Ben Auerbach
Mentors: Mingyao Li, PhD and Garret FitzGerald, MD, FRS

Thesis Title: Applications of Single-Cell Genomics in the Study of Circadian and Vascular Biology
Research and Lab Description: I had the opportunity to work with Mingyao Li, a biostatistician with an interest in single-cell omics, and Garret FitzGerald, a physician pharmacologist with an interest in circadian and vascular biology. Both are intensely curious and passionate about science, and deeply care about training independent scientists. I am incredibly fortunate to have had the opportunity to work with them both. I studied vascular and circadian biology through the lens of single-cell RNA-sequencing. This encompassed both applied projects (studying atherosclerosis and circadian misalignment), as well as a computational method development project (a statistical tool to measure a cell’s circadian time from a snapshot of its mRNA).
Mentor Comment: Ben is highly intelligent but also curious, imaginative, innovative, persistent and independent. These features will combine with focus to provide a strong foundation for his promising scientific career. It has always been a great pleasure to work with Ben. 

Will Bone
Mentors: Benjamin Voight, PhD and Marylyn Ritchie, PhD
Saul Winegrad Award for Outstanding Dissertation

Thesis Title: Dissecting complex disease pleiotropy through multi-trait association studies
Research and Lab Description: My work focused on using multi-trait genetic association methods to better understand the genetic etiology of cardiometabolic diseases. I could not have asked for a better training environment than the Ritchie and Voight labs. Ben and Marylyn were excellent mentors, and my labmates taught me so much during my PhD.
Post PhD Plans: Computational Biologist at Recursion Pharmaceuticals
Mentor Comment: Will is positively a rock-star academician and colleague. He has contributed to GCB in every possible way: from teaching, service on GCB committees, undergraduate mentorship, and productivity in both lead and collaborative scientific scholarship. Will is a thinker and a listener who never shies away from asking good questions in group meetings and seminars and always thinks carefully about other people’s work. While he will be sorely missed, we are both super excited for him as he takes his next career steps.

Yun Hao
Mentors: Li Shen, PhD, FAIMBE and Jason Moore, PhD

Thesis Title: Knowledge-Guided Deep Learning Models of Drug Toxicity Improve Interpretation
Research and Lab Description: My thesis research focuses on developing computational models to improve the interpretability of drug and chemical toxicity prediction. The Moore and Shen labs provided me a remarkable environment to conduct my thesis research.
Post PhD Plans: Genomics Scientist at Simons Foundation
Mentor Comment: Yun’s computational research has pushed the boundaries of explainable AI for understanding the relationship between toxic chemical exposure and risk of disease.

Ben Heil
Mentors: John Holmes, PhD, FACE, FACMI and Casey Greene, PhD

Thesis Title: Neural nets are not all you need: evaluating the effects of deep learning on transcriptomic analysis
Research and Lab Description: My thesis research centered around various applications of machine learning to biology as part of Casey Greene's lab. The things that make Greenelab special are the supportive atmosphere, the emphasis on reproducible research, and the freedom in selecting research topics.
Post PhD Plans: Machine Learning Scientist at Visa Research in Austin
Mentor Comment: Dr. Heil took a rigorous approach to understanding where deep learning does, and doesn’t, contribute to success in building predictors from transcriptomic data. His careful experimental designs revealed the presence of signal that could be captured by non-linear methods, but also that current non-linear modeling strategies did not outperform linear ones, raising important questions for the future of our field.

Ariel Hippen
Mentors: Casey Greene, PhD and John Wherry, PhD

Thesis Title: Using computationally-derived metadata to unlock the tumor microenvironment in high-grade serous ovarian cancer
Research and Lab Description: I used single-cell and bulk transcriptomics methods to profile the tumor microenvironment of high-grade serous ovarian cancer and study the relationship between tumor composition and survival. The Greene lab is full of the most diligent, rigorous and insightful people I’ve ever met; it’s been a privilege to work with them.
Post PhD Plans: Postdoctoral Fellow at Colorado University
Mentor Comment: Dr. Hippen led a project to understand the cellular basis of transcriptomic subtypes of high-grade serous ovarian cancer, through which she rigorously evaluated existing methods and implemented new software for single-cell RNA-seq analysis. She also contributed heavily to work understanding how equitably scientists are recognized.

Derek Kelly
Mentor: Sarah Tishkoff, PhD

Thesis Title: The Molecular Basis of Human Adaptation in sub-Saharan Africa
Research and Lab Description: The Tishkoff Lab studies the genotypic and phenotypic diversity of indigenous human populations in Sub-Saharan Africa. I studied how genetic variation affects gene expression and other traits in Africans, and how evolution has shaped that variation.
Post PhD Plans: Postdoctoral Fellow at the University of Pennsylvania
Mentor Comment: Derek was an exceptional PhD student in a number of ways, showing independence, intellectual curiosity, creativity, drive, and initiative. His focus on studying genomic diversity under-represented populations in human genetics is of particular importance for promoting health equity. In addition to his research skills, Derek was active with teaching, mentoring, scientific outreach, and delighting the lab with his skills on the piano.

David Nicholson
Mentor: Casey Greene, PhD

Thesis Title: Unmasking the Language of Science through Textual Analyses on Biomedical Preprints and Published Papers
Post PhD Plans: Data Scientist at Digital Science
Mentor Comment: Dr. Nicholson led a challenging project at the intersection of computational biology and linguistics to understand how researchers use preprints to describe findings. The software packages and webservers that he developed are helping understand modern scientific discourse and shaping where researchers decide to submit their findings for peer review.

Jingya Qiu
Mentor: Andy Minn, MD, PhD

Thesis Title: Evolution of Inflammatory Memory and Therapy-Resistant States in Cancer Cells
Research and Lab Description: The Minn Lab is an inter-disciplinary group of incredible scientists investigating mechanisms of immunotherapy resistance with diverse hypotheses and approaches. My thesis work used multi-omic sequencing technologies and analysis of human clinical data to observe how cancer cell epigenomes evolve and adapt in response to inflammatory stimuli, and examined how these molecular alterations promotes resistance to cancer immunotherapy.
Post PhD Plans: I'm planning on doing a postdoc to broaden our budding understanding of how cells and tissues form memories of inflammation, and how these memories impact human health and disease.
Mentor Comment: I am immensely proud of Jingya not only for what she has scientifically accomplished but also for how she has done it. She is talented on so many levels and complements this with being a thoughtful, generous, and kind team player. She makes everyone around her better! I and everyone in the lab will miss her and will always be rooting for her happiness and success.

Joseph Aicher
Mentors: Yoseph Barash, PhD and Elizabeth Bhoj, MD, PhD

Thesis Title: Improving molecular diagnosis of suspected Mendelian disorders with RNA splicing analysis
Post PhD Plans: Completing Medical School Requirements
Mentor Comment: Joseph contributed his exceptional math and coding skills to several projects in both the Barash and the Bhoj labs. While his research focused on improving rare disease diagnostics using RNA sequencing, Joseph was able to be extremely productive in other "projects", including an internship at Amazon, house renovation, and two adorable kids! We wish him much success in his future career as a Physician Scientist.

Jason Xu
Mentor: Kai Tan, PhD

Thesis Title: Identification and targeting of treatment resistant progenitor populations in T-cell Acute Lymphoblastic Leukemia
Research and Lab Description: My thesis identified risk-stratifying genetic signatures and novel therapeutic targets in chemotherapy refractory T-cell acute lymphoblastic leukemia, a type of pediatric leukemia. The Kai Tan lab allowed me to integrate high-dimensional genomics approaches with unique patient samples to ask clinically pressing questions; I was also very fortunate to receive mentorship from the David Teachey lab, which was instrumental to bridge our findings one step closer to patient care.
Post PhD Plans: Completing Medical School Requirements
Mentor Comment: It has been a pleasure to mentor Jason! His thesis project has made significant contributions to the field of leukemia biology and inspired future investigations. Jason has also established himself as having high leadership potential, effective scientific communication skills, and critical thinking.