Psychiatric Genomics Postdoctoral Fellow
Icahn School of Medicine at Mount Sinai, New York, NY USA
May 2016 – Present
• Multi-modal genomic data integration spanning human, cellular and murine systems of ASD.
• Reconstruct brain-based gene networks and find key driver genes in major psychiatric disorders.
• Build biologically plausible mechanistic models of disease for experimental & clinical validation.
• Development and assessment of blood-based transcriptome biomarkers.
• Statistical consultant for double blind crossover clinical trials.
Bioinformatics and Genomics PhD Research Fellow
University of Southampton, Southampton, United Kingdom
Aug. 2013 – May 2016
• Identification of genes and pathways involved in major psychiatric diseases.
• Statistical analyses and data integrations (transcriptome, proteome, clinical & neuroimaging).
• Emphasis on genome-wide blood-based transcriptome biomarker discovery.
• Network pharmacogenomics to understand drug mechanism of action.
University of California San Diego (UCSD), San Diego, CA USA
July 2012 – Aug. 2013
• Support computational analysis of genomic datasets for UCSD academic investigators.
• Design of experiments and statistical modeling (pathway and gene network modeling).
• Develop NGS pipelines geared towards biomarker discovery.
Bioinformatics Associate Research Scientist
Centre of Genomic Regulation (CRG), Barcelona, Spain
Nov. 2008 – July 2012
• Develop statistical methods for estimating the influence of epistasis on protein evolution.
• Statistical genetics of population-specific pathogenic mutations.
PhD Bioinformatics and Genomics (emphasis neuroscience)
University of Southampton, Faculty of Medicine, Southampton, UK
Sept. 2013 – Feb. 2016
Doctoral Thesis: Blood-based Transcriptome Biomarker Discovery in Psychiatric Disorders.
BSc Behavior, Ecology, Evolution and Systematics
Department of Biology, Illinois State University, USA
Aug. 2002 – May 2006
- Breen MS*, Ozcan S, Ramsey J, Rustogi N, Gottschalk M, Webster M et al. Insights into the molecular changes associated with postnatal human brain development: an integrated transcriptomics and proteomics study. 2017. Under review.
- Breen MS*, Thomas K, Baldwin D, Lipinska G. Predicting PTSD diagnosis using support vector machine learning – the role of sleep, memory and adrenergic metabolites. 2017. Under review.
- Breen MS*, Tylee D, Maihofer A, Neylan T, Mehta D, Binder E, et al. PTSD blood transcriptome mega-analysis: Shared inflammatory pathways across biological sex and modes of trauma. 2017. Article in press.
- Breen MS*, Uhlmann A, Bahn S, Stein DJ. Parallel changes in serum proteins and diffusion tensor imaging biomarkers in methamphetamine-associated psychosis. Scientific Reports. 2017 January; 7:47333. DOI: 10.1038/srep43777. PMID: 5333148.
- Breen MS*, Stein DJ, Baldwin DS. Systematic review of blood transcriptome profiling and neuropsychiatric disorders: guidelines for biomarker discovery. Psychopharmacol Clin Exp. 2016 Sept; 31: 373–381. DOI: 10.1002/hup.2546
- Breen MS*, White CH, Shekhtman T, Lin K, Looney D, Woelk CH, Kelsoe JR. Identification of lithium responsive genes and gene networks in bipolar disorder patient derived lymphoblastoid cell lines. Pharmacogenomics Journal. 2016 Jul; 00:1-8. DOI: 10.1038/tpj.2016.50. PMID: 27401222
- Breen MS*, Uhlmann A, Nday C, Glatt SJ, Mitt M, Metsalpu A et al. Candidate gene networks and blood-biomarkers of methamphetamine-associated psychosis: an integrative RNA-sequencing report. Transl Psychiatry. 2016 May; 6:e802. DOI: 10.1038/tp.2016.67. PMID: 27163203
- Breen MS*, Beliakova-Bethell N, Mujica-Parodi L, Carlson J, Ensign W, Woelk C, et al. Acute psychological stress induces short-term variable immune response. Brain, Behavior, and Immunity. 2016 Mar; 53:172-82. DOI: 10.1016/j.bbi.2015.10.008. PMID: 26476140
- Breen MS*, Maihofer A, Glatt ST, Chandler SD, Tsuang M, Risbrough V, et al. Gene networks specific for innate immunity define post-traumatic stress disorder. Molecular Psychiatry. 2015 Dec; 20(12):1538-45. DOI: 10.1038/mp.2015.9. PMID: 25754082
- Howard JH, Williams BL, Breen MS*, Nishiguchi MK. Adaptation to both host and environment in an environmentally transmitted symbiosis: Comparative genomics of Vibrio spp. from different host squid and geographic locations. Vei et Milieu – Life and Environment. 2015, 65(4):187-200.
- Breen MS*, Kemena C, Vlasov P, Notredame C, Kondrashov, F Epistasis not needed to explain low dn/ds. Nature. 2013 May 30;497(7451):E1-2; discussion E2-3. DOI: 10.1038/nature12219. PMID: 23719465
- Breen MS*, Kemena C, Vlasov P, Notredame C, Kondrashov, F. Epistasis as the primary factor in molecular evolution. Nature. 2012 Oct; 490(7421): 535-8. DOI:10.1038/nature11510. PMID: 23064225
- Breen MS*, Kondrashov, F. Mitochondrial pathogenic mutations are population-specific. Biology Direct. 2010 Dec 31;5:68. doi:10.1186/1745-6150-5-68. PMID: 21194457
HONORS AND AWARDS
2014 – Engineering and Physical Sciences Research Counsel Grant (£6,000)
2014 – Worldwide University Network Research Mobility Grant (£3,000)
2014 – Marie Curie Travel Award Grant (£3,000)
2014 – Visiting Research Fellow, University of Cape Town, SA
2015 – Wessex UK Immunology Research Award for Young Investigators
2015 – Wessex UK Medical Research Award for Young Investigators
2015 – European College of Neuropsychopharmacology (ECNP) Travel Award
2015 – Annual Adventures in Research Grant; Co-PI (£20,000)
2016 – Seaver Autism Center for Research and Treatment Fellowship
2017 – Autism Science Foundation Fellowship
2017 – Mindich Child Health and Development Pilot Grant Award
SELECTED INTERNATIONAL PRESENTATIONS
2014 – Banyuls sur mer, FR: The role of epistasis in molecular evolution
2015 – Bristol, UK: Innovations in PTSD prediction, diagnosis and therapy
2015 – Amsterdam, NL: NATO traumatic stress & anti-terrorism meeting
2015 – Cape Town, SA: Single sample estimates of confounding cells and tissues
2016 – Nice, FR: ECNP young scientist meeting
2017 – San Diego, CA: Society of Biological Psychiatry
2017 – Bethesda, MD (NIMH): Psychiatric genomics in the era of team science
2017 – Mainz, Germany: 3rd annual PTSD resilience research symposium
Ad Hoc Journal Reviewer: Psychoneuroendocrinology, Metabolic Brain Disease, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, Journal of Human Transcriptome, Progress in Neuro-Psychopharmacology & Biological Psychiatry, Nature Communications, Scientific Reports, Biological Psychiatry, Translational Psychiatry.
Genomic expertise: Transcriptome-wide RNA-sequencing and microarray gene expression techniques, Whole-genome genotype arrays, Mass-spectrometry proteomics (labelled and label-free techniques), 450K Methylation arrays, Neuroimaging data analysis (DTI, sMRI).
Statistical expertise: Supervised multivariate classification (i.e. machine-learning algorithms), Unsupervised gene network reconstruction algorithms (i.e. causal, bayesian and weighted), Mixed (effect) linear models, Molecular pathway and gene-set modelling, Protein interaction networks, Large-scale data integrations spanning genotypes, methylation, RNA-sequencing and proteomics, eQTL analyses, Genotype-based predictions of gene expression, Cellular deconvolution analysis and modelling heterogeneous tissues, Pharmacogenomics and drug mechanism of action, Modelling the transcriptome-proteome interface, Time-series data analysis, Statistical analyses for double-blind cross-over clinical trials.