Curriculum Vitae

I lead translational research studies that combine functional genomic and bio-statistical approaches in pursuit of risk factors, biomarkers, and molecular mechanisms underlying neurodevelopmental and neuropsychiatric disorders. My work strikes an important balance between hypothesis-driven research and exploration while utilizing patient-derived tissues, including peripheral blood, umbilical cord blood, postmortem brain tissue and neuronal cell culture systems. One of my main strengths is my ability to design and analyze large datasets generated from high-throughput genetics/genomics approaches in a rigorous and reproducible manner under a prism  of computational, bioinformatics and machine learning methods. These studies bring together scientists with varied expertise, including academic and industry researchers, psychiatrists, geneticists, immunologists and bioinformaticians.

Research topicsComputational biology, bioinformatics, machine learning, clinical trials, transcriptomics, proteomics, normal brain development, neurodevelopment, posttraumatic stress disorder.


POSITIONS AND EMPLOYMENT

2017 – Present                   Statistical Consultant
|                                             
    National Institute of Mental Health and U.S. Dept. of Veteran Affairs
|                                                
   Genomic Biomarker Clinical Trials

2016 – Present                   Postdoctoral Fellow in Psychiatric Genomics
                                               
Icahn School of Medicine at Mount Sinai, New York, NY USA
|                                                  
Depts. Psychiatry, Genetics and Genomic Sciences

2014 – 2016                          Bioinformatics and Genomics PhD Research Fellow
|                                                 University of Southampton, Southampton, United Kingdom
|                                                   
Faculty of Medicine and Dept. Psychiatry

Jan. 2014 – Mar. 2014     Visiting Research Fellow
|                                                 University of Cape Town, Cape Town, South Africa
|                                                   Dept. Psychiatry and Mental Health

2012 – 2014                         Bioinformatics Analyst
|                                                 VA San Diego, University of California San Diego, La Jolla, CA USA
|                                                   Dept. Psychiatry

2008 – 2012                         Bioinformatics Associate Research Scientist
                                               
Centre of Genomic Regulation, Barcelona, ES
|                                                    Comparative and Evolutionary Genomics

2006 – 2008                         Bioinformatics Research Associate
|                                               
University of California San Diego, La Jolla, CA USA
|                                                   Dept. of Genetics and Genomic Sciences

EDUCATION

2014 – 2016                       PhD Bioinformatics and Genomics (emphasis neuroscience)
                                                University of Southampton, Faculty of Medicine, Southampton, UK
Doctoral Thesis:              Blood-based Transcriptome Biomarker Discovery in Psychiatric Disorders.

MANUSCRIPTS UNDER REVIEW ON PREPRINT (*corresponding author)

19.   Golden C, Breen MS, Koro L, Sonar S, Niblo K, Browne A et al. Disruption of the KH1 domain leads to transcriptional alterations and attentional deficits in rats.  2018. Under review.

18.    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.  2018. Under review.

17.    Breen MS, Thomas K, Baldwin D, Lipinska G. Predicting PTSD diagnosis using support vector machine learning – the role of sleep, memory and adrenergic metabolites.  2018. Under review.

PRIMARY PUBLICATIONS

16.    Breen MS*, Wingo A, Koen N, Donald K, Zar H, Ressler K et al. Gene expression in cord blood links genetic risk for neurodevelopmental disorders with prenatal maternal psychological distress and adverse outcomes in early childhoodBrain, Behavior, and Immunity (2018). Ahead of print.

15.   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. Neuropsychopharmacology. 2017 Nov; 1:13. DOI: 10.1038/npp.2017.220. PMID: 28925389.

14.    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 Jan; 7:47333. DOI: 10.1038/srep43777. PMID: 5333148.

13.    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. PMID: 27650405

12.    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

11.    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

10.    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

9.    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

8.    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.

7.    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

6.    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

5.    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

CO-AUTHOR CONTRIBUTIONS TO PEER-REVIEWED PUBLICATIONS

4.  White C, Beliakova-Bethell N, Lada S, Breen MS, Hurst T, Spina C et al. Transcriptional Modulation of Human Endogenous Retroviruses in Primary CD4+ T Cells Following Vorinostat Treatment. Frontiers in Immunology (2018). Apr 12;9:603. DOI:10.3389/fimmu.2018.00603. PMID: 29706951.

3. Manolakopoulos S, Kontos G, Breen MS, Kourikou A, Deutsch M et al. Immunological Parameters For Prediction Of Sustained Response After Nucleoside Analogs (NAs) Discontinuation In Patients With Hbeag-Negative Chronic Hepatitis B. Hepatology. 2016 Oct; 64: 314A-314A.

2. Nievergelt CM, Maihofer AX, Mustapic M, Breen MS et al. Genome-Wide Association Study in Combat-Exposed Marines Identifies a Novel Risk Factor for PTSD. Biological Psychiatry. 2014 May; 75:9: 149S-150S.

1. Wood O, Woo J, Seumois G, Savelyeva N, McCann KJ, Singh D, Jones T, Breen MS et al. Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors. Oncotarget. 2016 Aug 8;7:35. DOI 10.18632/oncotarget.10788. PMID: PMC5302866.


HONORS AND AWARDS

2014 – Engineering and Physical Sciences Research Counsel Grant
2014 – Worldwide University Network Research Mobility Grant
2014 – Marie Curie Travel Award Grant
2014 – Visiting Research Fellow, University of Cape Town, SA
2015 – Wessex UK Immunology Research Award for Young Investigators
2015 – Wellcome Trust Sanger Insitute Travel Award
2015 – Wessex UK Medical Research Award for Young Investigators
2015European College of Neuropsychopharmacology (ECNP) Travel Award
2015 – Annual Adventures in Research Grant; Co-PI
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 – Hinxton, UK: Computational Neuropsychiatry
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
2016 – Southampton, UK: Anxiety, Targeting the Mechanisms of Menace
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
2018 – New York, NY:  Society of Biological Psychiatry

TEACHING EXPERIENCE

2014 –  Lecturer, University of Southampton: Machine-learning applications in biomedical research.
2015 –  Bioinformatics Mentor, University of Southampton: Genomics mentor for various undergraduate students.
2015 – Demonstrator, University of Cape Town: Genome mapping and alignment.
2015 – Lecturer, University of Southampton: UK 100K Genomes Project Masters Genomic Course.
2016 – Graduate Student Mentor, Icahn School of Medicine at Mount Sinai: Genomics mentor for various graduate students.

Ad Hoc Journal Reviewer: Biological Psychiatry, Molecular Psychiatry, Translational Psychiatry, Nature Neuroscience, 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.

Keywords: transcriptomics, RNA-sequencing, proteomics, genotype arrays, supervised multivariate classification (i.e. machine-learning algorithms), unsupervised gene network reconstruction algorithms (i.e. causal, bayesian and weighted), mixed (effect) linear models,  pathway and gene-set modelling, protein interaction networks,  multi-omic data integration, eQTL analysis, RNA editing, deconvolution analysis and modelling of heterogeneous tissues, pharmacogenomics and drug mechanism of action, randomized clinical trial.

 

 

 

 

 

 

 

 

 

 

 

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