yusuke1997/dblp-id-title huggingface dataset:
Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes
HeRA: an atlas of enhancer RNAs across human tissues
GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
MeRNA: a database of metal ion binding sites in RNA structures
BioModels - 15 years of sharing computational models in life science
INFRAFRONTIER - providing mutant mouse resources as research tools for the international scientific community
20 years of the SMART protein domain annotation resource
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods
ModBase, a database of annotated comparative protein structure models, and associated resources
The ChEMBL bioactivity database: an update
An update on LNCipedia: a database for annotated human lncRNA sequences
lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs
NetGO: improving large-scale protein function prediction with massive network information
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs
EVA: evaluation of protein structure prediction servers
Molecular footprints of human immunoglobulin gene evolution: a new sequence family
SuperDRUG2: a one stop resource for approved/marketed drugs
mCSM-membrane: predicting the effects of mutations on transmembrane proteins
The GenBank genetic sequence databank
MspI polymorphism at the human complement component C6 gene (C6)
Genenames.org: the HGNC and VGNC resources in 2017
A promoter trap in embryonic stem (ES) cells selects for integration of DNA into CpG islands
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity
Database for exploration of functional context of genes implicated in ovarian cancer
CellMarker: a manually curated resource of cell markers in human and mouse
A rapid classification protocol for the CATH Domain Database to support structural genomics
LectomeXplore, an update of UniLectin for the discovery of carbohydrate-binding proteins based on a new lectin classification
S/MARt DB: a database on scaffold/matrix attached regions
R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation
dbSUPER: a database of super-enhancers in mouse and human genome
KINARI-Web: a server for protein rigidity analysis
CoMet - a web server for comparative functional profiling of metagenomes
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences
PlanMine - a mineable resource of planarian biology and biodiversity
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs
Bioactivity of anti-angiogenic ribozymes targeting Flt-1 and KDR mRNA
An Eco R1 polymorphism of a human platelet factor 4 (PF4) gene
MutationDistiller: user-driven identification of pathogenic DNA variants
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum
Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update
PDBFlex: exploring flexibility in protein structures
CSM-lig: a web server for assessing and comparing protein-small molecule affinities
ETCM: an encyclopaedia of traditional Chinese medicine
AMIGene: Annotation of MIcrobial Genes
HotRegion: a database of predicted hot spot clusters
LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations
COVTree: Coevolution in OVerlapped sequences by Tree analysis server
Conducting Research on the Web: 2007 Update for the Bioinformatics Links Directory
LPSN - list of prokaryotic names with standing in nomenclature
eRAM: encyclopedia of rare disease annotations for precision medicine
The Database of Interacting Proteins: 2004 update
Application of a rapid gel method to the sequencing of fragments of 16S ribosomal RNA from Escherichia coli
The Molecule Pages database
IsoFinder: computational prediction of isochores in genome sequences
TMB-Hunt: a web server to screen sequence sets for transmembrane ß-barrel proteins
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins
Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis
PINTA: a web server for network-based gene prioritization from expression data
Subunit structure of alpha-satellite DNA containing chromatin from African green monkey cells
DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data
AlignMe - a membrane protein sequence alignment web server
The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data
TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data
COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps
SensiPath: computer-aided design of sensing-enabling metabolic pathways
miRBase: tools for microRNA genomics
CoPub: a literature-based keyword enrichment tool for microarray data analysis
VarCards: an integrated genetic and clinical database for coding variants in the human genome
Bac Dive in 2022: the knowledge base for standardized bacterial and archaeal data
Ribosomal Database Project: data and tools for high throughput rRNA analysis
TopFIND 2.0 - linking protein termini with proteolytic processing and modifications altering protein function
ZOOM Lite: next-generation sequencing data mapping and visualization software
BepI restriction endonuclease, a new isoschisomer of FnuDII
FusionGDB: fusion gene annotation DataBase
The Eukaryotic Promoter Database (EPD): recent developments
MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis
Theatre: a software tool for detailed comparative analysis and visualization of genomic sequence
Improving the accuracy of predicting secondary structure for aligned RNA sequences
CeNDR, the Caenorhabditis elegans natural diversity resource
PhEVER: a database for the global exploration of virus-host evolutionary relationships
The nucleotide sequence of Euglena cytoplasmic phenylalanine transfer RNA. Evidence for possible classifications of Euglena among the animal rather than the plant kingdom
Los Alamos sequence analysis package for nucleic acids and proteins
Genetic regulation of delta-aminolevulinate dehydratase during erythropoiesis
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs
ExpressYourself: a modular platform for processing and visualizing microarray data
LncTarD: a manually-curated database of experimentally-supported functional lncRNA?target regulations in human diseases
PRODORIC: state-of-the-art database of prokaryotic gene regulation
R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
Isolation and mapping of a polymorphic DNA sequence (pCMM66) on chromosome 14 [D14S22]
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species
Phospho.ELM: a database of phosphorylation sites - update 2008
The Rat Genome Database (RGD): developments towards a phenome database
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming
ICM: a web server for integrated clustering of multi-dimensional biomedical data
dNTPpoolDB: a manually curated database of experimentally determined dNTP pools and pool changes in biological samples
PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database
PhenoHM: human-mouse comparative phenome-genome server
Nucleosomal histone protein protects DNA from iron-mediated damage
PRGdb: a bioinformatics platform for plant resistance gene analysis
rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes
GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms
RNAspider: a webserver to analyze entanglements in RNA 3D structures
15 years of GDR: New data and functionality in the Genome Database for Rosaceae
MetaPath Online: a web server implementation of the network expansion algorithm
InBase, the Intein Database
Lynx: a knowledge base and an analytical workbench for integrative medicine
EcoCyc: fusing model organism databases with systems biology
Analysis of the rat JE gene promoter identifies an AP-1 binding site essential for basal expression but not for TPA induction
PROMISE: a database of bioinorganic motifs
Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets
LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse
YeastRGB: comparing the abundance and localization of yeast proteins across cells and libraries
dbDNV: a resource of duplicated gene nucleotide variants in human genome
The Eukaryotic Promoter Database EPD: the impact of in silico primer extension
AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms
The ProDom database of protein domain families
Static benchmarking of membrane helix predictions
The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes
A DNA analysis program designed for computer novices working in an industrial-research environment
Molecular cloning and sequencing of pheU, a gene for Escherichia coli tRNAPhe
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes
The distribution and query systems of the RCSB Protein Data Bank
The reactome pathway knowledgebase 2022
ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Co-expression pattern from DNA microarray experiments as a tool for operon prediction
G4LDB: a database for discovering and studying G-quadruplex ligands
DNAproDB: an expanded database and web-based tool for structural analysis of DNA?protein complexes
Formal description of a DNA oriented computer language
Heterogeneous base distribution in mitochondrial DNA of Neurospora crassa
Saccharomyces genome database provides new regulation data
InvFEST, a database integrating information of polymorphic inversions in the human genome
Temperature dependence of the joining by T4 DNA ligase of termini produced by type II restriction endonucleases
OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update
PubChem 2019 update: improved access to chemical data
The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization
Histone modifications in the yeast S. Cerevisiae
Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
Keeping pace with the data: 2008 update on the Bioinformatics Links Directory
DOMAC: an accurate, hybrid protein domain prediction server
ECMDB: The E. coli Metabolome Database
Virgil: a database of rich links between GDB and GenBank
CATH: an expanded resource to predict protein function through structure and sequence
The Comprehensive Microbial Resource
ProTherm, version 4.0: thermodynamic database for proteins and mutants
miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale
WholeCellKB: model organism databases for comprehensive whole-cell models
euGenes: a eukaryote genome information system
DNA Data Bank of Japan: 30th anniversary
MITOMAP: a human mitochondrial genome database
The neXtProt knowledgebase on human proteins: 2017 update
The Genomic HyperBrowser: an analysis web server for genome-scale data
RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes
HIV-1, human interaction database: current status and new features
NRMD: Nuclear Receptor Mutation Database
MethHC: a database of DNA methylation and gene expression in human cancer
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics
Motif3D: relating protein sequence motifs to 3D structure
f POP: footprinting functional pockets of proteins by comparative spatial patterns
REBASE - restriction enzymes and DNA methyltransferases
PEDB: the Prostate Expression Database
ButterflyBase: a platform for lepidopteran genomics
Editorial: the 15th annual Nucleic Acids Research Web Server issue 2017
On the statistical significance of nucleic acid similarities
Gibbs Recursive Sampler: finding transcription factor binding sites
TransFind - predicting transcriptional regulators for gene sets
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022
CSDBase: an interactive database for cold shock domain-containing proteins and the bacterial cold shock response
ADGO 2.0: interpreting microarray data and list of genes using composite annotations
The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection
GeneTrail - advanced gene set enrichment analysis
RFLPs at the D19S19 locus of human chromosome 19 linked to myotonic dystrophy (DM)
RHYTHM - a server to predict the orientation of transmembrane helices in channels and membrane-coils
The Rat Genome Database, update 2007 - Easing the path from disease to data and back again
VIDA: a virus database system for the organization of animal virus genome open reading frames
Polymerase chain reaction (PCR) for detection of RsaI polymorphism at the D3S32 locus
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
T1DBase: integration and presentation of complex data for type 1 diabetes research
RTPrimerDB: the Real-Time PCR primer and probe database
Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2
CutDB: a proteolytic event database
Inhibition of DNA synthesis at the hemimethylated pBR322 origin of replication by a cell membrane fraction
Pseudofam: the pseudogene families database
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12
GOblet: a platform for Gene Ontology annotation of anonymous sequence data
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse
RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
VARAdb: a comprehensive variation annotation database for human
SRF and MCM1 have related but distinct DNA binding specificities
webPDBinder: a server for the identification of ligand binding sites on protein structures
KUPS: constructing datasets of interacting and non-interacting protein pairs with associated attributions
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database
NP-MRD: the Natural Products Magnetic Resonance Database
LegumeIP V3: from models to crops - an integrative gene discovery platform for translational genomics in legumes
Oligonucleotide duplexes containing 2'-amino-2'-deoxycytidines: thermal stability and chemical reactivity [published erratum appears in Nucleic Acids Res 1994 Feb 25;22(4): 701]
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information
MVP: a microbe-phage interaction database
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota
IMGT/GeneInfo: enhancing V(D)J recombination database accessibility
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0
PROTINFO: new algorithms for enhanced protein structure predictions
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
TRACTS: a program to map oligopurine.oligopyrimidine and other binary DNA tracts
IsoBase: a database of functionally related proteins across PPI networks
The RDP (Ribosomal Database Project) continues
Cloning and nucleotide sequence of a cDNA encoding the antifungal- protein of Aspergillus giganteus and preliminary characterization of the native gene
CADgene: a comprehensive database for coronary artery disease genes
Evidence for Z-form RNA by vacuum UV circular dichroism
Endonuclease G from mammalian nuclei is identical to the major endonuclease of mitochondria
Improved RNA sequencing method to determine immunoglobulin mRNA sequence
GEPS: the Gene Expression Pattern Scanner
Gramene: a growing plant comparative genomics resource
Eco Cyc: encyclopedia of Escherichia coli genes and metabolism
A high-capacity column for affinity purification of sequence-specific DNA-binding proteins
UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions
MicroScope - an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies
Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications
MDS_IES_DB: a database of macronuclear and micronuclear genes in spirotrichous ciliates
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics
KAAS: an automatic genome annotation and pathway reconstruction server
VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes
R. S. WebTool, a web server for random sampling-based significance evaluation of pairwise distances
Identification of preferential target sites for human DNA methyltransferases
Fluorescence modification of Escherichia coli 5S RNA
MaizeGDB 2018: the maize multi-genome genetics and genomics database
Sequence polymorphism in the human alpha-2-macroglobulin (A2M) gene
The UCSC Genome Browser database: 2017 update
ArrayExpress update - trends in database growth and links to data analysis tools
CDD: a Conserved Domain Database for protein classification
MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data
COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference
Functional analysis of the transcription factor ER71 and its activation of the matrix metalloproteinase-1 promoter
Thera-SAbDab: the Therapeutic Structural Antibody Database
The Multi-Q web server for multiplexed protein quantitation
PEP: Predictions for Entire Proteomes
A variant Tc4 transposable element in the nematode C. elegans could encode a novel protein
AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses
LipidSuite: interactive web server for lipidomics differential and enrichment analysis
PCDDB: new developments at the Protein Circular Dichroism Data Bank
SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements
RBO Aleph: leveraging novel information sources for protein structure prediction
Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas
BASC: an integrated bioinformatics system for Brassica research
psRNATarget: a plant small RNA target analysis server (2017 release)
PEP-FOLD: an online resource for de novo peptide structure prediction
The database of the smallest known auto-replicable RNA species: viroids and viroid-like RNAs
ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining
STRING 8 - a global view on proteins and their functional interactions in 630 organisms
ALFRED: an allele frequency database for diverse populations and DNA polymorphisms - an update
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation
Evidence that covalent complex formation between BCNU-treated oligonucleotides and E. coli alkyltransferases requires the O6- alkylguanine function
Stability of adriamycin-induced DNA adducts and interstrand crosslinks
GoGene: gene annotation in the fast lane
yMGV: a cross-species expression data mining tool
ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery
YMDB: the Yeast Metabolome Database
ClusPro: a fully automated algorithm for protein-protein docking
IMGT, the international ImMunoGeneTics database®
agriGO: a GO analysis toolkit for the agricultural community
EuroPhenome: a repository for high-throughput mouse phenotyping data
SuperCYPsPred - a web server for the prediction of cytochrome activity
PAIR: the predicted Arabidopsis interactome resource
ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences
Efficient and selective initiation by yeast RNA polymerase B in a dinucleotide-primed reaction
LassoProt: server to analyze biopolymers with lassos
Updates to BioSamples database at European Bioinformatics Institute
NLRscape: an atlas of plant NLR proteins
Evaluation of 2'-hydroxyl protection in RNA-synthesis using the H- phosphonate approach
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution
FlyBase: enhancing Drosophila Gene Ontology annotations
RCD+: Fast loop modeling server
TumorFusions: an integrative resource for cancer-associated transcript fusions
CGDB: a database of circadian genes in eukaryotes
Molecular weight determination program
Riboswitch finder tool for identification of riboswitch RNAs
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions
MobiDB: 10 years of intrinsically disordered proteins
JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures
Data structures for DNA sequence manipulation
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
Structural features in TAR RNA of human and simian immunodeficiency viruses: a phylogenetic analysis
CSEA-DB: an omnibus for human complex trait and cell type associations
RPG: the Ribosomal Protein Gene database
The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences
Virus Variation Resource - improved response to emergent viral outbreaks
AAindex: Amino Acid Index Database
POGO-DB - a database of pairwise-comparisons of genomes and conserved orthologous genes
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering
Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera