yusuke1997/dblp-id-title huggingface dataset:
Comparison of Convolutional Neural Networks and Transformers for the Classification of Images of COVID-19, Pneumonia and Healthy Individuals as Observed with Computed Tomography
A Soft Coprocessor Approach for Developing Image and Video Processing Applications on FPGAs
Viewing Experience Model of First-Person Videos
Optimization by Simmulated Annealing
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
Product release is a rate-limiting step during cleavage by the catalytic RNA subunit of Escherichia coli RNase P [published erratum appears in Nucleic Acids Res 1993 Apr 11;21(7): 1686]
Fast analysis of DNA and protein sequence on Apple IIe: restriction sites search, alignment of short sequence and dot matrix analysis
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties
STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database
Minisatellite instability at the Adh locus reveals somatic polymorphism in amphioxus
TSGene: a web resource for tumor suppressor genes
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
Nematode.net update 2011: addition of data sets and tools featuring next-generation sequencing data
Nanobase.org: a repository for DNA and RNA nanostructures
InsectBase 2.0: a comprehensive gene resource for insects
scEnhancer: a single-cell enhancer resource with annotation across hundreds of tissue/cell types in three species
AutoPSI: a database for automatic structural classification of protein sequences and structures
Haemophilia B: database of point mutations and short additions and deletions, 7th edition
Lineage Landscape: a comprehensive database that records lineage commitment across species
AAgAtlas 1.0: a human autoantigen database
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning
Extension of CyanoBase. CyanoMutants: repository of mutant information on Synechocystis sp. strain PCC6803
A new reference implementation of the PSICQUIC web service
A HindIII RFLP at the FTHP1 locus on chromosome 6
The MetaCyc Database
DyNAVacS: an integrative tool for optimized DNA vaccine design
IMGT, the international ImMunoGeneTics database
SAHG, a comprehensive database of predicted structures of all human proteins
Characterization of (CA)n microsatellites with degenerate sequencing primers
Approaches to sequence analysis of 125I-labeled RNA
The Negatome database: a reference set of non-interacting protein pairs
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes
Peryton: a manual collection of experimentally supported microbe-disease associations
ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context
Organization and partial sequence of a DNA region of the Rhizobium leguminosarum symbiotic plasmid pRL6JI containing the genes fixABC, nifA, nifB and a novel open reading frame
YPD-A database for the proteins of Saccharomyces cerevisiae
New data and features for advanced data mining in Manteia
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
SymD webserver: a platform for detecting internally symmetric protein structures
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes
SilkSatDb: a microsatellite database of the silkworm, Bombyx mori
COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia
soaPDB : a web application for searching the Protein Data Bank, organizing results, and receiving automatic email alerts
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
REDfly 2.0: an integrated database of cis -regulatory modules and transcription factor binding sites in Drosophila
Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles
Protection of (dA.dT) cluster regions in the DNAase I cleavage of DNA by specific interaction with netropsin
FISH - family identification of sequence homologues using structure anchored hidden Markov models
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
PPISearch: a web server for searching homologous protein-protein interactions across multiple species
RNAcentral: a hub of information for non-coding RNA sequences
Synthesis of decadeoxyribonucleotides containing N6-methyladenine, N4- methylcytosine, and 5-methylcytosine: recognition and cleavage by restriction endonucleases (nucleosides and nucleotides part 74)
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization
ARIAweb: a server for automated NMR structure calculation
P4P: a peptidome-based strain-level genome comparison web tool
A restriction enzyme from Fusobacterium nucleatum 4H which recognizes GCNGC
Revised nucleotide sequence of the sporulation gene spoVE from Bacillus subtilis
Analysis of trp repressor-operator interaction by filter binding
MeDAS: a Metazoan Developmental Alternative Splicing database
Comparative transcriptomics across the prokaryotic tree of life
Beyond protein expression, MOPED goes multi-omics
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats
Brassica ASTRA: an integrated database for Brassica genomic research
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures
Arabidopsis nucleolar protein database (AtNoPDB)
miRBase: microRNA sequences, targets and gene nomenclature
FungiDB: an integrated functional genomics database for fungi
ALADYN: a web server for aligning proteins by matching their large-scale motion
Structural organization of the Amy locus in seven strains of Drosophila melanogaster
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors
A replication-deficient HIV-1 DNA used for quantitation of the polymerase chain reaction (PCR)
Candidate gene prioritization with Endeavour
rMAPS: RNA map analysis and plotting server for alternative exon regulation
The topology of the promoter of RNA polymerase II- and III-transcribed genes is modified by the methylation of 5'-CG-3' dinucleotides
AutozygosityMapper: Identification of disease-mutations in consanguineous families
COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures
TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions
AvaII polymorphism in the human LDL receptor gene
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells
JCat: a novel tool to adapt codon usage of a target gene to its potential expression host
ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies
SSRPrimer and SSR Taxonomy Tree : Biome SSR discovery
Atomic force microscopy of oriented linear DNA molecules labeled with 5nm gold spheres
Algorithms for the search of amino acid patterns in nucleic acid sequences
The interaction of ethidium with synthetic double-stranded polynucleotides at low ionic strength
MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering
DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome
The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures
EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering
The Radiation Hybrid Database
Codon usage tabulated from the international DNA sequence databases
The TIGRFAMs database of protein families
IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data
The UCSC Archaeal Genome Browser
Gene3D: modelling protein structure, function and evolution
MINAS - a database of M etal I ons in N ucleic A cid S
NRPSpredictor2 - a web server for predicting NRPS adenylation domain specificity
PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
APPRIS 2017: principal isoforms for multiple gene sets
The tL structure within the leader region of Escherichia coli ribosomal RNA operons has post-transcriptional functions
AWESOME: a database of SNPs that affect protein post-translational modifications
Structural elements of rps0 mRNA involved in the modulation of translational initiation and regulation of E. coli ribosomal protein S15
euHCVdb: the European hepatitis C virus database
SigCom LINCS: data and metadata search engine for a million gene expression signatures
BioPortal: ontologies and integrated data resources at the click of a mouse
Automatic reading of DNA sequencing gel autoradiographs using a large format digital scanner
SuperTarget goes quantitative: update on drug-target interactions
BRENDA in 2019: a European ELIXIR core data resource
Manipulating multiple sequence alignments via MaM and WebMaM
SpliceInfo: an information repository for mRNA alternative splicing in human genome
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
DOOR: a database for prokaryotic operons
MEROPS: the peptidase database
BRAD V3.0: an upgraded Brassicaceae database
STAMP: a web tool for exploring DNA-binding motif similarities
CRISPRedict: a CRISPR-Cas9 web tool for interpretable efficiency predictions
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure
DOMINE: a database of protein domain interactions
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis
The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics
CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies
Energy directed folding of RNA sequences
The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing
GotEnzymes: an extensive database of enzyme parameter predictions
A convenient and adaptable package of computer programs for DNA and protein sequence management, analysis and homology determination
Shiny GATOM: omics-based identification of regulated metabolic modules in atom transition networks
ArchDB 2014: structural classification of loops in proteins
SpermatogenesisOnline 1.0: a resource for spermatogenesis based on manual literature curation and genome-wide data mining
Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation
oPOSSUM: integrated tools for analysis of regulatory motif over-representation
MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases
Nucleotide sequence of the intronless gene expressing a member of the globin VIIB subfamily from Chironomus thummi (Diptera)
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
ArrayProspector: a web resource of functional associations inferred from microarray expression data
RADAR: a web server for RNA data analysis and research
Natural and engineered nicking endonucleases - from cleavage mechanism to engineering of strand-specificity
Nucleotide sequence of the Saccharomyces cerevisiae CLN1 and CLN2 genes
Compilation of tRNA sequences
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions
pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature
waviCGH: a web application for the analysis and visualization of genomic copy number alterations
Extrachromosomal circular ribosomal DNA in the yeast Saccharomyces carlsbergensis
openSputnik - a database to ESTablish comparative plant genomics using unsaturated sequence collections
VFDB 2016: hierarchical and refined dataset for big data analysis - 10 years on
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)
MEROPS: the protease database
SledgeHMMER: a web server for batch searching the Pfam database
ExplorEnz: the primary source of the IUBMB enzyme list
Repeat polymorphisms in the interleukin-4 gene (IL4)
DAMPD: a manually curated antimicrobial peptide database
PubChem: a public information system for analyzing bioactivities of small molecules
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
The RESID Database of protein structure modifications: 2000 update
BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis
Complete nucleotide sequence of the gene encoding the regulatory subunit of 3', 5'-cyclic AMP-dependent protein kinase from the yeast Saccharomyces cerevisiae
The ProDom database of protein domain families: more emphasis on 3D
The Pancreatic Expression Database: 2018 update
Hedgehog Signaling Pathway Database: a repository of current annotation efforts and resources for the Hh research community
Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research
Visualization of RNA crystal growth by atomic force microscopy
eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities
GEL, a DNA sequencing project management system
Protein segment finder: an online search engine for segment motifs in the PDB
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions
The protein common interface database (ProtCID) - a comprehensive database of interactions of homologous proteins in multiple crystal forms
chipD: a web tool to design oligonucleotide probes for high-density tiling arrays
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions
Analysis Tool Web Services from the EMBL-EBI
FootPrinter: a program designed for phylogenetic footprinting
GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group
GLAMM: Genome-Linked Application for Metabolic Maps
Transient expression of DNA in Drosophila via electroporation
Phylogenetic relationships and altered genome structures among Tetrahymenamitochondrial DNAs
The Structure Superposition Database
VARIDT 1.0: variability of drug transporter database (Corrigendum)
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
SPACER: server for predicting allosteric communication and effects of regulation
The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms
Cloning simulation in the cage environment
PhyleasProg: a user-oriented web server for wide evolutionary analyses
ICM Web: the interactive chromatin modeling web server
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation
Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB
PHEPS: web-based pH-dependent Protein Electrostatics Server
NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes
DEEP - A tool for differential expression effector prediction
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
Thermal denaturation of nucleosomal core particles
SMMRNA: a database of small molecule modulators of RNA
Two Taq I RFLPs for human alpha-2 macroglobulin (alpha 2M) using a full length cDNA probe
iSyTE 2.0: a database for expression-based gene discovery in the eye
The Mouse Genome Database (MGD): integrating biology with the genome
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks
The Ocean Gene Atlas: exploring the biogeography of plankton genes online
Catalytic site identification - a web server to identify catalytic site structural matches throughout PDB
Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
Regenerating livers of old rats contain high levels of C/EBPalpha that correlate with altered expression of cell cycle associated proteins
RetrOryza: a database of the rice LTR-retrotransposons
Adenovirus DNA replication in vitro: site-directed mutagenesis of the nuclear factor I binding site of the Ad2 origin
Developments in FINDbase worldwide database for clinically relevant genomic variation allele frequencies
Gene3D: structural assignments for the biologist and bioinformaticist alike
KmerKeys: a web resource for searching indexed genome assemblies and variants
MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
Computer management of oligonucleotide synthesis on cellulose filters
The University of Minnesota Biocatalysis/Biodegradation Database: improving public access
CENTROIDFOLD: a web server for RNA secondary structure prediction
CoPub update: CoPub 5.0 a text mining system to answer biological questions
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces
modEnrichr: a suite of gene set enrichment analysis tools for model organisms
Comparison of the A-T rich regions and the Bacillus subtilis RNA polymerase binding sites in phage phi 29 DNA
A PstI RFLP for the human retinoic acid receptor in 17q21
The EMBL data library
Gene expression variations are predictive for stochastic noise
RAID v2.0: an updated resource of RNA-associated interactions across organisms
NOBAI: a web server for character coding of geometrical and statistical features in RNA structure
Virus Variation Resource - recent updates and future directions
LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs
Low stringency-PCR (LS-PCR) allows entirely internally standardized DNA quantitation
GenBank
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics
CSCD: a database for cancer-specific circular RNAs
ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs
3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy
WormBase 2012: more genomes, more data, new website
WEGO: a web tool for plotting GO annotations
PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach
Common structural features of the Ro RNP associated hY1 and hY5 RNAs
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs
SOP 3 v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF
DIALIGN-TX and multiple protein alignment using secondary structure information at GOBICS
HuGeMap: a distributed and integrated Human Genome Map database
BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome
The tmRNA Website
The PRESAGE database for structural genomics
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
DNA bending in the ternary nucleoprotein complex at the c-fos promoter
Isolation and sequence of cDNA clones coding for a member of the family of high mobility group proteins (HMG-T) in trout and analysis of HMG-T- mRNA's in trout tissues
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics
Human miR-1271 is a miR-96 paralog with distinct non-conserved brain expression pattern
CentrosomeDB: a new generation of the centrosomal proteins database for Human and Drosophila melanogaster
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000
Ribosomal protein gene cluster analysis in eubacterium genomics: homology between Sinorhizobium meliloti strain 1021 and Bacillus subtilis
MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
A relational database system for the maintenance and verification of the Los Alamos sequence library
GRAPE: GRaphical Abstracted Protein Explorer
INTERFEROME v2.0: an updated database of annotated interferon-regulated genes
MIPS: a database for protein sequences and complete genomes
Protein Information Resource: a community resource for expert annotation of protein data
SUMMER: a Mendelian randomization interactive server to systematically evaluate the causal effects of risk factors and circulating biomarkers on pan-cancer survival
VirusMINT: a viral protein interaction database
3dSS: 3D structural superposition
CDD: a curated Entrez database of conserved domain alignments
The Quest for Orthologs orthology benchmark service in 2022
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update
LocalMove: computing on-lattice fits for biopolymers
CyloFold: secondary structure prediction including pseudoknots
Interactions between 30s ribosomal proteins and 50s subunits of Escherichia coli
IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions
BSRD: a repository for bacterial small regulatory RNA
A server and database for dipole moments of proteins
Curved DNA without AA/TT dinucleotide step
IndelFR: a database of indels in protein structures and their flanking regions
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis
Structural organization and nucleotide sequence of mouse c-myb oncogene: activation in ABPL tumors is due to viral integration in an intron which results in the deletion of the 5' coding sequences
BioGPS and MyGene.info: organizing online, gene-centric information
Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems
FOLD-RATE: prediction of protein folding rates from amino acid sequence
High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12