yusuke1997/dblp-id-title huggingface dataset:
BiologicalNetworks: visualization and analysis tool for systems biology
LncACTdb 2.0: an updated database of experimentally supported ceRNA interactions curated from low- and high-throughput experiments
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
AgBase: supporting functional modeling in agricultural organisms
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data
Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure
The TP53 website: an integrative resource centre for the TP53 mutation database and TP53 mutant analysis
CAT constructions with multiple unique restriction sites for the functional analysis of eukaryotic promoters and regulatory elements
iPDA: integrated protein disorder analyzer
REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
TBDB: a database of structurally annotated T-box riboswitch: tRNA pairs
Phydbac (phylogenomic display of bacterial genes): an interactive resource for the annotation of bacterial genomes
Distinctive patterns of translational reinitiation in the lac repressor mRNA: bridging of long distances by out-of-frame translation and RNA secondary structure, effects of primary sequence
SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
FlyTED: the Drosophila Testis Gene Expression Database
CEBS update: curated toxicology database with enhanced tools for data integration
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
IS6110, an IS-like element of Mycobacterium tuberculosis complex
HMG I/Y regulates long-range enhancer-dependent transcription on DNA and chromatin by changes in DNA topology
A single amino acid change of translation termination factor eRF1 switches between bipotent and omnipotent stop-codon specificity
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
BSDD: Biomolecules Segment Display Device's web-based interactive display tool
Network portal: a database for storage, analysis and visualization of biological networks
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences
Pseudouridylation of yeast ribosomal precursor RNA
Recovery of YAC-end sequences through complementation of an Escherichia coli pyrF mutation
PCR amplification of DNA sequences from nitrocellulose-bound, immunostained bacterial colonies
PRINTS prepares for the new millennium
Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides
MDPD: an integrated genetic information resource for Parkinson's disease
CRISPRz: a database of zebrafish validated sgRNAs
PATRIC, the bacterial bioinformatics database and analysis resource
MEPD: medaka expression pattern database, genes and more
JiffyNet: a web-based instant protein network modeler for newly sequenced species
SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes
Isolation of rare transcripts by representational difference analysis
LitSuggest: a web-based system for literature recommendation and curation using machine learning
NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database
Pathema: a clade-specific bioinformatics resource center for pathogen research
Isolation and characterization of maize genes coding for zein proteins of the 21000 dalton size class
RPS: a comprehensive database of RNAs involved in liquid-liquid phase separation
OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data
DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements
FLYSNPdb: a high-density SNP database of Drosophila melanogaster
Human PAML browser: a database of positive selection on human genes using phylogenetic methods
microbioTA : an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus
A convenient and adaptable package of DNA sequence analysis programs for microcomputers
Transterm: a database of messenger RNA components and signals
(PS)2: protein structure prediction server version 3.0
BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking
WebFR3D - a server for finding, aligning and analyzing recurrent RNA 3D motifs
HMDD v2.0: a database for experimentally supported human microRNA and disease associations
Recent updates and developments to plant genome size databases
MYBS: a comprehensive web server for mining transcription factor binding sites in yeast
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics
Isolation and mapping of a polymorphic DNA sequence MCT128.1 on chromosome 11 [D11S285]
Visualization of the protein-coding regions with a self adaptive spectral rotation approach
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport
DiseaseMeth: a human disease methylation database
The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform
The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish
FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets
3D-partner: a web server to infer interacting partners and binding models
AutoClass@IJM: a powerful tool for Bayesian classification of heterogeneous data in biology
R obi NA : a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
SuperFly: a comparative database for quantified spatio-temporal gene expression patterns in early dipteran embryos
PROTAC-DB: an online database of PROTACs
antiSMASH 2.0 - a versatile platform for genome mining of secondary metabolite producers
The CATH database: an extended protein family resource for structural and functional genomics
SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation
taveRNA: a web suite for RNA algorithms and applications
IDBD: Infectious Disease Biomarker Database
BIND: the Biomolecular Interaction Network Database
tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data
DNA double-strand break repair in cell-free extracts from Ku80-deficient cells: implications for Ku serving as an alignment factor in non-homologous DNA end joining
Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery
EPD in its twentieth year: towards complete promoter coverage of selected model organisms
KinaMetrix: a web resource to investigate kinase conformations and inhibitor space
The European Large Subunit Ribosomal RNA database
The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources
GeneCAT - novel webtools that combine BLAST and co-expression analyses
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine
Partial nucleotide sequence of a 3.4 kb fragment from the rat ribosomal DNA nontranscribed spacer
ENCODE whole-genome data in the UCSC Genome Browser
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments
The non-histone proteins of the rat liver nucleus and their distribution amongst chromatin fractions as produced by nuclease digestion
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome
SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches
Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks
CNVxplorer: a web tool to assist clinical interpretation of CNVs in rare disease patients
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models
SigMol: repertoire of quorum sensing signaling molecules in prokaryotes
Structural requirements for binding of bovine tRNATrp with avian myeloblastosis virus DNA polymerase
Pcons.net: protein structure prediction meta server
WormBase 2016: expanding to enable helminth genomic research
miRandola 2017: a curated knowledge base of non-invasive biomarkers
Identification of high affinity Tbf1p-binding sites within the budding yeast genome
Database of protein sequence alignments: PIR-ALN
Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data
SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways
InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence
The tmRNA database (tmRDB)
SRPDB: Signal Recognition Particle Database
5S rRNA Data Bank
E2F-1 represses transcription of the human telomerase reverse transcriptase gene
ProTox-II: a webserver for the prediction of toxicity of chemicals
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets
GeneTrees: a phylogenomics resource for prokaryotes
SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data
COG database update: focus on microbial diversity, model organisms, and widespread pathogens
Sequence resources at the Candida Genome Database
HTPSELEX - a database of high-throughput SELEX libraries for transcription factor binding sites
Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
DIANA-microT web server: elucidating microRNA functions through target prediction
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists
The DynaMine webserver: predicting protein dynamics from sequence
ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps
ADPriboDB 2.0: an updated database of ADP-ribosylated proteins
MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database
ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae
Proteins Plus : interactive analysis of protein-ligand binding interfaces
Kabat Database and its applications: 30 years after the first variability plot
The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community
PCMDB: a curated and comprehensive resource of plant cell markers
'ZSTATS' - a statistical analysis for potential Z-DNA sequences
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation
NetAffx: Affymetrix probesets and annotations
GeNemo: a search engine for web-based functional genomic data
miRGator v3.0: a microRNA portal for deep sequencing, expression profiling and mRNA targeting
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes
RNAhybrid: microRNA target prediction easy, fast and flexible
ArrayExpress update - from bulk to single-cell expression data
Small RNA database
OrfPredictor: predicting protein-coding regions in EST-derived sequences
REVERSE: a user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments
AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome
PAR-3D: a server to predict protein active site residues
CRdb: a comprehensive resource for deciphering chromatin regulators in human
Update of KDBI: Kinetic Data of Bio-molecular Interaction database
Complex Portal 2022: new curation frontiers
BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
CASTp 3.0: computed atlas of surface topography of proteins
Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers
Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1
Islander: a database of precisely mapped genomic islands in tRNA and tmRNA genes
GWASdb: a database for human genetic variants identified by genome-wide association studies
A new synthesis of inosine from 5-amino-1-beta-D-ribofuranosyl-4- imidazole-carboxamide
A Taq I polymorphism for the human transforming growth factor alpha gene (TGFA)
OperonDB: a comprehensive database of predicted operons in microbial genomes
NORSp: predictions of long regions without regular secondary structure
DNA synthesis, methylation and degradation during conjugation in Tetrahymena thermophila
The Mouse Genome Database (MGD): updates and enhancements
ELM 2016 - data update and new functionality of the eukaryotic linear motif resource
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
The EMBL Nucleotide Sequence Database: major new developments
SEQAID: a DNA sequence assembling program based on a mathematical model
The European ribosomal RNA database
T-psi-C: user friendly database of tRNA sequences and structures
psRNATarget: a plant small RNA target analysis server
Identification and visualization of protein binding regions with the ArDock server
TRANSFAC: a database on transcription factors and their DNA binding sites
ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes
Swiss EMBnet node web server
Moderately repeated mouse Y chromosomal sequence families present distinct types of organization and evolutionary change
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways
OncoBase: a platform for decoding regulatory somatic mutations in human cancers
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
CaspR: a web server for automated molecular replacement using homology modelling
ARED Organism: expansion of ARED reveals AU-rich element cluster variations between human and mouse
Nucleotide sequence of the psbH gene of the cyanobacterium Synechocystis 6803
The PIR-International Protein Sequence Database
The Rat Genome Database 2009: variation, ontologies and pathways
A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system
AFLP-based mRNA fingerprinting
Ensembl 2006
eProS - a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles
Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires
UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions
The nucleotide sequences of the 5S rRNAs from the purple bacteria Ectothiorhodospira halophila and Ectothiorhodospira vacuolata
ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy
Web3DMol: interactive protein structure visualization based on WebGL
Binding MOAD, a high-quality protein-ligand database
DBD2BS: connecting a DNA-binding protein with its binding sites
Molecular Probe Data Base (MPDB)
PatMatch: a program for finding patterns in peptide and nucleotide sequences
CNCDatabase: a database of non-coding cancer drivers
The European Nucleotide Archive in 2021
The solution structure of the circular trinucleotide cr(GpGpGp) determined by NMR and molecular mechanics calculation
MyDGR: a server for identification and characterization of diversity-generating retroelements
Sequence of an isoleucine tRNA from Mycoplasma mycoides sp. Capri
The carbohydrate-active enzymes database (CAZy) in 2013
MAGNET: MicroArray Gene expression and Network Evaluation Toolkit
Nuclear magnetic resonance studies on yeast tRNAPhe. III. Assignments of the iminoproton resonances of the tertiary structure by means of nuclear Overhauser effect experiments at 500 MHz
TDR Targets: a chemogenomics resource for neglected diseases
Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases
Nucleotide sequence of the gene coding for quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus
LincSNP 2.0: an updated database for linking disease-associated SNPs to human long non-coding RNAs and their TFBSs
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation
Construction of bacteriophage T7 late promoters with point mutations and characterization by in vitro transcription properties
ERGDB: Estrogen Responsive Genes Database
CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects
Studies on human tRNA. I. The rapid, large scale isolation and partial fractionation of placenta and liver tRNA
Triplex affinity capture of a single copy clone from a yeast genomic library
Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins
GTRD: an integrated view of transcription regulation
Polbase: a repository of biochemical, genetic and structural information about DNA polymerases
MimoDB 2.0: a mimotope database and beyond
PCE: web tools to compute protein continuum electrostatics
Isolation and mapping of a polymorphic DNA sequence pHBI18P2 on chromosome 11 [D11S147]
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources
UniProt: the universal protein knowledgebase in 2021
SWORD2: hierarchical analysis of protein 3D structures
The BIG Data Center: from deposition to integration to translation
Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags
G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands
Gendoo: Functional profiling of gene and disease features using MeSH vocabulary
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes
miRecords: an integrated resource for microRNA-target interactions
ChEMBL web services: streamlining access to drug discovery data and utilities
TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies
The 27th annual Nucleic Acids Research database issue and molecular biology database collection
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells
Rice SNP-seek database update: new SNPs, indels, and queries
Nucleotide sequence of a cyclodextrin glucosyltransferase gene, cgtA, from Bacillus licheniformis
Isolation and mapping of a polymorphic DNA sequence (pEFD85.7) on chromosome 15 [D15S37]
DeepBlue epigenomic data server: programmatic data retrieval and analysis of epigenome region sets
The SBASE protein domain library, release 6.0: a collection of annotated protein sequence segments
PLAZA 3.0: an access point for plant comparative genomics
The Pfam protein families database: towards a more sustainable future
NCI: a server to identify non-canonical interactions in protein structures
Intercalative binding to DNA of antitumour drugs derived from 3-nitro- 1, 8-naphthalic acid
KFC Server: interactive forecasting of protein interaction hot spots
The Proteins API: accessing key integrated protein and genome information
The tmRDB and SRPDB resources
Human DNA sequences exhibiting gamete-specific hypomethylation
SCMD: Saccharomyces cerevisiae Morphological Database
iELM - a web server to explore short linear motif-mediated interactions
AluGene: a database of Alu elements incorporated within protein-coding genes
ASAP: the Alternative Splicing Annotation Project
A spite specific endonuclease from thermus thermophilus 111, Tth111I
NPRD: Nucleosome Positioning Region Database
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC
ECgene: genome annotation for alternative splicing
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro
patcHwork: a user-friendly pH sensitivity analysis web server for protein sequences and structures
Kinetoplast-associated DNA topoisomerase in Crithidia fasciculata: crosslinking of mitochondrial topoisomerase II to both minicircles and maxicircles in cells treated with the topoisomerase inhibitor VP16
Computer graphics program to reveal the dependence of the gross three- dimensional structure of the B-DNA double helix on primary structure
TMA Navigator: network inference, patient stratification and survival analysis with tissue microarray data
wwLigCSRre: a 3D ligand-based server for hit identification and optimization
iSPOT: a web tool to infer the interaction specificity of families of protein modules
CSRDB: a small RNA integrated database and browser resource for cereals
3did: identification and classification of domain-based interactions of known three-dimensional structure
Computer programs to analyze DNA and amino acid sequence data
PomBase: a comprehensive online resource for fission yeast
The PlantsP and PlantsT Functional Genomics Databases
The ERGOTM genome analysis and discovery system
RNALogo: a new approach to display structural RNA alignment
SpliceDB: database of canonical and non-canonical mammalian splice sites
Swimming into peptidomimetic chemical space using pepMMsMIMIC
PCAT: an integrated portal for genomic and preclinical testing data of pediatric cancer patient-derived xenograft models
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands
CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization
RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects
A new restriction endonuclease from Acetobacter pasteurianus
E2F mediates induction of the Sp1-controlled promoter of the human DNA polymerase B-subunit gene POLE2
PHYTOPROT: a database of clusters of plant proteins
Enzymatic synthesis of DNA complementary to mitochondrial mRNA via reverse transcription
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
PepCyber: P~PEP: a database of human protein-protein interactions mediated by phosphoprotein-binding domains
YMDB 2.0: a significantly expanded version of the yeast metabolome database
SEPPA 3.0 - enhanced spatial epitope prediction enabling glycoprotein antigens