yusuke1997/dblp-id-title huggingface dataset:
Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations
DriverDB: an exome sequencing database for cancer driver gene identification
CryptoDB: the Cryptosporidium genome resource
CancerSCEM: a database of single-cell expression map across various human cancers
The Legume Information System (LIS): an integrated information resource for comparative legume biology
Atlas of Genetics and Cytogenetics in Oncology and Haematology, an Interactive Database
Epidermodysplasia verruciformis associated human papillomaviruses present a subgenus-specific organization of the regulatory genome region
Proximity and accessibility studies of histones in nuclei and free nucleosomes
InterPro in 2011: new developments in the family and domain prediction database
The 20 years of PROSITE
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
OPTIMIZER: a web server for optimizing the codon usage of DNA sequences
The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data
Collection of published 5S and 5.8S RNA sequences and their precursors
Translocatome: a novel resource for the analysis of protein translocation between cellular organelles
HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes
CEP: a conformational epitope prediction server
SuperPred 3.0: drug classification and target prediction - a machine learning approach
ESTHER, the database of the /?hydrolase fold superfamily of proteins
The Zebrafish Insertion Collection (ZInC): a web based, searchable collection of zebrafish mutations generated by DNA insertion
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases
HUNT: launch of a full-length cDNA database from the Helix Research Institute
Structure of yeast regulatory gene LEU3 and evidence that LEU3 itself is under general amino acid control
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods
Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors
RNAMST: efficient and flexible approach for identifying RNA structural homologs
pTARGET: a web server for predicting protein subcellular localization
GalaxySite: ligand-binding-site prediction by using molecular docking
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing
The PIR-International databases
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA
Public web-based services from the European Bioinformatics Institute
ProteinDBS: a real-time retrieval system for protein structure comparison
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers
EzCatDB: the Enzyme Catalytic-mechanism Database
EMAGE: a spatial database of gene expression patterns during mouse embryo development
PatchDock and SymmDock: servers for rigid and symmetric docking
The i5k Workspace@NAL - enabling genomic data access, visualization and curation of arthropod genomes
Complementary non-radioactive assays for investigation of human flap endonuclease 1 activity
The Immune Epitope Database (IEDB): 2018 update
Both histone H4 genes of Physarum polycephalum are interrupted by an intervening sequence
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists
The Ligand Gated Ion Channel Database
EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data
Cloning and sequence of the rat retinoblastoma (Rb) gene cDNA
A common philosophy and FORTRAN 77 software package for implementing and searching sequence databases
Processing of chimeric introns in dicot plants: evidence for a close cooperation between 5' and 3' splice sites
TOXRIC: a comprehensive database of toxicological data and benchmarks
IUPHAR-DB: updated database content and new features
DB-PABP: a database of polyanion-binding proteins
U12DB: a database of orthologous U12-type spliceosomal introns
Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema
FragmentStore - a comprehensive database of fragments linking metabolites, toxic molecules and drugs
FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis
NESbase version 1.0: a database of nuclear export signals
MERAV: a tool for comparing gene expression across human tissues and cell types
Some substrate properties of analogues of oligothymidylates with p-s- C5' bonds
PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
mirDIP 4.1 - integrative database of human microRNA target predictions
iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations
A rapid and efficient one-tube PCR-based mutagenesis technique using Pfu DNA polymerase
Sequence of the cDNA coding for ammodytoxin B
A highly specific terminal uridylyl transferase modifies the 3'-end of U6 small nuclear RNA
RNAtips: analysis of temperature-induced changes of RNA secondary structure
Pfam: clans, web tools and services
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL
DDBJ launches a new archive database with analytical tools for next-generation sequence data
MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing
APPRIS: annotation of principal and alternative splice isoforms
Improvements to services at the European Nucleotide Archive
The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers
Conformation of the synthetic DNA poly(amino2dA-dT) duplex in high-salt and aqueous alcohol solutions
The transcription factor YY1 binds to negative regulatory elements in the human cytomegalovirus major immediate early enhancer/promoter and mediates repression in non-permissive cells
Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level
Detection of the XbaI RFLP within the retinoblastoma locus by PCR
XSuLT: a web server for structural annotation and representation of sequence-structure alignments
Taverna: a tool for building and running workflows of services
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
DIGICALC: a restriction fragment analysis program
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments
GeneNet: a database on structure and functional organisation of gene networks
DrugComb: an integrative cancer drug combination data portal
A new class of genome rare cutters
Transterm: a database of mRNAs and translational control elements
MIPS: analysis and annotation of proteins from whole genomes
The reactome pathway knowledgebase
Heatmapper: web-enabled heat mapping for all
SMART 5: domains in the context of genomes and networks
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection
GOBASE - a database of mitochondrial and chloroplast information
The Molecular Biology Database Collection: 2005 update
MaizeGDB update: new tools, data and interface for the maize model organism database
VIPERdb v3.0: a structure-based data analytics platform for viral capsids
PedAM: a database for Pediatric Disease Annotation and Medicine
Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics
IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
Sequence of pp42/MAP kinase, a serine/threonine kinase regulated by tyrosine phosphorylation
HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses
DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data
GMrepo: a database of curated and consistently annotated human gut metagenomes
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity
Web 3DNA - a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
REBASE-restriction enzymes and methylases
PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
GeneSigDB - a curated database of gene expression signatures
GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide
Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data
mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures
Rhea - a manually curated resource of biochemical reactions
PDBSite: a database of the 3D structure of protein functional sites
miRGen: a database for the study of animal microRNA genomic organization and function
The Cancer Epitope Database and Analysis Resource (CEDAR)
ICDS database: interrupted CoDing sequences in prokaryotic genomes
The PMDB Protein Model Database
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis
GeneNet in 2005
The basic repeat unit of a Chironomus Balbiani ring gene
S1-sensitive sites in the supercoiled double-stranded form of tomato golden mosaic virus DNA component B: identification of regions of potential alternative secondary structure and regulatory function
Spectroscopic studies of (m5dC-dG)3: thermal stability of B- and Z- forms
CYGD: the Comprehensive Yeast Genome Database
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease
i GNM 2.0: the Gaussian network model database for biomolecular structural dynamics
BacFITBase: a database to assess the relevance of bacterial genes during host infection
A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens
The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context
ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia
PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level
NONCODE 2016: an informative and valuable data source of long non-coding RNAs
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences
Tomato Expression Database (TED): a suite of data presentation and analysis tools
PredictProtein - an open resource for online prediction of protein structural and functional features
Fine-mapping of DNA damage and repair in specific genomic segments
InterProScan: protein domains identifier
DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology
StellaBase : The Nematostella vectensis Genomics Database
WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research
PARSESNP: a tool for the analysis of nucleotide polymorphisms
Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors
DrugCentral 2023 extends human clinical data and integrates veterinary drugs
Computer programs in nucleic acid synthesis: synthetic strategy development using solid-phase chemical techniques with data storage, retrieval and analysis capabilities
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences
CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins
Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes
NPInter v2.0: an updated database of ncRNA interactions
PADS Arsenal: a database of prokaryotic defense systems related genes
The complex portal - an encyclopaedia of macromolecular complexes
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics
DroSpeGe: rapid access database for new Drosophila species genomes
PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria
Rfam: Wikipedia, clans and the "decimal" release
SENTRA, a database of signal transduction proteins
ProClass Protein Family Database
MeDBA: the Metalloenzyme Data Bank and Analysis platform
NEBcutter: a program to cleave DNA with restriction enzymes
Haplogrep 3 - an interactive haplogroup classification and analysis platform
MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome
TIGRFAMs and Genome Properties in 2013
Equimolar addition of oligoribonucleotides with T4 RNA ligase
ChemBank : a small-molecule screening and cheminformatics resource database
Uniclust databases of clustered and deeply annotated protein sequences and alignments
Gene Ontology Annotations and Resources
BRENDA in 2015: exciting developments in its 25th year of existence
Synthesis and physicochemical properties of two analogs of poly(dA): poly(2-aminopurine-9-beta-D-deoxyribonucleotide) and poly 2-amino- deoxyadenylic acid
Multidimensional gene search with Genehopper
RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development
Novel developments with the PRINTS protein fingerprint database
antiSMASH 6.0: improving cluster detection and comparison capabilities
Adepth: new representation and its implications for atomic depths of macromolecules
Metabolic PathFinding: inferring relevant pathways in biochemical networks
TWAS Atlas: a curated knowledgebase of transcriptome-wide association studies
ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues
IUPHAR-DB: new receptors and tools for easy searching and visualization of pharmacological data
Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum
Analysis of chromatin structure of rat alpha1-acid glycoprotein gene; changes in DNase I hypersensitive sites after thyroid hormone, glucocorticoid hormone and turpentine oil treatment
Editorial: the 21st annual Nucleic Acids Research Web Server Issue 2023
FFAS03: a server for profile-profile sequence alignments
PubChem 2023 update
DeepNeo: a webserver for predicting immunogenic neoantigens
In vivo co-localisation of MBNL protein with DMPK expanded-repeat transcripts
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas
The Gene Ontology (GO) project in 2006
Identification of genome edited cells using CRISPRnano
PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks
ConoServer: updated content, knowledge, and discovery tools in the conopeptide database
Ice -COLD-PCR enables rapid amplification and robust enrichment for low-abundance unknown DNA mutations
ATTED-II provides coexpressed gene networks for Arabidopsis
RNAstructure: web servers for RNA secondary structure prediction and analysis
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
The current status and portability of our sequence handling software
FGF: A web tool for Fishing Gene Family in a whole genome database
RaftProt V2: understanding membrane microdomain function through lipid raft proteomes
Analysis of the rearrangements associated with carcinogen-induced activation of the hamster thymidine kinase gene
Use of oligonucleotides to define the site of interstrand cross-links induced by Adriamycin
Should nucleotide sequence analyzing computer algorithms always extend homologies by extending homologies?
Bacteriophage T4 DNA packaging genes 16 and 17
SilkDB v2.0: a platform for silkworm ( Bombyx mori ) genome biology
DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes
15 years of PhosphoSitePlus®: integrating post-translationally modified sites, disease variants and isoforms
mreps: efficient and flexible detection of tandem repeats in DNA
3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome
DEQOR: a web-based tool for the design and quality control of siRNAs
TcoF-DB v2: update of the database of human and mouse transcription co-factors and transcription factor interactions
PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes
The ITS2 Database II: homology modelling RNA structure for molecular systematics
MISTIC2: comprehensive server to study coevolution in protein families
Reciprocal recombination products of VK-JK joining reactions in human lymphoid cell lines
iMOTdb - a comprehensive collection of spatially interacting motifs in proteins
Oli2go: an automated multiplex oligonucleotide design tool
FoXS: a web server for rapid computation and fitting of SAXS profiles
CLICK - topology-independent comparison of biomolecular 3D structures
The Pfam protein families database in 2019
STRBase: a short tandem repeat DNA database for the human identity testing community
Ensembl 2022
Systematic sequencing of the Escherichia coli genome: analysis of the 0- 2.4 min region
DNA Data Bank of Japan (DDBJ) update report 2021
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed -1 ribosomal frameshifting
RNAssess - a web server for quality assessment of RNA 3D structures
Nucleotide sequence of a full-length cDNA (PST-1) for aryl sulfotransferase from rat liver
Knowledge-based simulation of genetic regulation in bacteriophage lambda
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments
Exploration and analysis of R-loop mapping data with RLBase
SLiMSearch 2.0: biological context for short linear motifs in proteins
Project Score database: a resource for investigating cancer cell dependencies and prioritizing therapeutic targets
AllerCatPro 2.0: a web server for predicting protein allergenicity potential
ALFRED: an allele frequency resource for research and teaching
The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant
Genome Variation Map: a data repository of genome variations in BIG Data Center
EWAS Data Hub: a resource of DNA methylation array data and metadata
FlyNets and GIF-DB, two internet databases for molecular interactions in Drosophila melanogaster
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons
PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information
CEGA - a catalog of conserved elements from genomic alignments
CytoSVM: an advanced server for identification of cytokine-receptor interactions
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets
Mammalian promoter element function in the fission yeast Schizosaccharomyces pombe
The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments
piRNA cluster database: a web resource for piRNA producing loci
Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA
Haemophilia B: database of point mutations and short additions and deletions--fourth edition, 1993
PIPs: human protein-protein interaction prediction database
SCUDO: a tool for signature-based clustering of expression profiles
CeDR Atlas: a knowledgebase of cellular drug response
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats
VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era
siVirus: web-based antiviral siRNA design software for highly divergent viral sequences
Duplication of single stranded DNA catalyzed by calf thymus DNA polymerase alpha
alpha 1-Fetoprotein mRNA of rat yolk sac and hepatoma
ProteinDBS v2.0: a web server for global and local protein structure search
DrugBank: a knowledgebase for drugs, drug actions and drug targets
ProBiS: a web server for detection of structurally similar protein binding sites
Keio Mutation Database (KMDB) for human disease gene mutations
ppdb: a plant promoter database
Thunor: visualization and analysis of high-throughput dose-response datasets
Update of the G2D tool for prioritization of gene candidates to inherited diseases
Isolation and computer-aided characterization of MmeI, a type II restriction endonuclease from Methylophilus methylotrophus
Eukaryotic topoisomerase II preferentially cleaves alternating purine- pyrimidine repeats
ProFunc: a server for predicting protein function from 3D structure
rVISTA 2.0: evolutionary analysis of transcription factor binding sites
The 23S Ribosomal RNA Mutation Database (23SMDB)
ChromDB: The Chromatin Database
OrthoDB in 2020: evolutionary and functional annotations of orthologs
AlterORF: a database of alternate open reading frames
IMGT ® , the international ImMunoGeneTics information system ® 25 years on
The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes
IntroVerse: a comprehensive database of introns across human tissues
BioCatalogue: a universal catalogue of web services for the life sciences
The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI
MirDIP 5.2: tissue context annotation and novel microRNA curation
Extension of a flexible computer program for handling DNA sequence data
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
Matrix program to analyze primary structure homology
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies
IEDB-3D: structural data within the immune epitope database
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy
The upstream activating sequence for L-leucine gene regulation in Saccharomyces cerevisiae
Aminoacylation of tRNA Trp from beef liver, yeast and E. coli by beef pancrease tryptophan-tRNA ligase. Stoichiometry of tRNATrp binding
PILGRM: an interactive data-driven discovery platform for expert biologists
TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
Sequence microheterogeneity of the three small subunit ribosomal RNA genes of Babesia bigemina: expression in erythrocyte culture