yusuke1997/dblp-id-title huggingface dataset:
Root nodule specific gene regulation: analysis of the soybean nodulin N23 gene promoter in heterologous symbiotic systems
Genes and proteins of Escherichia coli K-12
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S -nitrosylation
3did Update: domain-domain and peptide-mediated interactions of known 3D structure
ProtoNet: hierarchical classification of the protein space
ACNUC: a nucleic acid sequence data base and analysis system
MTR3D: identifying regions within protein tertiary structures under purifying selection
mirDNMR: a gene-centered database of background de novo mutation rates in human
Apple software for analysis of the size of restriction fragments
WeGET: predicting new genes for molecular systems by weighted co-expression
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB
Ensembl 2015
DNA sequence handling programs in BASIC for home computers
The Eukaryotic Promoter Database (EPD)
GPCRDB: information system for G protein-coupled receptors
ENCODE Data in the UCSC Genome Browser: year 5 update
The Autophagy Database: an all-inclusive information resource on autophagy that provides nourishment for research
Web-based platform for analysis of RNA folding from high throughput chemical probing data
Dinucleotide repeat polymorphism in the human surfactant-associated protein 3 gene (SFTP3)
DiRE: identifying distant regulatory elements of co-expressed genes
dbSNP: a database of single nucleotide polymorphisms
GOBASE: the organelle genome database
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
Identification and characterization of the RAD51 gene from the ciliate Tetrahymena thermophila
PathwAX: a web server for network crosstalk based pathway annotation
HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project
Gene Expression Atlas at the European Bioinformatics Institute
DNA assembly using bis-peptide nucleic acids (bisPNAs)
PROPHECY - a database for high-resolution phenomics
Progenetix: 12 years of oncogenomic data curation
Developmental progress and current status of the Animal QTLdb
SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs
The Transporter Classification Database
Structural basis of microRNA length variety
CARNAC: folding families of related RNAs
Current Comparative Table (CCT) automates customized searches of dynamic biological databases
The commercially available restriction enzyme BspHI is blocked by overlapping methylation
ExPASy: SIB bioinformatics resource portal
Organization, sequence and nuclease hypersensitivity of repetitive elements flanking the chicken apoVLDLII gene: extended sequence similarity to elements flanking the chicken vitellogenin gene
Antiviral activity of polynucleotides: copolymers of inosinic acid and N2-dimethylguanylic of 2-methylthioinosinic acid
Multiple sequence alignment with the Clustal series of programs
FASTR3D: a fast and accurate search tool for similar RNA 3D structures
KEGG for taxonomy-based analysis of pathways and genomes
ChloroplastDB: the Chloroplast Genome Database
IPAVS: Integrated Pathway Resources, Analysis and Visualization System
Database of mutations that alter the large tumor antigen in simian virus 40
BCNTB bioinformatics: the next evolutionary step in the bioinformatics of breast cancer tissue banking
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
ATP hydrolysis activity of the DEAD box protein Rok1p is required for in vivo ROK1 function
CDD: a Conserved Domain Database for the functional annotation of proteins
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data
Recent improvements of the ProDom database of protein domain families
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
EffectiveDB - updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
dbSAP: single amino-acid polymorphism database for protein variation detection
R3D-BLAST: a search tool for similar RNA 3D substructures
Synthesis and reactivity of intermediates formed in the T4 RNA ligase reaction
COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures
The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse
RSITE: a computer program to predict the recognition sequence of a restriction enzyme
GeMprospector - online design of cross-species genetic marker candidates in legumes and grasses
Organelle DB: a cross-species database of protein localization and function
THREaD Mapper Studio: a novel, visual web server for the estimation of genetic linkage maps
Eukaryotic genome size databases
QualitySNPng: a user-friendly SNP detection and visualization tool
SuperPred: drug classification and target prediction
SAGD: a comprehensive sex-associated gene database from transcriptomes
DNA helicase IV from HeLa cells
YOGY: a web-based, integrated database to retrieve protein orthologs and associated Gene Ontology terms
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
ExInt: an Exon/Intron database
Fungal names: a comprehensive nomenclatural repository and knowledge base for fungal taxonomy
RFLP detected at the 8924 locus by a thyroglobulin cDNA probe
PROMALS web server for accurate multiple protein sequence alignments
APD2: the updated antimicrobial peptide database and its application in peptide design
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data
HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA
SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts
Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
Cloning and sequencing of a rearranged V lambda gene from a Burkitt's lymphoma cell line expressing kappa light chains
E1DS: catalytic site prediction based on 1D signatures of concurrent conservation
The Vertebrate Genome Annotation (Vega) database
A novel class of human type I interferons
Protein Ontology: a controlled structured network of protein entities
DBcat: a catalog of 500 biological databases
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice
T1DBase, a community web-based resource for type 1 diabetes research
MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes
UniHI: an entry gate to the human protein interactome
A proton NMR study of a DNA dumb-bell structure with hairpin loops of only two nucleotides: d(CACGTGTGTGCGTGCA)
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
RNAiFold: a web server for RNA inverse folding and molecular design
Integrating functional genomic information into the Saccharomyces Genome Database
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Nucleotide sequence of genes for a 5.8S and 25S rRNA from rape seed (Brassica napus)
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information
GPCRDB information system for G protein-coupled receptors
Histone Sequence Database: a compilation of highly-conserved nucleoprotein sequences
RNA-Redesign: a web server for fixed-backbone 3D design of RNA
Initiation of transcription in nuclei isolated from adenovirus infected cells
MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments
IDR: the ImmunoDeficiency Resource
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
The European Large Subunit Ribosomal RNA Database
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach
PMAP: databases for analyzing proteolytic events and pathways
Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names
AAindex: Amino Acid index database
PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes
Gene: a gene-centered information resource at NCBI
SubViral RNA: a database of the smallest known auto-replicable RNA species
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants
Rat Genome Database (RGD): mapping disease onto the genome
Gene Ontology annotations at SGD: new data sources and annotation methods
Introduction of restriction enzyme sites in protein-coding DNA sequences by site-specific mutagenesis not affecting the amino acid sequence: a computer program
Complete nucleotide sequence of a viroid isolated from Etrog citron, a new member of hop stunt viroid group
ATACdb: a comprehensive human chromatin accessibility database
Biallelic Bgl II DNA polymorphism of the human p53 oncogene
Supragenic loop organization: mapping in Drosophila embryos, of scaffold-associated regions on a 800 kilobase DNA continuum cloned from the 14B-15B first chromosome region
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
SCOPPI: a structural classification of protein-protein interfaces
GPCRsignal: webserver for analysis of the interface between G-protein-coupled receptors and their effector proteins by dynamics and mutations
mirTools: microRNA profiling and discovery based on high-throughput sequencing
Equilibrium binding of carcinogens and antitumor antibiotics to DNA: site selectivity, cooperativity, allosterism
ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures
Formation of a G-tetrad and higher order structures correlates with biological activity of the RelA (NF-kappaB p65) 'antisense' oligodeoxynucleotide
The personal genome browser: visualizing functions of genetic variants
MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome
Rapid and efficient cosmid cloning
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites
Identification of a novel murine IAP-promoted placenta-expressed gene
Histone variant macroH2A contains two distinct macrochromatin domains capable of directing macroH2A to the inactive X chromosome
The effect of site specific methylation on restriction endonuclease cleavage (update)
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides
The Global Genome Biodiversity Network (GGBN) Data Portal
Activation of RuvC Holliday junction resolvase in vitro
IARC Database of p53 gene mutations in human tumors and cell lines: updated compilation, revised formats and new visualisation tools
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation
SuperSite: dictionary of metabolite and drug binding sites in proteins
NONCODE v2.0: decoding the non-coding
PHEMTO: protein pH-dependent electric moment tools
oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species
COMPASS server for remote homology inference
FeatureExtract - extraction of sequence annotation made easy
Introducing the PRIDE Archive RESTful web services
PROBEmer: a web-based software tool for selecting optimal DNA oligos
Polymerase chain reaction (PCR) for detection of MspI polymorphism at the D3S2 locus
NCBI Viral Genomes Resource
A fast homology program for aligning biological sequences
HitPredict: a database of quality assessed protein-protein interactions in nine species
MethylomeDB: a database of DNA methylation profiles of the brain
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes
MGnify: the microbiome analysis resource in 2020
Floral tissue of Petunia hybrida (V30) expresses only one member of the chalcone synthase multigene family
Utilization of sequence libraries on a 16-bit mini computer with particular reference to high speed searching
SGDB: a database of synthetic genes re-designed for optimizing protein over-expression
CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts
Expanded versions of the 16S and 23S ribosomal RNA mutation databases (16SMDBexp and 23SMDBexp) [published erratum appears in Nucleic Acids Res 1998 Feb 15;26(4): following 1134]
The SBASE protein domain library, release 2.0: a collection of annotated protein sequence segments
ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
Alignment-Annotator web server: rendering and annotating sequence alignments
European Nucleotide Archive in 2016
ORegAnno 3.0: a community-driven resource for curated regulatory annotation
OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs
CellTracer: a comprehensive database to dissect the causative multilevel interplay contributing to cell development trajectories
Glycan fragment database: a database of PDB-based glycan 3D structures
ANNIE: integrated de novo protein sequence annotation
NBRP databases: databases of biological resources in Japan
Coupling of transcription and replication machineries in λ DNA replication initiation: evidence for direct interaction of Escherichia coli RNA polymerase and the λO protein
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions
DDBJ progress report
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization
Sequence landscapes
A mutation in NPS1/STH1, an essential gene encoding a component of a novel chromatin-remodeling complex RSC, alters the chromatin structure of Saccharomyces cerevisiae centromeres
The PRIDE database and related tools and resources in 2019: improving support for quantification data
MetalPDB in 2018: a database of metal sites in biological macromolecular structures
An RNA folding rule
The imprinted gene and parent-of-origin effect database
Nonisotopic SSCP and competitive PCR for DNA quantification: p53 in breast cancer cells
SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support
TissGDB: tissue-specific gene database in cancer
Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies
FireProt: web server for automated design of thermostable proteins
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
ProteoVision: web server for advanced visualization of ribosomal proteins
CPDB: a database of circular permutation in proteins
CancerResource - updated database of cancer-relevant proteins, mutations and interacting drugs
Cell Taxonomy: a curated repository of cell types with multifaceted characterization
HubMed: a web-based biomedical literature search interface
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
ImmuneRegulation: a web-based tool for identifying human immune regulatory elements
A computer program package for storing and retrieving DNA/RNA and protein sequence data
The Encyclopedia of DNA elements (ENCODE): data portal update
Entrez Gene: gene-centered information at NCBI
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data
GRAMM-X public web server for protein-protein docking
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software
AutDB: a platform to decode the genetic architecture of autism
Proofreading in trans by an aminoacyl-tRNA synthetase: a model for single site editing by isoleucyl-tRNA synthetase
TFAM 1.0: an online tRNA function classifier
Making your database available through Wikipedia: the pros and cons
Gallus GBrowse: a unified genomic database for the chicken
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
The Stanford Microarray Database: data access and quality assessment tools
New and continuing developments at PROSITE
Isolation of cDNAs encoding human manganese superoxide dismutase
PI 2 PE: protein interface/interior prediction engine
Identification of the origin and direction of replication of the broad-host-range plasmid pLS1
Construction of a human chromosome 4 YAC pool and analysis of artificial chromosome stability
PSORTdb: a protein subcellular localization database for bacteria
Organising multi-dimensional biological image information: the BioImage Database
FINDbase: a worldwide database for genetic variation allele frequencies updated
Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices
The mitBASE human dataset structure
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs
PRINTS and its automatic supplement, prePRINTS
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery
Synthesis of DNA via deoxynucleoside H-phosphonate intermediates
Selectome: a database of positive selection
NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL
HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues
Bisulfite genomic sequencing: systematic investigation of critical experimental parameters
NetVenn: an integrated network analysis web platform for gene lists
MAXAMIZE. A DNA sequencing strategy advisor
Dinucleotide repeat polymorphism in the human tubulin alpha 1 (testis specific) gene (TUBA1)
Codon usage tabulated from the international DNA sequence databases; its status 1999
PCSD: a plant chromatin state database
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies
DriverDBv3: a multi-omics database for cancer driver gene research
'Enhancer-constitutive' vectors for the expression of recombinant antibodies
A critical analysis of a left-handed double helix model for B-DNA fibers
Specific cleavage of kinetoplast minicircle DNA from Leishmania tarentolae by mung bean nuclease and identification of several additional minicircle sequence classes
The sequence of the Saccharomyces cerevisiae gene PHO2 codes for a regulatory protein with unusual aminoacid composition
SuperToxic: a comprehensive database of toxic compounds
Onto-CC: a web server for identifying Gene Ontology conceptual clusters
ConoDictor: a tool for prediction of conopeptide superfamilies
A method for the enzymatic synthesis and purification of [alpha-32P] nucleoside triphosphates
Plant editosome database: a curated database of RNA editosome in plants
The mouse Gene Expression Database (GXD): 2011 update
COXPRESdb: a database to compare gene coexpression in seven model animals
BetaCavityWeb: a webserver for molecular voids and channels
Vertebrate MitBASE: a specialised database on vertebrate mitochondrial DNA sequences
An experimental study of Saccharomyces cerevisiae U3 snRNA conformation in solution
An efficient and accurate integration of mini-Mu transposons in vitro: a general methodology for functional genetic analysis and molecular biology applications
BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal
PmiRKB: a plant microRNA knowledge base
GWIPS-viz: 2018 update
Molecular characterization of a novel form of (A gamma delta beta)zero-thalassemia deletion with a 3' breakpoint close to those of HPFH-3 and HPFH-4: insights for a common regulatory mechanism
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods
TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
KnotGenome: a server to analyze entanglements of chromosomes
The Universal Protein Resource (UniProt) in 2010
HMPDACC: a Human Microbiome Project Multi-omic data resource
An algorithm for studying cooperative transitions in DNA
Cyclebase.org - a comprehensive multi-organism online database of cell-cycle experiments
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
SuperPred: update on drug classification and target prediction
Spontaneous and double-strand break-induced recombination, and gene conversion tract lengths, are differentially affected by overexpression of wild-type or ATPase-defective yeast Rad54
The complete nucleotide sequence of the potexvirus white clover mosaic virus
BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles
Polymerase chain reaction (PCR) for detection of MspI polymorphism at the D3S30 locus
Variable methylation of the ribosomal RNA genes of the rat
Ensembl 2019
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand
Cooperative assembly of proteins in the ribosomal GTPase centre demonstrated by their interactions with mutant 23S rRNAs
SMART 4.0: towards genomic data integration
One-Block CYRCA: an automated procedure for identifying multiple-block alignments from single block queries
QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
16S rRNA oligonucleotide catalog data base
SC2disease: a manually curated database of single-cell transcriptome for human diseases
TRANSFAC®: transcriptional regulation, from patterns to profiles
3Drefine: an interactive web server for efficient protein structure refinement
Vertebrate histone genes: nucleotide sequence of a chicken H2A gene and regulatory flanking sequences
EMBL Nucleotide Sequence Database: developments in 2005
OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines
ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
Targeted RNA fingerprinting: the cloning of differentially-expressed cDNA fragments enriched for members of the zinc finger gene family