yusuke1997/dblp-id-title huggingface dataset:
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria
Dinucleotide repeat polymorphisms at the D7S435 and D7S440 loci
KinMutBase, a database of human disease-causing protein kinase mutations
Microcomputer programs for graphic analysis of nucleic acid and protein sequences
GeneFriends: a human RNA-seq-based gene and transcript co-expression database
PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences
ParticleStats: open source software for the analysis of particle motility and cytoskeletal polarity
ONQUADRO: a database of experimentally determined quadruplex structures
FAN: fingerprint analysis of nucleotide sequences
MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation
MeMotif: a database of linear motifs in α-helical transmembrane proteins
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data
RTCGD: retroviral tagged cancer gene database
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins
EpiRegio: analysis and retrieval of regulatory elements linked to genes
The ribonuclease P database
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009
U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome
Oracle Database 10 g : a platform for BLAST search and Regular Expression pattern matching in life sciences
probeBase: an online resource for rRNA-targeted oligonucleotide probes
Phytozome: a comparative platform for green plant genomics
The La antigen inhibits the activation of the interferon-inducible protein kinase PKR by sequestering and unwinding double-stranded RNA
NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
GPCRDB: an information system for G protein-coupled receptors
STRING v10: protein-protein interaction networks, integrated over the tree of life
Translesional synthesis on DNA templates containing the 2'-deoxyribonolactone lesion
Ensembl Genomes 2013: scaling up access to genome-wide data
Human Proteinpedia: a unified discovery resource for proteomics research
KOMODO: a web tool for detecting and visualizing biased distribution of groups of homologous genes in monophyletic taxa
iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains
Haemophilia B: database of point mutations and short additions and deletions--eighth edition
MirGeneDB 2.1: toward a complete sampling of all major animal phyla
Kabat Database and its applications: future directions
A new generation of JASPAR, the open-access repository for transcription factor binding site profiles
MITOP: database for mitochondria-related proteins, genes and diseases
Splicing of a C. elegans myosin pre-mRNA in a human nuclear extract
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities
A new version of the RDP (Ribosomal Database Project)
CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
Post-PCR sterilization: a method to control carryover contamination for the polymerase chain reaction
LIPID MAPS online tools for lipid research
Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription
The sequence read archive: explosive growth of sequencing data
TRED: a transcriptional regulatory element database, new entries and other development
A novel 3' extension technique using random primers in RNA-PCR
dbPSHP: a database of recent positive selection across human populations
DDInter: an online drug-drug interaction database towards improving clinical decision-making and patient safety
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants
FATCAT 2.0: towards a better understanding of the structural diversity of proteins
Isolation and mapping of a polymorphic DNA sequence pMLJ14 on chromosome 14 [D14S13]
IMGT, the International ImMunoGeneTics database
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
DeepRefiner: high-accuracy protein structure refinement by deep network calibration
NRED: a database of long noncoding RNA expression
The omics discovery REST interface
AcrFinder: genome mining anti-CRISPR operons in prokaryotes and their viruses
PepX: a structural database of non-redundant protein-peptide complexes
HEXEvent: a database of Human EXon splicing Events
PubTator: a web-based text mining tool for assisting biocuration
In vivo transcription from multiple spacer rRNA gene promoters during early development and evolution of the intergenic spacer in the brine shrimp Artemia
MitoBreak: the mitochondrial DNA breakpoints database
An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules
Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations
The human (PEDB) and mouse (mPEDB) Prostate Expression Databases
Structure and expression of the Euglena gracilis nuclear gene coding for the translation elongation factor EF-1 alpha
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing
FoldamerDB: a database of peptidic foldamers
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database
LYRA, a webserver for lymphocyte receptor structural modeling
PhycoCosm, a comparative algal genomics resource
GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications
Viscometric analysis of the interaction of bisphenanthridinium compounds with closed circular supercoiled and linear DNA
The reciprocal recombination product of a VK-JK joining reaction remains on chromosome 2p12
The genome portal of the Department of Energy Joint Genome Institute: 2014 updates
WormBase: a multi-species resource for nematode biology and genomics
3V: cavity, channel and cleft volume calculator and extractor
ENCODE whole-genome data in the UCSC Genome Browser: update 2012
SelTar base , a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology
MODBASE: a database of annotated comparative protein structure models and associated resources
The RNA Virus Database
BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases
The tmRNA Website: invasion by an intron
Single copy probe CRI-L1065 (D6S21) maps to 6cen-6q21
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
ActionMap: a web-based software that automates loci assignments to framework maps
Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database
The international nucleotide sequence database collaboration
SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry
D7S448 detects a HindIII polymorphism located in the centromere region of chromosome 7
Computer methods to locate signals in nucleic acid sequences
HMDD v3.0: a database for experimentally supported human microRNA-disease associations
PCAF interacts with XBP-1S and mediates XBP-1S-dependent transcription
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks
Use of n-butanol for efficient recovery of minute amounts of small RNA fragments and branched nucleotides from dilute solutions
Identifying synonymous regulatory elements in vertebrate genomes
FunTree: advances in a resource for exploring and contextualising protein function evolution
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs
TRANSFAC: an integrated system for gene expression regulation
Direct selection of stabilised yeast URA3 transformants with 5- fluorouracil
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse
Prediction of protein structures, functions and interactions using the IntFOLD7, MultiFOLD and ModFOLDdock servers
BacMet: antibacterial biocide and metal resistance genes database
GabiPD: the GABI primary database - a plant integrative 'omics' database
BIND - The Biomolecular Interaction Network Database
Sequence homologies among the three yolk polypeptide (Yp) genes in Drosophila melanogaster
REPK: an analytical web server to select restriction endonucleases for terminal restriction fragment length polymorphism analysis
Walking of antitumor bifunctional trinuclear Pt II complex on double-helical DNA
Identification of the 10Sa RNA structural gene of Mycobacterium tuberculosis
Minimotif Miner 3.0: database expansion and significantly improved reduction of false-positive predictions from consensus sequences
Marfan Database (third edition): new mutations and new routines for the software
Fluorescence studies of the accessibility of the 3' ends of the ribosomal RNAs in Escherichia coli ribosomes and subunits
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
STCRDab: the structural T-cell receptor database
Membranome: a database for proteome-wide analysis of single-pass membrane proteins
ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability
The PROSITE database, its status in 1995
WormBase: a modern Model Organism Information Resource
A large database DNA sequence handling program with generalized searching specifications
HIstome - a relational knowledgebase of human histone proteins and histone modifying enzymes
Primary structure of the soybean nodulin-23 gene and potential regulatory elements in the 5'-flanking regions of nodulin and leghemoglobin genes
The nucleotide sequence of a Drosophila melanogaster enolase gene
The Pfam protein families database
PopHumanVar: an interactive application for the functional characterization and prioritization of adaptive genomic variants in humans
Recent enhancements to the Blocks Database servers
Common structural features of the genes for two stable RNAs from Halobacterium halobium
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data
SEanalysis 2.0: a comprehensive super-enhancer regulatory network analysis tool for human and mouse
PharmGKB: the Pharmacogenetics Knowledge Base
miRNEST 2.0: a database of plant and animal microRNAs
The Soybean Genome Database (SoyGD): a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max
REPAIRtoire - a database of DNA repair pathways
A web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications
CFM-ID 4.0 - a web server for accurate MS-based metabolite identification
DGIdb 2.0: mining clinically relevant drug-gene interactions
Wanda: a database of duplicated fish genes
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse
SPASCER: spatial transcriptomics annotation at single-cell resolution
Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites
CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria
Interactive microbial distribution analysis using BioAtlas
CUPSAT: prediction of protein stability upon point mutations
Viral RNA annealing activities of the nucleocapsid protein of Moloney murine leukemia virus are zinc independent
SysZNF: the C2H2 zinc finger gene database
DockCoV2: a drug database against SARS-CoV-2
BioProfiling.de: analytical web portal for high-throughput cell biology
Double-stranded cucumovirus associated RNA 5: experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophore sis
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering
SEQ: a nucleotide sequence analysis and recombination system
ZOVER: the database of zoonotic and vector-borne viruses
DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data
MetaboLights: a resource evolving in response to the needs of its scientific community
TFClass: expanding the classification of human transcription factors to their mammalian orthologs
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes
PlaMoM: a comprehensive database compiles plant mobile macromolecules
ArrayExpress - a public database of microarray experiments and gene expression profiles
MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis
The PROSITE database, its status in 1997
MGA repository: a curated data resource for ChIP-seq and other genome annotated data
The Mouse Gene Expression Database (GXD)
SwissTargetPrediction: a web server for target prediction of bioactive small molecules
The role of DNA polymerase beta in determining sensitivity to ionizing radiation in human tumor cells
PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties
ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics
MAGEST: MAboya Gene Expression patterns and Sequence Tags
The European Nucleotide Archive in 2017
CodonO: codon usage bias analysis within and across genomes
EcoGene: a genome sequence database for Escherichia coli K-12
Conformational studies of (2'-5') polynucleotides: theoretical computations of energy, base morphology, helical structure, and duplex formation
Identification of a putative RNA dependent RNA polymerase encoded by a yeast double stranded RNA virus
siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins
Metalloregulation of the cyanobacterial smt locus: identification of SmtB binding sites and direct interaction with metals
KEGG Atlas mapping for global analysis of metabolic pathways
COSMIC: somatic cancer genetics at high-resolution
MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation
CKAAPs DB: a conserved key amino acid positions database
Biological Magnetic Resonance Data Bank
Database resources of the National Center for Biotechnology
HorA web server to infer homology between proteins using sequence and structural similarity
AMIC@: All MIcroarray Clusterings @ once
SIGNOR 3.0, the SIGnaling network open resource 3.0: 2022 update
ProSAT2 - Protein Structure Annotation Server
Galaxy7TM: flexible GPCR-ligand docking by structure refinement
AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets
The FoldX web server: an online force field
AREsite: a database for the comprehensive investigation of AU-rich elements
LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana
Multiple interdependent regulatory sites in the mouse c-fos promoter determine basal level transcription: cell type-specific effects
FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB
INFEVERS: the Registry for FMF and hereditary inflammatory disorders mutations
CancerGenes: a gene selection resource for cancer genome projects
YMF: a program for discovery of novel transcription factor binding sites by statistical overrepresentation
ChiTaRS-3.1 - the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions
EuPathDB: the eukaryotic pathogen genomics database resource
RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements
BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference
LitCovid in 2022: an information resource for the COVID-19 literature
EpoDB: a database of genes expressed during vertebrate erythropoiesis
Analysis of the attachment of replicating DNA to a nuclear matrix in mammalian interphase nuclei
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition
Interactive computer programs in sequence data analysis
COUGER - co-factors associated with uniquely-bound genomic regions
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets
MutationTaster2021
Editorial: the 18th annual Nucleic Acids Research web server issue 2020
WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches
Modulation of enzymatic activities of Escherichia coli DnaB helicase by single-stranded DNA-binding proteins
BriX: a database of protein building blocks for structural analysis, modeling and design
Computer-based image analysis of one-dimensional electrophoretic gels used for the separation of DNA restriction fragments
PhysBinder: improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties
Positive regulation of the colicin E1 gene by cyclic AMP and cyclic AMP receptor protein
BeetleBase: the model organism database for Tribolium castaneum
Complete nucleotide sequence of the ribosomal RNA tandem repeat unit from Giardia intestinalis
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer
RPF: a quality assessment tool for protein NMR structures
PROSITE, a protein domain database for functional characterization and annotation
ADHDgene: a genetic database for attention deficit hyperactivity disorder
NAPP: the Nucleic Acid Phylogenetic Profile Database
The wild-type nucleotide sequence of the rpoBC-attenuator region of Escherichia coli DNA and its implications for the nature of the rifd18 mutation
EvoDesign: de novo protein design based on structural and evolutionary profiles
cat RAPID omics v2.0 : going deeper and wider in the prediction of protein-RNA interactions
MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
Protein Data Bank: the single global archive for 3D macromolecular structure data
RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
ncFANs v2.0: an integrative platform for functional annotation of non-coding RNAs
CRAMdb: a comprehensive database for composition and roles of microbiome in animals
A computer package for DNA sequence analysis
Araport: the Arabidopsis Information Portal
RefSeq: an update on mammalian reference sequences
GoPubMed: exploring PubMed with the Gene Ontology
MITOMAP: a human mitochondrial genome database - 2004 update
Proteome-pI: proteome isoelectric point database
Onto-Tools: new additions and improvements in 2006
BhairPred: prediction of ß-hairpins in a protein from multiple alignment information using ANN and SVM techniques
iProX: an integrated proteome resource
VectorBase: a data resource for invertebrate vector genomics
Delila system tools
Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics
Information Commons for Rice (IC4R)
Nucleotide sequence of the integrase (IN) gene of an endogenous murine leukemia retroviral DNA
IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis
NACDDB: Nucleic Acid Circular Dichroism Database
Solution structure of human U1 snRNA. Derivation of a possible three- dimensional model
Deciphering key features in protein structures with the new ENDscript server
GREENC: a Wiki-based database of plant lncRNAs
GenBank: update
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions
A novel method for the genome-wide high resolution analysis of DNA damage
Multilevel regulation of histone gene expression during the cell cycle in tobacco cells
Circular dichroism spectra of twelve short DNA restriction fragments of known sequence: a comparison of measured and calculated spectra
Genome organization of the killer plasmid pGK12 from Kluyveromyces lactis
MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002
5S Ribosomal RNA Data Bank
DNA polymerase I and a protein complex bind specifically to E. coli palindromic unit highly repetitive DNA: implications for bacterial chromosome organization
miRGen 2.0: a database of microRNA genomic information and regulation
PlantNATsDB: a comprehensive database of plant natural antisense transcripts
Studies on the structure of replicative intermediates in bacteriophage M13 single stranded DNA synthesis
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007
The Protein Information Resource
Dragon ERE Finder version 2: a tool for accurate detection and analysis of estrogen response elements in vertebrate genomes
MarkerDB: an online database of molecular biomarkers
EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)
SureChEMBL: a large-scale, chemically annotated patent document database
VIGOR extended to annotate genomes for additional 12 different viruses
VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics
PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics
PseudoBase: structural information on RNA pseudoknots
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces
NONCODEv4: exploring the world of long non-coding RNA genes
PALS db: Putative Alternative Splicing database
MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm
DNA intercalation without flipping in the specific ThaI-DNA complex
Structural and transcriptional analysis of a human subtelomeric repeat
The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019
VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
The Papillomavirus Episteme: a central resource for papillomavirus sequence data and analysis
5'SAGE: 5'-end Serial Analysis of Gene Expression database
Genew: the Human Gene Nomenclature Database, 2004 updates
Two members of an HNF1 homeoprotein family are expressed in human liver
IR study of base stacking interactions
O6-methylguanine in the SV40 origin of replication inhibits binding but increases unwinding by viral large T antigen
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
MIPS: a database for protein sequences, homology data and yeast genome information
DLEB: a web application for building deep learning models in biological research
GESS: a database of global evaluation of SARS-CoV-2/hCoV-19 sequences
WebGeSTer DB - a transcription terminator database