Will Matthew M - OmicsDI

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Genomics (65)
Proteomics (50)
Transcriptomics (39)
Unknown (29)
Metabolomics (3)
Models (1)
Genomic (1)

Organisms

Homo sapiens (71)
Mus musculus (15)
Drosophila melanogaster (13)
Escherichia coli (4)
Saccharomyces cerevisiae (2)
Candida albicans (2)
Rattus norvegicus (2)
Danio rerio (2)
Neurospora crassa (1)
Macaca mulatta (1)
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Mycobacterium tuberculosis (1)
Oncorhynchus mykiss (1)
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Bacteria (1)
Chlamydomonas reinhardtii (1)
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Human alphaherpesvirus 1 strain 17 (1)

Repository

biostudies-arrayexpress (59)
EGA (46)
MassIVE (38)
pride (10)
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Tissue

Kidney (2)
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Whole body (1)

Disease

Renal fibrosis (2)
Disease free (1)
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Technology Type

Mass Spectrometry (10)
Shotgun proteomics (8)
Illumina HiSeq 2000 (5)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (2)
Mass spectrometry (2)
Data-dependent acquisition (2)
AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Bottom-up proteomics (1)
Chemical cross-linking coupled with mass spectrometry proteomics (1)

Instrument Platform

LTQ Orbitrap Velos (10)
GC-MS (9)
GC MS (6)
Illumina HiSeq 2500 (3)
TimsTOF Pro (3)
LTQ Orbitrap Elite (2)
Orbitrap Fusion Lumos (2)
Q Exactive Plus (2)
FACSAria III (BD Sciences) (1)
HPC (1)
10x Genomics Chromium (1)
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NextSeq 500 (1)
LTQ FT (1)
MaXis (1)
Agilent 7890A GC with 5975C inert XL MSD (1)
LTQ Orbitrap (1)
LTQ Orbitrap XL (1)
LTQ Velos (1)
Q Exactive (1)
Various (1)
Exactive (Thermo Scientific) (1)
Flow injection analysis MS - negative (1)
Flow injection analysis MS - positive (1)

Publication Date

2013 (18)
2016 (17)
2015 (12)
2014 (7)
2018 (6)
2011 (6)
2022 (6)
2017 (6)
2010 (5)
2012 (4)
2023 (4)
2019 (4)
2009 (3)
2026 (2)
2025 (2)
2007 (2)
2021 (2)
2024 (2)
2005 (1)
2020 (1)
2006 (1)
2004 (1)

UNIPROT ID/AC

9823.ENSSSCP00000000410 (1)
9823.ENSSSCP00000000606 (1)
9823.ENSSSCP00000000717 (1)
9823.ENSSSCP00000001244 (1)
9823.ENSSSCP00000002108 (1)
9823.ENSSSCP00000003829 (1)
9823.ENSSSCP00000003865 (1)
9823.ENSSSCP00000005050 (1)
9823.ENSSSCP00000005769 (1)
9823.ENSSSCP00000007309 (1)
9823.ENSSSCP00000008216 (1)
9823.ENSSSCP00000009166 (1)
9823.ENSSSCP00000009441 (1)
9823.ENSSSCP00000009732 (1)
9823.ENSSSCP00000011053 (1)
9823.ENSSSCP00000011561 (1)
9823.ENSSSCP00000012903 (1)
9823.ENSSSCP00000013237 (1)
9823.ENSSSCP00000014399 (1)
9823.ENSSSCP00000015012 (1)
9823.ENSSSCP00000016046 (1)
9823.ENSSSCP00000016065 (1)
9823.ENSSSCP00000018879 (1)
9823.ENSSSCP00000019251 (1)
9823.ENSSSCP00000019299 (1)
9823.ENSSSCP00000019489 (1)
9823.ENSSSCP00000019502 (1)
9823.ENSSSCP00000019566 (1)
9823.ENSSSCP00000019793 (1)
9823.ENSSSCP00000020128 (1)

CHEBI ID

CHEBI:10072 (1)
CHEBI:1148 (1)
CHEBI:11814 (1)
CHEBI:12936 (1)
CHEBI:12962 (1)
CHEBI:133083 (1)
CHEBI:1387 (1)
CHEBI:14314 (1)
CHEBI:144330 (1)
CHEBI:15318 (1)
CHEBI:15344 (1)
CHEBI:15346 (1)
CHEBI:15351 (1)
CHEBI:15354 (1)
CHEBI:15355 (1)
CHEBI:15380 (1)
CHEBI:15414 (1)
CHEBI:15422 (1)
CHEBI:15468 (1)
CHEBI:1547 (1)
CHEBI:15473 (1)
CHEBI:15487 (1)
CHEBI:15517 (1)
CHEBI:15531 (1)
CHEBI:15533 (1)
CHEBI:15539 (1)
CHEBI:15551 (1)
CHEBI:15552 (1)
CHEBI:15555 (1)
CHEBI:15584 (1)

Metabolite Name

(4R)-4-Hydroxy-L-glutamic acid (1)
(R)-3-Hydroxybutyric acid (1)
(S)-3-Hydroxybutyric acid (1)
1,3-Diaminopropane (1)
1-Methyl-L-histidine (1)
1-Methylhistamine (1)
1-Methylnicotinamide (1)
2,3-Dihydroxypropanoic acid (1)
2,3-Dihydroxypropyl hexopyranoside (1)
2,3-Diphospho-D-glyceric acid (1)
2,3-Pyridinedicarboxylic acid (1)
2,5-Dihydroxybenzaldehyde (1)
2,5-Dihydroxybenzoic acid (1)
2-(Hydroxymethyl)butanoic acid (1)
2-Amino-3-methoxybenzoic acid (1)
2-Aminoadipic acid (1)
2-Deoxy-5-cytidylic acid (1)
2-Deoxy-D-ribonic acid (1)
2-Deoxy-D-ribose (1)
2-Deoxyadenosine (1)
2-Deoxyadenosine 5-triphosphate (1)
2-Deoxycytidine (1)
2-Deoxycytidine 5-diphosphate (1)
2-Deoxyguanosine (1)
2-Deoxyguanosine 5-diphosphate (1)
2-Deoxyguanosine 5-triphosphate (1)
2-Deoxyinosine (1)
2-Deoxyribose-5-phosphate (1)
2-Deoxyuridine (1)
2-Deoxyuridine 5-monophosphate (1)

IsPrivate

False (1)

Model Flag

Non Kinetic (1)

Study type

Transcription profiling by array (21)
ChIP-seq (17)
RNA-seq of coding RNA (5)
Comparative genomic hybridization by array (3)
Other (3)
Genotyping by array (2)
DNA-seq (2)
RNA-seq of non coding RNA (2)
ATAC-seq (1)
RNA-seq of coding RNA from single cells (1)
RNA-seq of total RNA (1)

Release Date

2013 (20)
2014 (8)
2015 (7)
2011 (7)
2012 (5)
2010 (5)
2016 (4)
2023 (4)
2022 (4)
2025 (3)
2020 (3)
2009 (3)
2024 (3)
2021 (3)
2018 (2)
2007 (2)
2026 (1)
2006 (1)
2004 (1)
2019 (1)
2017 (1)

Lab affiliation

Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA Department of Medicine – Renal Division, Brigham and Women’s Hospital, Boston, MA (2)
Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo 2007, Sydney, NSW, Australia (1)
Department of Genome Science, University of Washington, Seattle, USA (1)
Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA USA (1)
Future Biomanufacturing Research Hub University of Manchester (1)
School of Life Sciences and Proteomics and Metabolomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia (1)
Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario,Canada (1)
University of Washington Department of Chemistry (1)
Woods Hole Oceanographic Institute, Marine Chemistry and Geochemistry Woods Hole, MA (1)

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Differences in county-level cardiovascular disease mortality rates due to damage caused by hurricane Matthew and the moderating effect of social capital: a natural experiment.

Not available

S-EPMC9830798 | biostudies-literature

Transcription profiling of Drosophila developmental time series

Michelle N. Arbeitman, Eileen E. M. Furlong, Farhad Imam, Eric Johnson, Brian H. Null, Bruce S. Baker, Mark A. Krasnow, Matthew P. Scott, Ronald W. Davis and Kevin P. White. Gene Expression During the Life Cycle of Drosophila melanogaster, Science, 297: 2270-2275, 2002. This work can be accessed fro...

ORGANISM(S): Drosophila melanogaster

2004-11-06 | E-FLYC-6 | biostudies-arrayexpress

FIREWACh: High-throughput Functional Detection of Transcriptional Regulatory Modules in Mammalian Cells

We report a new method called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), a high-throughput functional assay for directly identifying active promoter and enhancer elements. FIREWACh simultaneously assessed over 80,000 DNA fragments derived from M-bM-^@M-^...

ORGANISM(S): Mus musculus

2014-03-22 | E-GEOD-54863 | biostudies-arrayexpress

Phase II study of gemcitabine, carboplatin, and bevacizumab in patients with advanced unresectable or metastatic urothelial cancer.

Not available

S-EPMC3574268 | biostudies-literature

Dreyfuss2013 - Genome-Scale Metabolic Model - N.crassa iJDZ836

Dreyfuss2013 - Genome-Scale Metabolic Model - N.crassa iJDZ836 Genome-scale metabolic model of the filamentous fungus Neurospora crassa This model is described in the article: Reconstruction and Validation of a Genome-Scale Metabo...

2005-01-01 | MODEL1212060001 | BioModels

MaHPIC Experiment HuC - Metabolomics of plasma samples from human volunteers infected with Plasmodium vivax

Project Description:
The Malaria Host-Pathogen Interaction Center (MaHPIC) is a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (HHSN272201200031C, 2012-2017; see http://w...

2018-06-19 | MTBLS665 | MetaboLights

Pharmacokinetic analysis of a novel human EGFRvIII:CD3 bispecific antibody in plasma and whole blood using a high-resolution targeted mass spectroscopy approach

Bi-specific single change antibody fragments (bi-scFv) represent an emerging class of biotherapeutics. We recently developed a fully human bi-scFv (EGFRvIII:CD3 bi-scFv) with the goal of redirecting CD3-expressiong T cells to recognize and destroy malignant, EGFR-expressing glioma. In mice, we showe...

ORGANISM(S): Homo Sapiens Mus Musculus

PXD012472 | panorama

Strategies for treating acute pain in patients with opioid dependence: a scoping review protocol.

Not available

S-EPMC10860028 | biostudies-literature

Expanding the Catalog of Enhancer Marks In Vivo

While the majority of protein-coding genes in the human genome have been identified, the location of the regulatory sequences that control their expression in time and space remains poorly defined. The importance of identifying these elements is underscored by a growing number of studies (such as GW...

ORGANISM(S): Mus musculus

2014-04-16 | E-GEOD-37151 | biostudies-arrayexpress

24 Hour Response of M. tuberculosis Erdman TMCC 107 to 20 micromolar clofazimine

3 sets of CFZ-exposed bacteria were compared to 3 sets of bacteria treated with vehicle (DMSO) for 24 hours in an aerated drug killing model.

ORGANISM(S): Mycobacterium tuberculosis

2020-07-22 | E-MTAB-9350 | biostudies-arrayexpress

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