Li Benjamin B - OmicsDI

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Unknown (143)
Transcriptomics (62)
Proteomics (38)
Genomics (24)
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Organisms

Homo sapiens (40)
Mus musculus (33)
Bombyx mori (21)
Klebsiella pneumoniae (21)
Schizosaccharomyces pombe (21)
Human immunodeficiency virus 1 (21)
Oryza sativa Indica Group (21)
Sinorhizobium meliloti BL225C (21)
Vitis (21)
Sus scrofa domesticus (21)
Ostreococcus tauri (21)
Saccharomyces cerevisiae (21)
Synechocystis sp. PCC 6803 (21)
Olavius algarvensis Gamma 1 endosymbiont (21)
Vitis vinifera (21)
Saccharopolyspora erythraea (21)
Staphylococcus aureus (21)
Rattus norvegicus (21)
Rattus rattus (21)
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synthetic construct (1)
Caenorhabditis elegans (1)
Arabidopsis thaliana (1)

Organisms

Mus musculus (2)

Repository

biostudies-arrayexpress (74)
pride (21)
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Cell culture (5)
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Disease

Not Available (2)
Prostate adenocarcinoma (2)
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Hutchinson-Gilford Progeria Syndrome (1)
Healthy (1)
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Technology Type

Mass Spectrometry (21)
Shotgun proteomics (16)
Affinity purification coupled with mass spectrometry proteomics (12)
Mass spectrometry (6)
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Illumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - Illuminus (1)
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Instrument Platform

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Instrument (2)
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Liquid Chromatography MS - negative - hilic (2)
FACSAria (BD) (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 3000 (1)
Exactive Plus (1)
Orbitrap Exploris 480 (1)
LTQ Orbitrap Elite (1)
LTQ Orbitrap (1)
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Liquid Chromatography MS - Negative (LC-MS (Negative)) (1)
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ACQUITY TQD (Waters) (1)
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Nuclear Magnetic Resonance (NMR) - (1)

Publication Date

2011 (17)
2016 (14)
2013 (10)
2014 (8)
2021 (8)
2022 (8)
2015 (7)
2012 (7)
2020 (7)
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2010 (6)
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2025 (4)
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2008 (2)
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UNIPROT ID/AC

P04003 (1)
Q15485 (1)
O00187 (1)
P01024 (1)
P06681 (1)
P0C0L4 (1)
P0C0L5 (1)
P02741 (1)

CHEBI ID

CHEBI:27838 (2)
CHEBI:27410 (2)
CHEBI:53210 (2)
CHEBI:24809 (2)
CHEBI:21557 (2)
CHEBI:15891 (2)
CHEBI:28683 (2)
CHEBI:16668 (2)
CHEBI:15356 (2)
CHEBI:17126 (2)
CHEBI:16797 (2)
CHEBI:17822 (2)
CHEBI:6650 (2)
CHEBI:28300 (2)
CHEBI:16811 (2)
CHEBI:18237 (2)
CHEBI:24898 (2)
CHEBI:29016 (2)
CHEBI:17154 (2)
CHEBI:27570 (2)
CHEBI:28044 (2)
CHEBI:16450 (2)
CHEBI:506227 (1)
CHEBI:18132 (1)
CHEBI:192175 (1)
CHEBI:85457 (1)
CHEBI:85459 (1)
CHEBI:73063 (1)
CHEBI:2682 (1)
CHEBI:73066 (1)

Metabolite Name

Theronine (1)
Adenosylhomocysteine (1)
Pentoic acid* (1)
Methylprednisolone (1)
Lansoprazole (1)
Domperidone (1)
Ticlopidine (1)
Amphotericin B (1)
2-Octenoylcarnitine CAR(8:1) (1)
Acetyl-methionine (1)
Glutathione (reduced) (1)
Indole 3-carboxylic acid (1)
IsoLeucine (1)
Phytanate (1)
Phenylalanylhydroxyproline* (1)
N-methylhydroxyproline** (1)
4-hydroxy-2-oxoglutaric acid (1)
O-acetylhomoserine (1)
Citramalate (1)
N2-methylguanosine (1)
[18O1]-NR (1)
[18O1, D3]-MeNam (1)
[D4]-NA (1)
[18O1]-Nam (1)
[13C10]-NAD (1)
[13C10]-NADP (1)
[13C5]-NMN (1)
[13C5]-NAR (1)
[13C5]-NAMN (1)
NR (1)

First Public Date

2024 (1)
2014 (1)

Modelling Approach

Ordinary differential equation model (1)

Lab affiliation

Imperial College London (5)
The University of Melbourne (3)
Raymond H. Wittcoff Distinguished Professor and Head Department of Biochemistry and Molecular Biophysics Washington University School of Medicine St. Louis, MO 63110 United States of America (1)
Imperial College London, The Francis Crick Institute (1)
Center for Proteomics & Artificial Intelligence Center for Clinical Mass Spectrometry Allegheny Health Network Cancer Institute 100 S Jackson Ave., Pittsburgh, PA 15202 (1)
Penn Epigenetics Institute Department of Biochemistry and Biophysics Smilow Center for Translational Research University of Pennsylvania School of Medicine (1)
Department of Chemistry, Imperial College London, UK Chemical Glycobiology Laboratory, The Francis Crick Institute, London, UK (1)
Professor, Gilula Chair in Chemical Biology, The Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute 10550 North Torrey Pines Rd, La Jolla, CA 92037 (1)
Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China (1)
Depts. of Pharmacology and Neurology, Boston University School of Medicine (1)
Department of Chemistry, Imperial College London, UK; Chemical Glycobiology Laboratory, The Francis Crick Institute, London (1)
Department of Anatomy and Neurobiolog; Department of Pharmacology, Physiology and Biophysics; Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA (1)
Raymond H. Wittcoff Distinguished Professor and Head Department of Biochemistry and Molecular Biophysics Washington University School of Medicine St. Louis, MO 63110 (1)
Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania (1)
The Scripps Research Institute (1)

IsPrivate

False (1)

Modification

N6 (1)

Study type

Transcription profiling by array (38)
RNA-seq of coding RNA (8)
ChIP-seq (6)
Methylation profiling by high throughput sequencing (5)
ChIP-chip by tiling array (3)
Methylation profiling by array (3)
RNA-seq of non coding RNA (3)
Spatial transcriptomics by high-throughput sequencing (2)
RNA-seq of total RNA (2)
Comparative genomic hybridization by array (1)
Other (1)
Single nucleus RNA sequencing (1)

Release Date

2013 (21)
2011 (20)
2022 (20)
2021 (17)
2016 (16)
2023 (14)
2025 (13)
2012 (13)
2018 (13)
2014 (11)
2015 (10)
2020 (10)
2024 (9)
2010 (8)
2019 (6)
2017 (6)
2009 (3)
2026 (2)
2008 (2)
2006 (1)
2007 (1)
2001 (1)

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Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial

Fecal microbiota transplantation (FMT) represents a potential strategy to overcome resistance to immune checkpoint inhibitors in patients with refractory melanoma; however, the role of FMT in first-line treatment settings has not been evaluated. We conducted a multicenter phase I trial combining ...

2025-02-27 | MTBLS711 | MetaboLights

Clovamide, a hydroxycinnamic acid amide, is a resistance factor against Phytophthora spp. in Theobroma cacao

The hydroxycinnamic acid amides (HCAAs) are a diverse group of plant specialized phenylpropanoid metabolites distributed widely in the plant kingdom and are known to be involved in tolerance to abiotic and biotic stress. The HCAA clovamide is reported in a small number of distantly related species. ...

2020-12-17 | MTBLS2154 | MetaboLights

Skin Deep: Early Mucosal Responses in Blue Catfish (Ictalurus furcatus) Skin to Aeromonas hydrophila Infection

Fish skin is a critical regulatory organ, serving not only as a physical barrier to pathogen entry, but also as a sophisticated integrator of aquatic environmental, social and nutritional cues through roles in immunity, osmoregulation, and endocrine signaling. Integral to the complexity of teleost s...

ORGANISM(S): Ictalurus furcatus

2014-06-17 | E-GEOD-42491 | biostudies-arrayexpress

Expression analysis of C. elegans wild-type N2 and rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutants

Investigation of whole genome gene expression level changes in C. elegans rsks-1, daf-2, daf-2 rsks-1 and daf-16; daf-2 rsks-1 mutant compared to the wild-type N2 strain. The mutants have altered longevity phenotypes. The mutants analyzed in this study are further described in Di Chen, Patrick Wai-...

ORGANISM(S): Caenorhabditis elegans

2013-11-14 | E-GEOD-52340 | biostudies-arrayexpress

Identification of megakaryoblastic leukemia-1 (Mkl1) target genes in 4T1 mammary carcinoma cells

The present study was designed to identify Mkl1 target genes whose expression requires either the B1 site of Mkl1 and serum response factor (SRF), respectively, or the SAP domain of Mkl1. For this purpose, we obtained the transcriptomes of four stable 4T1 cell lines that either overexpress full leng...

ORGANISM(S): Mus musculus

2016-07-15 | E-GEOD-59459 | biostudies-arrayexpress

SMN and Symmetric Arginine Dimethylation of RNAP II CTD Control Termination

The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) subunit POLR2A is a platform for modifications specifying the recruitment of factors that regulate transcription, mRNA processing, and chromatin remodeling. Here, we show that a CTD arginine residue (R1810 in human) that is conserved acr...

ORGANISM(S): Homo sapiens

2015-12-31 | E-GEOD-73379 | biostudies-arrayexpress

Transcription profiling by array of HC11 mammary epithelial cell strains stably expressing different variants of the transcriptional regulator megakaryoblastic leukemia-1 (Mkl1)

We have previously shown that HC11 mammary epithelial cells react strongly to the overexpression of megakaryoblastic leukemia-1 (Mkl1) with induction of tenascin-C expression. The present study was designed to find genes co-regulated with tenascin-C by Mkl1 in a SAP domain-dependent manner and witho...

ORGANISM(S): Mus musculus

2014-02-06 | E-GEOD-44907 | biostudies-arrayexpress

Sphingosine-1-phosphate Phosphatase 2 Regulates Pancreatic Islet B-cell Endoplasmic Reticulum Stress and Proliferation

Sphingosine-1-phosphate (S1P) is a sphingolipid metabolite that regulates basic cell functions through metabolic and signaling pathways. Intracellular metabolism of S1P is controlled, in part, by two homologous S1P phosphatases, 1 and 2, which are encoded by Sgpp1 and Sgpp2, respectively. S1P phosph...

ORGANISM(S): Mus musculus

2016-07-25 | E-GEOD-73131 | biostudies-arrayexpress

A Widening Divide: Cigarette Smoking Trends Among People With Substance Use Disorder And Criminal Legal Involvement.

Not available

S-EPMC10157835 | biostudies-literature

Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells

Krönke J, Udeshi ND, Narla A, Grauman P, Hurst SN, McConkey M, Svinkina T, Heckl D, Comer E, Li X, Ciarlo C, Hartman E, Munshi N, Schenone M, Schreiber SL, Carr SA, Ebert BL. Science 2014, 343, 301-305. doi:10.1126/science.1244851. Lenalidomide is a drug with clinical efficacy in multiple myeloma an...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2015-01-26 | MSV000079017 | MassIVE

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