Ryan A S AS - OmicsDI

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Unknown (2185)
Transcriptomics (200)
Proteomics (139)
Genomics (73)
Metabolomics (20)
Models (4)
Genomic (4)
Clinical (2)

Organisms

Homo sapiens (204)
Mus musculus (67)
Drosophila melanogaster (14)
Arabidopsis thaliana (12)
Saccharomyces cerevisiae (12)
Glycine max (9)
Rattus norvegicus (5)
synthetic construct (4)
Danio rerio (4)
Populus trichocarpa x Populus deltoides (3)
Vitis vinifera (3)
Helicobacter pylori (3)
Caenorhabditis elegans (3)
Amphimedon queenslandica (2)
Ruegeria pomeroyi DSS-3 (2)
Felis catus (2)
Schizosaccharomyces pombe (2)
Salmonella enterica subsp. enterica serovar Typhimurium (2)
Hypsibius dujardini (1)
Mnemiopsis leidyi (1)
Sinorhizobium meliloti 1021 (1)
Salmonella enterica subsp. enterica serovar Paratyphi A (1)
Vibrio parahaemolyticus (1)
Pimephales promelas (1)
Macaca nemestrina (1)
Strongylocentrotus purpuratus (1)
Platynereis dumerilii (1)
Thalassiosira pseudonana (1)
Neisseria meningitidis MC58 (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (1)

Organisms

Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028 (1)
Salmonella enterica subsp. enterica serovar Paratyphi A (1)
Salmonella enterica subsp. enterica serovar Typhi (1)

Repository

biostudies-arrayexpress (230)
pride (102)
EGA (43)
MassIVE (29)
MetaboLights (18)
BioModels (4)
dbGaP (4)
PanoramaPublic (4)
ENA (3)
GNPS (2)
iProX (1)

Tissue

Cell culture (29)
Epithelial cell (15)
Heart (6)
Liver (5)
Permanent cell line cell (5)
Blood serum (4)
Blood cell (3)
Blood plasma (3)
Bone marrow (2)
Bone marrow macrophage (2)
Embryonic stem cell (2)
Fibroblast (2)
HeLa cell (2)
Hepatocyte (2)
Lung (2)
Stem cell (2)
Type II pneumocyte (2)
Amniotic fluid (1)
B cell (1)
Barrett's esophagus (1)
Blood (1)
Blood vessel (1)
Blood vessel endothelial cell (1)
Brain (1)
Bronchoalveolar lavage (1)
Brown adipose tissue (1)
Cardiomyocyte cell line (1)
Cell line cell (1)
JURKAT cell (1)
T cell (1)

Disease

Colon cancer (8)
COVID-19 (3)
Cardiovascular system disease (3)
Pancreatic ductal adenocarcinoma (3)
Mitochondrial complex I deficiency (2)
Infiltrating ductal carcinoma (2)
Neuroblastoma (2)
Cervix carcinoma (2)
Non-alcoholic steatohepatitis (2)
Hypotension (1)
Phyllodes tumor (1)
Schizophrenia (1)
Gastroesophageal Reflux (1)
Rectal Cancer (1)
Acute leukemia (1)
Amyotrophic lateral sclerosis (1)
Cardiovascular system (1)
Esophagus adenocarcinoma (1)
Heart disease (1)
Influenza (1)
Interstitial lung disease (1)
Mitochondrial metabolism disease (1)
Multiple myeloma (1)
Myocardial ischemia (1)
Obesity (1)
Psoriasis (1)
Thrombocytopenia (1)

Technology Type

Mass Spectrometry (102)
Shotgun proteomics (58)
Affinity purification coupled with mass spectrometry proteomics (18)
Mass spectrometry (17)
Bottom-up proteomics (13)
Data-independent acquisition (13)
Gel-based experiment (11)
Data-dependent acquisition (6)
SWATH MS (3)
Top-down proteomics (3)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
Affymetrix 6.0, Illumina Genome Analyzer II (1)
Illumina Genome Analyzer II (1)
Illumina HiSeq 2000 (1)
NMR spectroscopy (1)
Affinity proteomics (1)
Olink affinity proteomics (1)

Instrument Platform

Q Exactive Plus (7)
Orbitrap Fusion Lumos (5)
Illumina HiSeq 2500 (3)
GenePix 4000B [Axon Instruments] (2)
Illumina NovaSeq 6000 (2)
Q Exactive HF (2)
QExactive (2)
TimsTOF Pro (2)
Q Exactive (2)
Scanning of was performed on an Axon 4000B scanner (1)
NextSeq 500 (1)
ITQ 1100 (1)
Thermo Fisher Scientific (MA, USA) Q Exactive hybrid quadrupole-orbitrap mass spectrometer (1)
Thermo Fisher Scientific (MA, USA) Vanquish Horizon Duo ultra-high performance liquid chromatography (UHPLC) system with an Accucore C18 column with 150 mm length, 2.1 mm internal diameter, and 2.6 µm particle size (1)
Agilent 8890 GC coupled to a 5977 Inert Plus MSD (1)
LCQ Deca XP Plus (1)
LTQ (1)
LTQ Orbitrap (1)
LTQ Orbitrap Elite (1)
LTQ Orbitrap Velos (1)
Orbitrap Eclipse (1)
Orbitrap Fusion (1)
Orbitrap Fusion Lumos ETD (Thermo Scientific instrument model) (1)
Q Exactive HF-X (1)
Q Exactive UHMR (1)
Q-Exactive HFX (1)
QSTAR Elite (1)
TimsTOF Pro 2 (1)
TripleTOF 5600 (1)
TripleTOF 6600 (1)

Publication Date

2014 (43)
2016 (37)
2012 (30)
2025 (26)
2022 (26)
2010 (24)
2011 (23)
2023 (19)
2021 (19)
2008 (17)
2013 (16)
2015 (14)
2019 (13)
2020 (12)
2026 (11)
2024 (10)
2009 (10)
2017 (9)
2018 (8)
2007 (6)
2005 (4)
2004 (4)
2006 (3)
2003 (1)

CHEBI ID

CHEBI:15741 (7)
CHEBI:15756 (5)
CHEBI:16015 (5)
CHEBI:16704 (5)
CHEBI:16857 (5)
CHEBI:17234 (5)
CHEBI:17368 (5)
CHEBI:17568 (5)
CHEBI:17596 (5)
CHEBI:17754 (5)
CHEBI:17821 (5)
CHEBI:17992 (5)
CHEBI:22660 (5)
CHEBI:27897 (5)
CHEBI:30769 (5)
CHEBI:32816 (5)
CHEBI:7916 (5)
CHEBI:15354 (4)
CHEBI:15428 (4)
CHEBI:15603 (4)
CHEBI:15729 (4)
CHEBI:15891 (4)
CHEBI:15940 (4)
CHEBI:16643 (4)
CHEBI:16708 (4)
CHEBI:16737 (4)
CHEBI:16919 (4)
CHEBI:16958 (4)
CHEBI:17053 (4)
CHEBI:17196 (4)

Metabolite Name

Glycerol (4)
Inosine (4)
Sucrose (4)
Uracil (4)
Xanthine (4)
Adenine (3)
Adenosine (3)
Arginine (3)
Creatine (3)
Glucose (3)
Glucose (3)
Glutamine (3)
Guanine (3)
Isoleucine (3)
Leucine (3)
Methionine (3)
Pantothenic acid (3)
Phenylalanine (3)
Phenylalanine (3)
Tryptophan (3)
Tryptophan (3)
Uric acid (3)
Valine (3)
2-Hydroxybutyric acid (2)
2-phosphoglyceric acid (2)
3,5,7-Trimethyl-2E,4E,6E,8E-undecatetraene (2)
3E,5E-tridecadienoic acid (2)
4,7-dioxo-octanoic acid (2)
4-Hydroxybenzoic acid (2)
Acetoacetic acid (2)

First Public Date

2014 (2)
2017 (1)

Modelling Approach

Constraint-based model (3)
Ordinary differential equation model (1)

Study status

Recruiting (2)

Lab affiliation

Core Facility for Medical Bioanalytics Proteomics Platform Tübingen (PxP) Institute for Ophthalmic Research Eberhard-Karls University of Tuebingen Elfriede-Aulhorn-Str. 7 D-72076 Tuebingen. Germany. (7)
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 (6)
The University of Melbourne (5)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (3)
Boston University (2)
CRUK -CRUK Scotland nstitute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (2)
Department of Biochemistry & Pharmacology, University of Melbourne, Australia (2)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany (2)
Department of Chemistry and Biochemistry, Brigham Young University (2)
MS Omics, Biohub Chicago, USA (2)
School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia (2)
Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia (2)
1 Life Sciences Institute, Dublin City University, Glasnevin, Dublin 9, Ireland. 2 School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. 3 SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, Limerick, Ireland (1)
1Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia 2Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia 3Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Melbourne, VIC, 3052, Australia (1)
Assistant Professor & K12 Scholar Translational Glycobiology Institute, Department of Translational Medicine Florida International University | Herbert Wertheim College of Medicine (1)
Biochemistry and Molecular Genetics (1)
Biologics R&D Group/ Biomedical Program CSIRO Manufacturing Bayview Ave/ Research Way, Clayton, VIC3168 Australia (1)
Boston College (1)
Boston University School of Medicine (1)
CRUK -CRUK Scotland Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (1)
CRUK Beatson Institute (1)
CVRTI, University of Utah (1)
CVRTI, University of Utah (lab head) (1)
Cell Signalling & Immunology, School of Life Sciences, University of Dundee (1)
Cell Signalling and Immunology School of Life Sciences University of Dundee United Kingdom (1)
Center for Alzheimer's and Related Dementias (CARD), NIA and NINDS, NIH, Bethesda, Maryland, USA. (1)
Center for Network Systems Biology, Boston University (1)
Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA (1)
Chair of Immunobiology, Yale University (1)
Charles Perkins Centre, University of Sydney (1)

Keyword

Ablation Techniques (1)
Anti-obesity Medications (1)
Bariatric Endoscopy (1)
Bariatric Surgery (1)
Bilio-pancreatic diversion (BPD) (1)
Bilio-pancreatic diversion with duodenal switch (BPD-DS) (1)
Endoluminal sleeves (1)
Endoscopic Metabolic and Bariatric Therapies (EMBT) (1)
Endoscopic Sleeve Gastroplasty (ESG) (1)
Endoscopic Suturing (1)
Gastric peroral endoscopic myotomy (G-POEM) (1)
Gastroplasty with endoscopic myotomy (GEM) (1)
Gut Hormones (1)
Intragastric balloon (IGB) (1)
Laparoscopic adjustable gastric banding (LAGB) (1)
Laparoscopic sleeve gastrectomy (LSG) (1)
Pathophysiology of obesity (1)
Primary Obesity Surgery Endolumenal (POSE) (1)
Pylorus sparing antral myotomy (PSAM) (1)
Restorative Obesity Surgery Endoluminal (ROSE) (1)
Roux-en-Y gastric bypass (RYGB) (1)
Submucosal Tunneling Procedures (1)
Tissue Plication (1)
Weight Loss Diets (1)

IsPrivate

False (4)

Model Flag

Non Kinetic (2)

Classification

bacteria (3)

Modification

N6 (3)
N6-dimethyl-L-lysine (3)
15.994915 (1)
57.021464 (1)

Study type

Transcription profiling by array (102)
RNA-seq of coding RNA (45)
ChIP-seq (19)
Other (13)
RNA-seq of non coding RNA (10)
Methylation profiling by array (9)
Unknown experiment type (6)
ChIP-chip by tiling array (6)
Methylation profiling by high throughput sequencing (6)
Transcription profiling by tiling array (3)
Proteomic profiling by array (3)
Comparative genomic hybridization by array (2)
DNA-seq (2)
Genotyping by array (1)
MicroRNA profiling by high throughput sequencing (1)
ATAC-seq (1)
MicroRNA profiling by array (1)
Observational (1)
Observational patient registry (1)

Release Date

2022 (302)
2021 (250)
2023 (220)
2024 (216)
2025 (207)
2020 (177)
2019 (152)
2018 (137)
2016 (119)
2014 (94)
2017 (92)
2015 (91)
2013 (63)
2012 (61)
2011 (55)
2010 (55)
2026 (32)
2008 (31)
2009 (27)
2007 (9)
2006 (8)
2005 (6)
2004 (6)
2002 (2)
2003 (1)
2000 (1)
1999 (1)

Location

Australia (1)
United States (1)

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A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms

INTRODUCTION: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus - hyphae penetrate through tissue bar...

2017-02-20 | MTBLS370 | MetaboLights

Protocol for a randomized controlled trial to evaluate a year-long (NICU-to-home) evidence-based, high dose physical therapy intervention in infants at risk of neuromotor delay.

Not available

S-EPMC10508609 | biostudies-literature

Comparative Genomic Analysis of PhoP Regulon in S. Typhi and S. Typhimurium

Transcriptional profiling of three sequenced S. enterica strains: S. Typhimurium LT2, S. Typhi CT18, and S. Typhi Ty2 in PhoP-inducing and non-inducing conditions in vitro, and compared these results to profiles of phoP-/Q- mutants derived from S. Typhimurium LT2 and S. Typhi Ty2. Two-condition expe...

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

2010-05-06 | E-GEOD-17670 | biostudies-arrayexpress

Quality of care for HIV infection provided by Ryan White Program-supported versus Non-Ryan White Program-supported facilities.

Not available

S-EPMC2535568 | biostudies-literature

High-throughput gene expression profiling of Salmonella enterica serovar Paratyphi A in the blood of bacteremic patients in Bangladesh

In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1798 S. Paratyphi A mRNA...

ORGANISM(S): Salmonella enterica subsp. enterica serovar Paratyphi A

2010-09-06 | E-GEOD-22958 | biostudies-arrayexpress

Feasibility of Daily Assessments of Chemotherapy Toxicities to Predict Daily Exercise Behavior During a Home-Based Exercise Intervention.

Not available

S-EPMC12056855 | biostudies-literature

Identification of a novel Bromodomain / Casein Kinase II / TAF-containing complex as a regulator of mitotic condensin function

ABSTRACT: Condensin is a central regulator of mitotic genome structure, with mutants showing poorly condensed chromosomes and profound segregation defects. Here we identify the fission yeast NCT complex, comprising the Nrc1 BET-family tandem bromodomain protein (SPAC631.02), Casein Kinase II (CKII) ...

ORGANISM(S): Schizosaccharomyces pombe

2014-01-10 | E-GEOD-53955 | biostudies-arrayexpress

Transcription profiling of in vivo-derived CMS4-met cells and the in vitro-derived CMS4.sel cells using CMS4 cells as a reference sample

The CMS4 sarcoma, kindly provided by A. DeLeo (University of Pittsburgh, Pittsburgh, PA), is a solid tumor of BALB/c (H-2d) origin, which grows aggressively in naive, syngeneic hosts following a s.c. transplant. Although the parental tumor cell line forms few metastatic foci in the lungs following i...

ORGANISM(S): Mus musculus

2005-05-08 | E-MEXP-286 | biostudies-arrayexpress

Dietary Composition, Meal Timing, and Cancer-Related Fatigue: Insights From the Women's Healthy Eating and Living Study.

Not available

S-EPMC11136880 | biostudies-literature

Advances in Precision Oncology: Targeted Thorium-227 Conjugates As a New Modality in Targeted Alpha Therapy.

Not available

S-EPMC7475103 | biostudies-literature

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