Team

Principal Investigator

Malachi Griffith, PhD

Role: Principle Investigator

Bio: Dr. Griffith is an Assistant Professor of Medicine and Assistant Director of the McDonnell Genome Institute at Washington University School of Medicine. He has more than 13 years of experience in the fields of genomics, bioinformatics, data mining, and cancer research. His research is focused on improving our understanding of cancer biology and the development of personalized medicine strategies for cancer using genomics and informatics technologies. He develops bioinformatics and statistical methods for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction.

Obi L. Griffith, PhD

Role: Principle Investigator

Bio: Dr. Griffith is Assistant Professor of Medicine (Oncology) and Assistant Director of the McDonnell Genome Institute at Washington University. Dr. Griffith’s research is focused on the development of personalized medicine strategies for cancer. He develops bioinformatics tools and methods for the analysis of high throughput sequence data and identification of biomarkers for diagnostic, prognostic and drug response prediction. Dr Griffith is on the board of directors for the Cancer Genomics Committee, Steering Committee for the Global Alliance for Genomic Health, co-chair of the Variant Interpretation for Cancer Consortium, and editorial board for Cell Reports. He has published over 85 studies, received numerous research awards and honors and held several large grants from the NIH including a K22 Transition Career Development Award and U01 for Development of Informatics Technologies for Cancer Research. He has mentored more than 30 bioinformatics trainees and taught hundreds more as an instructor for Cold Spring Harbor Laboratories and the Canadian Bioinformatics Workshops.

Faculty

Kilannin Krysiak, PhD

Role: Instructor in Medicine

Bio: Dr. Krysiak is an Instructor in Medicine in the Division of Oncology. Her work focuses on the analysis and interpretation of genomic and transcriptomic sequence data produced from a variety of cancer types. Her primary interest is in the use of genomic data to improve the current standards of patient care. Since joining the McDonnell Genome Institute in 2014 she has been involved in comprehensive analysis of cancer patient cohorts as well as small and n-of-1 studies. In collaboration with the Genomics Tumor Board, she has led the analysis of case studies in order to better understand the molecular underpinnings of multiple hematologic cancers. Currently, her primary project is leading the analysis of >400 cases of follicular lymphoma in order to identify genomic events which can predict clinical outcomes for patients with this type of cancer. Applying her experience with these analyses and her predoctoral work on the genetics of myelodysplastic syndromes, she has been part of the team of developers and researchers that created and is actively expanding the open-source, community driven Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase.

Postdoctoral Researchers

Alex Wagner, PhD

Role: Postdoctoral Fellow

Bio: Dr. Wagner is an NCI Ruth L. Kirschstein NRSA Postdoctoral Fellow at the McDonnell Genome Institute at Washington University School of Medicine. His research interests are in facilitating the interpretation of genomic variants in a clinical context. He leads development of the Drug Gene Interaction Database, and is a primary contributor to other projects centered on interpretations of genomic variants (Database of Curated Mutations, Clinical Interpretations of Variants in Cancer) and Genomic Visualizations in R. Alex is an active member of the Global Alliance for Genomics and Health (GA4GH), and is leading an effort to aggregate and normalize the disparate knowledgebases of the GA4GH Variant Interpretation for Cancer Consortium. He is also currently studying the role of genomic variants in cancers and leading a study characterizing relapsed Small Cell Lung Cancers with Drs. Obi Griffith, Malachi Griffith, and Ramaswamy Govindan.

Arpad Danos, PhD

Role: Postdoctoral Researcher

Bio: Dr. Danos is a postdoctoral researcher in the Griffith Lab at the McDonnell Genome Institute at Washington University School of Medicine. He received undergraduate degrees in mathematics and physics at the University of Chicago. He performed graduate studies in the fields of Diabetes and Cancer Metabolism and received his PhD from the Committee on Molecular Metabolism and Nutrition and the University of Chicago. He also spent time working in IT as well as teaching science and mathematics, and received the Wayne C. Booth graduate student prize for excellence in teaching while at University of Chicago. His interests include applying and developing mathematical techniques to areas of basic and clinical cancer research, and at the Griffith Lab, his projects include working on the Clinical Interpretations of Variants in Cancer (CIViC) knowledgebase, as well as characterization of novel mutations important for cancer which exist in non-coding space.

Felicia Gomez, PhD

Role: Postdoctoral Researcher

Bio: Dr. Gomez is a postdoctoral researcher in the Griffith and Fehniger Laboratories at the McDonnell Genome Institute and The Department of Medicine – Division of Oncology. Dr. Gomez is leading a deep sequencing analysis of Hodgkin lymphoma genomes with the goal of describing somatic events characteristic of this malignancy. Dr. Gomez collaborates with members of the Griffith and Fehniger laboratories, as well was the Washington University Genomics Tumor Board on projects related to the genomics of Hodgkin and Non-Hodgkin lymphomas. Dr. Gomez’s research goals include developing strategies to translate genomic data into improved patient care. She is specifically interested in working toward the inclusion of diverse human populations in translational genomic research. Dr. Gomez also has a leadership role in the Department of Medicine as the co-chair of the Trainee Inclusion and Cultural Awareness Task Force. In this role she works to identify challenges related to diversity and inclusion that Medicine trainees face and the implementation of solutions to these challenges.

Graduate Students

Yang-Yang Feng, BSc

Role: Medical Student/MD5

Bio: Yang-Yang is a medical student at Washington University in St. Louis, and is currently conducting a year of research in the Griffith Lab. He completed his undergraduate at Yale University in 2016, where he obtained a B.S. in Molecular Biophysics and Biochemistry. Broadly speaking, he is interested in applying mathematical and computational techniques to investigating the fundamental principles of cancer immunology and translating these discoveries into novel immmunotherapies. More specifically, he is involved in a diverse set of projects in the lab, including CIViC, DGIdb, pVACtools, Regtools, and various collaborative clinical efforts.

Kelsy Cotto, BSc

Role: Graduate Student

Bio: Kelsy is a graduate student in the Molecular Cell Biology program at Washington University in St. Louis. She completed her undergraduate degree at Mercer University in 2016, where she earned a B.S. in Biochemistry and Molecular Biology. she is interested in developing methods to analyze multiple types of sequencing data in order to better understand regulatory mutations and splicing within cancer, with the hope of identifying novel biomarkers. Currently, she is involved with DGIdb, Regtools, and analysis of large scale clinical cohorts.

Erica Barnell, BSc

Role: Graduate Student

Bio: Erica graduated from Cornell University in 2013 with a dual degree in Biological Sciences and Applied Economics & Management. In 2013, Erica matriculated into the MD/PhD Program at the Washington University School of Medicine. She has completed her first two years of medical school and is currently in her second year of her PhD with a focus on Molecular Genetics and Genomics. Within the Griffith lab, Erica is focused on developing a CIViC capture panel for direct evaluation of clinically relevant tumors linked to clinical relevances summaries.

Katie Campbell, BSc

Role: Graduate Student

Bio: Katie is a PhD candidate in the Molecular Cell Biology program at Washington University in St. Louis. She graduated from Penn State University in 2014 with honors in Biochemistry. Katie has been awarded positions in the Precision Medicine and Cancer Biology Pathways at Washington University, and is interested in utilizing genomics and informatics approaches to study cancer and tumor immunology in order to understand mechanisms of drug and treatment sensitivity. Her thesis research is focused on characterizing models of and defining therapeutic opportunities in head and neck cancer. Katie has also contributed to other projects in the lab, including CIViC, GenVisR, pVACtools, and DGIdb, as well as analyzing cancer case studies for the Washington University Genomics Tumor Board. Katie’s additional talents include saying the alphabet backwards, standing on her head, and regularly drinking large amounts of coffee.

Ben Ainscough, BSc

Role: Graduate Student

Bio: Ben is a PhD candidate in the Human and Statistical Genetics program at Washington University in St. Louis. His research is focused on computational method development to improve the detection of biologically important somatic variants. Specifically, he is interested in applying machine learning algorithms to improve genomic analysis and enable precision medicine. Additionally, he led the team to create the Database of Curated Mutations, and is a primary contributor to DGIdb and CIViC. Ben graduated from Brigham Young University majoring in Bioinformatics with University Honors. In his free time, Ben enjoys mountain biking, watching BYU sports, and spending time with his wife and daughter.

Cody Ramirez, BSc

Role: Graduate Student

Bio: Cody is a PhD candidate in the Human and Statistical Genetics program at Washington University in St. Louis. He graduated from St. Edward’s University in 2014 with a degree in Bioinformatics. He is interested in utilizing patient genomic profiles to study and predict personalized immunotherapy treatments through bioinformatic analysis and machine learning models. He is currently focused on characterizing the genetic landscape and identifying personalized treatment plans in follicular lymphoma.

Jasreet Hundal, MSc

Role: Graduate Student

Bio: Jasreet is a PhD candidate in the Human and Statistical Genetics program at Washington University in St. Louis. She graduated from Georgia Institute of Technology with a Masters in Bioinformatics in 2009, and thereafter worked as a Staff Scientist/Bioinformatician at the McDonnell Genome Institute for about four years, before deciding to join WashU as a PhD student. She gained a lot of experience in comprehensive analysis of large-scale cancer sequencing projects during her work at MGI. Her current graduate research primarily focuses on developing sequence analysis methods for the design of cancer vaccines and personalized immunotherapy regimens. She has been heavily involved in helping design cancer vaccines for a number of clinical trials at Washington University School of Medicine, and has led the team to develop pVACtools/pVACseq – a cancer immunogenomics pipeline for selection and visualization of neoantigens. She is also interested in applying machine learning methods to better predict patient response during immunotherapy trials.

Staff

Zachary L. Skidmore, MEng

Role: Staff Scientist/Bioinformatician

Bio: Zach is a staff scientist at the McDonnell Genome Institute at Washington University in Saint Louis. His undergraduate work was completed at the Ohio State University where he obtained a B.Sc. in molecular biology. His Graduate work was performed at the University of Illinois where he obtained a M.eng in bioinformatics. His research focus is in the realm of cancer biology where he uses and develops tools and techniques to aid in the analysis and interpretation of cancer sequencing data. He leads maintenance/development on the bioconductor package GenVisR, a graphics program designed to visualize cohort level genomic data. He is the creator and a primary instructor for the Genomic Data Visualization and Interpretation workshop course and is the webmaster for many of the griffith lab websites. Currently his primary research project is the genomic evaluation of non-cirrhotic hepatocellular carcinoma.

Susanna Kiwala, MEng

Role: Programmer Analyst

Bio: Susanna is a Programmer Analyst at the McDonnell Genome Institute at Washington University in St. Louis. She obtained her M.eng in Computer Science from Southern Illinois University in Edwardsville. She is the lead software developer for the Clinical Interpretations of Variants in Cancer project, the Drug Gene Interaction Database, and pVACtools.

Jason Kunisaki, BSc

Role: Data Analyst/Bioinformatician

Bio: Jason is post-baccalaureate premedical student who recently graduated from Washington University in St. Louis with a degree in Genomics and Computational Biology. As an aspiring physician scientist, his research interests lie in the development and application of computational tools to effectively analyze large sequencing datasets. Through this, he is able to identify and characterize novel genomic events as diagnostic and prognostic biomarkers in cancer, which can support improved personalized strategies against the disease. Over the years, he has contributed to several development projects including DoCM, GenVisR, and Regtools. He has also been heavily involved a number of cohort-level investigations spanning several cancer types such as hepatocellular carcinoma (cirrhotic, noncirrhotic, fibrolamellar, and mixed fibrolamellar), adult T-cell leukemia, and osteosarcoma.

Lee Trani, BSc

Role: Research Technician

Bio: Lee is a research technician at the McDonnell Genome Institute at Washington University in Saint Louis. His primary focus is data quality analysis and manual review of variants for cancer investigations. He is also involved with developing scripts to automate pipelines and procedures for the quality control production group.

Jason Walker, BSc, BA, MEng (summer 2018)

Role: Biomedical Informatics Project Manager

Bio: Jason Walker is a Biomedical Informatics Project Manager at the McDonnell Genome Institute. He works with the Griffith Lab to translate grant objectives and analysis goals into well defined development milestones for software engineers to iterate on projects, achieving consistent progress while maintaining best practices in software development methodologies. His responsibilities include overseeing the integration and adaptation of numerous bioinformatics tools for cancer genomics automated analysis of high-throughput DNA and RNA sequence data. In addition to large-scale research projects, he works with a CLIA licensed laboratory on clinical-grade, CAP-accredited analysis workflows for reporting somatic variants in cancer patient genomes.

Lynzey Kujan

Role: Lab Assistant/Staff Curator

Bio: Lynzey Kujan is a Staff Curator at the McDonnell Genome Institute at Washington University in Saint Louis. She obtained her BS in Biomedical and Mechanical Engineering from Saint Louis University. She is the lead curator for the Clinical Interpretations of Variants in Cancer project (CIViC). She has also contributed to the CyclinE project as well.

Joshua McMichael

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Adam Coffman

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Students

Nick Spies, BSc

Role: Medical Student/MA

Bio: Nick is an MD candidate at Washington University School of Medicine. He graduated from WUSTL in 2014 with a degree in genomics and computational biology. Since 2013, Nick has been working in the lab on projects that hope to bridge the gap between research and medicine. These include DGIdb, CIViC, and multiple cancer sequencing projects. He is focused on expanding the applications of clinical sequencing, and hopes to continue this work throughout his career.

Kaitlin Clark

Role: Undergraduate Student

Bio: Kaitlin Clark is an second year undergraduate at Washington University in St. Louis pursuing a Bachelor of Science degree in Computational Biology and Genomics. She joined the Griffith Lab as a curator for the Clinical Interpretation of Variants in Cancer (CIViC) project last year. Her ongoing interests concern the enablement of precision medicine through the identification of clinically relevant variants that aid in better prognosis and diagnosis of cancer syndromes and the development of web resources to aid in the interpretation and discovery of such clinically relevant variants. Currently Kaitlin curates information relating to von-Hippel Lindau disease (VHLD), a neoplastic syndrome resulting from the inactivation of the VHL tumor suppressor gene. Her project aides to the overall goal of the CIViC project by developing a comprehensive web source of VHL variants. In the future Kaitlin hopes to pursue an MD/PhD in integrative genomics.

Alumni

Robert Lesurf, PhD

Role: Postdoctoral Researcher

Bio: Dr Lesurf was a Postdoc with Obi Griffith and Elaine Mardis at the McDonnell Genome Institute of Washington University where he led several investigations into the genomic architecture of cancer. In one project, he focused on studying genomic features associated with response to trastuzumab in HER2-positive breast cancer. In a series of other projects, he worked to identify highly validated regulatory sites within the human genome to update the ORegAnno database and design a novel regulome capture reagent. He initiated ongoing studies with this reagent in conjunction with targeted sequencing of TCGA breast cancer samples to identify recurrent alterations in the regulatory regions of the disease. Robert is now a Data Scientist at the Ontario Institute of Cancer Research.

Connor Liu, BSc

Role: Medical Student/MA

Bio: Connor completed his first two years of medical school at Washington University in St. Louis and is currently pursuing a year of research as a Howard Hughes medical fellow. He graduated from Washington University in 2013 where he obtained a B.A. in Biology and Biochemistry. As a medical student, his scientific and clinical interests in oncology led him to join the Griffith lab in 2016 where he has contributed to a number of projects including CIVIC and pVACtools. His current focus is on using bioinformatic strategies to develop personalized treatments for glioblastoma.

Avinash Ramu, MSc

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Past Members

Lei Chen
Shou Han
Shaopeng Liu
Rachel Bilski
Greg Spies
Ju Heon Maeng
Alex Wollam