EdinOmics

Case Studies

A selection of publications highlighting the different groups we collaborate with and the many systems metabolomics and proteomics can be applied to.

2022

On-line untargeted metabolomics monitoring of an E. coli succinate fermentation process

Cortada-Garcia J, Haggarty J, Moses T, Daly R, Arnold SA, Burgess K

Biotechnology and Bioengineering. 2022 July, https://doi.org/10.1002/bit.28173

Rapid HILIC-Z ion mobility mass spectrometry (RHIMMS) method for untargeted metabolomics of complex biological samples

Pičmanová M, Moses T, Cortada-Garcia J , Barrett G, Florance H, Pandor S, Burgess K

Metabolomics. 2022 Feb 28, 18(3):16.

 

2021

Metabolic Alterations in Preneoplastic Development Revealed by Untargeted Metabolomic Analysis

Myllymäki H, Johansson JA, Porro EG, Elliot A, Moses T*, Feng Y*

Frontiers in Cell and Developmental Biology. 2021 Aug 03, 9: 684036.

 

2020

Boosting the Synthesis of Pharmaceutically Active Abietane Diterpenes in S. sclarea Hairy Roots by Engineering the GGPPS and CPPS Genes

Vaccaro MC, Alfieri M, De Tommasi N, Moses T, Goossens A, Leone A

Frontiers in Plant Science. 2020 June 18, 11: 924.

A systematic comparison of triterpenoid biosynthetic enzymes for the production of oleanolic acid in Saccharomyces cerevisiae

Dale MP, Moses T, Johnston EJ, Rosser SJ

PLoS One. 2020 May 01, https://doi.org/10.1371/journal.pone.0231980.

Trichoplein controls endothelial cell function by regulating autophagy

Martello A, Lauriola A, Mellis D, Parish E, Dawson JC, Imrie L, Vidmar M, Gammoh N, Mitic T, Brittan M, Mills N, O Carragher N, D’Arca D, Caporali A

EMBO Reports. 2020 Apr 26, 21: e48192.

 

2019

Shotgun proteomics analysis of nanoparticle-synthesising Desulfovibrio alaskensis in response to platinum and palladium

Capeness M, Imrie L, Muhlbauer LF, Le Bihan T, Horsfall LE

Microbiology. 2019 Jul 30, 165: 1282–1294.

Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics

Imrie L, Le Bihan T, O'Toole A, Hickner PV, Dunn WA, Weise B, Rund SSC

PLoS One. 2019 Jul 29, 14(7): e0220225.

Quantitative Phosphoproteomic Using Titanium Dioxide Micro-Columns and Label-Free Quantitation

Barrios-Llerena ME, Le Bihan T

Methods in Molecular Biology. 2019 Apr 13, 1977: 35-42.

 

2018

Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis

Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ

FEBS Letters. 2018 Dec 07, 593(3): 319-338.

Redox regulation of pyruvate kinase M2 by cysteine oxidation and S-nitrosation

Mitchell AR, Yuan M, Morgan HP, McNae IW, Blackburn EA, Le Bihan T, Homem RA, Yu M, Loake GJ, Michels PA, Wear MA, Walkinshaw MD

Biochemical Journal. 2018 Oct 31, 475(20): 3275-3291.

 

2017

Sumoylation of the Plant Clock Transcription Factor CCA1 Suppresses DNA Binding

Hansen LL, Imrie L, Le Bihan T, van den Burg HA, van Ooijen G

Journal of Biological Rhythms. 2017 Nov 27, 32(6): 570-582.

A structurally distinct TGF-β mimic from an intestinal helminth parasite potently induces regulatory T cells

Johnston CJC, Smyth DJ, Kodali RB, White MPJ, Harcus Y, Filbey KJ, Hewitson JP, Hinck CS, Ivens A, Kemter AM, Kildemoes AO, Le Bihan T, Soares DC, Anderton SM, Brenn T, Wigmore SJ, Woodcock HV, Chambers RC, Hinck AP, McSorley HJ, Maizels RM

Nature Communications. 2017 Nov 23, 8(1): 1741.

Nucleoredoxin guards against oxidative stress by protecting antioxidant enzymes

Kneeshaw S, Keyani R, Delorme-Hinoux V, Imrie L, Loake GJ, Le Bihan T, Reichheld JP, Spoel SH

Proceedings of the National Academy of Sciences USA. 2017 Aug 1, 114(31): 8414-8419.

Sex differences in leucocyte telomere length in a free-living mammal

Watson RL, Bird EJ, Underwood S, Wilbourn RV, Fairlie J, Watt K, Salvo-Chirnside E, Pilkington JG, Pemberton JM, McNeilly TN, Froy H, Nussey DH

Molecular Ecology. 2017 Jan 27, 26(12): 3230-3240.

 

2016

Method Specific Calibration Corrects for DNA Extraction Method Effects on Relative Telomere Length Measurements by Quantitative PCR

Seeker LA, Holland R, Underwood S, Fairlie J, Psifidi A, Ilska JJ, Bagnall A, Whitelaw B, Coffey M, Banos G, Nussey DH

PLoS One. 2016 Oct 10, 11(10): e0164046.

Protein Co-Expression Analysis as a Strategy to Complement a Standard Quantitative Proteomics Approach: Case of a Glioblastoma Multiforme Study

Kanonidis EI, Roy MM, Deighton RF, Le Bihan T

PLoS One. 2016 Aug 29, 11(8): e0161828.

Data from quantitative label free proteomics analysis of rat spleen

Dudekula K, Le Bihan T

Data Brief. 2016 Jun 4, 8:494-500.

Identification of S-Nitrosothiols by the Sequential Cysteine Blocking Technique

Homem RA, Le Bihan T, Yu M, Loake GJ

Methods in Molecular Biology. 2016 Apr 20, 1424: 163-74.

Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy

Creedon H, Gómez-Cuadrado L, Tarnauskaitė Ž, Balla J, Canel M, MacLeod KG, Serrels B, Fraser C, Unciti-Broceta A, Tracey N, Le Bihan T, Klinowska T, Sims AH, Byron A, Brunton VG

Oncotarget. 2016 Mar 8, 7(10): 11539-52.

Lifelong leukocyte telomere dynamics and survival in a free-living mammal

Fairlie J, Holland R, Pilkington JG, Pemberton JM, Harrington L, Nussey DH

Aging Cell. 2016 Feb 15, 15(1): 140-8.

 

2015

Cell populations can use aneuploidy to survive telomerase insufficiency

Millet C, Ausiannikava D, Le Bihan T, Granneman S, Makovets S

Nature Communications. 2015 Oct 22, 6: 8664.

Rock geochemistry induces stress and starvation responses in the bacterial proteome

Bryce CC, Le Bihan T, Martin SF, Harrison JP, Bush T, Spears B, Moore A, Leys N, Byloos B, Cockell CS

Environmental Microbiology. 2015 Oct 16, 18(4): 1110-21.

Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri

Le Bihan T, Hindle M, Martin SF, Barrios-Llerena ME, Krahmer J, Kis K, Millar AJ, van Ooijen G

Proteomics. 2015 Jun 9, 15(23-24): 4135-44.

Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana

Krahmer J, Hindle MM, Martin SF, Le Bihan T, Millar AJ

Methods in Enzymology. 2015 May 11, 551: 405-31.

 

2014

Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution

Hector RD, Burlacu E, Aitken S, Le Bihan T, Tuijtel M, Zaplatina A, Cook AG, Granneman S

Nucleic Acids Research. 2014 Oct 29, 42(19): 12138-54.

The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species

Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, Simpson TI, Le Bihan T, Millar AJ

BMC Genomics. 2014 Aug 2, 15: 640.

The proteomic response in glioblastoma in young patients

Deighton RF, Le Bihan T, Martin SF, Barrios-Llerena ME, Gerth AM, Kerr LE, McCulloch J, Whittle IR

Journal of Neuro-Oncology. 2014 May 18, 119(1): 79-89.

Impact of age on the cerebrovascular proteomes of wild-type and Tg-SwDI mice

Searcy JL, Le Bihan T, Salvadores N, McCulloch J, Horsburgh K

PLoS One. 2014 Feb 26, 9(2): e89970.

 

2013

Functional analysis of the rodent CK1tau mutation in the circadian clock of a marine unicellular alga

van Ooijen G, Martin SF, Barrios-Llerena ME, Hindle M, Le Bihan T, O'Neill JS, Millar AJ

BMC Molecular and Cell Biology. 2013 Oct 15, 14: 46.

Telomeres, a busy platform for cell signaling

Gardano L, Pucci F, Christian L, Le Bihan T, Harrington L

Frontiers in Oncology. 2013 Jun 10, 3: 146.

Photobacterium profundum under pressure: a MS-based label-free quantitative proteomics study

Le Bihan T, Rayner J, Roy MM, Spagnolo L

PLoS One. 2013 May 31, 8(5): e60897.

PI3K/Akt1 signalling specifies foregut precursors by generating regionalized extra-cellular matrix

Villegas SN, Rothová M, Barrios-Llerena ME, Pulina M, Hadjantonakis AK, Le Bihan T, Astrof S, Brickman JM

eLife. 2013 Dec 24, 2: e00806.

 

2012

Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry

Martin SF, Munagapati VS, Salvo-Chirnside E, Kerr LE, Le Bihan T

Journal of Proteome Research. 2012 Jan 1, 11(1): 476-86.

 

2011

Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri

Le Bihan T, Martin SF, Chirnside ES, van Ooijen G, Barrios-Llerena ME, O'Neill JS, Shliaha PV, Kerr LE, Millar AJ

Journal of Proteomics. 2011 Sep 6, 74(10): 2060-70.

Circadian clock parameter measurement: characterization of clock transcription factors using surface plasmon resonance

O'Neill JS, van Ooijen G, Le Bihan T, Millar AJ

Journal of Biological Rhythms. 2011 Apr 30, 26(2): 91-8.