yusuke1997/dblp-id-title huggingface dataset:
GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals
APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features
The Bloom's and Werner's syndrome proteins are DNA structure-specific helicases
RSRE: RNA structural robustness evaluator
AnimalTFDB: a comprehensive animal transcription factor database
OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures
WashU Epigenome Browser update 2019
MpoxRadar: a worldwide MPXV genomic surveillance dashboard
Obligatory activator-polymerase addition order at promoters
GenoBase: comprehensive resource database of Escherichia coli K-12
iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species
Oestrogen facilitates the binding of ubiquitous and liver-enriched nuclear proteins to the apoVLDL II promoter in vivo
The InterPro protein families database: the classification resource after 15 years
DNA data bank of Japan (DDBJ) progress report
PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes
ArrayExpress update - from an archive of functional genomics experiments to the atlas of gene expression
AraPheno: a public database for Arabidopsis thaliana phenotypes
RMD: a rice mutant database for functional analysis of the rice genome
Protein C deficiency: summary of the 1995 database update
CNIT: a fast and accurate web tool for identifying protein-coding and long non-coding transcripts based on intrinsic sequence composition
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis
RSAT 2011: regulatory sequence analysis tools
Genomes OnLine Database (GOLD) v.8: overview and updates
Dinucleotide repeat polymorphisms at the D11S419 and CD3D loci
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
Cationic lipid-mediated co-transfection of insect cells
POBO, transcription factor binding site verification with bootstrapping
Database for bacterial group II introns
TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms
The gene encoding topoisomerase II from Plasmodium falciparum
GenePublisher: automated analysis of DNA microarray data
GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs
IRSOM2: a web server for predicting bifunctional RNAs
2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions
AthaMap, integrating transcriptional and post-transcriptional data
The HSSP database of protein structure-sequence alignments and family profiles
A DNA sequence analysis package for the IBM personal computer
DrugBank 5.0: a major update to the DrugBank database for 2018
OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms
From genomics to chemical genomics: new developments in KEGG
MAGIIC-PRO: detecting functional signatures by efficient discovery of long patterns in protein sequences
SOBA: sequence ontology bioinformatics analysis
The Mouse Genome Database: enhancements and updates
BioInfo3D: a suite of tools for structural bioinformatics
GUIDANCE: a web server for assessing alignment confidence scores
AGenDA: gene prediction by cross-species sequence comparison
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans
GenBank 2023 update
SABIO-RK - database for biochemical reaction kinetics
The 1999 SWISS-2DPAGE database update
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica
RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links
The Gibbs Centroid Sampler
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility
Nucleotide sequence of porcine rotavirus (OSU strain) gene segments 7, 8, and 9
WITHDRAWN - a resource for withdrawn and discontinued drugs
Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease
AlloDriver: a method for the identification and analysis of cancer driver targets
DIGGER: exploring the functional role of alternative splicing in protein interactions
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA
New synthetic routes to protected purine 2'-O-methylriboside-3'-O- phosphoramidites using a novel alkylation procedure
IRESite: the database of experimentally verified IRES structures (www.iresite.org)
Modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-tRNA synthetase
EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies
LISTA, a comprehensive compilation of nucleotide sequences encoding proteins from the yeast Saccharomyces
mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome
The Comparative Toxicogenomics Database: update 2019
PROSESS: a protein structure evaluation suite and server
LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites
NLSdb - major update for database of nuclear localization signals and nuclear export signals
Gene discovery using the maize genome database ZmDB
PubChem in 2021: new data content and improved web interfaces
The non-redundant Bacillus subtilis (NRSub) database: update 1998
EcoCyc: A comprehensive view of Escherichia coli biology
PLEXdb: gene expression resources for plants and plant pathogens
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services
EPIXplorer: A web server for prediction, analysis and visualization of enhancer-promoter interactions
mmCSM-AB: guiding rational antibody engineering through multiple point mutations
New photoactivatable structural and affinity probes of RNAs: specific features and applications for mapping of spermine binding sites in yeast tRNA(Asp) and interaction of this tRNA with yeast aspartyl-tRNA synthetase
The EROP-Moscow oligopeptide database
PDCM Finder: an open global research platform for patient-derived cancer models
Nucleotide sequence of 5' portion of srfA that contains the region required for competence establishment in Bacillus subtilus
LZerD webserver for pairwise and multiple protein-protein docking
Cloning and sequencing of the 3' half of a potato virus Y (O strain) genome encoding the 5k protein, protease, polymerase and coat protein
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases
GermOnline, a cross-species community knowledgebase on germ cell differentiation
MEF/ELF4 transactivation by E2F1 is inhibited by p53
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe
DNA polymerase alpha and models for proofreading
ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics
KinG: a database of protein kinases in genomes
Editorial: Nucleic Acids Research annual Web Server Issue in 2014
DSAP: deep-sequencing small RNA analysis pipeline
MOPED: Model Organism Protein Expression Database
sRNATarBase 3.0: an updated database for sRNA-target interactions in bacteria
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins
KEGG for representation and analysis of molecular networks involving diseases and drugs
EDomics: a comprehensive and comparative multi-omics database for animal evo-devo
Meiotic role of SWI6 in Saccharomyces cerevisiae
iDog: an integrated resource for domestic dogs and wild canids
ALTER: program-oriented conversion of DNA and protein alignments
ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
PlantMarkers - a database of predicted molecular markers from plants
Isolation and characterization of the human catalase gene
tRFdb: a database for transfer RNA fragments
Purification and properties of human DNA helicase VI
Tools for comparative protein structure modeling and analysis
The RDP-II (Ribosomal Database Project)
Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications
Sequence of a cDNA clone encompassing the complete mature human prostate specific antigen (PSA) and an unspliced leader sequence
MIPS: a database for genomes and protein sequences
CryptoDB: a Cryptosporidium bioinformatics resource update
The IPD and IMGT/HLA database: allele variant databases
Promoter variation in the ribosomal RNA genes in Drosophila melanogaster strains
EcID. A database for the inference of functional interactions in E. coli
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation
Allele dynamics plots for the study of evolutionary dynamics in viral populations
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
Alliance of Genome Resources Portal: unified model organism research platform
firestar - advances in the prediction of functionally important residues
WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
web-rMKL: a web server for dimensionality reduction and sample clustering of multi-view data based on unsupervised multiple kernel learning
Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes
SporeWeb: an interactive journey through the complete sporulation cycle of Bacillus subtilis
MoonProt 3.0: an update of the moonlighting proteins database
The NCBI Taxonomy database
RiceNet v2: an improved network prioritization server for rice genes
Histone and histone fold sequences and structures: a database
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
RetroRules: a database of reaction rules for engineering biology
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet
Solution structures of DNA-bound gyrase
RNAPhaSep: a resource of RNAs undergoing phase separation
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data
The role of Region II in the RNA polymerase factor N (54)
Voronoia 4-ever
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning
Database Resources of the BIG Data Center in 2019
The control of lambda DNA terminase synthesis
Sentra, a database of signal transduction proteins
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus
mRNALoc: a novel machine-learning based in-silico tool to predict mRNA subcellular localization
DNA Data Bank of Japan (DDBJ) in XML
The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons
PATRIC: The VBI PathoSystems Resource Integration Center
RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs
MiMeDB: the Human Microbial Metabolome Database
Methionyl-tRNA synthetase from Bacillus stearothermophilus: structural and functional identities with the Escherichia coli enzyme
enoLOGOS: a versatile web tool for energy normalized sequence logos
The Protein Information Resource: an integrated public resource of functional annotation of proteins
dbCRID: a database of chromosomal rearrangements in human diseases
Development of a superior strategy for computer-assisted nucleotide sequence analysis
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes
Mouse Phenome Database
PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins
Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines
InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information
D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples
ASIAN: a web server for inferring a regulatory network framework from gene expression profiles
DNA Data Bank of Japan in the age of information biology
FlyBase at 25: looking to the future
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements
Synthesis of low molecular weight RNA components A, C and D by polymerase II in alpha-amanitin-resistant hamster cells
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts
MitoNuc and MitoAln: two related databases of nuclear genes coding for mitochondrial proteins
The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse
Tractor_DB (version 2.0): a database of regulatory interactions in gamma-proteobacterial genomes
PrePPI: a structure-informed database of protein-protein interactions
Identification and characterization of the human XIST gene promoter: implications for models of X chromosome inactivation
Xanthusbase: adapting wikipedia principles to a model organism database
Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes
AMPDB: the Arabidopsis Mitochondrial Protein Database
Database of non-canonical base pairs found in known RNA structures
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines
OverGeneDB: a database of 5′ end protein coding overlapping genes in human and mouse genomes
ProtChemSI: a network of protein-chemical structural interactions
Accumulation of H/ACA snoRNPs depends on the integrity of the conserved central domain of the RNA-binding protein Nhp2p
Biomedical term mapping databases
Polyribosome binding of rabbit globin messenger RNA and messenger ribonucleoprotein labelled with bacteriophage-T4 RNA ligase and 5'-[32P] phosphocytidine 3'-phosphate
Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
RASP: an atlas of transcriptome-wide RNA secondary structure probing data
Human protein reference database as a discovery resource for proteomics
UKPMC: a full text article resource for the life sciences
Genome Maps, a new generation genome browser
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species
Complete nucleotide sequence of a sea urchin actin gene
PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples
iPfam: a database of protein family and domain interactions found in the Protein Data Bank
The Eukaryotic Linear Motif resource: 2022 release
Nucleotide sequence and LexA regulation of the Escherichia coli recN gene
A selective recognition mode of a nucleic acid base by an aromatic amino acid: L-phenylalanine-7-methylguanosine 5'-monophosphate stacking interaction
SWISS-MODEL: an automated protein homology-modeling server
FUGOID: functional genomics of organellar introns database
Allele-specific methylation and expression of an imprinted U2af1-rs1 (SP2) gene
Frog: a FRee Online druG 3D conformation generator
Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community
GRASP v2.0: an update on the Genome-Wide Repository of Associations between SNPs and phenotypes
SPICA: Swiss portal for immune cell analysis
MethDB - a public database for DNA methylation data
The UniProt Consortium: The Universal Protein Resource (UniProt)
The Database of Ribosomal Cross-links: an update
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences
Towards pathogenomics: a web-based resource for pathogenicity islands
The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression
Inducible expression based on regulated recombination: a single vector strategy for stable expression in cultured cells
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome
The Protein Data Bank
O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins
Editorial: The 16th annual Nucleic Acids Research web server issue 2018
Bio-TDS: bioscience query tool discovery system
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations
Gene3D: merging structure and function for a Thousand genomes
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
The UCSC Genome Browser Database: update 2006
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm
p53 activates the PANK1/ miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins
The mouse Gene Expression Database (GXD): updates and enhancements
APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived networks
POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level
PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins
Proteome- pI 2.0: proteome isoelectric point database update
rSNPBase: a database for curated regulatory SNPs
MetalPDB: a database of metal sites in biological macromolecular structures
MetaboAnalyst 3.0 - making metabolomics more meaningful
TRDB - The Tandem Repeats Database
MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics
snoDB: an interactive database of human snoRNA sequences, abundance and interactions
snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs
WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans
Crosslinking of the anticodon of P site bound tRNA to C-1400 of E.coli 16S RNA does not require the participation of the 50S subunit
A program for the identification of tRNA-like structures in DNA sequence data
LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
Detection of SstI restriction site polymorphism in human APOC3 by the polymerase chain reaction
The integrated microbial genomes system: an expanding comparative analysis resource
Sequence and position requirements for uridylate-rich downstream elements of polyadenylation signals
pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information
CauloBrowser: A systems biology resource for Caulobacter crescentus
UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models
KEYnet: a keywords database for biosequences functional organization
WashU Epigenome Browser update 2022
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis
HGVbase: a curated resource describing human DNA variation and phenotype relationships
The ENZYME data bank in 1999
FusionGDB 2.0: fusion gene annotation updates aided by deep learning
Nucleotide sequence of the mitochondrial genome of Paramecium
Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses
TFClass: a classification of human transcription factors and their rodent orthologs
GtRNAdb: a database of transfer RNA genes detected in genomic sequence
Characterization of the origins of replication of bacteriophage phi 29 DNA
The Histone Database
UniPrime2: a web service providing easier Universal Primer design
EcoCyc: Encyclopedia of Escherichia coli genes and metabolism
Aminoacyl-tRNA synthetases database Y2K
A program package applicable to the detection of overlaps between restriction maps
KBERG: KnowledgeBase for Estrogen Responsive Genes
OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes
Forum domain in Drosophila melanogaster cut locus possesses looped domains inside
SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants
GeneMANIA update 2018
ProAct: quantifying the differential activity of biological processes in tissues, cells, and user-defined contexts
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data
Alkaline deoxyribonucleases released from Neurospora crassa mycelia: two activities not released by mutants with multiple sensitivities to mutagens
R E MUS: a tool for identification of unique peptide segments as epitopes
The GOA database: Gene Ontology annotation updates for 2015
Factor D is a selective single-stranded oligodeoxythymidine binding protein
AAindex: amino acid index database, progress report 2008
SuperScent - a database of flavors and scents
The Gene Expression Barcode 3.0: improved data processing and mining tools
RaptorX-Property: a web server for protein structure property prediction
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes
TPMD: a database and resources of microsatellite marker genotyped in Taiwanese populations
Characteristics of trypanosome variant antigen genes active in the tsetse fly
DNA swivel enzyme activity in a nuclear membrane fraction
Open Targets Platform: new developments and updates two years on
14-3-3 associates with and activates the MEF2D transcription factor during muscle cell differentiation
The InterPro database, an integrated documentation resource for protein families, domains and functional sites
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017
WebGMAP: a web service for mapping and aligning cDNA sequences to genomes
Simple ClinVar: an interactive web server to explore and retrieve gene and disease variants aggregated in ClinVar database
Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human
Aquila: a spatial omics database and analysis platform
The IMG/M data management and analysis system v.7: content updates and new features
EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities
INDELSCAN: a web server for comparative identification of species-specific and non-species-specific insertion/deletion events