2025 VAI Epigenomics Workshop

Sandipan Brahma, Ph.D., is an assistant professor in the Department of Genetics, Cell Biology & Anatomy at the University of Nebraska Medical Center and a member of the Fred & Pamela Buffett Cancer Center in Omaha, NE. His research focuses on understanding how chromatin structure and nucleosome dynamics regulate gene expression during normal development and in cancer, with particular emphasis on ATP-dependent nucleosome remodeling. To address these questions, the Brahma Lab employs advanced structural epigenomics techniques integrated with bioinformatics and biochemical approaches. Established in 2023, the lab is currently supported by an NIH R00 award. Sandipan received his training under Dr. Blaine Bartholomew at Southern Illinois University and the University of Texas MD Anderson Cancer Center, and later with Dr. Steve Henikoff at Fred Hutch Cancer Center, where he specialized in biochemical and genomic studies of chromatin remodeling mechanisms. In addition to his research, Sandipan is committed to mentoring the next generation of scientists in both experimental biology and computational analysis. He also develops interactive learning modules focused on genome-wide chromatin profiling and bioinformatics tools.

Dr. Brad Dickson received his Ph.D. in chemistry from Clemson University, where he studied enhanced sampling algorithms for molecular dynamics simulations. After studying path sampling techniques at UT Austin, in 2009 Brad began working with adaptive bias methods as a postdoctoral researcher at École Normale Supérieure de Lyon. Brad has deployed these adaptive schemes to probe kinase dynamics while at Purdue University, and to inform drug discovery efforts against epigenetic targets while working in the Center for Integrative Chemical Biology and Drug Discovery at University of North Carolina Chapel Hill. In 2015, Dr. Dickson joined the Rothbart Laboratory at Van Andel Institute (VAI), where he used computational biophysics to inform on the complex mechanics underlying chromatin accessibility, interaction and function. He is now a staff scientist at VAI.

Dr. Kristin Gallik earned her B.S. in biological sciences at Wayne State University in 2014. Dr. Gallik then completed her Ph.D. at the University of Illinois at Chicago in the Molecular, Cell, and Developmental Biology/Neuroscience Program. Her research implemented a wide range of imaging techniques from live confocal microscopy to high-pressure freeze/freeze substitution serial transmission electron microscopy. In learning the art of microscopy, Dr. Gallik also discovered her passion for image analysis. Now that she is a part of the Optical Imaging Core at VAI, she spends her time learning new analysis approaches and teaching fellow VAI scientists different methods of quantitative image analysis. She enjoys solving the challenges each data set brings.

Dr. Josh Jang has a Ph.D. in molecular genetics and genomics from Washington University in St. Louis and a B.S. in health promotion and disease prevention from University of Southern California. His graduate work focused on characterizing transposable elements’ contribution to oncogenic potential in cancer cell line models, as well as other projects that established and optimized targeted epigenetic technologies using CRISPR-Cas9 technology. In 2020, Dr. Jang joined Van Andel Institute as a VAI Fellow under Drs. Peter A. Jones and Stephen B. Baylin.

Dr. Derek Janssens explores the factors that give rise to blood cancers with the goal of informing improved diagnosis and treatment strategies. His research has contributed to powerful new methods that enable scientists to better study the complex factors that drive cancer development.

Shixin Liu obtained his Ph.D. in chemistry at Harvard University, conducted postdoctoral research at University of California, Berkeley, and has been on the faculty of The Rockefeller University since 2016, where he is now associate professor and head of the Laboratory of Nanoscale Biophysics & Biochemistry. Dr. Liu’s group mainly leverages single-molecule biophysical techniques to visualize the real-time dynamics of DNA- and chromatin-based processes such as replication and transcription. His research program continues to push the boundaries of biochemical complexity and quantitative dimension in their experimental systems, shedding new light on the molecular mechanisms underlying genetic and epigenetic inheritance. Dr. Liu has received several early-career awards including an NIH Director’s New Innovator award and a Vilcek Prize for Creative Promise.

Dr. Tim Triche, Jr., earned his A.B. in chemistry from Cornell University, followed by an M.S. in biostatistics and a Ph.D. in statistical genetics from University of Southern California. Prior to joining Van Andel Institute’s Department of Epigenetics in 2017, he served as a postdoctoral fellow in the Jane Anne Nohl Division of Hematology at USC’s Norris Comprehensive Cancer Center, where he studied the roles of cellular and immune senescence in benign and malignant blood disorders, including acute myeloid leukemia and pediatric leukemia. He has been a key member of The Cancer Genome Atlas Research Network since 2011, and has contributed to more than a dozen of the consortium’s publications in journals such as Nature and Cell. As a statistician with interests in both basic and translational research, Dr. Triche’s work focuses on improving patient outcomes and quality of life through the design of randomized clinical trials, which are critical components of moving promising therapies from the lab to the doctor’s office.

Dr. Weifang Wu is a postdoctoral research fellow at the Fred Hutchinson Cancer Center in Dr. Steven Henikoff’s lab. She earned her Ph.D. in Dr. Robin Allshire’s lab at the University of Edinburgh, where she discovered that nuclear spatial organization as an epigenetic factor defining centromere identity. Her current research focuses on gene expression regulation through transcription and RNA splicing. Dr. Wu developed KAS-CUT&Tag, a method for mapping protein binding to single-stranded DNA regions, including transcription bubbles. This technique reveals that RNA polymerase II backtracking serves as a dynamic transcriptional checkpoint during initiation, ensuring accurate and efficient transcription through chromatin. She also discovered a chromatin-guide splicing mechanism, where the splicing factor U2AF2 directly binds to chromatin, ensuring accurate exon inclusion during transcription. By combining advanced epigenomic profiling tools with computational analysis, Dr. Wu’s research provides a deeper understanding of how cells maintain gene expression fidelity.

Ye Zheng is a tenure-track assistant professor in the Bioinformatics and Computational Biology Department of the University of Texas MD Anderson Cancer Center and an NIH/NHGRI K99/R00 fellow. Dr. Zheng received her postdoctoral training at the Fred Hutchinson Cancer Center from both molecular biology and quantitative modeling perspectives mentored by Dr. Steven Henikoff. Before her postdoctoral training, Dr. Zheng received a Ph.D. in statistics from the University of Wisconsin–Madison under the supervision of Dr. Sündüz Keleş. At MD Anderson Cancer Center, Dr. Zheng leads a hybrid research group. Her quantitative research group is dedicated to the statistical modeling and computational pipeline development using bulk and single-cell transcriptomics, proteomics, epigenomics, and 3D genomics data to address biological and clinical challenges. Her wet lab specializes in the epigenomic profiling of the Formalin-Fixed, Paraffin-Embedded (FFPE) samples.

Dr. Derek Janssens explores the factors that give rise to blood cancers with the goal of informing improved diagnosis and treatment strategies. His research has contributed to powerful new methods that enable scientists to better study the complex factors that drive cancer development.

Dr. Huilin Li uses cryo-electron microscopy (cryo-EM) to reveal the most basic building blocks of DNA replication and other systems vital for life. He has been at the vanguard of cryo-EM for more than 20 years, and his research has implications for some of the world’s most critical public health concerns, including tuberculosis, cancer, mental illness and many more.

Dr. J. Andrew Pospisilik seeks to understand how we become whom we become, and how our disease susceptibility is defined from early on in life, even before conception, with the long-term goal of being able to predict lifelong health outlook at birth.

Dr. Xiaobing Shi investigates the mechanisms that regulate DNA and gene expression to better understand how they impact cancer development. His research has led to the discovery of several new “readers” of epigenetic marks that may serve as targets for cancer treatment.

Dr. Evan Worden leverages VAI’s powerful suite of cryo-electron microscopes to explore the complex molecular interactions that give rise to cancer. To date, his research has revealed novel insights into poorly understood regulatory elements in the genetic code and illuminated how aberrations in these processes can transform healthy cells into malignant ones.