PhD Students

2017

Photo of Noel Kosarek Noel Kosarek, BS

Mentors: Michael Whitfield, PhD & Patricia Pioli, PhD

Education: Lafayette College - Biology

My research interests include gene expression and noncoding RNA analysis of patients suffering from rare autoimmune diseases and cancers. Outside of the lab I enjoy skiing, hiking, running, and hanging out with my two bunnies, Rosalind Fur-anklin and Fuzz Aldrin.


Photo of Marek Svoboda Marek Svoboda, BA(MD-PhD)

Mentors: Giovanni Bosco, PhD

Education: Columbia University-Nueroscience

Before starting my MD-PhD studies at Dartmouth, I graduated from Columbia University with B.A. in Neuroscience and Behavior. I am interested in Neurology in the clinic, and Neuroscience in the lab. More specifically, I am using both wet lab and computational techniques to study the underlying genetics, molecular interactions, and resulting phenotypic changes related to memory impairment in fruit fly and mouse models.


Photo of Yuka Morioshi Yuka Morioshi, BS

Mentors: Jiang Gui, PhD & Margaret Karagas, PhD

Carnegie-Mellon University - Statistics

My research interests include the statistical modeling of population health data and infectious disease epidemiology. In a time where collaboration is encouraged to produce optimal results, QBS recognizes that biostatistics, bioinformatics, and epidemiology may be integrated to make further advancements in biomedical research.


Photo of Quang Nguyen Quang Nguyen, BS

Mentors: Anne Hoen, PhD & Rob Frost, PhD

Education: Bates College - Biological Chemistry and Mathematics

I am currently interested in analyzing high-throughput sequencing data as well as learning more about applying analytics to epidemiological problems.


Photo of Robert Quon Robert Quon, BS, MHS

Mentors: Barbara Jobst, PhD, MD

Education: Creighton University, Biology and Psychology, •Johns Hopkins University, MHS Mental Health, Certificate in Gerontology

My research interests are in decoding how the brain works, in order to outline the etiology of neuropathology. I will utilize my skills in biostatistics, bioinformatics, and epidemiology to enhance the detection of chronic neurological conditions with the hope of delaying or preventing its progression.


Photo of Xin Ran Xin Ran, B.Eng, MS

Mentors: James O'Malley, PhD

Education: Beijing Jiaotong University - Biomedical Engineering, Certificate in Interpreting • University of Pennsylvania - MS Bioengineering

My research interest lies in biostatistics especially the topics of tackling with high dimensional data and missing data. When I was working on my Master's thesis, I became interested in biostatistics and realized the importance for Bioengineers to be equipped with statistical skills. I'm looking forward to life in New Hampshire and the diverse outdoor activities.


Photo of Benjamin Ricard Benjamin Ricard, BS, MS

Mentors: Saeed Hassanpour, PhD

Education: Texas State University, Biochemistry •Texas State University, MS Biochemistry

I am interested in application of statistical methods to understand contemporary problems in data science, particularly the 'omic' fields and finance.

Awards

  • Graduate student of the year, Department of Chemistry and Biochemistry, Texas State University
  • Chartered Financial Analyst (CFA) Global Competition Regional Finalist
  • William Lowell Putnam Mathematical Competition Representative of Texas State University

Photo of Qingyuan Song Qingyuan Song, BS, MS

Mentors: Saeed Hassanpour, PhD

Education: University of Pittsburgh, Biology • Carnegie Mellon University, MS Computational Biology

My research interests include the study of genetic diseases such as cancers, using the combination of computational, statistical and machine learning methods, along with my background knowledge in biological sciences. Besides, I'm looking forward to go camping, kayaking, ice skating, skiing and explore nature around New Hampshire.


Photo of Yiwei Yuan Yiwei Yuan, BS

Mentors: Michael Whitfield, PhD

Education: Fudan University, Biological

My research interests are human health and biomedicine-associated data mining and analysis. I would like to explore biological and health problems in interdisciplinary way and am happy to have the chance to work with a variety of faculty members in QBS.


2016

Photo of Carly Bobak Carly Bobak, BA, MSc

Mentors: Jane Hill, PhD and James O'Malley, PhD

Education: University of Guelph - Applied Mathematics and Statistics with a Co-op Option, Certificate in Business, University of Guelph - MSc Applied Mathematics

While studying applied mathematics and statistics at the University of Guelph, I quickly realized that mathematical thinking provides important insight in a variety of disciplines, but particularly in the realm of biomedical science. Ever since I've been passionate about data-driven approaches to research in human health, particularly in the realm of infectious disease. When I'm not thinking about science (do we ever really stop thinking about science?) you can usually find me hanging out with my dog, throwing spontaneous dinner parties, or dragging my peers out to various different adventures throughout the New England area.


Photo of Guanqing Chen Guanqing Chen, BS, MA

Mentor: James O'Malley, PhD

Education: Nanyang Technological University, Singapore - Mathematics and Statistics, University of Rochester - MA Statistics

My research interests are causal inference, network analysis and longitudinal data analysis. I like QBS because this integrated interdisciplinary program in biostatistics, bioinformatics and epidemiology will broaden my knowledge base, strengthen my skills in translational sciences and lay a solid foundation for pursuing my career in biomedical and translational research.


Photo of Monica Espinoza Monica Espinoza, BS

Mentor: Michael Whitfield

Education: University of California Irvine - Biology

My research interests include genomics, biostatistics, rare diseases, and the human microbiome- interests that I have combined in my work with Dr. Michael Whitfield. The Whitfield lab studies Scleroderma, a rare autoimmune disease characterized by fibrosis and heightened immune response in various organ systems of the body. In his lab, I am currently exploring the potential associations of the epithelial microbiome with the host immune response presented in patients with Scleroderma (SSc). This is part of an investigative effort to elucidate the potential environmentally-driven etiology of SSc. As a 2016-2017 Burroughs Wellcome Scholar, I was given the opportunity to explore the possibility of a hybrid PhD, one that includes laboratory science and data science training. These opportunities only became available to me through the encouragement of cross-training in the multidisciplinary space that QBS offers. Outside of school, I can be found socializing with friends or exploring the New England area.

Photo of Yasmin Kamal Yasmin Kamal, BS (MD-PhD)

Mentors: Christopher Amos, PhD and Robert Frost, PhD

Education: Smith College - Biochemistry and Neuroscience

My research interests are cancer immuno-genomics. The Amos lab in genomic medicine was a perfect fit for me given my interests in genomics. Dr. Amos and my co-mentor Dr. Robert Frost have been excellent mentors. Working in the Amos lab, I was able to mesh my biochemistry and medical background to design a project focused on the application of immunotherapy in various types of cancer. Specifically, I am examining the interaction of immune cells in the tumor microenvironment with neoplastic cells using sequencing data and determining the impact of immune cells on driving cancer pathophysiology�specifically identifying unique immune signatures indicative of metastasis. In the Amos lab, I am able to collaborate with clinicians, immunologists, surgeons, and bioinformaticians, and am challenged to use a variety of tools to tackle key questions in cancer immunology.


Jai Woo Lee, BS, MS

Mentor:Jiang Gui, PhD

Education: Carnegie Mellon University - Mathematics and Computer Science, Dartmouth College - MS Computer Science

I am originally from South Korea, and I usually enjoy walking or hiking, and/or listening to any kind of music or political podcasts. Before entering graduate programs at Dartmouth College, I mainly focused on graph theory and its application with/to computational methods in Operations Research in the field of Theoretical Computer Science. My current research interests lie in utilizing and developing statistical and computational methods in Bioinformatics, Biostatistics, or Machine Learning to analyze biomedical data related to various fields of Epidemiology. Thanks to enthusiastic faculty and broad scope of interesting research areas in Quantitative Biomedical Sciences (QBS) program, I have worked on statistical and computational methods to study protein-protein interaction, to learn more about the application of Multifactor Dimensionality Reduction (MDR), and to analyze placental metal concentrations data collected by the New Hampshire Birth Cohort Study.


Photo of Jennifer Luyapan Jennifer Luyapan, BS

Mentors: Christopher Amos, PhD and Michael Passarelli, PhD

Education: University of California Davis - Cell Biology

My research interests include genetic epidemiology and cancer prevention. My research background includes genetics, protein biochemistry, cancer biology and clinical trial research. I am studying the association of genetic variations of folate metabolism genes and colorectal adenoma recurrence to better understand folate metabolism and how it can influence colorectal adenoma development.


Photo of Daniel Mattox Daniel Mattox, BS

Mentor: Christopher Bailey-Kellogg, PhD

Education: University of North Carolina at Chapel Hill - Quantitative Biology

My research is focused around integrating computational and experimental approaches to protein design. More specifically, I am interested designing and applying novel computational tools to aid and supplement experiments. In the Bailey-Kellogg Lab, I am working to better understand glycan-protein interactions and possible roles for lectins in bioengineering. Outside of research, I enjoy exploring the beautiful New England countryside through any number of outdoor sports.

Awards

  • NIH-Dartmouth Big Data to Knowledge (BD2K) Fellow​

Photo of Meghan Muse Meghan Muse, BS

Mentors: Brock Christensen, PhD and Diane Gilbert-Diamond, ScD

Education: Dartmouth College - Biology

I am interested in studying maternal and child health through the lens of bioinformatics and epidemiology. I chose the QBS program at Dartmouth because it provides the unique opportunity to be cross trained in these fields as well as the field of biostatistics. Outside of the lab, I enjoy running, hiking, and taking advantage of all the other outside activities that New Hampshire has to offer.


Photo of Xingyu Zheng Xingyu Zheng, BS

Mentors: Christopher Amos, PhD and Robert Frost, PhD

Education: Fudan University - Biology

My research interests are bioinformatics and biostatistics, especially cancer genomics and statistical genomics. I chose QBS because it's an interdisciplinary program which is so exciting and I enjoy analyzing big data. I'm working in the Amos lab. Dr. Amos and Dr. Robert Frost co-mentor me and give much help and advice to me. Outside of the lab, I like walking around and really love the trees all around here which bring surprises in all seasons.


2016

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

Photo of Jason Wells Jason Wells, BS

Mentor: Todd Miller, PhD

Education: University of California, Davis - Genetics

I have a background in genetics and genomics research. Previous projects that I have worked on mainly focused on muscular dystrophy from a genomics perspective. My current interests include using genomic and bioinformatic approaches to study various aspects of cancer.


Photo of Lia Harrington 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.


Photo of Katherine Antosca Katherine Antosca, BS

Mentor: Todd MacKenzie, PhD and George O'Toole, PhD

Education: University of New Hampshire, Durham - Mathematics

My current research interests center around the function of the microbiome. I am currently evaluating the role of breastfeeding and probiotics in the development of the gut microbiome of children with Cystic Fibrosis. We hope to determine the specific mechanisms associated with better health outcomes of Cystic Fibrosis patients. I am also creating a program to provide insight into the metabolic function of unclassified microbes within the microbiome.


Photo of David Chen David Chen BS, MS

Mentor: Brock Christensen, PhD

Education: Pacific Lutheran University - Biology • University of Michigan-Ann Arbor -MS Biochemistry

My main research interest is integrating epigenetic (DNA methylation) and proteo-genomic data sets for cancer subgroup identification and downstream characterization using machine learning and statistical approaches. My most recent research projects are related to identifying somatic alteration biomarkers in homologous recombination DNA repair-deficient cancers. My ongoing work includes profiling DNA methylation and proteomics in triple negative breast cancer and integrating multiple tumor molecular profiles for predictive analytics. Through the Burroughs-Wellcome Big Data in Life Sciences training program, I also had the opportunity of collecting primary data from patient tumor and cell line biospecimens for subsequent data analytics. In addition to my research, I participate in the teaching/curriculum design of biostatistics, epidemiology, and machine learning courses at both the undergraduate and graduate level at Dartmouth.

Awards

  • Burroughs-Wellcome Big Data in Life Sciences Training Grant, 2016-18
  • Genome Informatics Travel Award, 2017
  • Analytics and Big Data Summit Financial Support, 2018

Photo of Jennifer Franks Jennifer Franks, BS

Mentor: Michael Whitfield, PhD

Education: Purdue University - Genetics, Applied Statistics

My research interests are human genetics, computational immunology, machine learning, and statistical methods for high-dimensional data. My current projects in the Whitfield lab focus on classifying intrinsic molecular subtypes and characterizing the immune repertoire in patients with systemic sclerosis. I really enjoy working with Michael Whitfield because I am able to generate data at the bench and also analyze results using novel computational methods. Through the Big Data in the Life Sciences Training Program funded by Burroughs-Wellcome, I am able to collaborate with Chris Bailey-Kellogg using sequence and structural models to explore cross-reactivity in the adaptive immune system.


Photo of Sara N. Lundgren Sara N. Lundgren, BA

Mentors: Brock Christensen, PhD and Anne Hoen, PhD

Education: University of Chicago - Comparative Human Development

I came to Dartmouth in 2014 to begin interdisciplinary training in epidemiology, bioinformatics, and biostatistics after studying Comparative Human Development at UChicago. As a student in both the Christensen Lab and the Hoen Lab, I will gain experience working on epigenomic and human microbiome projects including the assessment of exposures such as aspects of diet and lifestyle. A particular research interest is to characterize the variation in breast milk and its association with both maternal and infant health using the New Hampshire Birth Cohort Study. I enjoy working with Dr. Christensen and Dr. Hoen because they encourage students to form their own research interests and goals, so I am able to focus on the questions I find the most intriguing!


Photo of Ellen Nutter 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

Photo of Mavra Nasir Mavra Nasir, BS, MS

Mentor: Jane Hill, PhD

Education: McGill Univsersity - Biology • New York University - MS Bioinformatics

In the Hill lab, my current project is focused on developing breath-based diagnostic for cystic fibrosis patients with polymicrobial lung infections.This involves analysis of volatile organic compounds (VOCs) produced by Pseudomonas aeruginosa and Staphylococcus aureus infection in cystic fibrosis patients using GCXGC -TOFMS. Analysis of volatile organic compounds (VOCs) in the breath that can be used to distinguish between antibiotic-sensitive and antibiotic-resistant strains of S. aureus, particularly MRSA and VRSA using GCXGC -TOFMS Development and application of machine learning methods for fingerprinting VOC profiles.


2013

See QBS Alumni


2012

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.


Photo of Qian Yang Qian Yang, BE, MEM

Mentor: Tor Tosteson, PhD

Education: University of Michigan‐Shanghai Jiao Tong University (UM‐SJTU) Joint Institute, Shanghai Jiao Tong University - Electrical and Computer Engineering •Thayer School of Engineering, Dartmouth College- MEM Engineering Management

Now a fourth year QBS PhD candidate, I am a member of the Biomedical Statistical Science Laboratory (BSSL) directed by Dr. Tor Tosteson. My current research focuses on joint modeling of longitudinal medical cost and survival. My research interests also involve decision analytic modeling and comparative effectiveness research. I enjoy the emphasis of novel statistical methodology and their application to real healthcare data and challenges which is the hallmark of our lab.

Photo of James Rudd James Rudd, BS, MS

Mentor: Jennifer Doherty, PhD

Education: North Carolina Central University - Music • North Carolina Central University - MS Computer Science

I received my MS in Computer Science from North Carolina Central University and joined the Quantitative Biomedical Sciences program in order to better integrate my computation background with biostatistical and epidemiological frameworks. My research interests involve the use of bioinformatics to solve epidemiological problems. As a member of the Doherty lab, I am working to model molecular subtypes of ovarian cancer and have been awarded an F31 fellowship from the National Cancer Institute.