yusuke1997/dblp-id-title huggingface dataset:
Database for mobile group II introns
MovieMaker: a web server for rapid rendering of protein motions and interactions
KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007
MyHits: improvements to an interactive resource for analyzing protein sequences
SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
StyI RFLP of the human platelet derived growth factor (PDGF) A-chain gene
cDNA sequence of the env gene of a pathogenic equine infectious anemia lentivirus variant
Gramene 2013: comparative plant genomics resources
BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature
CPPsite 2.0: a repository of experimentally validated cell-penetrating peptides
Transcriptome visualization and data availability at the Saccharomyces Genome Database
The Transporter Classification Database: recent advances
Molecular modelling study of changes induced by netropsin binding to nucleosome core particles
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
UniCarbKB: building a knowledge platform for glycoproteomics
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees
Nucleotide sequence of a 16S ribosomal RNA gene from Neisseria gonorrhoeae
CORG: a database for COmparative Regulatory Genomics
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions
Ensembl 2021
PromoSer: improvements to the algorithm, visualization and accessibility
Hubba: hub objects analyzer - a framework of interactome hubs identification for network biology
Organization and upstream DNA sequence of the mouse protease inhibitor gene
Sequence comparison by exponentially-damped alignment
The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis
deconSTRUCT: general purpose protein database search on the substructure level
PlantRNA, a database for tRNAs of photosynthetic eukaryotes
MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search
Non-contact positions impose site selectivity on Cre recombinase
Multiplex strand displacement amplification (SDA) and detection of DNA sequences from Mycobacterium tuberculosis and other mycobacteria
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response
HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project
CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Thermodynamic behaviour of the heptadecadeoxynucleotide d(CGCGCGTTTTTCGCGCG) forming B and Z hairpins in aqueous solution
GTRD: a database on gene transcription regulation - 2019 update
Methylphosphonate mapping of phosphate contacts critical for RNA recognition by the human immunodeficiency virus tat and rev proteins
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays
Extensive mitochondrial specific transcription of the Brassica campestris mitochondrial genome
qPrimerDB: a thermodynamics-based gene-specific qPCR primer database for 147 organisms
SCOR: Structural Classification of RNA, version 2.0
NCBI's Database of Genotypes and Phenotypes: dbGaP
ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry
The neXtProt knowledgebase in 2020: data, tools and usability improvements
cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function
A rapid method of non-radioactive detection of DNA-fragments in dried agarose gels
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap
SUMOsp: a web server for sumoylation site prediction
AlloReverse: multiscale understanding among hierarchical allosteric regulations
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants
CATH: expanding the horizons of structure-based functional annotations for genome sequences
Primary and secondary structure of a new viroid 'species' (CbVd 1) present in the Coleus blumei cultivar 'Bienvenue'
STRAW: Species TRee Analysis Web server
WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar
Identification of proteins interacting with the enhancer of human U2 small nuclear RNA genes
Nucleotide sequence of Clostridium difficile toxin B gene
PDBsum additions
The FALC-Loop web server for protein loop modeling
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex
RSAT 2022: regulatory sequence analysis tools
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade
NAR Breakthrough Article: The Vertebrate Genome Annotation browser 10 years on
PROMISCUOUS: a database for network-based drug-repositioning
NMPdb: Database of Nuclear Matrix Proteins
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters
EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments
Web services at the European Bioinformatics Institute-2009
PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update
CausalMGM: an interactive web-based causal discovery tool
The Degradome database: expanding roles of mammalian proteases in life and disease
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database
SZGR 2.0: a one-stop shop of schizophrenia candidate genes
DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web
YEASTRACT: an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae
SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition
BiG-FAM: the biosynthetic gene cluster families database
Nucleotide sequence of the murD gene encoding the UDP-MurNAc-L-Ala-D- Glu synthetase of Escherichia coli
GeneSpeed: protein domain organization of the transcriptome
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data
DRESIS: the first comprehensive landscape of drug resistance information
FastContact: a free energy scoring tool for protein-protein complex structures
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
CancerSEA: a cancer single-cell state atlas
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature
pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins
RTKdb: database of receptor tyrosine kinase
The complete nucleotide sequence of a rice 17S rRNA gene
The BioMart community portal: an innovative alternative to large, centralized data repositories
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer
PromAn: an integrated knowledge-based web server dedicated to promoter analysis
WebInterViewer: visualizing and analyzing molecular interaction networks
Human uracil DNA N-glycosidase: studies in normal and repair defective cultured fibroblasts
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species
SH3-Hunter: discovery of SH3 domain interaction sites in proteins
Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes
GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments
FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking
TAM 2.0: tool for MicroRNA set analysis
GENSTYLE: exploration and analysis of DNA sequences with genomic signature
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes
ConjuPepDB: a database of peptide-drug conjugates
Pathway Commons, a web resource for biological pathway data
HARMONY: a server for the assessment of protein structures
PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes
MutScreener: primer design tool for PCR-direct sequencing
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface
METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters
The 2013 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
Software and database for the analysis of mutations in the human WT1 gene
Aging Chart: a community resource for rapid exploratory pathway analysis of age-related processes
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets
BIS2Analyzer: a server for co-evolution analysis of conserved protein families
Construction of a genomic DNA 'feature map' by sequencing from nested deletions: application to the HLA class I region
VarAFT: a variant annotation and filtration system for human next generation sequencing data
BioMart Central Portal - unified access to biological data
SCOP database in 2004: refinements integrate structure and sequence family data
T3DB: a comprehensively annotated database of common toxins and their targets
DrugBank: a comprehensive resource for in silico drug discovery and exploration
Supercoiling in prokaryotic and eukaryotic DNA: changes in response to topological perturbation of plasmids in E. coli and SV40 in vitro, in nuclei and in CV-1 cells
IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species
Related transposons in C.elegans and D.melanogaster
GeneDB: a resource for prokaryotic and eukaryotic organisms
Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes
The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes
New tools at the Candida Genome Database: biochemical pathways and full-text literature search
Efficient algorithms for folding and comparing nucleic acid sequences
A novel in vivo assay for the analysis of protein-protein interaction
Two-dimensional graphic analysis of DNA sequence homologies
CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase
BRENDA, the enzyme database: updates and major new developments
Nucleotide sequence of the gene for elongation factor EF-1 alpha from the extreme thermophilic archaebacterium Thermococcus celer
rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks
Malaria.tools - comparative genomic and transcriptomic database for Plasmodium species
LitInspector: literature and signal transduction pathway mining in PubMed abstracts
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
CombFunc: predicting protein function using heterogeneous data sources
Telomere directed fragmentation of mammalian chromosomes
cDNA encoding a human homolog of yeast ubiquitin 1
diArk - the database for eukaryotic genome and transcriptome assemblies in 2014
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data
In vivo transcription of the E. coli uvrB gene: both promoters are inducible by UV
Cloning and characterisation of a nuclear, site specific ssDNA binding protein
LegumeIP 2.0 - a platform for the study of gene function and genome evolution in legumes
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides
DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates
ACLAME: A CLAssification of Mobile genetic Elements
sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach
KARMA: a web server application for comparing and annotating heterogeneous microarray platforms
THGS: a web-based database of Transmembrane Helices in Genome Sequences
MIPS: curated databases and comprehensive secondary data resources in 2010
cisRED: a database system for genome-scale computational discovery of regulatory elements
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
Isolation and mapping of a polymorphic DNA sequence (cMCOE32) on chromosome 2 [D2S53]
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs
A collection of programs for nucleic acid and protein analysis, written in FORTRAN 77 for IBM-PC compatible microcomputers
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria
CSTEA: a webserver for the Cell State Transition Expression Atlas
O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins
EVmiRNA: a database of miRNA profiling in extracellular vesicles
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
EURISCO: The European search catalogue for plant genetic resources
DNAvisualization.org: a serverless web tool for DNA sequence visualization
Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protein
C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms
The SysteMHC Atlas project
MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons
PROBFIND: a computer program for selecting oligonucleotide probes from peptide sequences
The aminoacyl-tRNA Synthetase Data Bank (AARSDB)
Memoir: template-based structure prediction for membrane proteins
CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics
GWIDD: Genome-wide protein docking database
mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance
A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species
SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology
BμG@Sbase - a microbial gene expression and comparative genomic database
ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites
IBS 2.0: an upgraded illustrator for the visualization of biological sequences
NCBI BLAST: a better web interface
PCDDB: the protein circular dichroism data bank, a repository for circular dichroism spectral and metadata
GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis
The release of high mobility group protein H6 and protamine gene sequences upon selective DNase I degradation of trout testis chromatin
A mutation spectra database for bacterial and mammalian genes
Locus Reference Genomic: reference sequences for the reporting of clinically relevant sequence variants
The European Nucleotide Archive
IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq
hMYH cell cycle-dependent expression, subcellular localization and association with replication foci: evidence suggesting replication-coupled repair of adenine: 8-oxoguanine mispairs
The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae
WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes
FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas
GDB: the Human Genome Database
TreeDomViewer: a tool for the visualization of phylogeny and protein domain structure
PharmGED: Pharmacogenetic Effect Database
The observation of the local ordering characteristics of spermidine- condensed DNA: atomic force microscopy and polarizing microscopy studies
AgBase: a unified resource for functional analysis in agriculture
Increasing the Fokl cleavage specificity from 5 to 7 base pairs by two-step methylation
Carbohydrate Structure Suite (CSS): analysis of carbohydrate 3D structures derived from the PDB
Bcl-1 RFLP at the human hepatic lipase gene locus (CIPC)
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions
OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates
Cube-DB: detection of functional divergence in human protein families
SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts
VisANT: data-integrating visual framework for biological networks and modules
G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery
Keio Mutation Database for eye disease genes (KMeyeDB)
PromoterCAD: data-driven design of plant regulatory DNA
WAR: Webserver for aligning structural RNAs
Assigning genomic sequences to CATH
TreeFam: a curated database of phylogenetic trees of animal gene families
Genonets server - a web server for the construction, analysis and visualization of genotype networks
Persistence of bovine papillomavirus (pBPV-1) as an extrachromosomal element in tissues of microinjected Xenopus laevis
Subspecies of DNA polymerase alpha from calf thymus with different fidelity in copying synthetic template-primers
Assembly information services in the European Nucleotide Archive
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones
The Gene Resource Locator: gene locus maps for transcriptome analysis
The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information
A frequent Pvu II RFLP of the human gastrin releasing peptide gene
APC gene: database of germline and somatic mutations in human tumors and cell lines
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
RNAmutants: a web server to explore the mutational landscape of RNA secondary structures
Identification and characterization of negative regulatory elements of the human telomerase catalytic subunit (hTERT) gene promoter: possible role of MZF-2 in transcriptional repression of hTERT
Expanded protein information at SGD: new pages and proteome browser
UFCG: database of universal fungal core genes and pipeline for genome-wide phylogenetic analysis of fungi
Comparative Toxicogenomics Database (CTD): update 2021
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0
PINA v2.0: mining interactome modules
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
The interaction of RNA polymerase and lac repressor with the lac control region
ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization
Alternative pathways for editing non-cognate amino acids by aminoacyl- tRNA synthetases
Nucleotide sequences of tRNA genes in Streptomyces lividans 66
The EcoCyc and MetaCyc databases
The IPD-IMGT/HLA Database
CVCDAP: an integrated platform for molecular and clinical analysis of cancer virtual cohorts
IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis
The Natural Products Atlas 2.0: a database of microbially-derived natural products
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria
The Molecular Biology Database Collection: 2008 update
CATH: increased structural coverage of functional space
MetaCrop 2.0: managing and exploring information about crop plant metabolism
The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog
MycoCosm portal: gearing up for 1000 fungal genomes
Unusual anticodon loop structure found in E.coli lysine tRNA
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes
TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
ChEMBL: towards direct deposition of bioassay data
The BioGRID Interaction Database: 2011 update
RADAR: a rigorously annotated database of A-to-I RNA editing
Rapid turnover of the histone-ubiquitin conjugate, protein A24
The iceLogo web server and SOAP service for determining protein consensus sequences
Sequence of a ubiquitin carboxyl extension protein of Nicotiana tabacum
Nucleotide sequence of gene 2 of the UK tissue culture adapted strain of bovine rotavirus
Search and sequence analysis tools services from EMBL-EBI in 2022
NGPhylogeny.fr: new generation phylogenetic services for non-specialists
PAT: a comprehensive database of prokaryotic antimicrobial toxins
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems
RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12
S4: structure-based sequence alignments of SCOP superfamilies
Role of transcript and interplay between transcription and replication in triplet-repeat instability in mammalian cells
<tt>CRISPRloci: </tt> comprehensive and accurate annotation of CRISPR-Cas systems
DBcat: a catalog of biological databases
Target Explorer: an automated tool for the identification of new target genes for a specified set of transcription factors
HOWDY: an integrated database system for human genome research
Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC
MAVID multiple alignment server
P-MITE: a database for plant miniature inverted-repeat transposable elements
ClinVar: public archive of interpretations of clinically relevant variants
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes
Human BAC Ends
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models
HCAD, closing the gap between breakpoints and genes
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features
NutriChem: a systems chemical biology resource to explore the medicinal value of plant-based foods
Differential detection of multiple DNA-binding complexes using dissimilar polyanion competitors
Nucleotide sequence of the gene coding for cyclophilin/peptidyl-prolyl cis-trans isomerase of Neurospora crassa
OriDB, the DNA replication origin database updated and extended
CDD/SPARCLE: the conserved domain database in 2020
Animal-APAdb: a comprehensive animal alternative polyadenylation database
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
Conformational change of Escherichia coli initiator methionyl-tRNAfMet upon binding to methionyl-tRNA formyl transferase
Polypurine/polypyrimidine sequence elements of the murine homeo box loci, Hox-1, -2 and -3
AlignMe: an update of the web server for alignment of membrane protein sequences
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters