Dr Simone Coughlan


 
researcher
 

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