Current Team

Shawn is a research associate in the Xia laboratory. He received his Bachelor’s degree from Cuiying Honors College, Lanzhou University in 2020. Jiangshan has a broad interest in genomics, epigenomics, evolution, and bioinformatics. Previously, Jiangshan worked on the evolutionary history of the plant PINOID gene family at Lanzhou University, as well as G-quadruplexes (G4) distribution across the human genome at the Institute of Biophysics, Chinese Academy of Sciences. In the Xia lab, Jiangshan will mainly work on 3D genome organization by combining methods of experiments and bioinformatics. Outside the lab, Jiangshan enjoys music and Chinese calligraphy.

Social link: X, @baijiangshan1

Favorite bio-molecule: G-quadruplex

Parmida is a Ph.D. student at MIT EECS. Broadly she is interested in developing/deploying machine learning and statistical methods to solve problems in (single-cell) biology. In her master's thesis conducted under Caroline Uhler's advice, she sought to analyze and create an embedding for the 3D genome organization in mouse embryos, using in situ genomic sequencing data. She obtained her bachelor's degree in Mathematics at the University of Michigan (class of 2021).

Favorite bio-molecule: mRNA

Farhan is a PhD student in the Mechanical Engineering/Bioengineering program at MIT. He’s interested in understanding the genotype-phenotype relationship through novel single-cell technologies and machine learning algorithms. He’s working primarily under the supervision of Prof. Elazer Edelman at the Institute of Medical Engineering and Science (IMES) where he uses CRISPR-based perturbation, single-cell RNA-seq readout and language models to extract the underlying pattern of genetic network dynamic in the progression of pathophysiology.

Favorite bio-molecule: chlorophyll

Xinyu Ling is currently a Jane Coffin Childs - Merck Postdoctoral Fellow in the Xia lab. He obtained his Ph.D. from the School of Pharmaceutical Sciences at Peking University, where he specialized in chemical biology and was guided by Professor Tao Liu. During his doctoral studies, Xinyu made significant strides in genetic code expansion technology, particularly in the realm of gene editing. He developed an innovative CRISPR-nucleic acid chemical conjugation platform which significantly enhances gene editing efficiency. Furthermore, he established the RENAPT system for precise in situ protein labeling. Following his Ph.D., Dr. Ling joined Professor Sidi Chen's lab at Yale University, where he established an in situ CRISPR screening approach for immune cells, a pivotal step toward identifying novel drug targets. His current passion involves utilizing chemical biology techniques to develop novel genomic technologies for understanding genome regulation mechanisms, demystifying gene regulation network formation, and devising synthetic gene regulation circuits for gene therapy applications.

Favorite bio-molecule: 4-(2-azidoethoxy)-l-phenylalanine (also termed as AeF)

Qingji Lyu is a Postdoctoral Fellow in the Xia lab. She obtained her Ph.D. degree from China Agricultural University, where she studied X-chromosome dosage compensation in mammalian embryos under the guidance of Prof. Jianhui Tian and Prof. Lei An. Throughout her Ph.D. training, she is passionate about the molecular biology of gene expression and its impact on development and diseases. In the Xia lab, she will focus on developing novel genomic tools to advance our understanding of gene regulation mechanisms.

Favorite bio-molecule: non-coding RNAs

Fifi is currently a concurrent undergraduate and Masters student at the University of Southern California pursuing degrees in Neuroscience and Stem Cells and Regenerative Medicine, respectively. She has previously conducted research to study early aging and drug-aided rejuvenation against aging in the mammalian hippocampus. She continues to be very interested in exploring transcriptomic profiles of diseased/aging biological systems and in silico small-molecule drug screening targeting the profile using machine learning.

Favorite bio-molecule: Brain-Derived Neurotrophic Factor (BDNF)

Jimin Tan is a graduate student studying computational biomedicine at NYU Grossman School of Medicine, co-mentored by Dr. David Fenyo and Dr. Aristotelis Tsirigos. He graduated from Grinnell College in 2018 with a double major in mathematics and computer science. He then studied at NYU Center for Data Science from 2018 to 2020 and received an M.S. degree in data science. He is broadly interested in using machine learning to understand biological systems. In the past, he worked on projects related to computer vision, natural language processing, and genomics. His recent projects include chromatin organization prediction and in silico genetic screening using machine learning models (C.Origami), tissue microenvironment study on high-plex fluorescence imaging using self-supervised learning, and machine learning-aided prognosis using X-ray/MRI imaging with semi-supervised learning. He looks to continue his exploration in genomics in the Xia Lab.

Social link: X, @tan_jimin

Favorite bio-molecule: CCCTC-binding factor (CTCF)

Bailey is currently an undergraduate student at MIT pursuing a degree in bioengineering and chemistry. She is dedicated to researching microbiology, genetics, and immunology. She has previously conducted work in biological research studies at Arizona State University (2020-2022) emphasizing cell permeability and computational simulations. During that time she was awarded as an ISEF finalist (2021) and was designated “Future Innovator of the Year” by the Arizona Governor’s Celebration of Innovation forum (2021). 

Favorite bio-molecule: Epinephrine/Adrenaline 

Bo Xia is Gene Regulation Observatory Fellow and a Principal Investigator at the Broad Institute of MIT and Harvard. He is also a Junior Fellow of the Harvard University Society of Fellows. Xia’s career started as an independent research associate in Dr. Chengqi Yi’s lab at Peking University, leading the development of chemical technologies for analyzing epigenomes. Xia received his Ph.D. degree from NYU School of Medicine in 2022, co-mentored by Drs. Itai Yanai and Jef D. Boeke. During Ph.D., Xia pioneered a few innovative studies on genome regulation and its impact on human development and evolution, including revealing the genetic basis of tail-loss evolution in humans and apes. He is a recipient of multiple prestigious awards, including the 2020 Regeneron Prize for Creative Innovation, the Harold M. Weintraub Graduate Student Award (2022), and the NIH Director's Early Independence Award (2022). 

Social link: X, @BoXia7

Favorite bio-molecule: 5-formylcytosine

Bingham Zheng recently received her Bachelor of Science in computational biology from the University of Pittsburgh. Bingham is primarily interested in using applied machine learning and data science to explore regulatory systems and mechanisms in genomics. She is very excited to be working on what she loves and is eager to keep learning.

Favorite bio-molecule: Pseudouridine