yusuke1997/dblp-id-title huggingface dataset:
Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE
COFECO: composite function annotation enriched by protein complex data
The RNA modification database
Accurate quantification of transcriptome from RNA-Seq data by effective length normalization
Scooby-domain: prediction of globular domains in protein sequence
PlantGDB, plant genome database and analysis tools
Isolation and characterization of the human tyrosine aminotransferase gene
The Enhanced Microbial Genomes Library
Biogenesis of mitochondria: the mitochondrial gene (aap1) coding for mitochondrial ATPase subunit 8 in Saccharomyces cerevisiae
DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations
CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning
Sequence similarity of putative transposases links the maize Mutator autonomous element and a group of bacterial insertion sequences
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Intelligent computational assistance for experiment design
Characterization of a human cDNA encoding a widely expressed and highly conserved cysteine-rich protein with an unusual zinc-finger motif
Microcomputer programs for DNA sequence analysis
Replication of proto-oncogenes early during the S phase in mammalian cell lines
GRNdb: decoding the gene regulatory networks in diverse human and mouse conditions
Digital development: a database of cell lineage differentiation in C. elegans with lineage phenotypes, cell-specific gene functions and a multiscale model
The European Bioinformatics Institute's data resources 2014
IMG/M 4 version of the integrated metagenome comparative analysis system
ClusterCAD: a computational platform for type I modular polyketide synthase design
A database of germline p53 mutations in cancer-prone families
mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes
SCOPE: a web server for practical de novo motif discovery
The PDB data uniformity project
Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences
SilkDB: a knowledgebase for silkworm biology and genomics
jPOSTrepo: an international standard data repository for proteomes
SwissSidechain: a molecular and structural database of non-natural sidechains
The database of experimentally supported targets: a functional update of TarBase
WorfDB: the Caenorhabditis elegans ORFeome Database
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net
Principle of codification for quick comparisons with the entire biomolecule databanks and associated programs in FORTRAN 77
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
An improved method for the separation and quantitation of the modified nucleosides of transfer RNA
GIF-DB, a WWW database on gene interactions involved in Drosophila melanogaster development
NNcon: improved protein contact map prediction using 2D-recursive neural networks
REBASE: a database for DNA restriction and modification: enzymes, genes and genomes
Double replica southwestern
A novel functional genomics approach identifies mTERT as a suppressor of fibroblast transformation
Applications of parallel processing algorithms for DNA sequence analysis
Primer Design Assistant (PDA): a web-based primer design tool
Improved programs for DNA and protein sequence analysis on the IBM personal computer and other standard computer systems
EpiToolKit - a web server for computational immunomics
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3
CLIC: clustering analysis of large microarray datasets with individual dimension-based clustering
SpatialDB: a database for spatially resolved transcriptomes
The Zebrafish Information Network (ZFIN): the zebrafish model organism database
The SWISS-2DPAGE database: what has changed during the last year
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
The SLiMDisc server: short, linear motif discovery in proteins
Panzea: an update on new content and features
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database
PLIP: fully automated protein-ligand interaction profiler
FlyRNAi: the Drosophila RNAi screening center database
Gene Ontology Consortium: going forward
Protein structure prediction servers at University College London
In vitro suppression of an amber mutation by a chemically aminoacylated transfer RNA prepared by runoff transcription
GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries
CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design
Genome3D: exploiting structure to help users understand their sequences
XPC and human homologs of RAD23: intracellular localization and relationship to other nucleotide excision repair complexes
Targetfinder.org: a resource for systematic discovery of transcription factor target genes
The Biomolecular Interaction Network Database and related tools 2005 update
siRNA Selection Server: an automated siRNA oligonucleotide prediction server
An in vitro screening technique for DNA polymerases that can incorporate modified nucleotides. Pseudo-thymidine as a substrate for thermostable polymerases
SPARCS: a web server to analyze (un)structured regions in coding RNA sequences
An inexpensive semi-automated sequence reader for the Apple II computer
ELM - the database of eukaryotic linear motifs
CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography
Polynucleotide fragments from the 28S ribosomal RNA of insects
The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA)
Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome
1H NMR of valine tRNA modified bases. Evidence for multiple conformations
EASED: Extended Alternatively Spliced EST Database
OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels
Complete nucleotide sequence of the peroxisomal acyl CoA oxidase from the alkane-utilizing yeast Candida maltosa
SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis
GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs
LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser
Computer analysis and structure prediction of nucleic acids and proteins
TISdb: a database for alternative translation initiation in mammalian cells
MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map
High EDTA concentrations cause entrapment of small DNA molecules in the compression zone of pulsed field gels, resulting in smaller than expected insert sizes in YACs prepared from size selected DNA
Incorporation of 2'-amido-nucleosides in oligodeoxynucleotides and oligoribonucleotides as a model for 2'-linked conjugates
Novel short interspersed repeat in human DNA
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences
Involvement of protein kinase C in the control of tRNA modification with queuine in HeLa cells
qPrimerDepot: a primer database for quantitative real time PCR
DynOmics: dynamics of structural proteome and beyond
TRANSCompel®: a database on composite regulatory elements in eukaryotic genes
Petabyte-scale innovations at the European Nucleotide Archive
NPASS database update 2023: quantitative natural product activity and species source database for biomedical research
EMAGE mouse embryo spatial gene expression database: 2010 update
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites
The NIP7 protein is required for accurate pre-rRNA processing in human cells
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams
PERCEPTRON: an open-source GPU-accelerated proteoform identification pipeline for top-down proteomics
Preparation of nested deletions in single-strand DNA using oligonucleotides containing partially random base sequences
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
InterPro in 2022
GWAS Central: an expanding resource for finding and visualising genotype and phenotype data from genome-wide association studies
MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species
Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013
IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
FuzPred: a web server for the sequence-based prediction of the context-dependent binding modes of proteins
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions
Inferring the functional effect of gene expression changes in signaling pathways
GalaxyRefine: protein structure refinement driven by side-chain repacking
iPPI-DB: an online database of modulators of protein-protein interactions
LIST-S2: taxonomy based sorting of deleterious missense mutations across species
SilencerDB: a comprehensive database of silencers
PrDOS: prediction of disordered protein regions from amino acid sequence
COVID19 Drug Repository: text-mining the literature in search of putative COVID19 therapeutics
The European Nucleotide Archive in 2018
ChIPprimersDB: a public repository of verified qPCR primers for chromatin immunoprecipitation (ChIP)
Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
Common terminal repeats of the macronuclear DNA are absent from the micronuclear DNA in hypotrichous ciliate, Stylonychia pustulata
LncTarD 2.0: an updated comprehensive database for experimentally-supported functional lncRNA-target regulations in human diseases
SMART: recent updates, new developments and status in 2015
CysView: protein classification based on cysteine pairing patterns
DSHIFT: a web server for predicting DNA chemical shifts
Polymerase chain reaction (PCR) for detection of MspI polymorphism at the D3S6 locus
MAPU 2.0: high-accuracy proteomes mapped to genomes
Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T)
iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
PiRaNhA: a server for the computational prediction of RNA-binding residues in protein sequences
R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops
Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus
WEBSAGE: a web tool for visual analysis of differentially expressed human SAGE tags
Compilation of small ribosomal subunit RNA structures
Alternative translation start sites are conserved in eukaryotic genomes
MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence
ArchDB: automated protein loop classification as a tool for structural genomics
BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences
Retrotransposition of the I factor, a non-long terminal repeat retrotransposon of Drosophila, generates tandem repeats at the 3' end
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation
Bacteriome.org - an integrated protein interaction database for E. coli
Pfold: RNA secondary structure prediction using stochastic context-free grammars
ProteomicsDB: a multi-omics and multi-organism resource for life science research
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service
The Nuclear Receptor Resource: a growing family
MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence
CORUM: the comprehensive resource of mammalian protein complexes - 2019
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
Recognizing and validating ligands with CheckMyBlob
Rfam: an RNA family database
Signal search analysis server
The DisGeNET knowledge platform for disease genomics: 2019 update
A method for the analysis of newly synthesized tritiated mRNA
SGAtools: one-stop analysis and visualization of array-based genetic interaction screens
A general database for DNA sequence changes induced by mutagenesis of several bacterial and mammalian genes
Sputnik: a database platform for comparative plant genomics
BLASTO: a tool for searching orthologous groups
Dali server: structural unification of protein families
Brain Catalog: a comprehensive resource for the genetic landscape of brain-related traits
A simple method for global sequence comparison
The Human Disease Ontology 2022 update
An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein three-dimensional structure data
OligoWiz 2.0 - integrating sequence feature annotation into the design of microarray probes
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison
KineticDB: a database of protein folding kinetics
ALFRED: an allele frequency database for diverse populations and DNA polymorphisms
ASpedia: a comprehensive encyclopedia of human alternative splicing
CATH: comprehensive structural and functional annotations for genome sequences
MethyCancer: the database of human DNA methylation and cancer
Identification of proteins of Escherichia coli and Saccharomyces cerevisiae that specifically bind to C/C mismatches in DNA
DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs
Highly redundant function of multiple AT-rich sequences as core promoter elements in the TATA-less RPS5 promoter of Saccharomyces cerevisiae
YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information
RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
FLAGdb ++ : a database for the functional analysis of the Arabidopsis genome
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts
MBGD update 2013: the microbial genome database for exploring the diversity of microbial world
ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling
RSAT: regulatory sequence analysis tools
Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites
HotSprint: database of computational hot spots in protein interfaces
miRNAFold: a web server for fast miRNA precursor prediction in genomes
The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database
DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
Approach to identification of a point mutation in apo B100 gene by means of a PCR-mediated site-directed mutagenesis
The HHpred interactive server for protein homology detection and structure prediction
Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format
rrn DB: documenting the number of rRNA and tRNA genes in bacteria and archaea
Unraveling allosteric landscapes of allosterome with ASD
ArchPRED: a template based loop structure prediction server
FuzDB: a new phase in understanding fuzzy interactions
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings
R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures
A new general approach for the simultaneous chemical synthesis of large numbers of oligonucleotides: segmental solid supports
Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs
The UCSC Genome Browser Database
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals
Construction of cDNA coding for human von Willebrand factor using antibody probes for colony-screening and mapping of the chromosomal gene
The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
The YH database: the first Asian diploid genome database
<mds_ies_db>: a database of ciliate genome rearrangements
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis
PseudoBase: a database with RNA pseudoknots
Multi-CSAR: a web server for scaffolding contigs using multiple reference genomes
HAGR: the Human Ageing Genomic Resources
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level
Arena3Dweb: interactive 3D visualization of multilayered networks
Recombinant DNA data management at the restriction and functional site level
Nucleic Acids Research annual Web Server Issue in 2009
Sequence analysis of the BZLF 1 gene of Epstein-Barr virus derived from a new variant isolated in Taiwan
ChEMBL: a large-scale bioactivity database for drug discovery
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
Primary structure and functional organization of Drosophila 1731 retrotransposon
The DNA sequence of the gene and genetic control sites for the excreted B. subtilis enzyme beta-glucanase
PheLiGe: an interactive database of billions of human genotype-phenotype associations
DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes
ModBase, a database of annotated comparative protein structure models and associated resources
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
SynDB: a Synapse protein DataBase based on synapse ontology
Gene3D: comprehensive structural and functional annotation of genomes
AMDB: a database of animal gut microbial communities with manually curated metadata
GlyNest and CASPER: two independent approaches to estimate 1 H and 13 C NMR shifts of glycans available through a common web-interface
FlyBase: integration and improvements to query tools
Modification interference approach to detect ribose moieties important for the optimal activity of a ribozyme
Serial Expression Analysis: a web tool for the analysis of serial gene expression data
g: Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments
A multiple sequence alignment program
The ABCD database: a repository for chemically defined antibodies
Oligonucleotide mapping: evaluation of its sensitivity by computer- simulation
Visualizing RAD51-mediated joint molecules: implications for recombination mechanism and the effect of sequence heterology
Biological SOAP servers and web services provided by the public sequence data bank
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
RNA molecules containing exons originating from different members of the cytochrome P450 2C gene subfamily (CYP2C) in human epidermis and liver
The RIKEN integrated database of mammals
DDBJ Database updates and computational infrastructure enhancement
Thermostable polynucleotide phosphorylases from Bacillus stearothermophilus and Thermus aquaticus
PLANT-PIs: a database for plant protease inhibitors and their genes
SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology
A novel human cytochrome P450 gene (P450IIB): chromosomal localization and evidence for alternative splicing
The RCSB Protein Data Bank: new resources for research and education
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data
PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
The SUPERFAMILY database in 2007: families and functions
Coding strategy differences between constant and variable segments of immunoglobulin genes
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome
PANGEA: a new gene set enrichment tool for Drosophila and common research organisms
EMAGE - Edinburgh Mouse Atlas of Gene Expression: 2008 update
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics
PK-DB: pharmacokinetics database for individualized and stratified computational modeling
INE: a rice genome database with an integrated map view
Nucleic acid sequence database computer system
FIDEA: a server for the functional interpretation of differential expression analysis
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
SV40 large tumor antigen (T antigen): database of mutants
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions
Ensembl Genomes 2016: more genomes, more complexity
The nucleotide sequence of formylmethionine tRNA from Mycoplasma mycoides sp. capri
UK CropNet: a collection of databases and bioinformatics resources for crop plant genomics
Deficiency of a novel mismatch repair activity in a bladder tumor cell line
MitoP2: the mitochondrial proteome database - now including mouse data
CottonMD: a multi-omics database for cotton biological study
Simplified computer programs for search of homology within nucleotide sequences
HieranoiDB: a database of orthologs inferred by Hieranoid
Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling
G2Cdb: the Genes to Cognition database
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA
PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures
PhosPhAt goes kinases - searchable protein kinase target information in the plant phosphorylation site database PhosPhAt
Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database
Ensembl 2013
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks
NCBI GEO: mining tens of millions of expression profiles - database and tools update
UTGB/medaka: genomic resource database for medaka biology
Xpro: database of eukaryotic protein-encoding genes
Sequence analysis of 5'[32P] labeled mRNA and tRNA using polyacrylamide gel electrophoresis
The coffee genome hub: a resource for coffee genomes