yusuke1997/dblp-id-title huggingface dataset:
The SV40 termination region exhibits an altered helical DNA conformation
ProOpDB : Pro karyotic Op eron D ata B ase
DrugSpaceX: a large screenable and synthetically tractable database extending drug space
MyCLADE: a multi-source domain annotation server for sequence functional exploration
X: Map: annotation and visualization of genome structure for Affymetrix exon array analysis
FunARTS, the Fungal bioActive compound Resistant Target Seeker, an exploration engine for target-directed genome mining in fungi
PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins
ProTherm: Thermodynamic Database for Proteins and Mutants
BUSCA: an integrative web server to predict subcellular localization of proteins
A computer program to enter DNA gel reading data into a computer
The EMBL nucleotide sequence database
Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P
MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice
AutismKB: an evidence-based knowledgebase of autism genetics
Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure
MITOP, the mitochondrial proteome database: 2000 update
The RNAsnp web server: predicting SNP effects on local RNA secondary structure
dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers
Extracellular nucleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA
ConsensusPathDB - a database for integrating human functional interaction networks
RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications
CircaDB: a database of mammalian circadian gene expression profiles
ExoCarta 2012: database of exosomal proteins, RNA and lipids
PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution
The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms
UniProt: a hub for protein information
Formation of a DNA monofunctional cis-platinum adduct cross-linking the intercalating drug N-methyl-2, 7-diazapyrenium
Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals
Loopstructures in synthetic oligodeoxynucleotides
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants
Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA
cDNA sequence coding for human kidney catalase
Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences
IEDB-AR: immune epitope database - analysis resource in 2019
SomamiR: a database for somatic mutations impacting microRNA function in cancer
Novel families of interspersed repetitive elements from the human genome
A correction in the nucleotide sequence of the Tn903 kanamycin resistance determinant in pUC4K [published erratum appears in Nucleic Acids Res 1988 Aug 11;16(15): 7762]
Organelle DB: an updated resource of eukaryotic protein localization and function
OncoSplicing: an updated database for clinically relevant alternative splicing in 33 human cancers
NONCODEV5: a comprehensive annotation database for long non-coding RNAs
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration
The UCSC Proteome Browser
Synthesis and physical properties of anti-HIV antisense oligonucleotides bearing terminal lipophilic groups
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases
Nucleotide sequence of a mouse cDNA encoding the nonhistone chromosomal high mobility group protein-1 (HMG1)
A simple high yield method for the preparation of lambda gt10 DNA suitable for subcloning, amplification and direct sequencing
NXSensor web tool for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors
ProGMap: an integrated annotation resource for protein orthology
Galahad: a web server for drug effect analysis from gene expression
HUGE: a database for human KIAA proteins, a 2004 update integrating HUGEppi and ROUGE
ADVICE: Automated Detection and Validation of Interaction by Co-Evolution
MPlot - a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins
APID: Agile Protein Interaction DataAnalyzer
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer
ClinVar: improving access to variant interpretations and supporting evidence
UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
SODA: prediction of protein solubility from disorder and aggregation propensity
Transcriptional mapping of the ribosomal RNA region of mouse L-cell mitochondrial DNA
Newt-omics: a comprehensive repository for omics data from the newt Notophthalmus viridescens
DiseaseEnhancer: a resource of human disease-associated enhancer catalog
The integrated microbial genomes (IMG) system
Protein Peeling 2: a web server to convert protein structures into series of protein units
TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes
sc-PDB: a 3D-database of ligandable binding sites - 10 years on
The site-specific DNA endonuclease encoded by a group I intron in the Chlamydomonas pallidostigmatica chloroplast small subunit rRNA gene introduces a single-strand break at low concentrations of Mg2+
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
MOD i : a powerful and convenient web server for identifying multiple post-translational peptide modifications from tandem mass spectra
HHrep: de novo protein repeat detection and the origin of TIM barrels
The radiation hybrid database
A FastA based compilation of higher plant mitochondrial tRNA genes
MoMuLV proviral integrations identified by Sup-F selection in tumors from infected myc/pim bitransgenic mice correlate with activation of the gfi-1 gene
AlloMAPS 2: allosteric fingerprints of the AlphaFold and Pfam-trRosetta predicted structures for engineering and design
A kinetic model for subtractive hybridization
TIMEDB: tumor immune micro-environment cell composition database with automatic analysis and interactive visualization
miEAA: microRNA enrichment analysis and annotation
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
BacMap: an up-to-date electronic atlas of annotated bacterial genomes
RNALOSS: a web server for RNA locally optimal secondary structures
The three-dimensional folding of ribosomal RNA; localization of a series of intra-RNA cross-links in 23S RNA induced by treatment of Escherichia coli 50S ribosomal subunits with bis-(2-chloroethyl)- methylamine
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements
PIC: Protein Interactions Calculator
TFM-Explorer: mining cis -regulatory regions in genomes
CATNAP: a tool to compile, analyze and tally neutralizing antibody panels
Synthesis and hybridization analysis of a small library of peptide- oligonucleotide conjugates
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures
SCit: web tools for protein side chain conformation analysis
PepComposer: computational design of peptides binding to a given protein surface
RefSeq: an update on prokaryotic genome annotation and curation
DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry
PhenomicDB: a new cross-species genotype/phenotype resource
Electroporation of Haemophilus influenzae is effective for transformation of plasmid but not chromosomal DNA
ExInt: an Exon Intron Database
DEPCOD: a tool to detect and visualize co-evolution of protein domains
MFEprimer-2.0: a fast thermodynamics-based program for checking PCR primer specificity
CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine
ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability
FREP: a database of functional repeats in mouse cDNAs
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation
PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments
SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)
TcruziDB: an integrated, post-genomics community resource for Trypanosoma cruzi
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)
snpXplorer: a web application to explore human SNP-associations and annotate SNP-sets
The EMBL-EBI bioinformatics web and programmatic tools framework
DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data
The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species
The cleavage site for the restriction endonucleases BanI and HgiC I is 5' ...G decreases GPyPuCC ...3'
The SYSTERS protein sequence cluster set
SIFTS: Structure Integration with Function, Taxonomy and Sequences resource
PHAST: A Fast Phage Search Tool
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
WormBase 2014: new views of curated biology
Current status of the SWISS-2DPAGE database
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
MetaboAnalyst: a web server for metabolomic data analysis and interpretation
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998
RNAcentral: an international database of ncRNA sequences
T-Reg Comparator: an analysis tool for the comparison of position weight matrices
LINKER: a web server to generate peptide sequences with extended conformation
GIANT API: an application programming interface for functional genomics
Update of AMmtDB: a database of multi-aligned metazoa mitochondrial DNA sequences
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts
PHUSER (Primer Help for USER): a novel tool for USER fusion primer design
Mutagenesis in monkey cells of a vector containing a single d(GPG) cis- diamminedichloroplatinum(II) adduct placed on codon 13 of the human H- ras proto-oncogene
RepTar: a database of predicted cellular targets of host and viral miRNAs
WebGestalt: an integrated system for exploring gene sets in various biological contexts
MP: PD - a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data
dbCAN-PUL: a database of experimentally characterized CAZyme gene clusters and their substrates
The Rice PIPELINE: a unification tool for plant functional genomics
Comparative Toxicogenomics Database (CTD): update 2023
WebScipio: reconstructing alternative splice variants of eukaryotic proteins
Gephebase, a database of genotype-phenotype relationships for natural and domesticated variation in Eukaryotes
The comprehensive microbial resource
The nucleotide sequence of the cDNA encoding a chicken Deformed family homeobox gene, Chox-Z
The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group
GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information
Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC
StemChecker: a web-based tool to discover and explore stemness signatures in gene sets
RE-MuSiC: a tool for multiple sequence alignment with regular expression constraints
A strategy for sequence phylogeny research
NATsDB: Natural Antisense Transcripts DataBase
Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins
Genomes OnLine database (GOLD) v.7: updates and new features
Formation of ribosome-RNA initiation complexes with alfalfa mosaic virus RNA 4 and RNA 3
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data
Prediction of synonymous corrections by the BE-FF computational tool expands the targeting scope of base editing
3DNALandscapes : a database for exploring the conformational features of DNA
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection
PrimerZ: streamlined primer design for promoters, exons and human SNPs
The European database on small subunit ribosomal RNA
Expression of wild-type and mutant p53 proteins by recombinant vaccinia viruses
TIARA: a database for accurate analysis of multiple personal genomes based on cross-technology
MINT, the molecular interaction database: 2012 update
EHFPI: a database and analysis resource of essential host factors for pathogenic infection
DNAGEL: a computer program for determining DNA fragment sizes using a small computer equipped with a graphics tablet
Pocketome: an encyclopedia of small-molecule binding sites in 4D
GENCODE reference annotation for the human and mouse genomes
ClinVar: improvements to accessing data
The European Nucleotide Archive in 2020
MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides
Ensembl 2012
TTD: Therapeutic Target Database
dbDEPC 2.0: updated database of differentially expressed proteins in human cancers
IgBLAST: an immunoglobulin variable domain sequence analysis tool
The yeast protein encoded by PUB1 binds T-rich single stranded DNA
RosettaDesign server for protein design
The RESID Database of Protein Modifications: 2003 developments
SiteSeer: visualisation and analysis of transcription factor binding sites in nucleotide sequences
Saccharomyces Genome Database provides mutant phenotype data
A decade of web server updates at the bioinformatics links directory: 2003-2012
UniqueProt: creating representative protein sequence sets
ELM: the status of the 2010 eukaryotic linear motif resource
NCBI Peptidome: a new repository for mass spectrometry proteomics data
PTGL: a database for secondary structure-based protein topologies
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
Human single-nucleotide polymorphisms alter p53 sequence-specific binding at gene regulatory elements
PhosphoBase, a database of phosphorylation sites: release 2.0
mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers
EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles
Proteo3Dnet: a web server for the integration of structural information with interactomics data
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts
Genome-wide detection of alternative splicing in expressed sequences of human genes
RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures
CREME: Cis-Regulatory Module Explorer for the human genome
RNAmod: an integrated system for the annotation of mRNA modifications
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome
HGPD: Human Gene and Protein Database, 2012 update
RosettaAntibody: antibody variable region homology modeling server
Update of MmtDB: a Metazoa mitochondrial DNA variants database
The SBASE protein domain library, release 5.0: a collection of annotated protein sequence segments
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning
Elk-1 protein domains required for direct and SRF-assisted DNA-binding
NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning
ASDB: database of alternatively spliced genes
Progress with the PRINTS protein fingerprint database
BodyMap: a human and mouse gene expression database
Structural and functional analysis of a polyoma-related mammalian plasmid (L factor): the enhancer activity and plasmid establishment
Genenames.org: the HGNC resources in 2015
New features of the Blocks Database servers
dbDEPC: a database of Differentially Expressed Proteins in human Cancers
Yvis: antibody high-density alignment visualization and analysis platform with an integrated database
LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts
BSDB: the biomolecule stretching database
GENCODE: reference annotation for the human and mouse genomes in 2023
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
DISNOR: a disease network open resource
A convenient method for locating sets of related short sequences in DNA sequences of any length
The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones
Transcriptional activation of NFI/CTF1 depends on a sequence motif strongly related to the carboxyterminal domain of RNA polymerase II
CMPD: cancer mutant proteome database
The UCSC Table Browser data retrieval tool
A web-based genotyping resource for viral sequences
A novel assay for DNA ligase
Improvements to the GDB Human Genome Data Base
The gene S promoter of hepatitis B virus confers constitutive gene expression
MouseIndelDB: a database integrating genomic indel polymorphisms that distinguish mouse strains
Detection of protein similarities using nucleotide sequence databases
DDI-CPI , a server that predicts drug-drug interactions through implementing the chemical-protein interactome
ELM - the eukaryotic linear motif resource in 2020
Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences
NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites
The AP-1 site is required for basal expression but is not necessary for TPA-response of the human stromelysin gene
Therapeutic target database 2020: enriched resource for facilitating research and early development of targeted therapeutics
Pathways with PathWhiz
TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes
Pentamidine inhibits catalytic activity of group I intron Ca.LSU by altering RNA folding
HumanNet v3: an improved database of human gene networks for disease research
Nucleotide sequence of the lsp-dapB interval in Escherichia coli
Characterization of mouse 45S ribosomal RNA subspecies suggests that the first processing cleavage occurs 600 +/- 100 nucleotides from the 5' end and the second 500 +/- 100 nucleotides from the 3' end of a 13.9 kb precursor
Identification of two enhancer elements downstream of the human c-myc gene
ProteomeScout: a repository and analysis resource for post-translational modifications and proteins
Ensembl 2008
GDAP: a web tool for genome-wide protein disulfide bond prediction
Mfold web server for nucleic acid folding and hybridization prediction
rQuant.web: a tool for RNA-Seq-based transcript quantitation
NetworKIN: a resource for exploring cellular phosphorylation networks
Interactive computer programs for the graphic analysis of nucleotide sequence data
Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides
Gene for OTC: characterisation and linkage to Duchenne muscular dystrophy
Characterization and mapping of the double-stranded regions involved in activation of PKR within a cellular RNA from 3T3-F442A cells
The Transporter Classification Database (TCDB): 2021 update
MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures
Cancer driver drug interaction explorer
LSD 2.0: an update of the leaf senescence database
The IMB Jena Image Library of Biological Macromolecules
MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions
SigniSite : Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments
The primary transcript of the ribosomal repeating unit in yeast
Studies on the synthesis of a G-rich octaoligoisonucleotide (isoT)2(isoG)4(isoT)2 by the phosphotriester approach and its formation of G-quartet structure
P2CS: a database of prokaryotic two-component systems
The nucleotide sequence of a human immunoglobulin C gamma1 gene
Mouse genome database 2016
CisMols Analyzer: identification of compositionally similar cis -element clusters in ortholog conserved regions of coordinately expressed genes
The RNA Modification Database: 1999 update
ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteins
lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse
JINN, an integrated software package for molecular geneticists
SVC: structured visualization of evolutionary sequence conservation
The mouse Gene Expression Database (GXD): 2014 update
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification
KD4v: comprehensible knowledge discovery system for missense variant
1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans
TSTMP: target selection for structural genomics of human transmembrane proteins
3D-DART: a DNA structure modelling server
MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study
ConVarT: a search engine for matching human genetic variants with variants from non-human species
Facing growth in the European Nucleotide Archive
Origin and fate of repeats in bacteria
Shi BASE: an integrated database for comparative genomics of Shigella
dbSNP: the NCBI database of genetic variation
Automated Gene Ontology annotation for anonymous sequence data
FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts
LncExpDB: an expression database of human long non-coding RNAs
A convenient and adaptable microcomputer environment for DNA and protein sequence manipulation and analysis
The DExH/D protein family database
Trips-Viz: a transcriptome browser for exploring Ribo-Seq data
MicrobesOnline: an integrated portal for comparative and functional genomics
Lesion selectivity in blockage of lambda exonuclease by DNA damage
PROTINFO: secondary and tertiary protein structure prediction
ProTherm, version 2.0: thermodynamic database for proteins and mutants
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways
Inhibitory effects of 3'deoxycytidine 5'-triphosphate and 3'- deoxyuridine 5'-triphosphate on DNA-dependent RNA polymerases I and II purified from Dictyostelium discoideum cells
MIDAW: a web tool for statistical analysis of microarray data
MolliGen, a database dedicated to the comparative genomics of Mollicutes
A novel tenascin type III repeat is part of a complex of tenascin mRNA alternative splices
The orientation and dynamics of the C2'-OH and hydration of RNA and DNA.RNA hybrids
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations
Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts
FlyBase 101 - the basics of navigating FlyBase