yusuke1997/dblp-id-title huggingface dataset:
WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures
MIRU-VNTR plus : a web tool for polyphasic genotyping of Mycobacterium tuberculosis complex bacteria
IMGT/LIGM-DB, the IMGT ® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences
AlgPred: prediction of allergenic proteins and mapping of IgE epitopes
POSTAR2: deciphering the post-transcriptional regulatory logics
The translational signal database, TransTerm: more organisms, complete genomes
The MHC Motif Atlas: a database of MHC binding specificities and ligands
Éclair - a web service for unravelling species origin of sequences sampled from mixed host interfaces
Disruption of the Crithidia fasciculata RNH1 gene results in the loss of two active forms of ribonuclease H
FlyAtlas: database of gene expression in the tissues of Drosophila melanogaster
Spectroscopic properties of various 2'(3')-O-aminoacyldinucleoside phosphates analogous to the 3' terminus of AA-tRNA
Panzea: a database and resource for molecular and functional diversity in the maize genome
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
FlyBase: anatomical data, images and queries
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins
DBTSS: DataBase of Human Transcription Start Sites, progress report 2006
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database
PseudoChecker: an integrated online platform for gene inactivation inference
MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms
VISTA: computational tools for comparative genomics
rVarBase: an updated database for regulatory features of human variants
GlyProt: in silico glycosylation of proteins
DoChaP: the domain change presenter
OptiTope - a web server for the selection of an optimal set of peptides for epitope-based vaccines
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database
ProTherm, Thermodynamic Database for Proteins and Mutants: developments in version 3.0
Reproducible and inexpensive probe preparation for oligonucleotide arrays
Cloning and mapping of infA, the gene for protein synthesis initiation factor IF1
Radiation induced DNA double strand breaks are rejoined by ligation and recombination processes
PhytAMP: a database dedicated to antimicrobial plant peptides
A comparative study of G+C-rich satellite components of sheep and goat DNA
Characterisation of the adenovirus preterminal protein and its interaction with the POU homeodomain of NFIII (Oct-1)
OGRDB: a reference database of inferred immune receptor genes
FlyBase: establishing a Gene Group resource for Drosophila melanogaster
Synthesis of two diastereoisomeric p-nitrophenyl phosphodiesters of 2', 3'-secouridine and their affinity for phosphodiesterases
WebPrInSeS: automated full-length clone sequence identification and verification using high-throughput sequencing data
Recent additions and improvements to the Onto-Tools
Cell Model Passports - a hub for clinical, genetic and functional datasets of preclinical cancer models
RNA base-amino acid interaction strengths derived from structures and sequences
Exposome-Explorer 2.0: an update incorporating candidate dietary biomarkers and dietary associations with cancer risk
The Gene Ontology in 2010: extensions and refinements
Unusually wide co-factor tolerance in a metalloenzyme; divalent metal ions modulate endo?exonuclease activity in T5 exonuclease
CFam: a chemical families database based on iterative selection of functional seeds and seed-directed compound clustering
ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels
HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis
EGF-induced jun B-expression in transfected P19 embryonal carcinoma cells expressing EGF-receptors is dependent on Jun D
HACER: an atlas of human active enhancers to interpret regulatory variants
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data
Deep phenotyping: symptom annotation made simple with SAMS
Bovine Genome Database: new tools for gleaning function from the Bos taurus genome
The MiST2 database: a comprehensive genomics resource on microbial signal transduction
VIPERdb 2 : an enhanced and web API enabled relational database for structural virology
DDBJ in preparation for overview of research activities behind data submissions
A dynamic programming algorithm for finding alternative RNA secondary structures
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data
miRPathDB: a new dictionary on microRNAs and target pathways
A new approach to the synthesis of branched and branched cyclic oligoribonucleotides
ProClass protein family database
New approach for understanding genome variations in KEGG
Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation
ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations
PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference
MOsDB: an integrated information resource for rice genomics
Update on RefSeq microbial genomes resources
Maximizing sensitivity and specificity of PCR by pre-amplification heating
ADPriboDB: The database of ADP-ribosylated proteins
ViTa: prediction of host microRNAs targets on viruses
Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pK a of ionizable residues in proteins
PDBTM: Protein Data Bank of transmembrane proteins after 8 years
Structure and expression of a human gene coding for a 71 kd heat shock 'cognate' protein
RNAcanvas: interactive drawing and exploration of nucleic acid structures
The Nuclear Receptor Resource Project
INFO-RNA - a server for fast inverse RNA folding satisfying sequence constraints
Vienna RNA secondary structure server
The Universal Protein Resource (UniProt)
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
NetCSSP: web application for predicting chameleon sequences and amyloid fibril formation
Deoxyribonuclease II as a probe to sequence-specific chromatin organization: preferential cleavage in the 72 bp modulator sequence of SV40 minichromosome
FlyBase 102 - advanced approaches to interrogating FlyBase
EVEREST: a collection of evolutionary conserved protein domains
LGICdb: the ligand-gated ion channel database
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
Heavy metal ions in transcription factors from HeLa cells: Sp1, but not octamer transcription factor requires zinc for DNA binding and for activator function
RNAInter in 2020: RNA interactome repository with increased coverage and annotation
Amplification dynamics of human-specific (HS) Alu family members
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
mTM-align: a server for fast protein structure database search and multiple protein structure alignment
Norine: update of the nonribosomal peptide resource
QSCOP-BLAST - fast retrieval of quantified structural information for protein sequences of unknown structure
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
DisProt: the Database of Disordered Proteins
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
PocketAnnotate: towards site-based function annotation
UniHI 4: new tools for query, analysis and visualization of the human protein-protein interactome
The ProteomeXchange consortium at 10 years: 2023 update
ACFIS: a web server for fragment-based drug discovery
MUGEN mouse database; Animal models of human immunological diseases
EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles
CPHmodels-3.0 - remote homology modeling using structure-guided sequence profiles
MULocDeep web service for protein localization prediction and visualization at subcellular and suborganellar levels
FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs
Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents
PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif
IMG/M: a data management and analysis system for metagenomes
Database on the structure of small subunit ribosomal RNA
GeneMANIA Prediction Server 2013 Update
CMWeb: an interactive on-line tool for analysing residue-residue contacts and contact prediction methods
miRNATissueAtlas2: an update to the human miRNA tissue atlas
The European Bioinformatics Institute's data resources: towards systems biology
The Zebrafish Information Network: major gene page and home page updates
The Stanford Microarray Database: implementation of new analysis tools and open source release of software
PiER: web-based facilities tailored for genetic target prioritisation harnessing human disease genetics, functional genomics and protein interactions
ComiR: combinatorial microRNA target prediction tool
Cloning and sequencing of the matrix protein gene (M) of Sendai virus (strain Fushimi)
The complete sequence of the Bacillus amyloliquefaciens proviral H2, BamHI methylase gene
The MetaCyc database of metabolic pathways and enzymes
Tissue-specific regulation of mouse MicroRNA genes in endoderm-derived tissues
PUMA2 - grid-based high-throughput analysis of genomes and metabolic pathways
A comparison between mammalian and avian fast skeletal muscle alkali myosin light chain genes: regulatory implications
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics
Thermal denaturation of DNA from bromodeoxyuridine substituted cells
BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
PPDB, the Plant Proteomics Database at Cornell
The Ashbya Genome Database (AGD) - a tool for the yeast community and genome biologists
Génie: literature-based gene prioritization at multi genomic scale
ChemMaps.com v2.0: exploring the environmental chemical universe
A new bioinformatics analysis tools framework at EMBL-EBI
TICO: a tool for postprocessing the predictions of prokaryotic translation initiation sites
lncRNASNP v3: an updated database for functional variants in long non-coding RNAs
HHomp - prediction and classification of outer membrane proteins
LSD 3.0: a comprehensive resource for the leaf senescence research community
The Dfam database of repetitive DNA families
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server
Detection of latent sequence periodicities
Protein knot server: detection of knots in protein structures
Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9
SWISS-MODEL: homology modelling of protein structures and complexes
EpiFactors 2022: expansion and enhancement of a curated database of human epigenetic factors and complexes
Development of a heme protein structure-electrochemical function database
Preferential homogenization between adjacent and alternate subrepeats in wheat rDNA
PRODORIC: prokaryotic database of gene regulation
CCRXP: exploring clusters of conserved residues in protein structures
Conformational analysis of the trinucleoside diphosphate 3'd(A2'-5'A2'- 5'A). An NMR and CD study
The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters
EndoDB: a database of endothelial cell transcriptomics data
ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs
The secondary structure of mRNAs from Escherichia coli: its possible role in increasing the accuracy of translation
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations
Database on the structure of large subunit ribosomal RNA
DrugCentral 2021 supports drug discovery and repositioning
FIMM, a database of functional molecular immunology: update 2002
The Phytophthora Genome Initiative Database: informatics and analysis for distributed pathogenomic research
TMBETA-GENOME: database for annotated ß-barrel membrane proteins in genomic sequences
ViralZone: a knowledge resource to understand virus diversity
The Mouse Genome Database genotypes: : phenotypes
BLAST: at the core of a powerful and diverse set of sequence analysis tools
exoRBase: a database of circRNA, lncRNA and mRNA in human blood exosomes
The Gene Wiki in 2011: community intelligence applied to human gene annotation
Tonicity-responsive microRNAs contribute to the maximal induction of osmoregulatory transcription factor OREBP in response to high-NaCl hypertonicity
Specific spin-labeling of transfer ribonucleic acid molecules
GPS: a comprehensive www server for phosphorylation sites prediction
PLecDom: a program for identification and analysis of plant lectin domains
NGSmethDB 2017: enhanced methylomes and differential methylation
STITCH 4: integration of protein-chemical interactions with user data
QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants
DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes
SINEBase: a database and tool for SINE analysis
FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database
GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database
SeLOX - a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems
PanDrugs2: prioritizing cancer therapies using integrated individual multi-omics data
The HuRef Browser: a web resource for individual human genomics
GPS 6.0: an updated server for prediction of kinase-specific phosphorylation sites in proteins
SBR-Blood: systems biology repository for hematopoietic cells
The Human Phenotype Ontology in 2017
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
vissE.cloud: a webserver to visualise higher order molecular phenotypes from enrichment analysis
UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures
SuperHapten: a comprehensive database for small immunogenic compounds
SEPPA 2.0 - more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen
piRBase: a comprehensive database of piRNA sequences
MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing
Human aldolase B cDNA detects a Pvu II RFLP in healthy individuals
Therapeutic target database update 2014: a resource for targeted therapeutics
The guide RNA database
DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction
PSSweb: protein structural statistics web server
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies
Polymerase chain reaction (PCR) for detection of MspI and DraI polymorphism at the THRB gene
bNAber: database of broadly neutralizing HIV antibodies
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes
MetExplore: collaborative edition and exploration of metabolic networks
DINIES: drug-target interaction network inference engine based on supervised analysis
Transient expression in insect cells using a recombinant baculovirus synthesising bacteriophage T7 RNA polymerase
HProteome-BSite: predicted binding sites and ligands in human 3D proteome
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
Discovering causal signaling pathways through gene-expression patterns
Chromatin association and DNA binding properties of the c-fos proto- oncogene product
GPSy: a cross-species gene prioritization system for conserved biological processes - application in male gamete development
RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs
Ensembl 2017
MitoMiner: a data warehouse for mitochondrial proteomics data
PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR
The Antibody Registry: ten years of registering antibodies
Michigan molecular interactions r2: from interacting proteins to pathways
lncRNAfunc: a knowledgebase of lncRNA function in human cancer
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes
Nucleotide sequence of trnI(CAU) and rpl23 from Arabidopsis thaliana chloroplast genome [published erratum appears in Nucleic Acids Res 1992 Jul 25;20(14): 3814]
GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements
PRUNE and PROBE - two modular web services for protein-protein docking
STRING: known and predicted protein-protein associations, integrated and transferred across organisms
NPASS: natural product activity and species source database for natural product research, discovery and tool development
CAGm: a repository of germline microsatellite variations in the 1000 genomes project
A sensitive non-radioactive PCR-RFLP analysis for detecting point mutations at 12th codon of oncogene c-Ha-ras in DNAs of gastric cancer
BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations
Accessibility of chromatin to DNA polymerase I and location of the F1 histone
Isolation and mapping of a polymorphic DNA sequence (pMCOC14) on chromosome 4p [D4S124]
InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps
pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species
CircNet: a database of circular RNAs derived from transcriptome sequencing data
MAFFT-DASH: integrated protein sequence and structural alignment
Accurate and efficient N-6-adenosine methylation in spliceosomal U6 small nuclear RNA by HeLa cell extract in vitro
mmCSM-PPI: predicting the effects of multiple point mutations on protein-protein interactions
PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits
Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes
ProTarget: automatic prediction of protein structure novelty
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
COMBATdb: a database for the COVID-19 Multi-Omics Blood ATlas
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
iProClass: an integrated database of protein family, function and structure information
GAM: a web-service for integrated transcriptional and metabolic network analysis
Nucleotide sequences of 18S ribosomal RNA genes from the red algae Gracilaria tikvahiae McLachlan, Gracilaria verrucosa (Hudson) Papenfuss and Gracilariopsis sp
PPG: online generation of protein pictures and animations
Some characteristics of processing sites in ribosomal precursor RNA of yeast
Quorumpeps database: chemical space, microbial origin and functionality of quorum sensing peptides
Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research
DNAReplication: a database of information and resources for the eukaryotic DNA replication community
ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data
GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update
High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase
DIANA-miTED: a microRNA tissue expression database
A DNA recombinant database management system
ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry
The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining
Inhibition of SV40 gene expression by microinjected small antisense RNA and DNA molecules
PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots
3did: interacting protein domains of known three-dimensional structure
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data
TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration
Type material in the NCBI Taxonomy Database
The Protein Information Resource (PIR)
trome, trEST and trGEN: databases of predicted protein sequences
DNA Data Bank of Japan (DDBJ) for genome scale research in life science
Homophila: human disease gene cognates in Drosophila
SMDB: a Spatial Multimodal Data Browser
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels
BioLit: integrating biological literature with databases
RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data
FESD: a Functional Element SNPs Database in human
ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms
RBP-Var: a database of functional variants involved in regulation mediated by RNA-binding proteins
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
KNOTTIN: the database of inhibitor cystine knot scaffold after 10 years, toward a systematic structure modeling
TRAMPLE: the transmembrane protein labelling environment
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach
The 3' noncoding region of beta-globin mRNA is not essential for in vitro translation
RNAsoft: a suite of RNA secondary structure prediction and design software tools
GeneWeaver: data driven alignment of cross-species genomics in biology and disease
The ENCODE Project at UC Santa Cruz
PDBsum new things
deepBase v3.0: expression atlas and interactive analysis of ncRNAs from thousands of deep-sequencing data
Nucleotide sequence of the bacteriophage T5 DNA fragment containing a distal part of tRNA gene region
uORFdb - a comprehensive literature database on eukaryotic uORF biology
CRISPRlnc: a manually curated database of validated sgRNAs for lncRNAs
Pfam: multiple sequence alignments and HMM-profiles of protein domains
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases