Yu J J - OmicsDI

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Unknown (49818)
Proteomics (1313)
Transcriptomics (449)
Genomics (187)
Metabolomics (107)
Models (23)
Multiomics (12)
Genomic (3)
Other (2)
Methylation profiling (1)

Organisms

Homo sapiens (629)
Mus musculus (193)
Arabidopsis thaliana (28)
Rattus norvegicus (17)
Zea mays (10)
Saccharomyces cerevisiae (8)
Drosophila melanogaster (7)
Rattus rattus (6)
Escherichia coli (5)
Oryza sativa (5)
Gallus gallus (5)
Aplysia californica (4)
Yersinia pestis (4)
Glycine max (4)
Oryza sativa Japonica Group (4)
Bombyx mori (4)
Macaca mulatta (3)
Sus scrofa (3)
cellular organisms (2)
Aspergillus parasiticus (2)
Aspergillus flavus (2)
Populus trichocarpa x Populus deltoides (2)
Zea mays subsp. mays (2)
Caenorhabditis elegans (2)
Escherichia coli str. K-12 substr. MG1655 (2)
Pseudomonas syringae (1)
Burkholderia pseudomallei K96243 (1)
Pseudomonas syringae pv. syringae B728a (1)
Rhodococcus opacus (1)
Brassica oleracea (1)

Organisms

Mus musculus (6)
Homo sapiens (3)
Saussurea bogedaensis (2)
Pseudomonas sp. CES (1)
Campylobacter jejuni (1)
Pseudomonas aeruginosa (1)
Danio rerio (1)
Rattus norvegicus (1)

Repository

pride (810)
biostudies-arrayexpress (488)
iProX (388)
EGA (127)
MetaboLights (99)
MassIVE (66)
jPOST (28)
BioModels (23)
PeptideAtlas (16)
ENA (16)
GNPS (8)
geo (7)
PanoramaPublic (5)
dbGaP (3)
LINCS (3)
GPMDB (2)

Tissue

Cell culture (204)
Epithelial cell (61)
Brain (40)
Plant cell (30)
Liver (30)
Leaf (26)
Heart (24)
Permanent cell line cell (24)
Blood plasma (23)
Lung (20)
Kidney (20)
Whole body (19)
Urine (15)
Blood (15)
Testis (14)
Blood serum (13)
Embryonic stem cell (12)
B cell (12)
Plasma Non-glyco (11)
Macrophage (11)
Stem cell (11)
Hepatocyte (11)
HeLa cell (10)
Spleen (10)
Colon (10)
Fibroblast (9)
Blood cell (9)
Bone marrow (8)
Cell suspension culture (7)
Others (4)

Disease

Disease free (23)
Breast cancer (20)
Colon cancer (19)
Acute leukemia (17)
Cervix carcinoma (13)
Malignant neoplasm of ovary (8)
Prostate adenocarcinoma (7)
Non-small cell lung carcinoma (6)
Lung cancer (5)
Cardiovascular system disease (5)
Kidney cancer (5)
Type 2 diabetes mellitus (5)
Lung carcinoma (4)
Alzheimer's disease (4)
Malaria (4)
Skin melanoma (3)
Colitis (3)
Lymphoma (3)
Acute myeloid leukemia (3)
Brain cancer (3)
Liver cancer (3)
Not Available (2)
Disease (2)
Salmonella infectious disease (2)
HPV positive (1)
Colorectal cancer recurrence-free (1)
Diabetes mellitus (1)
Mammary tumor (1)
VSV infection (1)
Healthy (1)

Technology Type

Mass Spectrometry (810)
Shotgun proteomics (389)
Bottom-up proteomics (137)
Affinity purification coupled with mass spectrometry proteomics (101)
Mass spectrometry (81)
Data-dependent acquisition (72)
Gel-based experiment (52)
SWATH MS (35)
Top-down proteomics (35)
Data-independent acquisition (32)
Chemical cross-linking coupled with mass spectrometry proteomics (22)
SRM/MRM (11)
NMR spectroscopy (9)
Mass spectrometry assay (9)
Proteogenomics (9)
Mass spectrometry imaging (4)
Illumina HiSeq 2000 (3)
ELISA (3)
Chemiluminescence (3)
Immunopeptidomics (3)
DiaPASEF (3)
Illumina HiSeq 2000, ILLUMINA (2)
Illumina HiSeq 2000, HiSeq X Ten, Illumina HiSeq 2500, ILLUMINA (1)
Illumina HiSeq 2500, Illumina HiSeq 4000, ILLUMINA, NextSeq 500 (1)
Complete Genomics (COMPLETE_GENOMICS) (1)
Affymetrix OncoScan FFPE Express (1)
Illumina 2.5M, Illumina HiSeq 2000 (1)
AB SOLiD System 3.0 (1)
Illumina_670k - Illuminus, Affymetrix 6.0, Illumina 1.2M (1)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)

Instrument Platform

Illumina NovaSeq 6000 (23)
Q Exactive (21)
Orbitrap Fusion Lumos (10)
Illumina HiSeq 2000 (9)
Q Exactive HF (9)
LTQ Orbitrap Elite (9)
Orbitrap Eclipse (6)
Illumina Genome Analyzer IIx (4)
Illumina HiSeq 4000 (4)
Orbitrap Fusion (4)
Illumina HiSeq 2500 (3)
MS:1000031 (3)
Agilent 7890A GC with 5975C inert XL MSD (2)
LTQ Orbitrap Velos Pro (2)
LTQ FT (2)
Instrument (2)
Agilent Bioanalyzer 2100 (or TapeStation); Qubit 4 Fluorometer (Thermo Fisher Scientific) (1)
NanoDrop ND-1000 spectrophotometer (1)
RNeasy Plant Mini Kit (Qiagen) (1)
10X Genomics Chromium (1)
Agilent Bioanalyzer 2100 (1)
Agilent Microarray Scanner (1)
GenePix 4000A [Axon Instruments] (1)
GenePix 4000B [Axon Instruments] (1)
Illumina Genome Analyzer II (1)
NextSeq 2000 (1)
NextSeq 550 (1)
NextSeq 500 (1)
Xevo G2 Q-Tof (1)
MaXis (1)

Publication Date

2025 (219)
2022 (205)
2021 (148)
2023 (134)
2024 (126)
2026 (124)
2020 (120)
2019 (81)
2010 (79)
2013 (77)
2014 (68)
2015 (65)
2012 (60)
2016 (51)
2018 (50)
2011 (45)
2017 (38)
2009 (27)
2008 (19)
2007 (16)
2005 (9)
2006 (1)
2002 (1)
2004 (1)

UNIPROT ID/AC

Q6FG99 (15)
Q92841 (15)
Q92804-2 (15)
Q92804 (15)
Q92499 (15)
Q9BQG0 (15)
Q9UQ80 (15)
Q04695 (15)
Q01546 (15)
P52292 (15)
P05386-2 (15)
P05386 (15)
P02786 (15)
Q10567 (15)
P84098 (15)
P63010 (15)
P55209 (15)
Q9Y490 (15)
Q8NHW5 (15)
Q7KZF4 (15)
Q15149-9 (15)
Q15149-8 (15)
P06238 (1)
P20961 (1)
Q71SA3 (1)
P17246 (1)
P29598 (1)
Q01177 (1)
P00749 (1)
P00747 (1)

ENSEMBL ID

ENSG00000170477 (13)
ENSG00000247315 (7)
ENSG00000147251 (4)

CHEBI ID

CHEBI:11812 (13)
CHEBI:11596 (13)
CHEBI:77740 (13)
CHEBI:17594 (13)
CHEBI:17164 (13)
CHEBI:74393 (13)
CHEBI:77802 (13)
CHEBI:35621 (13)
CHEBI:58680 (13)
CHEBI:74631 (13)
CHEBI:15593 (13)
CHEBI:132957 (13)
CHEBI:74604 (13)
CHEBI:32528 (13)
CHEBI:58675 (13)
CHEBI:58083 (13)
CHEBI:73784 (13)
CHEBI:73898 (13)
CHEBI:320061 (13)
CHEBI:73888 (13)
CHEBI:74363 (13)
CHEBI:73771 (13)
CHEBI:231935 (13)
CHEBI:61904 (13)
CHEBI:15245 (13)
CHEBI:77843 (13)
CHEBI:15226 (13)
CHEBI:78236 (13)
CHEBI:73762 (13)
CHEBI:18394 (13)

Metabolite Name

Taurine (26)
Creatine (26)
Uridine (23)
Creatinine (23)
Betaine (21)
Adenosine (21)
Cytosine (21)
Adenine (20)
Cytidine (20)
Choline (19)
L-Tyrosine (19)
Hypoxanthine (19)
Inosine (18)
Thymidine (17)
Acetylcholine (16)
Uracil (15)
Valine (15)
Isoleucine (15)
Guanosine (15)
Glycerophosphocholine (15)
Leucine (14)
Carnosine (14)
L-Arginine (14)
Histamine (14)
Linoleic acid (14)
L-Glutamine (14)
L-Carnitine (14)
L-Valine (14)
Glycine (13)
L-Alanine (13)

First Public Date

2014 (6)
2024 (3)
2020 (3)
2025 (1)
2018 (1)
2016 (1)
2013 (1)

Modelling Approach

Constraint-based model (16)
Ordinary differential equation model (7)

Lab affiliation

J. Craig Venter Institute, Rockville, MD 20850 (12)
Wellcome Trust Sanger Institute (10)
Department of Convergence Medicine, Convergence Medicine Research Center/Biomedical Research Center, Asan Medical Center, Asan Institute for Life Sciences, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea. (9)
The Institute of Cancer Research (9)
Guangzhou Medical University (5)
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA. (4)
Alkali Soil Natural Environmental Science Center, Northeast Forestry University, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Ministry of Education, Harbin 150040, China (4)
Center of Molecular and Cellular Oncology, Yale University (4)
Westlake University (4)
Tsinghua University, China (4)
Zhejiang University (4)
Functional Proteomics, ICR (4)
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou 510060, China (3)
Yazhouwan National Laboratory, Sanya 572024, China (3)
Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Nanjing Medical University, Nanjing, Jiangsu, China (3)
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China (3)
Department of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA (3)
Professor. Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark (3)
Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, China (3)
Professor, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark (3)
J. Craig Venter Institute 9605 Medical Center Dr. Rockville, MD 20850 (3)
Harvard medical school (3)
School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China (3)
Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning 110122, China (3)
Ocean University of China (3)
St. Jude Children’s Research Hospital (3)
The Institute of Cancer Research, London (3)
Shanghaitech University (3)
State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China (2)
Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK (2)

IsPrivate

False (23)

Model Flag

Non Kinetic (2)

Submitter Keywords

FROG (2)
Immuno-oncology (2)

Classification

bacteria (2)

Modification

15.994915 (3)
57.021464 (3)
-17.026549 (2)
42.010565 (2)
Not available (2)
27.994915 (1)
31.989829 (1)
0.984016 (1)
58.005479 (1)
N6 (1)
2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (250)
RNA-seq of coding RNA (102)
ChIP-seq (29)
Unknown experiment type (17)
Methylation profiling by high throughput sequencing (14)
RNA-seq of coding RNA from single cells (13)
RNA-seq of non coding RNA (11)
Methylation profiling by array (9)
Comparative genomic hybridization by array (7)
Other (7)
ChIP-chip by tiling array (4)
Transcription profiling by tiling array (4)
MicroRNA profiling by array (4)
Transcription profiling by SAGE (2)
ChIP-chip by array (2)
ScATAC-seq (2)
Cell line - Single-cell sequencing (1)
RNA-seq of non coding RNA from single cells (1)
Differential (1)
Human - Single-cell sequencing (1)
High-throughput sequencing (1)
Genotyping by array (1)
Transcription profiling by RT-PCR (1)
DNA-seq (1)
Genotyping by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2025 (7426)
2022 (6719)
2023 (6001)
2024 (5900)
2021 (5272)
2020 (3801)
2019 (2742)
2018 (2414)
2017 (2072)
2016 (1697)
2015 (1398)
2014 (1069)
2026 (1003)
2013 (705)
2012 (568)
2011 (409)
2010 (360)
2009 (257)
2008 (171)
2007 (107)
2006 (52)
2005 (50)
2004 (36)
2003 (21)
2002 (19)
2000 (14)
2001 (8)
1998 (6)
1997 (5)
1999 (3)

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Steam-exploded okara ameliorates hepatic lipid metabolism in high-fat diet-induced obese C57BL/6J mice: Evidence from multi-omics characterization

Okara, a byproduct of soybean processing, possesses valuable nutritional and physiological properties. Steam explosion, an efficient physical modification technique, can increase the soluble dietary fiber (SDF) content in okara and potentially amplify its health benefits, such as anti-obesity eff...

2025-10-23 | MTBLS13154 | MetaboLights

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

BACKGROUND: Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value...

2022-05-18 | MTBLS3657 | MetaboLights

JBP1-seq: a fast and efficient method for genome-wide profiling of 5hmC

We developed a novel approach, J-binding protein 1 sequencing (JBP1-seq), that combines the benefits of an improved recombinant JBP1 protein, Nextera-based library construction, and nextgeneration sequencing (NGS) for genome-wide profiling of 5-hydroxymethylcytosine (5hmC). Compared with the orig...

ORGANISM(S): Homo sapiens

2014-11-26 | E-GEOD-61193 | biostudies-arrayexpress

gga-miR-148a-5p-Targeting PDPK1 Inhibits Proliferation and Cell Cycle Progression of Avain Leukosis Virus Subgroup J (ALV-J)-Infected Cells.

Not available

S-EPMC7769946 | biostudies-literature

Functionality of Class A and Class B J-protein co-chaperones with Hsp70.

Not available

S-EPMC4570866 | biostudies-literature

Utilizing Polymer Micelle to Control Dye J-aggregation and Enhance Its Theranostic Capability.

Not available

S-EPMC6906732 | biostudies-literature

Rapid detection of avian leukosis virus subgroup J by cross-priming amplification.