extended
DNA methylation in hereditary persistence of fetal hemoglobin (HPFH-2)
Rfam 12.0: updates to the RNA families database
Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins
SENT: semantic features in text
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association
The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments
Long 5' leaders inhibit removal of a 3' trailer from a precursor tRNA by mammalian tRNA 3' processing endoribonuclease
ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ
AgeFactDB - the JenAge Ageing Factor Database - towards data integration in ageing research
AHTPDB: a comprehensive platform for analysis and presentation of antihypertensive peptides
The sequence of the 3' non-coding region of the hexon mRNA discloses a novel adenovirus gene
The TriForC database: a comprehensive up-to-date resource of plant triterpene biosynthesis
PDBe: improved findability of macromolecular structure data in the PDB
NCBI Epigenomics: a new public resource for exploring epigenomic data sets
MIPSPlantsDB - plant database resource for integrative and comparative plant genome research
Sequence of two apparent pseudogenes of the major potato tuber protein, patatin
CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality
RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression
BitterDB: taste ligands and receptors database in 2019
Pomelo II: finding differentially expressed genes
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates
New developments in the InterPro database
VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes
WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes
Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster
The immunosuppressives FK 506 and cyclosporin A inhibit the generation of protein factors binding to the two purine boxes of the interleukin 2 enhancer
PRISM: protein interactions by structural matching
MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status
The nucleotide sequence of tobacco vein mottling virus RNA
iHOP web services
InterPro in 2017 - beyond protein family and domain annotations
BreCAN-DB: a repository cum browser of personalized DNA breakpoint profiles of cancer genomes
LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression
Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations
HERVd: the Human Endogenous RetroViruses Database: update
PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling
mutLBSgeneDB: mutated ligand binding site gene DataBase
SPLINT: a cubic spline interpolation program for the analysis of fragment sizes in one-dimensional electrophoresis gels
HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures
Nucleotide sequence of Bacillus phage Nf terminal protein gene
OrthoInspector 3.0: open portal for comparative genomics
ViMIC: a database of human disease-related virus mutations, integration sites and cis -effects
FunCoup 4: new species, data, and visualization
IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex
The yeast DNA polymerase I transcript is regulated in both the mitotic cell cycle and in meiosis and is also induced after DNA damage
GPCRsclass: a web tool for the classification of amine type of G-protein-coupled receptors
deepTools2: a next generation web server for deep-sequencing data analysis
The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease
Cleavage of yeast and bacteriophage T7 genomes at a single site using the rare cutter endonuclease I-Sce I
A semi-automated method for the reading of nucleic acid sequencing gels
Optimal conditions for directly sequencing double-stranded PCR products with sequenase
SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine
modMine: flexible access to modENCODE data
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
The MAPPER 2 Database: a multi-genome catalog of putative transcription factor binding sites
BioNumbers - the database of key numbers in molecular and cell biology
TargetRNA: a tool for predicting targets of small RNA action in bacteria
Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications
RNA Movies 2: sequential animation of RNA secondary structures
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences
PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification
Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
Multi-Harmony: detecting functional specificity from sequence alignment
ProteinCCD : enabling the design of protein truncation constructs for expression and crystallization experiments
ChroKit: a Shiny-based framework for interactive analysis, visualization and integration of genomic data
The PROSITE database, its status in 2002
E-RNAi: a web application for the multi-species design of RNAi reagents - 2010 update
(PS) 2 : protein structure prediction server
BRCC36A is epistatic to BRCA1 in DNA crosslink repair and homologous recombination in Arabidopsis thaliana
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases
PhyloDome - visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets
Reactome knowledgebase of human biological pathways and processes
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily
INMEX - a web-based tool for integrative meta-analysis of expression data
HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
RISSC: a novel database for ribosomal 16S'23S RNA genes spacer regions
Global Substance Registration System: consistent scientific descriptions for substances related to health
SIC: a tool to detect short inverted segments in a biological sequence
CEAS: cis -regulatory element annotation system
TargetIdentifier: a webserver for identifying full-length cDNAs from EST sequences
CTLPScanner: a web server for chromothripsis-like pattern detection
Norine, the knowledgebase dedicated to non-ribosomal peptides, is now open to crowdsourcing
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts
The LIFEdb database in 2006
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
RNA polymerase activity and template activity of chromatin after butyrate induced hyperacetylation of histones in Physarum
SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical-protein interactome
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses
The nucleotide sequence of pACYC184
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules
LGICdb: a manually curated sequence database after the genomes
PULDB: the expanded database of Polysaccharide Utilization Loci
GenePaint.org: an atlas of gene expression patterns in the mouse embryo
Graphite Web: web tool for gene set analysis exploiting pathway topology
G/C-modified oligodeoxynucleotides with selective complementarity: synthesis and hybridization properties
The UCSC Genome Browser database: 2021 update
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures
The Gene Ontology: enhancements for 2011
MeDReaders: a database for transcription factors that bind to methylated DNA
Locating transcribed and non-transcribed rDNA spacer sequences within the nucleolus by in situ hybridization and immunoelectron microscopy
ChickVD: a sequence variation database for the chicken genome
PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations
CATMA: a complete Arabidopsis GST database
The prediction of exons through an analysis of spliceable open reading frames
An improved sequencing method using Sequenase that is independent of template concentration
EmAtlas: a comprehensive atlas for exploring spatiotemporal activation in mammalian embryogenesis
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment
The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids
Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex
PBSword: a web server for searching similar protein-protein binding sites
Transterm - extended search facilities and improved integration with other databases
DBTSS provides a tissue specific dynamic view of Transcription Start Sites
MethBank 4.0: an updated database of DNA methylation across a variety of species
TcoFBase: a comprehensive database for decoding the regulatory transcription co-factors in human and mouse
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
MoKCa database - mutations of kinases in cancer
The interaction of ribonuclease T 1 with DNA
The BioGRID interaction database: 2017 update
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
The haemophilia A mutation search test and resource site, home page of the factor VIII mutation database: HAMSTeRS
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation