He Li L - OmicsDI

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Unknown (16011)
Models (622)
Proteomics (463)
Transcriptomics (252)
Genomics (101)
Metabolomics (69)
Multiomics (4)
Genomic (3)
Other (3)

Organisms

Homo sapiens (651)
Mus musculus (159)
Mammalia (65)
Saccharomyces cerevisiae (58)
Arabidopsis thaliana (36)
cellular organisms (31)
Escherichia coli (27)
Rattus (26)
Drosophila melanogaster (21)
Rattus norvegicus (21)
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Canis lupus familiaris (10)
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Murinae (3)
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Candidatus Palibaumannia cicadellinicola (2)
Chlamydomonas reinhardtii (2)
Homalodisca vitripennis (2)
Human immunodeficiency virus 1 (2)
Viridiplantae (2)

Organisms

Larimichthys crocea (1)
Mus musculus (1)

Repository

BioModels (622)
biostudies-arrayexpress (299)
pride (215)
iProX (137)
PeptideAtlas (90)
MetaboLights (67)
EGA (54)
MassIVE (19)
dbGaP (3)
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ENA (2)

Tissue

Cell culture (51)
Liver (44)
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Male Reproductive System (2)
Adrenal adenoma cell (2)

Disease

Diabetes mellitus (15)
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Disease free (6)
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Severe acute respiratory syndrome (3)
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Polycythemia due to hypoxia (2)
Not Available (2)
Alzheimer's disease (1)
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Andersen-Tawil syndrome (1)
Brugada syndrome (1)
Coronary artery disease (1)
Down syndrome (1)
Fatty liver disease (1)
Liver disease (1)
Mature T-cell and NK-cell lymphoma (1)
Neonatal abstinence syndrome (1)
Parkinson's disease (1)
Type 1 diabetes mellitus (1)
Type 2 diabetes mellitus (1)
Papillary thyroid carcinoma (1)

Technology Type

Mass Spectrometry (215)
Shotgun proteomics (109)
Mass spectrometry (49)
Bottom-up proteomics (33)
Affinity purification coupled with mass spectrometry proteomics (23)
Gel-based experiment (19)
Mass spectrometry assay (17)
Data-dependent acquisition (14)
Data-independent acquisition (13)
Chemical cross-linking coupled with mass spectrometry proteomics (7)
Top-down proteomics (5)
Affinity proteomics (4)
Mass spectrometry imaging (4)
Olink affinity proteomics (3)
SRM/MRM (3)
Illumina HiSeq 2000 (2)
Illumina HiSeq 2000, ILLUMINA (2)
All-ion fragmentation (2)
DiaPASEF (2)
SWATH MS (2)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
Proteogenomics (1)

Instrument Platform

Liquid Chromatography MS - negative - reverse phase (28)
Liquid Chromatography MS - positive - reverse phase (25)
LTQ Orbitrap Velos (15)
TripleTOF 5600 (12)
Illumina NovaSeq 6000 (9)
Liquid Chromatography MS - negative - reverse-phase (8)
Liquid Chromatography MS - positive - hilic (8)
Liquid Chromatography MS - positive - reverse-phase (8)
Illumina HiSeq 4000 (5)
Liquid Chromatography MS - negative (5)
Illumina HiSeq 2500 (4)
Illumina HiSeq 2000 (4)
Q Exactive HF (4)
Illumina Genome Analyzer (2)
Illumina Genome Analyzer II (2)
TripleTOF 6600 (2)
Instrument (2)
Orbitrap Eclipse (2)
Q Exactive Plus (2)
Scanning hardware (1)
Bruker maXis ESI Quadrupole TOF (1)
LTQ Orbitrap (1)
LTQ XL (1)
Orbitrap Ascend (1)
Orbitrap Astral (1)
Orbitrap Exploris 480 (1)
Orbitrap Fusion (1)
Orbitrap Fusion Lumos (1)
Q Exactive (1)
Q Exactive HF-X (1)

Publication Date

2005 (373)
2024 (309)
2022 (76)
2025 (72)
2015 (63)
2021 (59)
2023 (58)
2026 (50)
2014 (40)
2013 (40)
2012 (40)
2016 (36)
2011 (36)
2010 (33)
2019 (25)
2020 (24)
2008 (17)
2018 (12)
2017 (10)
2007 (7)
2009 (5)
2006 (5)
2004 (3)
2003 (1)
2027 (1)
2002 (1)
2001 (1)

UNIPROT ID/AC

P04637 (9)
Q00987 (9)
P24864 (8)
P01308 (7)
P07663 (7)
P06400 (6)
P24869 (6)
P26309 (6)
P53197 (6)
P00360 (5)
P00549 (5)
P00560 (5)
P00924 (5)
P00950 (5)
P04806 (5)
P06169 (5)
P12709 (5)
P14540 (5)
P16861 (5)
P16862 (5)
P20438 (5)
P24941 (5)
P30283 (5)
P38634 (5)
O00327 (4)
O15055 (4)
O15534 (4)
P00175 (4)
P00330 (4)
P00331 (4)

ENSEMBL ID

ENSBTAG00000000003.4 (1)
ENSBTAG00000000033.3 (1)
ENSBTAG00000000042.2 (1)
ENSBTAG00000000058.4 (1)
ENSBTAG00000000065.4 (1)
ENSBTAG00000000077.4 (1)
ENSBTAG00000000081.4 (1)
ENSBTAG00000000085.4 (1)
ENSBTAG00000000091.1 (1)
ENSBTAG00000000111.4 (1)
ENSBTAG00000000123.3 (1)
ENSBTAG00000000139.4 (1)
ENSBTAG00000000160.4 (1)
ENSBTAG00000000172.4 (1)
ENSBTAG00000000185.4 (1)
ENSBTAG00000000186.3 (1)
ENSBTAG00000000188.2 (1)
ENSBTAG00000000191.3 (1)
ENSBTAG00000000202.3 (1)
ENSBTAG00000000203.3 (1)
ENSBTAG00000000212.3 (1)
ENSBTAG00000000246.4 (1)
ENSBTAG00000000251.4 (1)
ENSBTAG00000000259.4 (1)
ENSBTAG00000000286.4 (1)
ENSBTAG00000000287.3 (1)
ENSBTAG00000000292.4 (1)
ENSBTAG00000000301.3 (1)
ENSBTAG00000000318.4 (1)
ENSBTAG00000000336.3 (1)

CHEBI ID

CHEBI:15422 (39)
CHEBI:16761 (33)
CHEBI:29108 (32)
CHEBI:33699 (26)
CHEBI:16908 (21)
CHEBI:15361 (19)
CHEBI:15846 (19)
CHEBI:16108 (19)
CHEBI:15996 (18)
CHEBI:17552 (18)
CHEBI:16027 (17)
CHEBI:17794 (17)
CHEBI:17234 (16)
CHEBI:18367 (16)
CHEBI:16001 (15)
CHEBI:16526 (14)
CHEBI:17665 (14)
CHEBI:17754 (14)
CHEBI:17835 (14)
CHEBI:18021 (14)
CHEBI:29052 (14)
CHEBI:15343 (13)
CHEBI:16236 (13)
CHEBI:16905 (13)
CHEBI:15351 (12)
CHEBI:16084 (12)
CHEBI:36080 (12)
CHEBI:16595 (11)
CHEBI:28013 (11)
CHEBI:15346 (10)

Metabolite Name

Adenine (13)
Adenosine (12)
Uridine (12)
Choline (11)
Hypoxanthine (11)
Inosine (11)
Citric acid (10)
Guanine (10)
Indole (10)
Creatine (9)
Cytidine (9)
Kynurenic acid (9)
L-Tyrosine (9)
Thymidine (9)
Uric acid (9)
1-Methyladenosine (8)
Deoxyinosine (8)
L-Arginine (8)
Nicotinic acid (8)
Pantothenic acid (8)
Riboflavin (8)
Cortisone (7)
Creatinine (7)
Cytosine (7)
Erucic acid (7)
Guanosine (7)
L-Phenylalanine (7)
Leucine (7)
Ornithine (7)
Porphobilinogen (7)

First Public Date

2025 (1)
2022 (1)

Modelling Approach

Ordinary differential equation model (561)
Constraint-based model (2)
Delayed differential equation model (2)

Lab affiliation

Biological Science Research Center, Southwest University, Chongqing, 400715, China (3)
Chinese Academy of Sciences Shanghai Institute of Materia Medica (3)
Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning 110122, China (3)
Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, 100069, China (2)
Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. (2)
Division of Medical Inflammation Research, Dept. Medical Biochemistry and Biophysics, Karolinska Institute, Sweden (2)
Huazhong University of Science and Technology (2)
Huazhong University of Science and Technology Union Shenzhen Hospital (2)
New Cornerstone Science Laboratory, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China (2)
Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China (2)
Sichuan Provincial People's Hospital (2)
State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China (2)
State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China. (2)
State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, Jiangsu, China (2)
The Fifth Affiliated Hospital of Guangzhou Medical University (2)
The First Affiliated Hospital of Fujian Medical University (2)
Westlake University (2)
Zhejiang University (2)
the First Affiliated Hospital of Chongqing Medical University (2)
, Dana-Farber Cancer Institute, Harvard Medical School 360 Longwood Avenue Longwood Center, LC4117 Boston, MA 02215 (1)
1. State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China 2. University of Chinese Academy of Sciences, Beijing 100101, China 3. KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming 650201, China (1)
1Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA 2Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA 3Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA (1)
Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China (1)
Associate Professor of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Minnesota, United States (1)
BGI-shenzhen (1)
Basic Medicine, Guangxi University of Chinese Medicine, Nanning, China (1)
Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, P.R. China (1)
Beijing proteome research center, Beijing, China (1)
Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders (Ministry of Education), Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China. (1)
Biological Science Research Center, Southwest University, Chongqing, 400715, China. (1)

IsPrivate

False (622)

Model Flag

Non Kinetic (72)
Non Miriam (14)
Sbml Extended (3)

Submitter Keywords

FROG (2)
Immuno-oncology (1)
TransQST (1)

Modification

Not available (2)
2x(15)N labeled L-lysine (1)
4x(15)N labeled L-arginine (1)
N6 (1)

Study type

Transcription profiling by array (139)
RNA-seq of coding RNA (58)
ChIP-seq (22)
Methylation profiling by high throughput sequencing (21)
RNA-seq of non coding RNA (12)
RNA-seq of coding RNA from single cells (7)
Other (6)
Transcription profiling by tiling array (5)
Comparative genomic hybridization by array (5)
ChIP-chip by tiling array (4)
Methylation profiling by array (4)
Genotyping by array (3)
MicroRNA profiling by array (2)
DNA-seq (2)
MRE-seq (1)
Unknown experiment type (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
RNAi profiling by array (1)
Transcription profiling by RT-PCR (1)
Proteomic profiling by array (1)
Genotyping by high throughput sequencing (1)

Release Date

2025 (2648)
2022 (2211)
2024 (2052)
2023 (2037)
2021 (1633)
2020 (1279)
2019 (848)
2018 (723)
2017 (610)
2016 (471)
2015 (385)
2026 (364)
2014 (314)
2013 (216)
2012 (170)
2011 (132)
2010 (92)
2009 (45)
2008 (34)
2007 (15)
2006 (10)
2005 (8)
2004 (7)
2003 (3)
2001 (2)
2002 (1)

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Methionine Intervention Induces PD-L1 Expression to Enhance the Immune Checkpoint Therapy Response in MTAP-deleted Osteosarcoma

Osteosarcoma (OS), a malignant bone tumor with limited treatment options, exhibits low sensitivity to immune checkpoint therapy (ICT). Through genomics and transcriptomics analyses, we have identified a subgroup of OS with methylthioadenosine phosphorylase (MTAP) deletion, which contributes to ICT r...

2026-06-09 | MTBLS11985 | MetaboLights

Cell wide response to air exposure in Desulfovibrio vulgaris Hildenborough

We investigated the effects of air exposure on Desulfovibrio vulgaris Hildenborough using microarrays. Keywords: stress response, time course Comparison of cells treated with air to untreated cells at 0,10,30,120,240 min.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2007-08-08 | E-GEOD-8196 | biostudies-arrayexpress

Cell wide response to low oxygen exposure in Desulfovibrio vulgaris Hildenborough

We investigated the effects of low level oxygen on Desulfovibrio vulgaris Hildenborough using microarrays. Keywords: time course, stress response Comparison of cells treated with 1000 ppm oxygen to untreated cells at 60,120,240 min.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2010-06-10 | E-GEOD-7816 | biostudies-arrayexpress

Salt/NaCl stress in Desulfovibrio vulgaris Hildenborough

This set of microarray data was used to investigate the effects of D. vulgaris adaptation to excess NaCl. Keywords: stress response, one time point (the mid-log phase for both control and treated cells) Comparison of cells treated with 250 Salt:NaCl to untreated cells at times of mid-log phase min.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2010-04-11 | E-GEOD-14343 | biostudies-arrayexpress

Ecdysone Response Timecourse in Kc Cells

Kc167 Cells were plated at 0.5x106/ml and grown at 23.50C. They were treated with 20-HE (Sigma) at a final concentration of 5x10-7M. The reference sample was total RNA isolated at 0 hr. after treatment. The experimental samples were total RNA isolated from cells treated for 1, 3, 6, 12, 24, and 48 h...

ORGANISM(S): Drosophila melanogaster

2008-06-12 | E-GEOD-11625 | biostudies-arrayexpress

pH stress in Desulfovibrio vulgaris Hildenborough

Using data from microarray experiments, we investigated the effects of excess NaCl on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with pH10 pH to untreated cells at times of 0,120,240,30,60 min.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2007-08-31 | E-GEOD-8197 | biostudies-arrayexpress

Protocol for a parallel assignment prospective, randomised, comparative trial to evaluate the safety and efficacy of intense pulsed light (IPL) combined with 3% diquafosol (DQS) ophthalmic solution in dry eye syndrome.

Not available

S-EPMC10465902 | biostudies-literature

DNA Cytosine Hydroxymethylation Levels Are Distinct Among Peripheral Blood Leukocytes

Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease related stress. We considered the hypothesis that the TET enzyme catalyzed hydroxymethylation of 5mC to 5hmC might vary among peripheral blood leukocytes and reflect t...

ORGANISM(S): Homo sapiens

2016-07-05 | E-GEOD-70519 | biostudies-arrayexpress

Subsets of visceral adipose tissue nuclei with discrete levels of 5-hydroxymethylcytosine

We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We devel...

ORGANISM(S): Sus scrofa

2016-07-20 | E-GEOD-73684 | biostudies-arrayexpress

Hydrogen peroxide Stress in Desulfovibrio vulgaris Hildenborough (REPLACED BY GSE21441)

Using data from microarray experiments, we investigated the effects of excess hydrogen peroxide on D. vulgaris. Keywords: stress response, time course Comparison of wild type and deletion mutant cells treated with 1 mM H2O2 to untreated cells at times of 0 and 120 min. See also Series GSE4447 (http...

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

2011-10-03 | E-GEOD-14345 | biostudies-arrayexpress

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