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Unknown
(1832)
Genomics
(625)
Transcriptomics
(502)
Proteomics
(286)
Metabolomics
(37)
Other
(5)
Genomic
(4)
Models
(3)
Methylation profiling
(1)
Organisms
Homo sapiens
(241)
Mus musculus
(169)
Caenorhabditis elegans
(91)
Drosophila melanogaster
(62)
Saccharomyces cerevisiae
(17)
Arabidopsis thaliana
(17)
Rattus norvegicus
(14)
Danio rerio
(13)
Gallus gallus
(10)
Glycine max
(8)
Escherichia coli
(6)
Zea mays
(5)
Macaca fascicularis
(4)
Oryza sativa
(4)
Streptomyces venezuelae
(4)
Escherichia coli str. K-12 substr. MG1655
(4)
Brassica napus
(4)
Thermotoga maritima MSB8
(3)
Corynebacterium glutamicum
(3)
Candida albicans
(3)
Sus scrofa
(3)
Saccharomyces cerevisiae SK1
(2)
Macaca mulatta
(2)
Solanum lycopersicum
(2)
Solanum chilense
(1)
Fusarium oxysporum f. sp. niveum
(1)
Tetranychus cinnabarinus
(1)
Rehmannia glutinosa
(1)
Epinephelus coioides
(1)
Apostichopus japonicus
(1)
Organisms
Homo sapiens
(89)
Mus musculus
(87)
Caenorhabditis elegans
(11)
Arabidopsis thaliana
(10)
Gallus gallus
(8)
Drosophila melanogaster
(8)
Rattus norvegicus
(7)
uncultured marine microorganism
(4)
Danio rerio
(4)
Oncorhynchus mykiss
(3)
seawater metagenome
(3)
Cupriavidus necator H16
(2)
Brassica napus
(2)
Prunus persica
(2)
Saccharomyces cerevisiae
(2)
Bos taurus
(2)
Colwellia sp. TT2012
(1)
Rimicaris leurokolos
(1)
Reaumuria trigyna
(1)
Pantoea ananatis LMG 2665
(1)
Human gammaherpesvirus 8
(1)
Dictyostelium discoideum AX4
(1)
Morus alba var. atropurpurea
(1)
Roseobacter denitrificans OCh 114
(1)
Rhizoctonia solani AG-3 Rhs1AP
(1)
Rickettsia conorii str. Malish 7
(1)
Phyllostachys violascens
(1)
Mayetiola destructor
(1)
Agrobacterium fabrum str. C58
(1)
Rhizophagus irregularis DAOM 181602=DAOM 197198
(1)
Repository
biostudies-arrayexpress
(594)
ENA
(368)
pride
(269)
geo
(122)
EGA
(49)
MetaboLights
(37)
MassIVE
(8)
iProX
(5)
dbGaP
(4)
jPOST
(4)
BioModels
(2)
PMR
(1)
Tissue
Cell culture
(81)
Epithelial cell
(19)
Blood plasma
(13)
Brain
(12)
Skin
(8)
Blood
(7)
Permanent cell line cell
(6)
Liver
(6)
Feces
(5)
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(5)
Lung
(5)
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(5)
Blood serum
(4)
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(4)
T cell
(4)
Whole body
(4)
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(3)
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(3)
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(3)
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(2)
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(2)
Gill
(2)
Neutrophil
(2)
Photosynthetic cell
(2)
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(2)
Rosette
(2)
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(2)
Cerebellum
(2)
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(2)
Primary cell
(2)
Disease
Colon cancer
(6)
COVID-19
(4)
Parkinson's disease
(4)
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(4)
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(4)
Atypical teratoid rhabdoid tumor
(3)
Bacterial sepsis
(3)
Membranous glomerulonephritis
(3)
Lung adenocarcinoma
(3)
Cervix carcinoma
(3)
Disease free
(3)
Brain glioblastoma multiforme
(2)
Melanoma
(2)
Malignant neoplasm of ovary
(2)
Lymphoma
(2)
Osteosarcoma
(2)
Human immunodeficiency virus infectious disease
(2)
Wounds and Injuries
(2)
None- acute control
(1)
Non-infected
(1)
Colorectal carcinoma
(1)
None- Acute Control
(1)
Normal
(1)
Encephalitis
(1)
Metabolic dysfunction-associated steatohepatitis
(1)
Critical COVID-19
(1)
Adult hepatocellular carcinoma
(1)
Uveal melanoma
(1)
Prediabetes syndrome
(1)
Idiopathic pulmonary fibrosis
(1)
Technology Type
Mass Spectrometry
(269)
Data-independent acquisition
(99)
Bottom-up proteomics
(93)
Shotgun proteomics
(88)
Mass spectrometry
(31)
Data-dependent acquisition
(30)
SWATH MS
(25)
Affinity purification coupled with mass spectrometry proteomics
(16)
DiaPASEF
(14)
Gel-based experiment
(12)
Mass spectrometry assay
(5)
All-ion fragmentation
(4)
Illumina HiSeq 2500
(3)
Chemical cross-linking coupled with mass spectrometry proteomics
(3)
ILLUMINA, Illumina HiSeq 2000
(2)
Illumina HiSeq 2000
(2)
Illumina MiSeq
(2)
SRM/MRM
(2)
Top-down proteomics
(2)
Illumina HiSeq 2500, ILLUMINA
(1)
Illumina HiSeq 2000, Illumina_2.5M
(1)
NMR spectroscopy
(1)
Affinity proteomics
(1)
MSE
(1)
Mass spectrometry imaging
(1)
HDMSE
(1)
Instrument Platform
Illumina NovaSeq 6000
(28)
Illumina HiSeq 2500
(13)
Illumina HiSeq 2000
(13)
NextSeq 500
(11)
NextSeq 550
(7)
Axon GenePix 4000B scanning hardware
(5)
Illumina HiSeq 4000
(5)
Illumina MiSeq
(4)
Illumina NovaSeq X
(3)
MinION
(3)
Sequel II
(2)
PromethION
(2)
Illumina Genome Analyzer IIx
(2)
NextSeq 2000
(2)
I.DOT (Dispendix), C.WASH (CYTENA), Qubit Fluorometer (Thermo Fisher Scientific), Agilent TapeStation 4200
(1)
BD FACSDiscover S8
(1)
Sequel IIe
(1)
Turbidostat
(1)
Linux platform. Galaxy https://usegalaxy.org/. R http://www.r-project.org/
(1)
Illumina iSeq2000 platform
(1)
454 GS 20
(1)
Sequel
(1)
G2565BA DNA microarray scanner [Agilent]
(1)
NextSeq 1000
(1)
NA
(1)
Illumina HiSeq X
(1)
FACS Aria
(1)
R
(1)
Illumina HiSeq 1500
(1)
Illumina HiSeq 3000
(1)
Publication Date
2013
(146)
2026
(92)
2025
(90)
2014
(76)
2011
(74)
2015
(68)
2024
(67)
2012
(57)
2021
(49)
2023
(46)
2022
(45)
2016
(40)
2010
(38)
2018
(35)
2019
(26)
2020
(25)
2017
(19)
2009
(19)
2008
(14)
2007
(4)
2006
(4)
2005
(3)
2004
(2)
UNIPROT ID/AC
Q0WB82
(2)
P0AAD4
(2)
Q7CH92
(2)
Q7CHI6
(2)
Q0WI04
(2)
P0AGD3
(2)
Q7CJI9
(2)
Q7CJ22
(2)
Q7CKU7
(2)
Q74WT5
(2)
Q0WJB5
(2)
P60752
(2)
Q0WH20
(2)
P0ABU7
(2)
Q0WIZ0
(2)
Q7CGI6
(2)
P0ABV2
(2)
Q0WBR9
(2)
Q7CH41
(2)
Q180F2
(2)
Q7CG73
(2)
P25519
(2)
P0C0L7
(2)
Q0WCN6
(2)
Q0WD20
(2)
Q0WAH3
(2)
P0ABI4
(2)
P13738
(2)
Q7CG77
(2)
P15042
(2)
CHEBI ID
CHEBI:25597
(2)
CHEBI:7644
(2)
CHEBI:28368
(2)
CHEBI:44505
(2)
CHEBI:71339
(2)
CHEBI:48622
(2)
CHEBI:58754
(2)
CHEBI:11993
(2)
CHEBI:20375
(2)
CHEBI:36148
(2)
CHEBI:20374
(2)
CHEBI:1838
(2)
CHEBI:24328
(2)
CHEBI:14323
(2)
CHEBI:39153
(2)
CHEBI:12156
(2)
CHEBI:20623
(2)
CHEBI:39151
(2)
CHEBI:2115
(2)
CHEBI:16120
(2)
CHEBI:18685
(2)
CHEBI:42060
(2)
CHEBI:342
(2)
CHEBI:44073
(2)
CHEBI:11002
(2)
CHEBI:15588
(2)
CHEBI:18686
(2)
CHEBI:133047
(2)
CHEBI:73912
(2)
CHEBI:17201
(2)
Metabolite Name
Tryptophan
(6)
Adenine
(6)
Aspartate
(5)
Methionine
(5)
Valine
(5)
Lysine
(5)
Isoleucine
(5)
Leucine
(5)
Glutamine
(5)
Arginine
(5)
Alanine
(5)
Inosine
(5)
Uridine
(5)
Guanine
(5)
Glutamine
(5)
AMP
(5)
N1-Methyl-2-pyridone-5-carboxamide
(4)
Tyrosine
(4)
Succinate
(4)
Phenylalanine
(4)
Lactate
(4)
Glutamate
(4)
2-hydroxyglutarate
(4)
Carnitine
(4)
Methionine
(4)
Dopamine
(4)
Tyramine
(4)
Serotonin
(4)
Acetylcholine
(4)
Xanthosine
(4)
First Public Date
2020
(42)
2022
(41)
2021
(38)
2019
(37)
2023
(34)
2024
(32)
2018
(24)
2026
(22)
2017
(21)
2013
(20)
2015
(17)
2025
(15)
2016
(12)
2014
(12)
2012
(1)
Modelling Approach
Constraint-based model
(2)
Lab affiliation
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
(24)
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
(3)
Aarhus University Department of Biomedicine DK-8000 Aarhus
(3)
Seer Inc.
(2)
Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna
(2)
Discovery Proteomics Facility, University of Oxford
(2)
Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
(2)
UCLA
(2)
International Institute of Molecular and Cell Biology, Laboratory of RNA-Protein Interactions - Dioscuri Centre, Warsaw, Poland
(2)
Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University of Munich (TUM) Gregor-Mendel-Strasse 4 85354 Freising Germany
(2)
WEHI
(2)
School of Biotechnology and Biomolecular Sciences The University of NSW Sydney NSW 2052 Australia
(2)
Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna
(2)
Pacific Northwest National Laboratory
(2)
DZNE Munich, Neuroproteomics, Feodor-Lynen-Str. 17, 81377 München, Germany
(2)
Department of Medical Biology, Medical University of Bialystok, Poland
(1)
Department of Oncology-Pathology, Karolinska Institutet
(1)
Systems Biology of Pain,Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Vienna
(1)
Laboratório de Biologia Molecular e Sistêmica de Trypanossomatídeos, Instituto Carlos Chagas-Fiocruz, Brazil
(1)
Institut für Biochemie FB08, B050 Justus-Liebig-Universität Gießen Heinrich-Buff-Ring 17 35392 Gießen Germany
(1)
German Cancer Research Center (DKFZ) Heidelberg
(1)
Mass spectrometry facility, Functional Proteomics, SFB 815 Core Unit, Goethe-Universität, Frankfurt am Main, Germany
(1)
Protim, Univ Rennes, Inserm, EHESP, Irset – UMR_S 1085
(1)
Clinical Proteomics Medizinisches Proteom-Center Ruhr-University Bochum and Department of Anesthesiology, Intensive Care Medicine and Pain Therapy University Hospital Knappschaftskrankenhaus Bochum
(1)
Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, UK. Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, UK.
(1)
Institute of Innate Immunity BMZ-II, Building 12, Room 2G408 University Hospital Bonn, University of Bonn
(1)
Necker Proteomics, Université Paris Cité - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, Paris, France.
(1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands and Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
(1)
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai
(1)
Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, Strasbourg, France
(1)
Tags
xref:PubMed:38253266
(8)
pathogen
(8)
pathogen:bacterium
(5)
xref:PubMed:35042798
(3)
xref:PubMed:40444635
(3)
xref:PubMed:37290815
(2)
xref:PubMed:35371069
(2)
xref:PubMed:38858365
(2)
xref:PubMed:25340333
(2)
xref:PubMed:34544361
(2)
xref:PubMed:25595182
(2)
xref:PubMed:39985376
(2)
xref:PubMed:28978483
(2)
xref:PubMed:36414416
(2)
xref:PubMed:33292867
(2)
xref:PubMed:36577373
(2)
xref:PubMed:29436395
(2)
xref:EuropePMC:PMC11308531
(2)
xref:PubMed:34039964
(2)
pathogen:virus
(2)
xref:PubMed:36891903
(1)
xref:PubMed:35867177
(1)
xref:PubMed:12200320
(1)
xref:PubMed:16349490
(1)
xref:PubMed:9554937
(1)
xref:PubMed:17098896
(1)
xref:PubMed:11431568
(1)
xref:PubMed:36204273
(1)
xref:PubMed:30248606
(1)
xref:PubMed:23879744
(1)
IsPrivate
False
(2)
Submitter Keywords
Not Peer Reviewed
(2)
FROG
(2)
Classification
bacteria
(5)
viruses
(2)
protozoa
(1)
Modification
15.994915
(2)
57.021464
(2)
32.056407
(1)
28.0313
(1)
Not available
(1)
Study type
ChIP-seq
(171)
RNA-seq of coding RNA
(131)
Transcription profiling by array
(90)
RNA-seq of non coding RNA
(53)
ChIP-chip by tiling array
(36)
Methylation profiling by high throughput sequencing
(13)
ChIP-chip by array
(12)
Other
(10)
DNA-seq
(9)
ATAC-seq
(7)
RNA-seq of coding RNA from single cells
(7)
Comparative genomic hybridization by array
(6)
Methylation profiling by array
(6)
Unknown experiment type
(5)
Transcription profiling by tiling array
(5)
High-throughput sequencing
(4)
Hi-C
(4)
Transcription profiling by RT-PCR
(3)
Transcription profiling by SAGE
(2)
Cell line - High-throughput sequencing
(2)
4C
(2)
RNA-seq of total RNA
(2)
CUT&TAG
(1)
Transcription profiling by MPSS
(1)
Cell line - Single-cell sequencing
(1)
One-color microarray
(1)
Animal - Single-cell sequencing
(1)
Human - High-throughput sequencing
(1)
Cell line - One-color microarray
(1)
Animal - High-throughput sequencing
(1)
Release Date
2025
(346)
2022
(262)
2023
(246)
2024
(237)
2021
(186)
2013
(164)
2020
(149)
2015
(117)
2014
(99)
2016
(86)
2019
(85)
2011
(83)
2012
(73)
2018
(66)
2017
(55)
2026
(54)
2010
(47)
2009
(25)
2008
(18)
2007
(8)
2006
(6)
2005
(5)
2004
(3)
2003
(2)
2000
(2)
2002
(1)
1999
(1)
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Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation.
Not available
S-EPMC7669280
|
biostudies-literature
Cite
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation.
Not available
S-EPMC6625853
|
biostudies-literature
Cite
Deep learning-enhanced R-loop prediction provides mechanistic implications for repeat expansion diseases.
Not available
S-EPMC11345597
|
biostudies-literature
Cite
Instance Segmentation of Multiple Myeloma Cells Using Deep-Wise Data Augmentation and Mask R-CNN.
Not available
S-EPMC8774909
|
biostudies-literature
Cite
Keras R-CNN: library for cell detection in biological images using deep neural networks.
Not available
S-EPMC7353739
|
biostudies-literature
Cite
Deep Learning R-Wave Detection for Electrocardiographic Gating in Cardiac MRI.
Not available
S-EPMC12728509
|
biostudies-literature
Cite
Electronic states of deep trap levels in a-plane GaN templates grown on r-plane sapphire by HVPE.
Not available
S-EPMC5959929
|
biostudies-literature
Cite
Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening.
Not available
S-EPMC6291153
|
biostudies-literature
Cite
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP.
Not available
S-EPMC7212772
|
biostudies-literature
Cite
Deep small RNA profiling of anthers of Brassica rapa R-o-18 and rdr2 mutant
Deep small RNA profiling of anthers of Brassica rapa R-o-18 and rdr2 mutant
PRJNA592710
|
ENA
Cite
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