yusuke1997/dblp-id-title huggingface dataset:
FIE2: a program for the extraction of genomic DNA sequences around the start and translation initiation site of human genes
Consensus alignment server for reliable comparative modeling with distant templates
Distinct cis-acting regions in U3 regulate trans-activation of the human spumaretrovirus long terminal repeat by the viral bel1 gene product
CAFE: aCcelerated Alignment-FrEe sequence analysis
Isolation and mapping of a polymorphic DNA sequence (pMCOC12) on chromosome 14 [D14S20]
PANTHER version 10: expanded protein families and functions, and analysis tools
GenoWatch: a disease gene mining browser for association study
Nucleotide sequence of a chromosomal rearranged lambda 2 immunoglobulin gene of mouse
dbVar and DGVa: public archives for genomic structural variation
BioUML - towards a universal research platform
M4T: a comparative protein structure modeling server
ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types
dictyBase: a new Dictyostelium discoideum genome database
A procedure to standardize CAT reporter gene assay
Update of TTD: Therapeutic Target Database
RNAcentral: a comprehensive database of non-coding RNA sequences
PFD: a database for the investigation of protein folding kinetics and stability
The Jpred 3 secondary structure prediction server
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications
Graphery: interactive tutorials for biological network algorithms
GEPAS: a web-based resource for microarray gene expression data analysis
Multiple whole genome alignments and novel biomedical applications at the VISTA portal
Ensembl Genomes: Extending Ensembl across the taxonomic space
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
piRTarBase: a database of piRNA targeting sites and their roles in gene regulation
WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
ExoLocator - an online view into genetic makeup of vertebrate proteins
Determination of size and orientation of DNA fragments cloned in phage M13 by S1 nuclease mapping
A high frequency RFLP identified by an anonymous single copy genomic clone at 13q14.1-13q14.2 [HGM8 assignment no. D13S22]
BISC: Binary SubComplexes in proteins database
ESTAnnotator: a tool for high throughput EST annotation
Studies on the association of the high mobility group non-histone chromatin proteins with isolated nucleosomes
The BioSample Database (BioSD) at the European Bioinformatics Institute
Nucleic acid binding and intracellular localization of unr, a protein with five cold shock domains
GISSD: Group I Intron Sequence and Structure Database
GEISHA: an evolving gene expression resource for the chicken embryo
PINA 3.0: mining cancer interactome
MMDB: 3D structures and macromolecular interactions
On the statistical assessment of similarities in DNA sequences
PromoterPlot: a graphical display of promoter similarities by pattern recognition
MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets
Modified reaction tubes for the sequential addition of reagents in PCR assays
The complete amino acid sequence of human fibroblast interferon as deduced using synthetic oligodeoxyribonucleotide primers of reverse transcriptase
MATRAS: a program for protein 3D structure comparison
The Reactome pathway knowledgebase
PubAngioGen: a database and knowledge for angiogenesis and related diseases
Major submissions tool developments at the European nucleotide archive
Expanded microbial genome coverage and improved protein family annotation in the COG database
The BioGRID interaction database: 2019 update
PHI-base: a new database for pathogen host interactions
TIMER2.0 for analysis of tumor-infiltrating immune cells
ProteinTools: a toolkit to analyze protein structures
SoyBase, the USDA-ARS soybean genetics and genomics database
SpBase: the sea urchin genome database and web site
ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition
RSAT 2015: Regulatory Sequence Analysis Tools
Laminin-database v.2.0: an update on laminins in health and neuromuscular disorders
GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources
WormBase: better software, richer content
The Adaptive Evolution Database (TAED): a phylogeny based tool for comparative genomics
Restriction analysis of spacers in ribosomal DNA of Drosophila melanogaster
GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes
RAPID: Resource of Asian Primary Immunodeficiency Diseases
ESEfinder: a web resource to identify exonic splicing enhancers
Updates in Rhea: SPARQLing biochemical reaction data
Database resources of the National Center for Biotechnology Information in 2023
ArrayExpress update - simplifying data submissions
FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum
Compilation of vertebrate-encoded transcription factors
Methylation of the T-DNA in Agrobacterium tumefaciens and in several crown gall tumors
A mercury-thiol affinity system for rapid generation of overlapping labeled DNA fragments for DNA sequencing
The use of a dipolar ion-exchanger for the fractionation of transfer ribonucleic acid
Subti Wiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information
OPM database and PPM web server: resources for positioning of proteins in membranes
NTDB: Thermodynamic Database for Nucleic Acids
e-RNA: a collection of web-servers for the prediction and visualisation of RNA secondary structure and their functional features
High mobility group proteins 1 and 2 are present in simian virus 40 provirions, but not in virions
Recent improvements to the SMART domain-based sequence annotation resource
OriDB: a DNA replication origin database
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
GenomeRNAi: a database for cell-based RNAi phenotypes
RNA CoSSMos: Characterization of Secondary Structure Motifs - a searchable database of secondary structure motifs in RNA three-dimensional structures
TSEMA: interactive prediction of protein pairings between interacting families
SAbDab: the structural antibody database
CCDB: a curated database of genes involved in cervix cancer
PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases
MERMAID: dedicated web server to prepare and run coarse-grained membrane protein dynamics
Exploring background mutational processes to decipher cancer genetic heterogeneity
DIANA-miRPath v3.0: deciphering microRNA function with experimental support
CovInter: interaction data between coronavirus RNAs and host proteins
MAGMA: analysis of two-channel microarrays made easy
Genus for biomolecules
TCMID 2.0: a comprehensive resource for TCM
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis
Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments
Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme
L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes
NTMG (N-terminal Truncated Mutants Generator for cDNA): an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants
The ORFanage: an ORFan database
The effect of preincubation of HeLa cell nuclei with ATP on the degradation of mononucleosomal DNA by micrococcal nuclease
MMDB: Entrez's 3D structure database
The ChEMBL database in 2017
ApiDB: integrated resources for the apicomplexan bioinformatics resource center
AISMIG - an interactive server-side molecule image generator
The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists
EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes
The cyclin-dependent kinase inhibitor p21 is regulated by RNA-binding protein PCBP4 via mRNA stability
Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes
The metabolic pathway collection from EMP: the enzymes and metabolic pathways database
An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data
Assignment of the 13C nuclear magnetic resonance spectrum of a short DNA-duplex with 1H-detected two-dimensional heteronuclear correlation spectroscopy
DDMGD: the database of text-mined associations between genes methylated in diseases from different species
SEA version 3.0: a comprehensive extension and update of the Super-Enhancer archive
The nucleotide sequences of 5S ribosomal RNAs from two plants: rape and white beet
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
IMG/M: integrated genome and metagenome comparative data analysis system
The Protein Naming Utility: a rules database for protein nomenclature
MetaMHC: a meta approach to predict peptides binding to MHC molecules
Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata
RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology
CX, DPX and PRIDE: WWW servers for the analysis and comparison of protein 3D structures
GeneFizz: a web tool to compare genetic (coding/non-coding) and physical (helix/coil) segmentations of DNA sequences. Gene discovery and evolutionary perspectives
iPath2.0: interactive pathway explorer
Synthesis of guanosine and its derivatives from 5-amino-1-beta-D- ribofuranosyl-4-imidazolecarboxamide. III. Formation of a novel cycloimidazole nucleoside and its cleavage reactions
SWEET-DB: an attempt to create annotated data collections for carbohydrates
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes
OrysPSSP: a comparative Platform for Small Secreted Proteins from rice and other plants
The Gene Sculpt Suite: a set of tools for genome editing
tRNADB-CE 2011: tRNA gene database curated manually by experts
DPVweb: a comprehensive database of plant and fungal virus genes and genomes
POWER: PhylOgenetic WEb Repeater - an integrated and user-optimized framework for biomolecular phylogenetic analysis
TROD: T7 RNAi Oligo Designer
XTMS: pathway design in an eXTended metabolic space
The eukaryotic linear motif resource - 2018 update
KOBAS server: a web-based platform for automated annotation and pathway identification
The IDB and IEDB: intron sequence and evolution databases
MISTIC: mutual information server to infer coevolution
The vertebrate genome annotation (Vega) database
The Gene Ontology Resource: 20 years and still GOing strong
PiDNA: predicting protein-DNA interactions with structural models
Molecular probe data base (MPDB)
The carboxyterminus of human c-myb protein stimulates activated transcription in trans
A comprehensive BAC resource
ARED 2.0: an update of AU-rich element mRNA database
XTalkDB: a database of signaling pathway crosstalk
Generation of circular RNAs and trans-cleaving catalytic RNAs by rolling transcription of circular DNA oligonucleotides encoding hairpin ribozymes
UbiBrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species
Characterization of an Arabidopsis thaliana DNA hypomethylation mutant
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
Ensembl Genomes 2020 - enabling non-vertebrate genomic research
Conformation of viroids
Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)
CellAtlasSearch: a scalable search engine for single cells
GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison
The Drosophila Hrb87F gene encodes a new member of the A and B hnRNP protein group
KEGG: Kyoto Encyclopedia of Genes and Genomes
ECO, the Evidence & Conclusion Ontology: community standard for evidence information
A bacterial methyltransferase M.EcoHK311 requires two proteins for in vitro methylation
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
The RCSB protein data bank: integrative view of protein, gene and 3D structural information
Location and sequence of the maize chloroplast gene for tRNAser (GCU); a third serine isoaccepting tRNA
genenames.org: the HGNC resources in 2011
The aMAZE LightBench: a web interface to a relational database of cellular processes
RSAT 2018: regulatory sequence analysis tools 20th anniversary
AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody-antigen structures and models
The Human Collagen Mutation Database 1998
CMCompare webserver: comparing RNA families via covariance models
The MemMoRF database for recognizing disordered protein regions interacting with cellular membranes
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
LOCATE: a mammalian protein subcellular localization database
PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
Structure of a pleiomeric form of poly d(AT): poly d(AT)
VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery
The KEGG databases at GenomeNet
Calorimetric measurements of the destabilisation of a ribosomal RNA hairpin by dimethylation of two adjacent adenosines
The mouse Gene Expression Database (GXD): 2019 update
Europe PMC in 2017
PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank
ISPIDER Central: an integrated database web-server for proteomics
Tools for the automatic identification and classification of RNA base pairs
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023
miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology
The CATH Database provides insights into protein structure/function relationships
Proteins Plus : a comprehensive collection of web-based molecular modeling tools
PLncDB V2.0: a comprehensive encyclopedia of plant long noncoding RNAs
SoRT 2 : a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra
ChannelsDB: database of biomacromolecular tunnels and pores
GWAB: a web server for the network-based boosting of human genome-wide association data
Opposing effects of Krüppel-like factor 4 (gut-enriched Krüppel-like factor) and Krüppel-like factor 5 (intestinal-enriched Krüppel-like factor) on the promoter of the Krüppel-like factor 4 gene
NONCODE: an integrated knowledge database of non-coding RNAs
BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products
The Homeodomain Resource: sequences, structures and genomic information
An improved bacterial colony lysis procedure enables direct DNA hybridisation using short (10, 11 bases) oligonucleotides to cosmids
FireProtDB: database of manually curated protein stability data
LOC3D: annotate sub-cellular localization for protein structures
H ++ 3.0: automating p K prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins
The International Genome Sample Resource (IGSR) collection of open human genomic variation resources
REDIdb: the RNA editing database
The genes coding for 4 snRNAs of Drosophila melanogaster: localization and determination of gene numbers
NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes
The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group
PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types
HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing
DIP: the Database of Interacting Proteins
The Database of Ribosomal Cross links (DRC)
Patscanui: an intuitive web interface for searching patterns in DNA and protein data
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database
HvrBase++: a phylogenetic database for primate species
SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool
ProtoMap: automatic classification of protein sequences and hierarchy of protein families
Mouse Genome Database (MGD) 2019
E3Miner: a text mining tool for ubiquitin-protein ligases
SugarBindDB, a resource of glycan-mediated host-pathogen interactions
RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins
Cell specific antiserum to chromosome scaffold proteins
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
QuadBase2: web server for multiplexed guanine quadruplex mining and visualization
Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues
Nucleosome packing in chromatin as revealed by nuclease digestion
Complexity: an internet resource for analysis of DNA sequence complexity
VirOligo: a database of virus-specific oligonucleotides
Physical characteristics in eucaryotic promoters
rrn DB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development
pFlexAna: detecting conformational changes in remotely related proteins
The G protein database, GproteinDb
Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
Histone H1 and HMG 14/17 are deposited nonrandomly in the nucleus
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes
CancerPPD: a database of anticancer peptides and proteins
Presence of a bi-directional S phase-specific transcription regulatory element in the promoter shared by testis-specific TH2A and TH2B histone genes
COMPASS server for homology detection: improved statistical accuracy, speed and functionality
ENdb: a manually curated database of experimentally supported enhancers for human and mouse
DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database
PCDB: a database of protein conformational diversity
Self-assembly of single and closely spaced nucleosome core particles
D 2 P 2 : database of disordered protein predictions
The European Bioinformatics Institute in 2018: tools, infrastructure and training
Preparative separation of the complementary strands of DNA restriction fragments by alkaline RPC-5 chromatography
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences
Antisense 2'-O-alkyl oligoribonucleotides are efficient inhibitors of reverse transcription
Site-specific dissection of E. coli chromosome by lambda terminase
Pest Alert Tool - a web-based application for flagging species of concern in metabarcoding datasets
New insights into the structure of abasic DNA from molecular dynamics simulations
HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Xenbase: a genomic, epigenomic and transcriptomic model organism database
The human-induced pluripotent stem cell initiative - data resources for cellular genetics
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud
RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures
The ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
Studies on the low molecular weight RNA associated with 28S ribosomal RNA from Crotalus durissus terrificus liver
CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates
MODOMICS: a database of RNA modification pathways - 2013 update
Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation
MOLE online 2.0: interactive web-based analysis of biomacromolecular channels
aBiofilm: a resource of anti-biofilm agents and their potential implications in targeting antibiotic drug resistance
FunCoup 3.0: database of genome-wide functional coupling networks
APPRIS WebServer and WebServices
Update of ASRP: the Arabidopsis Small RNA Project database
BAGEL: a web-based bacteriocin genome mining tool
BDB: biopanning data bank
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms
TMFunction: database for functional residues in membrane proteins
SRide: a server for identifying stabilizing residues in proteins
The Stanford Microarray Database
Quantum.Ligand.Dock: protein-ligand docking with quantum entanglement refinement on a GPU system
Contacts between mammalian RNA polymerase II and the template DNA in a ternary elongation complex
StemCellNet: an interactive platform for network-oriented investigations in stem cell biology
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
Update of NUREBASE: nuclear hormone receptor functional genomics
MmtDB: a Metazoa mitochondrial DNA variants database
SEAweb: the small RNA Expression Atlas web application
EDGAR 2.0: an enhanced software platform for comparative gene content analyses
PAST: fast structure-based searching in the PDB
NCBI Reference Sequences: current status, policy and new initiatives
Sequence of a new snRNA from the ciliate Tetrahymena thermophila
CRP: Cleavage of Radiolabeled Phosphoproteins
PUDGE: a flexible, interactive server for protein structure prediction
The Degradome database: mammalian proteases and diseases of proteolysis
ASAP, a systematic annotation package for community analysis of genomes
CSVS, a crowdsourcing database of the Spanish population genetic variability
PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination
ZmDB, an integrated database for maize genome research
5S ribosomal RNA database Y2K
The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research
DNA Data Bank of Japan (DDBJ) update report 2022
PlantQTL-GE: a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information
The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools