Thomas Stephen S

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Genomics (79)
Unknown (66)
Transcriptomics (47)
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Genomic (6)
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Organisms

Homo sapiens (98)
Mus musculus (11)
Arabidopsis thaliana (6)
Schizosaccharomyces pombe (5)
Saccharomyces cerevisiae (2)
Escherichia coli (2)
Arabidopsis (1)
Schistocerca gregaria (1)
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Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)
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Salmonella enterica subsp. enterica serovar Typhimurium (1)
Plasmodium falciparum 7G8 (1)
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Influenza A virus (A/Viet Nam/1203/2004(H5N1)) (1)
Influenza B virus (B/Memphis/13/2003) (1)
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Rattus norvegicus (1)

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EGA (77)
biostudies-arrayexpress (49)
pride (7)
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Tissue

Cell culture (1)

Disease

Coronary artery disease (1)
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Normal (1)
Not Available (1)
Influenza (1)
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Technology Type

Illumina 15K (8)
Mass Spectrometry (7)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
Mass spectrometry (3)
Bottom-up proteomics (3)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
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ILLUMINA, Illumina HiSeq 2500 (1)
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Instrument (1)
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5975C Series GC/MSD (Agilent) (1)

Publication Date

2011 (6)
2008 (6)
2016 (5)
2015 (5)
2024 (4)
2022 (4)
2012 (4)
2007 (4)
2025 (4)
2020 (3)
2014 (3)
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UNIPROT ID/AC

Q9LQT8 (1)
Q9MAA7 (1)

CHEBI ID

CHEBI:17992 (2)
CHEBI:29590 (1)
CHEBI:29605 (1)
CHEBI:30088 (1)
CHEBI:32902 (1)
CHEBI:32906 (1)
CHEBI:135063 (1)
CHEBI:15428 (1)
CHEBI:15891 (1)
CHEBI:16551 (1)
CHEBI:16610 (1)
CHEBI:16737 (1)
CHEBI:16811 (1)
CHEBI:16865 (1)
CHEBI:16919 (1)
CHEBI:17126 (1)
CHEBI:17148 (1)
CHEBI:17268 (1)
CHEBI:17754 (1)
CHEBI:229948 (1)
CHEBI:24265 (1)
CHEBI:27570 (1)
CHEBI:4167 (1)
CHEBI:62510 (1)
CHEBI:71182 (1)

Metabolite Name

Sucrose (2)
2-O-(alpha-D-glucopyranosyl)-D-glycerate (1)
Carnitine (1)
Creatine (1)
Creatinine (1)
D-glucose (1)
GABA (1)
Gluconate (1)
Glycerol (1)
Glycerophosphorylcholine (1)
Glycine (1)
Histidine (1)
Hydroxycotinine (1)
Methionine (1)
Myo-inositol (1)
N,N,N-Trimethyl-L-alanyl-L-proline betaine (TMAP) (1)
Putrescine (1)
Spermidine (1)
Taurine (1)
Trehalose (1)

IsPrivate

False (2)

Submitter Keywords

FAIR-AIML (1)
Machine Learning Model (1)

Modelling Approach

Computational model (1)
Ordinary differential equation model (1)

Study type

Transcription profiling by array (32)
RNA-seq of coding RNA (5)
Methylation profiling by array (4)
Other (2)
ChIP-seq (2)
Translation profiling (1)
ChIP-chip by array (1)
Comparative genomic hybridization by array (1)
MicroRNA profiling by array (1)

Release Date

2015 (11)
2021 (10)
2022 (9)
2019 (9)
2016 (8)
2023 (8)
2011 (6)
2008 (6)
2018 (6)
2024 (5)
2020 (5)
2014 (5)
2012 (5)
2017 (4)
2013 (4)
2007 (4)
2010 (3)
2025 (3)
2006 (2)
2026 (1)
2009 (1)

Lab affiliation

Associate Professor, Department of Chemistry Associate Professor, Thomas C. Jenkins Department of Biophysics Associate Professor, Department of Biology (1)
Department of Chemistry, Department of Biology (by courtesy), Thomas C.Jenkins Department of Biophysics (by courtesy), Johns Hopkins University (1)
Department of Chemistry, Johns Hopkins University (1)
Department of Electrical Engineering and Electronics University of Liverpool Liverpool (1)
EMBL, SCB, Heidelberg, Germany (1)
Johns Hopkins University Assistant Professor, Department of Chemistry Assistant Professor, Department of Biology (by courtesy) Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy) Preceptor, Chemistry-Biology Interface (CBI) Program (1)
Johns Hopkins University, Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA, Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA (1)

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Expression profiling by array of Salmonella enterica serovar Typhimurium (SL1344) qseC mutant x wild type

“Stress, survival and virulence: the multi-faceted host/microbial interactions.” Bacteria employ epinephrine and norepinephrine, which converge to distinct bacterial crucial processes, like survival and pathogenicity. A novel stress periplasmic membrane protein belonging to previously described BOF...

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

2012-05-31 | E-GEOD-38353 | biostudies-arrayexpress

An Intrinsically Disordered Region of Ubp10 Governs its Specificity for Deubiquitinating H2A/H2B Dimers over Nucleosomes

Histone modifications perform a vast array of functions in regulating gene expression, DNA replication, and repair. Monoubiquitination of histone H2B at K123 in yeast (K120 in humans) is an intriguing modification because it is deposited cotranscriptionally, mediates the installation of several othe...

ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast)

2025-07-16 | PXD051971 | Pride

Bayesian Adaptive Randomization Trial of Passive Scattering Proton Therapy and Intensity-Modulated Photon Radiotherapy for Locally Advanced Non-Small-Cell Lung Cancer.

Not available

S-EPMC6008104 | biostudies-literature

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

Microbial autotroph-heterotroph interactions influence biogeochemical cycles on a global scale, but the diversity and complexity of natural systems and their intractability to in situ manipulation make it challenging to elucidate the principles governing these interactions. The study of assembling p...

2014-06-24 | MTBLS75 | MetaboLights

Transcription profiling of synectin knock-out mouse primary endothelial cells before and after FGF2 induction

Transcriptional regulatory effects of synectin deletion in murine primary endothelial cells both before and after FGF2 induction.

ORGANISM(S): Mus musculus

2006-10-01 | E-MEXP-820 | biostudies-arrayexpress

Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains

Influenza virus polymerase transcribes or replicates the segmented RNA genome (vRNA) into respectively viral mRNA or full-length copies and initiates RNA synthesis by binding the conserved 3' and 5' vRNA ends (the promoter). In recent structures of promoter-bound polymerase, the cap-binding and endo...

ORGANISM(S): Influenza B virus (B/Memphis/13/03) Influenza A virus (A/Vietnam/1203/04(H5N1))

2016-01-04 | PXD002234 | Pride

Influenza Xl-ms Polymerase

ChIP-seq analysis of H3K4Me3- and H3K27Me3-marked chromatin in mesenchymal stem cells (MSCs), osteoblasts derived from MSCs and the osteosarcoma cell line U2OS

Many DNA-hypermethylated cancer genes are occupied by the polycomb (PcG) repressor complex in embryonic stem cells (ESCs). Their prevalence in the full spectrum of cancers, the exact context of chromatin involved, and their status in adult cell renewal systems are unknown. Using a genome-wide analys...

ORGANISM(S): Homo sapiens

2012-03-02 | E-GEOD-35573 | biostudies-arrayexpress

Geographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not been identified by conventional epidemiology yet potentially make a substantial contribution to cancer burden1. This pertains to clear cell renal cell carcinoma (ccRCC), fo...

2024-03-26 | MTBLS9394 | MetaboLights

Translation profiling of Schizosaccharomyces pombe size separated polysome fractions provides data on average numbers of associated ribosomes for most transcripts

To obtain translational profiles for all mRNAs, polysome preparations are separated according to their size using a sucrose gradient and the mRNAs in each fraction are identified and quantified with DNA microarrays. Starting with exponentially growing cells, we analyzed 12 polysome fractions using D...

ORGANISM(S): Schizosaccharomyces pombe

2007-03-22 | E-TABM-222 | biostudies-arrayexpress

Structural and Functional Determinants of Rodent and Human Surfactant Protein A: A Synthesis of Binding and Computational Data.