Mathematics, Statistics & Applied Mathematics

Expand all

Dr Simone Coughlan

Biography

I am a Lecturer in Genomics Data Science in the SFI Centre for Research Training in Genomics Data Science at the National University of Ireland, Galway. I have a PhD in bioinformatics (pathogen genomics) and have also worked as a bioinformatician in industry. My research interests include microbial genomics (including metagenomics), cancer and population genomics and structural variation discovery. My teaching interests include teaching methods to aid reproducibility (version control, workflow managers, containers, FAIR data principles) as well as teaching programming, cloud computing and bioinformatics analysis.

Peer Reviewed Journals

	Year	Publication
		'The gut virome in Irritable Bowel Syndrome differs from that of controls' Coughlan S;Das A;O'Herlihy E;Shanahan F;O'Toole PW;Jeffery IB; 'The gut virome in Irritable Bowel Syndrome differs from that of controls'. Gut Microbes, 13 (1) [DOI] [Details]
	(2020)	'Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption' Jeffery IB;Das A;O'Herlihy E;Coughlan S;Cisek K;Moore M;Bradley F;Carty T;Pradhan M;Dwibedi C;Shanahan F;O'Toole PW; (2020) 'Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption'. Gastroenterology, 158 (4) [DOI] [Details]
	(2018)	'Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus' Coughlan, S,Taylor, AS,Feane, E,Sanders, M,Schonian, G,Cotton, JA,Downing, T (2018) 'Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus'. Royal Society Open Science, 5 [DOI] [Details]
	(2017)	'Redeploying beta-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections' Waters, EM,Rudkin, JK,Coughlan, S,Clair, GC,Adkins, JN,Gore, S,Xia, GQ,Black, NS,Downing, T,O'Neill, E,Kadioglu, A,O'Gara, JP (2017) 'Redeploying beta-Lactam Antibiotics as a Novel Antivirulence Strategy for the Treatment of Methicillin-Resistant Staphylococcus aureus Infections'. Journal Of Infectious Diseases, 215 :80-87 [DOI] [Details]
	(2017)	'Tandem Amplification of the Staphylococcal Cassette Chromosome mec Element Can Drive High-Level Methicillin Resistance in Methicillin-Resistant Staphylococcus aureus' Gallagher, LA,Coughlan, S,Black, NS,Lalor, P,Waters, EM,Wee, B,Watson, M,Downing, T,Fitzgerald, JR,Fleming, GTA,O'Gara, JP (2017) 'Tandem Amplification of the Staphylococcal Cassette Chromosome mec Element Can Drive High-Level Methicillin Resistance in Methicillin-Resistant Staphylococcus aureus'. Antimicrobial Agents And Chemotherapy, 61 [DOI] [Details]
	(2017)	'Developing educational resources for population genetics in R: an open and collaborative approach' Kamvar, ZN,Lopez-Uribe, MM,Coughlan, S,Grunwald, NJ,Lapp, H,Manel, S (2017) 'Developing educational resources for population genetics in R: an open and collaborative approach'. Molecular Ecology Resources, 17 :120-128 [DOI] [Details]
	(2017)	'The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania' Coughlan, S,Mulhair, P,Sanders, M,Schonian, G,Cotton, JA,Downing, T (2017) 'The genome of Leishmania adleri from a mammalian host highlights chromosome fission in Sauroleishmania'. Scientific Reports, 7 [DOI] [Details]
	(2013)	'Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans' Neville BA;Sheridan PO;Harris HM;Coughlan S;Flint HJ;Duncan SH;Jeffery IB;Claesson MJ;Ross RP;Scott KP;O'Toole PW; (2013) 'Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans'. Plos One, 8 (7) [DOI] [Details]

Education

Year	Institution	Qualification	Subject
2016	NUIG Galway	PhD Bioinformatics	Pathogen genomics
2009	University of Limerick	BSc Industrial Biochemistry	Industrial Biochemistry
2011	University College Cork	MSc Bioinformatics with Systems Biology	Bioinformatics with Systems Biology

Current Postgraduate Students (Taught)

	Name	Degree	Primary Supervisor
	Aine Halpin	Msc	Y

Modules Taught

Term/Year	Module Title	Module Code	Subject / Desc
2020-2021	Foundations of Genomics Data Science	MA653	SFI Centre for Research Training in Genomics Data Science workshops
2021-2022	Foundations of Genomics Data Science	MA653	SFI Centre for Research Training in Genomics Data Science workshops
2019-2020	Medical Genomics II	MA5107	Bioinformatics
2020-2021	Medical Genomics II	MA5107	Cancer genomics
2019-2020	Mathematical Molecular Biology II	MA216	Mathematics

Internal Collaborators

	Name	Description of Collaboration
	Prof Piet Lens	Metagenomics of wastewater systems
	Dr Kate Reddington	Irish Coronavirus Sequencing Consortium
	Prof Corrado Santocanale	CRISPR Genetics Screens Cancer
	Prof Grace McCormack	Co-supervise PhD Student on genomics of Irish Honeybee
	Dr Conall Dennedy	Adrenocortical carcinoma genomics, co-supervise PhD Student
	Dr Emma Holian	Co-supervise PhD student on copy number alterations in breast cancer

About NUI Galway

Founded in 1845, we've been inspiring students for 175 years. NUI Galway has earned international recognition as a research-led university with a commitment to top quality teaching.