|Robert Frost, MS, PhD
Education: BS and MS Stanford University - Mechanical Engineering
QBS Mentor: Jason Moore, PhD
Thesis title: Statistical methods for gene set annotation optimization, unsupervised gene set testing and independent gene set filtering.
Current position: Assistant Professor of Biomedical Data Science, Division of Biostatistics, Geisel School of Medicine at Dartmouth
Research interests: Biomedical informatics, biostatistics, applied mathematics
||Matthew Davis, MPH, PhD
Education: BA Colby College - Chemistry • DC New York Chiropractic College • MPH, The Dartmouth Institute at Dartmouth College
QBS Mentor: Margaret Karagas
Thesis Title: Prenatal and childhood exposure to low-level arsenic in the US population
Current Position: Assistant Professor Department of Systems, Populations and Leadership at University of Michigan
Dr. Davis is a quantitatively-oriented health services researcher who has additional training in health informatics, epidemiology, and statistics. He is motivated by questions related to healthcare delivery and he uses rigorous methods to study important policy-relevant issues.
Dr. Davis's research has received national media attention. Articles about his research have appeared in outlets such as Forbes, The Huffington Post, USA Today, Time, The Atlantic, and Consumer Reports. His research has also been featured on television and radio broadcasts including NPR's Marketplace, the Today Show, and other national news outlets.
||Anala Gossai, HBSc, MPH, PhD
Education: University of Toronto, Trinity College - Immunology • Yale - MPH Epidemiology of Microbial Diseases
QBS Mentor: Margaret Karagas, PhD
Thesis title: Epidemiologic characterization of human polyomaviruses in adults from the United States, and their relation to cutaneous squamous cell carcinoma
Working with Dr. Margaret R. Karagas, I investigate the seroepidemiology of human polyomaviruses, and their relation to skin cancer, in a large population-based case-control study. I hope to extend my research into the New Hampshire Birth Cohort, where I'd like to explore the association between infant health and measures of polyomavirus immunity. Having been given the opportunity to address novel hypotheses at the level acceptable for peer-reviewed publications, develop collaborations with other labs worldwide, and attend multiple conferences yearly with additional support from graduate school travel awards, I have greatly enjoyed my time with my research group.
|David Qian, BS (MD-PhD), PhD
Education: Dartmouth College - Biophysical Chemistry, Economics
QBS Mentor: Christopher Amos, PhD
Thesis title: Characterization of cancer risk and response to immunotherapy through pathway-based genomic analyses
I am now doing clinical rotations in the final 2 years of the MD/PhD program following graduate study in QBS. I look forward to using my training in cancer genomics and big data as a physician-scientist who tailors precision therapy in one of the oncology specialties: medical oncology, surgical oncology, or radiation oncology. Current rotations will help guide that decision.Publications
- **Qian DC**, Busam JA, Xiao X, Eeles RA, Schumacher FR, Phelan CM, O'Mara TA, Amos CI (2016) "seXY: A tool for sex inference from genotype arrays". Bioinformatics [accepted]
- **Qian DC**, Xiao X, Byun J, Suriawinata AA, Her SC, Amos CI, Barth RJ Jr (2016) "PI3K/Akt/mTOR signaling and plasma membrane proteins are implicated in responsiveness to adjuvant dendritic cell vaccination for metastatic colorectal cancer". Clin Cancer Res [epub ahead of print]
- **Qian DC** , Han Y, Byun J, Shin HR, Hung RJ, McLaughlin JR, Landi MT, Seminara D, Amos CI (2016) "A novel pathway-based approach improves lung cancer risk prediction using germline genetic variations". Cancer Epidemiol Biomarkers Prev 25, 1208-1215.
- Halloran JW, Zhu D,**Qian DC**, Byun J, Gorlova OY, Amos CI, Gorlov IP (2015) "Prediction of the gene expression in normal lung tissue by the gene expression in blood". BMC Med Genomics 8, 77:1‒6
- Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, McLaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickebller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI (2015) "Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions". Hum Mol Genet 24, 7406‒7420.
- Cordell HJ, Han Y, Mells GF, Li Y, Hirschfield GM, Greene CS, Xie G, Juran BD, Zhu D, Qian DC, Floyd JA, Morley KI, Prati D, Lleo A, Cusi D; Canadian-US PBC Consortium; Italian PBC Genetics Study Group; UK-PBC Consortium, Gershwin ME, Anderson CA, et al. (2015) "International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways". Nat Commun 6, 8019:1‒11.
- Onyango EO, Kelly AR, Qian DC, Gribble GW (2015) "Novel Synthesis of 1-bromo-8-methylnaphthalene and 1-bromo-5-methylnaphthalene". J Org Chem 80, 5970‒5972.
|Britney Graham, BS, QBS MS
Education: New England College - Mathematics
QBS Mentor: Scott Williams, PhD
I chose the QBS program because I was intrigued by the multidisciplinary aspect of the research. This gave me the ability to apply my knowledge of mathematics in a practical setting. I am working on applying network theory to novel genetic associations. I like working with Scott Williams because he encourages me to think independently, yet offers my guidance when I need it. I have come a long way in understanding since I joined his lab.
|Jeffrey Thompson, BS, PhD
Education: University of Southern Maine - Computer Science
QBS Mentor: Carmen Marsit, PhD
Thesis title: Genomic and clinical data integration for improved cancer prognostic and predictive models
I'm originally from western Maine and prior to 2010 spent almost 15 years in the health publishing industry. Eventually I went back to school at the University of Southern Maine and during my undergrad, I joined the Congdon lab, where I developed a machine learning approach to inferring cis-regulatory modules of transcription factor binding sites. This research led me to become interested in all pre- and post-transcriptional regulation of genes and to notice that epigenetic data are underutilized by many projects that seek to unravel disease etiology. I joined the QBS program at Dartmouth because of its vision of a new type of researcher that can help connect specialists in different areas: epidemiology, biostatistics, and bioinformatics. Dr. Marsit has built a lab with people of diverse backgrounds to do research that cuts across all of these fields. As part of the Marsit Lab, I am developing new tools that enable integrative analyses of multiple, high-dimensional datasets using machine learning to reveal the connections between environmental exposure, epigenetic control, gene expression, and disease.
|Christiaan Rees, BS (MD-PhD), PhD
Education: University of Massachusetts, Dartmouth - Biology
QBS Mentor: Jane Hill, PhD
Thesis title: Thesis Title: Metabolic fingerprinting of Gram-negative pathogen groups with a focus on the identification of carbapenemase-producing Enterobacteriaceae
Working with Dr. Jane Hill, my research focused on the identification of metabolic fingerprints capable of identifying carbapenemase-producing Enterobacteriaceae (CRE), a critically-important pathogen group that contributes to substantial morbidity, mortality, and healthcare costs. Potential applications of this approach include the rapid identification of CRE from human specimens such as blood or sputum. Having completed my PhD, I now return to the MD program at the Geisel School of Medicine, with an anticipated graduation in 2020. I intend to use the next year of medical school (M3) to explore different career choices, and am grateful that my training through the QBS program has provided me with a useful set of skills irrespective of what specialty I eventually choose.
Awards, Abstracts, and Poster Presentations
- Dartmouth Graduate Studies Graduate Alumni Research Award
- Cystic Fibrosis Foundation Student Traineeship
- NIH BD2K T32 training grant
- Recent Publications
|Alexander Titus, BS, BA
Mentor: Brock Christensen, PhD
Education: University of Puget Sound - Biology, Biochemistry
I'm interested in data integration methods for 'omic' analyses. There is a growing volume of federally funded, publicly available data that were collected on different technologies. I develop methods to integrate these data sets together for analysis. Specifically, I'm interested in the prospects of combining genomic, transcriptomic, and proteomic data to identify the effect of miRNA-related genetic variation on disease phenotypes. Im also interested in reference-based and reference-free cell mixture deconvolution, using cell type specific methylation markers as additional parameters in modeling
Awards, Abstracts, and Poster Presentations
- NIH-Dartmouth Big Data to Knowledge (BD2K) Fellow
- Titus AJ*, Houseman EA*, Johnson KC, Christensen BC (2016) methyLiftover: cross-platform DNA methylation data integration. Bioinformatics. 32(16):2517-9. *co-first
- Titus AJ, Faill R, Das AK (In Press) Automatic identification of co-occurring patient events. Proceedings of the 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 579-86.
- Titus AJ, Faill R, Das AK (2016) Automatic identification of co-occurring patient events. Workshop on Methods and Applications in Healthcare Analytics. 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, Seattle, WA, USA. Oral Presentation.
- Titus AJ, Houseman EA, Johnson KC, Christensen BC (2016) methyLiftover: cross-platform DNA methylation data integration. Computational Life Sciences Workshop @ Bayer. Berlin, Germany. Poster
|Ellen Nutter, BS
Mentors:Tracy Onega, PhD, Giovanni Bosco, PhD and Jennifer Doherty, PhD
Education: University of Great Falls - Mathematics
My area of interest is translational research: participating in all the steps in the process from discovery to delivery is important to me. Here at Dartmouth I work with Jen Doherty's Cancer Epidemiology Laboratory and Tracy Onega's Population Health Laboratory. Working with both Dr. Doherty and Dr. Onega allows me to explore the spectrum of quantitative research topics. We work on a broad spectrum of topics from genetic association studies to geographic analyses pertaining to lung cancer screening usage for cancer prevention, prognosis, and treatment.
Awards, Abstracts, and Poster Presentations
- Big Data in the Life Sciences Trainee funded by Burroughs-Wellcome Fund Program
- Recent Publications
|Lia Harrington, BS, MS
Mentors: Saeed Hassanpour, PhD and Matthew Havrda, PhD
Education: Bucknell University - Nueroscience • University of Montana - MS Psychology
My research interest is in leveraging big data and bioinformatics tools to understand diseases, such as cancer. My current project is developing better predictive models of colon cancer risk via information text extraction from electronic medical data. In addition, through the Burroughs-Wellcome Fellowship, I am working with Dr. Havrda to better understand the biological basis of Parkinson's disease.
|Craig MacKenzie, BS, MS
Mentor: Gevorg Grigoryan, PhD
Education: University of New Hampshire Durham - Mathematics • University of Illinois - MS Mathematics
My research involves mining massive amounts existing data on proteins for the purpose of computationally designing novel proteins. More specifically, we have determined a small set of structural motifs capable of describing almost all structural interactions found in proteins (with known structures). We are now using sequence-structure relationships from these motifs to design novel proteins. Beyond this I'm interested in computationally designing proteins (and other molecules) for use in synthetic biology, nanomaterials and therapeutics. I have a bachelor's degree in Mathematics from the University of New Hampshire. The interesting and diverse research conducted by QBS faculty drew me to the program which I joined in 2012. When I joined the program I did not plan on working in the field of protein design, but got hooked after doing rotations in the labs of Chris Bailey-Kellogg and Gevorg Grigoryan my first year.