yusuke1997/dblp-id-title huggingface dataset:
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
MIPS: analysis and annotation of genome information in 2007
The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions
The neXtProt knowledgebase on human proteins: current status
A multi-fingerprint browser for the ZINC database
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses
Phospho.ELM: a database of phosphorylation sites - update 2011
dbRES: a web-oriented database for annotated RNA editing sites
Scalable web services for the PSIPRED Protein Analysis Workbench
Aspergillus Genomes and the Aspergillus Cloud
Annotating the human proteome: the Human Proteome Survey Database (HumanPSDTM) and an in-depth target database for G protein-coupled receptors (GPCR-PDTM) from Incyte Genomics
R-Coffee: a web server for accurately aligning noncoding RNA sequences
X-ray crystal structure of a dimethylene sulfone-bridged ribonucleotide dimer in a single-stranded state
PIDD: database for Protein Inter-atomic Distance Distributions
The PANTHER database of protein families, subfamilies, functions and pathways
inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data
ARED: human AU-rich element-containing mRNA database reveals an unexpectedly diverse functional repertoire of encoded proteins
The role of Schizosaccharomyces pombe Rad32, the Mre11 homologue, and other DNA damage response proteins in non-homologous end joining and telomere length maintenance
PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations
The Signal Recognition Particle Database (SRPDB)
The mitochondrial DNA polymerase as a target of oxidative damage
GBA server: EST-based digital gene expression profiling
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants
The UCSC Genome Browser database: 2019 update
G2PDeep: a web-based deep-learning framework for quantitative phenotype prediction and discovery of genomic markers
Ensembl 2009
Déjà vu: a database of highly similar citations in the scientific literature
Lynx web services for annotations and systems analysis of multi-gene disorders
Computer programs for nucleic acid sequence manipulation
APD: the Antimicrobial Peptide Database
Cell-type specific activity of two glucocorticoid responsive units of rat tyrosine aminotransferase gene is associated with multiple binding sites for C/EBP and a novel liver-specific nuclear factor
PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure
MetagenoNets: comprehensive inference and meta-insights for microbial correlation networks
StreptomeDB 2.0 - an extended resource of natural products produced by streptomycetes
IRESdb: the Internal Ribosome Entry Site database
The disease and gene annotations (DGA): an annotation resource for human disease
IMG/M: the integrated metagenome data management and comparative analysis system
SRPDB (Signal Recognition Particle Database)
Extending CATH: increasing coverage of the protein structure universe and linking structure with function
Nucleotide sequence of the human gamma cytoskeletal actin mRNA: anomalous evolution of vertebrate non-muscle actin genes
Synteny Portal: a web-based application portal for synteny block analysis
CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers
Quantitative PCR: validation of the use of a multispecific internal control
Nucleotide sequence of the infectious cloned DNA components of African cassava mosaic virus (Nigerian strain)
VBASE2, an integrative V gene database
DupScan: predicting and visualizing vertebrate genome duplication database
PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets
MiCroKiTS 4.0: a database of midbody, centrosome, kinetochore, telomere and spindle
DSSPcont: continuous secondary structure assignments for proteins
Sse8387I, a useful eight base cutter for mammalian genome analysis (influence of methylation on the activity of Sse8387I)
Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
The Addgene repository: an international nonprofit plasmid and data resource
MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data
BIC: a database for the transcriptional landscape of bacteria in cancer
Codon catalog usage is a genome strategy modulated for gene expressivity
IRESite - a tool for the examination of viral and cellular internal ribosome entry sites
CREAMMIST: an integrative probabilistic database for cancer drug response prediction
Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics
NOPdb: Nucleolar Proteome Database
NeXO Web: the NeXO ontology database and visualization platform
FGviewer: an online visualization tool for functional features of human fusion genes
Cloning and sequence analysis of gyrA gene of Klebsiella pneumoniae
Genomic database resources for Dictyostelium discoideum
DNA bending and unwinding due to the major 1, 2-GG intrastrand cross-link formed by antitumor cis-diamminedichloroplatinum(II) are flanking-base independent
rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA
LncBook: a curated knowledgebase of human long non-coding RNAs
Structural analysis of the mouse chromosomal gene encoding interleukin 4 which expresses B cell, T cell and mast cell stimulating activities
HuSiDa - the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells
DBTBS: a database of Bacillus subtilis promoters and transcription factors
Molecular Biology Database List
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function
NetworkAnalyst - integrative approaches for protein-protein interaction network analysis and visual exploration
Somatic point mutations in the p53 gene of human tumors and cell lines: updated compilation
SMOG@ctbp: simplified deployment of structure-based models in GROMACS
IXDB, an X chromosome integrated database
The UCSC Genome Browser database: 2022 update
GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers
HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm
Isolation and mapping of a polymorphic DNA sequence pEFZ18.2 on chromosome 14 [D14S17]
DBTGR: a database of tunicate promoters and their regulatory elements
eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping
The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts
Multiple genes encode the translation elongation factor EF-1 gamma in Saccharomyces cerevisiae
i SARST: an integrated SARST web server for rapid protein structural similarity searches
UTRome.org: a platform for 3'UTR biology in C. elegans
The human gene mutation database
SomaMutDB: a database of somatic mutations in normal human tissues
Genetic characterisation of hda1+, a putative fission yeast histone deacetylase gene
QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population
The mouse Gene Expression Database (GXD): 2007 update
PPT-DB: the protein property prediction and testing database
TreeFam: 2008 Update
Functional interaction between TFIIB and the Rpb9 (Ssu73) subunit of RNA polymerase II in Saccharomyces cerevisiae
Chemical and enzymatic biotin-labeling of oligodeoxyribonucleotides
A HindIII polymorphism in the 3' end of the human alpha 1(IV) collagen gene
primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies
ERGR: An ethanol-related gene resource
AOBase: a database for antisense oligonucleotides selection and design
GPRM: a genetic programming approach to finding common RNA secondary structure elements
MCPath: Monte Carlo path generation approach to predict likely allosteric pathways and functional residues
The UCSC Genome Browser database: 2016 update
The Comparative Toxicogenomics Database: update 2013
The Celera Discovery SystemTM
The Proteomics Identifications database: 2010 update
OpenXGR: a web-server update for genomic summary data interpretation
PlasMapper 3.0 - a web server for generating, editing, annotating and visualizing publication quality plasmid maps
RBPmap: a web server for mapping binding sites of RNA-binding proteins
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking
PROMISCUOUS 2.0: a resource for drug-repositioning
SGD: Saccharomyces Genome Database
BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes
PEDANT covers all complete RefSeq genomes
pKD: re-designing protein p K a values
Collection of mutant tRNA sequences
jpHMM: Improving the reliability of recombination prediction in HIV-1
ASRP: the Arabidopsis Small RNA Project Database
InBase: the Intein Database
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data
BitterDB: a database of bitter compounds
BRENDA, enzyme data and metabolic information
SchistoDB: an updated genome resource for the three key schistosomes of humans
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
Sequence and organization of barley yellow dwarf virus genomic RNA
MirZ: an integrated microRNA expression atlas and target prediction resource
MODBASE, a database of annotated comparative protein structure models
VIRGO: computational prediction of gene functions
HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor
DDBJ update: streamlining submission and access of human data
PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes
Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities
Gramene: a bird's eye view of cereal genomes
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays
Nucleotide sequence of the rice cytoplasmic aldolase cDNA
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Active nucleoprotein filaments of single-stranded binding protein and recA protein on single-stranded DNA have a regular repeating structure
Software.ncrna.org: web servers for analyses of RNA sequences
3DIV: A 3D-genome Interaction Viewer and database
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology
PREDITOR: a web server for predicting protein torsion angle restraints
Dual regulation of the Drosophila hsp26 promoter in vitro
The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions
Sequence specific cleavage of African green monkey alpha-satellite DNA by micrococcal nuclease
Initiation of HIV-2 reverse transcription: a secondary structure model of the RNA?tRNALys3 duplex
Olfactory Receptor Database: a database of the largest eukaryotic gene family
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
Alteration of apparent restriction endonuclease recognition specificities by DNA methylases
3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues
DynaMod: dynamic functional modularity analysis
Insertion (sufB) in the anticodon loop or base substitution (sufC) in the anticodon stem of tRNA(Pro)2 from Salmonella typhimurium induces suppression of frameshift mutations
MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes
Olfactory Receptor Database: a sensory chemoreceptor resource
PathPred: an enzyme-catalyzed metabolic pathway prediction server
Cloning and characterization of a single-stranded DNA binding protein that specifically recognizes deoxycytidine stretch
BIOLOG - a DNA sequence analysis system in PROLOG
Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures
The Diatom EST Database
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies
GeneView: a comprehensive semantic search engine for PubMed
BioModels: ten-year anniversary
PALI - a database of Phylogeny and ALIgnment of homologous protein structures
CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs
TREND: a platform for exploring protein function in prokaryotes based on phylogenetic, domain architecture and gene neighborhood analyses
Recode-2: new design, new search tools, and many more genes
Creation of a data base for sequences of ribosomal nucleic acids and detection of conserved restriction endonucleases sites through computerized processing
VisHiC - hierarchical functional enrichment analysis of microarray data
Yeast ochre suppressor SUQ5-ol is an altered tRNA Ser UCA
Theoretical study on the proton chemical shifts of hydrogen bonded nucleic acid bases
Complementation of defective translesion synthesis and UV light sensitivity in xeroderma pigmentosum variant cells by human and mouse DNA polymerase
GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis
POXO: a web-enabled tool series to discover transcription factor binding sites
transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels
Ubiquitous mammalian-wide interspersed repeats (MIRs) are molecular fossils from the mesozoic era
Lynx: a database and knowledge extraction engine for integrative medicine
ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online
Recent improvements to the PROSITE database
A cytological map of the human X chromosome - evidence for non-random recombination
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines
PHI-base update: additions to the pathogen-host interaction database
ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets
Seq2Logo : a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
NCBI GEO: mining millions of expression profiles - database and tools
GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization
Ensembl 2005
New tools and methods for direct programmatic access to the dbSNP relational database
Yeast Protein database (YPD): a database for the complete proteome of Saccharomyces cerevisiae
PEPVAC: a web server for multi-epitope vaccine development based on the prediction of supertypic MHC ligands
RNA binding characteristics and overall topology of the vaccinia poly(A) polymerase-processivity factor-primer complex
Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes
DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation
The Molecular Biology Database Collection: an updated compilation of biological database resources
IC 50 -to- K i : a web-based tool for converting IC 50 to K i values for inhibitors of enzyme activity and ligand binding
High-affinity RNA ligands to human alpha-thrombin
The Gypsy Database (GyDB) of mobile genetic elements
EcoCyc: an encyclopedia of Escherichia coli genes and metabolism
Binary vectors which allow the exchange of plant selectable markers and reporter genes
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
VnD: a structure-centric database of disease-related SNPs and drugs
GlycoMapsDB: a database of the accessible conformational space of glycosidic linkages
Bionemo: molecular information on biodegradation metabolism
A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources
CFEA: a cell-free epigenome atlas in human diseases
EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022
MS2PIP prediction server: compute and visualize MS2 peak intensity predictions for CID and HCD fragmentation
Sequence of mouse adenovirus type 1 DNA encoding the amino terminus of protein IVa2
The Candida Genome Database: The new homology information page highlights protein similarity and phylogeny
SEECancer: a resource for somatic events in evolution of cancer genome
C A DRE: the Central Aspergillus Data REpository 2012
Distal regulatory functions for the uvrC gene of E. coli
E-MSD: an integrated data resource for bioinformatics
PubChem Substance and Compound databases
WebTraceMiner: a web service for processing and mining EST sequence trace files
Cosmid 128 defines three RFLPs on chromosome 17q23-qter. [HGM9 no. D17S77]
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
The Sequence Read Archive: a decade more of explosive growth
PAT: a protein analysis toolkit for integrated biocomputing on the web
Synthesis and properties of oligonucleotides containing aminodeoxythymidine units
The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs
DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data
The pro alpha 2(V) collagen gene is evolutionarily related to the major fibrillar-forming collagens [published erratum appears in Nucleic Acids Res 1987 May 11;15(9): 3946]
The Proteome Analysis database: a tool for the in silico analysis of whole proteomes
Pfam: the protein families database
Isolation and mapping of a polymorphic DNA sequence pMHZ9 on chromosome 14 [D14S18]
TRANSPATH ® : an information resource for storing and visualizing signaling pathways and their pathological aberrations
mBodyMap: a curated database for microbes across human body and their associations with health and diseases
MGAlignIt: a web service for the alignment of mRNA/EST and genomic sequences
Nucleotide sequence encoding the 5' end of Xenopus laevis 18S rRNA
A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif
GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library
ARMADiLLO: a web server for analyzing antibody mutation probabilities
qPTM: an updated database for PTM dynamics in human, mouse, rat and yeast
TFSyntax: a database of transcription factors binding syntax in mammalian genomes
Erythroid-specific gene chromatin has an altered association with linker histones
An F factor based cloning system for large DNA fragments
Cluster-Buster: finding dense clusters of motifs in DNA sequences
WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences
SWAKK: a web server for detecting positive selection in proteins using a sliding window substitution rate analysis
LMPD: LIPID MAPS proteome database
MulPSSM: a database of multiple position-specific scoring matrices of protein domain families
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms
New genes for tRNA(Phe), tRNA(Leu), and tRNA(Thr) from Saccharomyces cerevisiae
NRSub: a non-redundant database for Bacillus subtilis
Fluorescent d(CGCGAATTCGCG): characterization of major groove polarity and study of minor groove interactions through a major groove semantophore conjugate
Homologous RNA recombination allows efficient introduction of site- specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs
SISYPHUS - structural alignments for proteins with non-trivial relationships
@TOME-2: a new pipeline for comparative modeling of protein-ligand complexes
Regular distribution of length heterogeneities within non-transcribed spacer regions of cloned and genomic rDNA of Saccharomyces cerevisiae
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
Complete cDNA sequence coding for human docking protein
Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pmel 17
A physical map of the genome of Mycoplasma mycoides subspecies mycoides Y with some functional loci
O-miner: an integrative platform for automated analysis and mining of -omics data
WormBook: the online review of Caenorhabditis elegans biology
Algorithms for restriction map comparisons
Editorial: the 19th annual Nucleic Acids Research web server issue 2021
ValidNESs: a database of validated leucine-rich nuclear export signals
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets
Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures
NUREBASE: database of nuclear hormone receptors
Editorial: Nucleic Acids Research annual Web Server Issue in 2015
Rfam: annotating non-coding RNAs in complete genomes
VFDB: a reference database for bacterial virulence factors
WormBase 2017: molting into a new stage
SNPbox: web-based high-throughput primer design from gene to genome
Nucleic acid secondary structure prediction and display
Victors: a web-based knowledge base of virulence factors in human and animal pathogens
The UCSC Genome Browser database: 2015 update
DISULFIND: a disulfide bonding state and cysteine connectivity prediction server
Advances in quantification and characterization of telomerase activity by the telomeric repeat amplification protocol (TRAP)
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
EzCatDB: the enzyme reaction database, 2015 update
MolSurfer: a macromolecular interface navigator
3DLigandSite: structure-based prediction of protein-ligand binding sites
SROOGLE: webserver for integrative, user-friendly visualization of splicing signals
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data
eQuilibrator - the biochemical thermodynamics calculator