yusuke1997/dblp-id-title huggingface dataset:
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
The SUPERFAMILY database in 2004: additions and improvements
VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees
NECTAR: a database of codon-centric missense variant annotations
The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms
Zinc(II) ions selectively interact with DNA sequences present at the TFIIIA binding site of the Xenopus 5S-RNA gene
Solid-phase synthesis of chelate-labelled oligonucleotides: application in triple-color ligase-mediated gene analysis
Xenbase: gene expression and improved integration
Aviator: a web service for monitoring the availability of web services
mCSM-NA: predicting the effects of mutations on protein-nucleic acids interactions
AraC-XylS database: a family of positive transcriptional regulators in bacteria
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs
The actinophage RP3 DNA integrates site-specifically into the putative tRNA(Arg)(AGG) gene of Streptomyces rimosus
Temperature and salt dependence of the gel migration anomaly of curved DNA fragments
NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions
The protein common assembly database (ProtCAD) - a comprehensive structural resource of protein complexes
i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly
PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data
Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV)
Assessment of major and minor groove DNA interactions by the zinc fingers of Xenopus transcription factor IIIA
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond
Analysis of the nucleic acid annealing activities of nucleocapsid protein from HIV-1
MARQ: an online tool to mine GEO for experiments with similar or opposite gene expression signatures
Complete nucleotide sequence of human glutamate dehydrogenase cDNA
IMGT®, the international ImMunoGeneTics information system®
antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences
OncoSearch: cancer gene search engine with literature evidence
Antisense properties of tricyclo-DNA
Database Resources of the National Center for Biotechnology Information
Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions
3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
SpliceDisease database: linking RNA splicing and disease
PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA
The Universal Protein Resource (UniProt) 2009
jMorp: Japanese Multi Omics Reference Panel
Improved cloning efficiency of polymerase chain reaction (PCR) products after proteinase K digestion
dictyBase - a Dictyostelium bioinformatics resource update
BEERE: a web server for biomedical entity expansion, ranking and explorations
VIPERdb: a relational database for structural virology
Double bands in DNA gel electrophoresis caused by bis-intercalating dyes
Molecular cloning of the mouse CCK gene: expression in different brain regions and during cortical development
CABS-flex: server for fast simulation of protein structure fluctuations
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11
The DARC site: a database of aligned ribosomal complexes
Update of KEYnet: a gene and protein names database for biosequences functional organisation
BayGenomics: a resource of insertional mutations in mouse embryonic stem cells
miRBase: integrating microRNA annotation and deep-sequencing data
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale
SA-Search: a web tool for protein structure mining based on a Structural Alphabet
PGDB: a curated and integrated database of genes related to the prostate
Translational enhancement of H-ferritin mRNA by interleukin-1 beta acts through 5' leader sequences distinct from the iron responsive element
SASBDB, a repository for biological small-angle scattering data
Helix geometry of single stranded DNA 'A' and 'B' forms from minimum energy conformations of dimeric subunits
ConsensusPathDB: toward a more complete picture of cell biology
PRGdb 4.0: an updated database dedicated to genes involved in plant disease resistance process
DISCO: a database of Deeply Integrated human Single-Cell Omics data
Termination of transcription in an 'in vitro' system is dependent on a polyadenylation sequence
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
kinDOCK: a tool for comparative docking of protein kinase ligands
The Unified Medical Language System (UMLS): integrating biomedical terminology
CDD: NCBI's conserved domain database
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research
A possible role of the 5' terminal sequence of 16S ribosomal RNA in the recognition of initiation sequences for protein synthesis
LocTree3 prediction of localization
InsectBase: a resource for insect genomes and transcriptomes
MetaCyc: a multiorganism database of metabolic pathways and enzymes
The iminoproton NMR spectrum of yeast tRNA-Phe predicted from crystal coordinates
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud
TargetRNA2: identifying targets of small regulatory RNAs in bacteria
The changes in proviral chromatin that accompany morphological variation in avian sarcoma virus-infected rat cells
Update of the viroid and viroid-like sequence database: addition of a hepatitis delta virus RNA section
The TIGR Rice Genome Annotation Resource: improvements and new features
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
ANTIMIC: a database of antimicrobial sequences
TRANSPATH: An integrated database on signal transduction and a tool for array analysis
HRTBLDb: an informative data resource for hormone receptors target binding loci
OrganellarGenomeDRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets
UCSC Genome Browser enters 20th year
Rapid one-step automated sequencing reactions for 16 DNA samples using Taq polymerase and fluorescent primers
CRISPRimmunity: an interactive web server for CRISPR-associated Important Molecular events and Modulators Used in geNome edIting Tool identifYing
A simple discontinuous buffer system for increased resolution and speed in gel electrophoretic analysis of DNA sequence
The SIDER database of drugs and side effects
DescribePROT: database of amino acid-level protein structure and function predictions
The bioinformatics resource for oral pathogens
H2DB: a heritability database across multiple species by annotating trait-associated genomic loci
DoriC 12.0: an updated database of replication origins in both complete and draft prokaryotic genomes
On the relationship between preferred termination codon contexts and nonsense suppression in human cells
Amino acid sequence of the testosterone-regulated mouse kidney RP2 protein deduced from its complementary DNA sequence
The mouse Gene Expression Database (GXD): 2017 update
MamPol: a database of nucleotide polymorphism in the Mammalia class
GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure
Stubb: a program for discovery and analysis of cis -regulatory modules
AnnotQTL: a new tool to gather functional and comparative information on a genomic region
Nucleotide sequence of 5S ribosomal RNA from Rhodococcus erythropolis
A direct selection strategy for shotgun cloning and sequencing in the bacteriophage M13
PEDANT genome database: 10 years online
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses
ASCancer Atlas: a comprehensive knowledgebase of alternative splicing in human cancers
PstI RFLP identified by an anonymous single copy genomic clone localized to chromosome 14 (HGM 9 provisional no. D14S14)
5S Ribosomal RNA Database
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
SynLeGG: analysis and visualization of multiomics data for discovery of cancer 'Achilles Heels' and gene function relationships
OnTarget: in silico design of MiniPromoters for targeted delivery of expression
Nucleotide sequence of the plastid 16S rRNA gene of the red alga Cyanidium caldarium
Multiple Oct2 isoforms are generated by alternative splicing
HOPPSIGEN: a database of human and mouse processed pseudogenes
AliWABA: alignment on the web through an A-Bruijn approach
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
CR2Cancer: a database for chromatin regulators in human cancer
siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
Sentra: a database of signal transduction proteins for comparative genome analysis
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences
Antibodies to hnRNP core proteins inhibit in vitro splicing of human beta-globin pre-mRNA
Alteration of the DNA double helix conformation upon incorporation of mispairs as revealed by energy computations and pathways of point mutations
Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals
CellFinder: a cell data repository
ATDB: a uni-database platform for animal toxins
Non-coding, mRNA-like RNAs database Y2K
mCSM-PPI2: predicting the effects of mutations on protein-protein interactions
SYNBIP: synthetic binding proteins for research, diagnosis and therapy
canSAR: updated cancer research and drug discovery knowledgebase
RegRNA: an integrated web server for identifying regulatory RNA motifs and elements
Mouse Tumor Biology (MTB): a database of mouse models for human cancer
EWASdb: epigenome-wide association study database
Dissection of the NF-Y transcriptional activation potential
Comparison of pneumolysin genes and proteins from Streptococcus pneumoniae types 1 and 2
o GNM: online computation of structural dynamics using the Gaussian Network Model
DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids
iPTMnet: an integrated resource for protein post-translational modification network discovery
The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts
The ENZYME data bank
Superior performance in protein homology detection with the Blocks Database servers
gcType: a high-quality type strain genome database for microbial phylogenetic and functional research
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine
SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases
The UCSC Genome Browser database: update 2011
RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data
PepSeeker: a database of proteome peptide identifications for investigating fragmentation patterns
The tmRNA website
Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment
Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes
Nucleotide sequence of Physarum U6 small RNA
Nucleotide sequence of the psbI gene of the cyanobacterium, Anacystis nidulans 6301
GLIDA: GPCR - ligand database for chemical genomics drug discovery - database and tools update
The reversible DNA-alkylating activity of duocarmycin and its analogues
pPyLT1 does not always dictate the formation of autonomously replicating elements in transgenic mice
SEM (Symmetry Equivalent Molecules): a web-based GUI to generate and visualize the macromolecules
MitBASE pilot: a database on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae
QuadBase: genome-wide database of G4 DNA - occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes
3DLigandSite: predicting ligand-binding sites using similar structures
Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Genomes OnLine Database (GOLD): a monitor of genome projects world-wide
CircleBase: an integrated resource and analysis platform for human eccDNAs
Evidence for the role of double-helical structures in the maturation of simian virus-40 messenger RNA
PASS2: a semi-automated database of Protein Alignments Organised as Structural Superfamilies
<tt>TADeus2</tt>: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure
NPInter v4.0: an integrated database of ncRNA interactions
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides
TCSBN: a database of tissue and cancer specific biological networks
Carbon-13 NMR in conformational analysis of nucleic acid fragments. 3. The magnitude of torsional angle epsilon in d(TpA) from CCOP and HCOP NMR coupling constants
Babelomics 5.0: functional interpretation for new generations of genomic data
PIECE: a database for plant gene structure comparison and evolution
PhD-SNPg: updating a webserver and lightweight tool for scoring nucleotide variants
Activation of transfer RNA-guanine ribosyltransferase by protein kinase C
ADDA: a domain database with global coverage of the protein universe
Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003
ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology
GAIA: G-quadruplexes in alive creature database
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators
A new method for the isolation of recombinant baculovirus
NCBI's LocusLink and RefSeq
Essential structural requirements for specific recognition of HIV TAR RNA by peptide mimetics of Tat protein
Dispensable role of the NF-kappa B sites in the UV-induction of the HIV- 1 LTR in transgenic mice
REPPER - repeats and their periodicities in fibrous proteins
Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling
KeyPathwayMinerWeb: online multi-omics network enrichment
High efficiency detection of bi-stranded abasic clusters in -irradiated DNA by putrescine
RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database
The human thyroglobulin gene is over 300 kb long and contains introns of up to 64 kb
Topoisomerase I is preferentially associated with normal SV40 replicative intermediates, but is associated with both replicating and nonreplicating SV40 DNAs which are deficient in histones
PMAP, PMAPS: DNA physical map constructing programs
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data
A DNA sequence handling program
Mouse Phenome Database (MPD)
Multiple mutations and frameshifts are the hallmark of defective hPMS2 in pZ189-transfected human tumor cells
rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation
AH-DB: collecting protein structure pairs before and after binding
On the epigenetic regulation of the human reelin promoter
The LightDock Server: Artificial Intelligence-powered modeling of macromolecular interactions
RNAbor: a web server for RNA structural neighbors
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009
EVALLER: a web server for in silico assessment of potential protein allergenicity
YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
The life sciences Global Image Database (GID)
A rapid method for measuring the steady state levels of mitochondrial RNA in whole mitochondria
tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers
The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database
SA-Mot: a web server for the identification of motifs of interest extracted from protein loops
A series of PDB related databases for everyday needs
The Molecular Biology Database Collection: 2002 update
Carp preproinsulin cDNA sequence and evolution of insulin genes
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases
The SNP Consortium website: past, present and future
GreenPhylDB: a database for plant comparative genomics
miRCarta: a central repository for collecting miRNA candidates
EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments
MOWServ: a web client for integration of bioinformatic resources
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing
PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
APAatlas: decoding alternative polyadenylation across human tissues
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
PlantsP: a functional genomics database for plant phosphorylation
CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics
Protonated pyrimidine-purine-purine triplex
AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes
GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
Web API for biology with a workflow navigation system
DEPICTER2: a comprehensive webserver for intrinsic disorder and disorder function prediction
MIPS PlantsDB: a database framework for comparative plant genome research
Requirement of chain initiation factor 3 and ribosomal protein S1 in translation of synthetic and natural messenger RNA
Formation of several specific nucleoprotein complexes on the human cytomegalovirus immediate early enhancer
STING Millennium: a web-based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence
REBASE - restriction enzymes and methylases
CABS-fold: server for the de novo and consensus-based prediction of protein structure
IDT SciTools: a suite for analysis and design of nucleic acid oligomers
ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes
SYSTOMONAS - an integrated database for systems biology analysis of Pseudomonas
3D-Fun: predicting enzyme function from structure
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era
Aptamer Database
HGVA: the Human Genome Variation Archive
Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
MPact: the MIPS protein interaction resource on yeast
CoCoCoNet: conserved and comparative co-expression across a diverse set of species
TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage
DILIMOT: discovery of linear motifs in proteins
The UCSC Genome Browser database: extensions and updates 2011
Molecular recognition of tRNA(Pro) by Escherichia coli proline tRNA synthetase in vitro
Protemot: prediction of protein binding sites with automatically extracted geometrical templates
FlyRNAi.org - the database of the Drosophila RNAi screening center: 2012 update
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data
The CGView Server: a comparative genomics tool for circular genomes
Computer programs for handling nucleic acid sequences
JAIL: a structure-based interface library for macromolecules
Enzyme-linked synthetic oligonucleotide probes: non-radioactive detection of enterotoxigenic Escherichia coli in faecal specimens
User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org
MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems
metaSHARK: a WWW platform for interactive exploration of metabolic networks
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection
HOCOMOCO: a comprehensive collection of human transcription factor binding sites models
AsMamDB: an alternative splice database of mammals
ESC: a comprehensive resource for SARS-CoV-2 immune escape variants
Atlas of Genetics and Cytogenetics in Oncology and Haematology, updated
GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools
ViPR: an open bioinformatics database and analysis resource for virology research
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications
TIRSF: a web server for screening gene signatures to predict Tumor immunotherapy response
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment
EcoCyc: a comprehensive database of Escherichia coli biology
iMolTalk: an interactive, internet-based protein structure analysis server
Eight different highly specific nucleosome phases on alpha-satellite DNA in the African green monkey
AcrHub: an integrative hub for investigating, predicting and mapping anti-CRISPR proteins
FABIAN-variant: predicting the effects of DNA variants on transcription factor binding
Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis
The RosettaDock server for local protein-protein docking
COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation
BodyMap incorporated PCR-based expression profiling data and a gene ranking system
Fast computer search for similar DNA sequences
EcoT14I RFLP found at the human amyloid beta protein gene locus