X. Shirley Liu received a PhD in Biomedical Informatics and a PhD minor in Computer Science from Stanford University in 2002. She is a Professor with the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and Harvard School of Public Health. Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.
Cliff Meyer received his PhD in Chemical Engineering from Princeton University in 2003. He is a computational biologist, with expertise in algorithm development, genomic data integration, cancer gene regulation, epigenetics and nuclear receptor biology. His work includes methodological research projects, collaborative research with experimental biologists, and the broad dissemination of research findings through review articles and software. He has contributed to the development of several widely used algorithms for ChIP-chip, ChIP-seq, MNase-seq, DNase-seq, DNA methylation and CRISPR screen data analysis. Through integrating genome-wide transcription factor binding, chromatin dynamics, and gene expression profiles, he has studied the specificity and function of transcription factors, and chromatin regulators, and has experience in large-scale genomic data integration.
Chen-Hao Chen received PhD in Biological and Biomedical Science from Harvard University in 2017. Chen-Hao is a computational biologist with expertise on integrating high dimensional omics data to decipher cancer mechanisms and genome-wide CRISPR-Cas9 knockout screens. He is now developing mathematical framework to model gene regulations.
Aashna received her masters in Computer and Information Sciences at the New York University. She is currently working on developing the Bioinformatics Pipelines for CIDC project with other members of the lab.
David Cohen received his M.S. in Bioinformatics from Northeastern University in late 2017. He is currently working on genomic research with other members of the lab. He has a bioinformatics and data analytics background and is interested in applying cutting edge technology in order to help understand and fight disease.
Len Taing received BA and MS in Computer Science from Harvard and MA in Psychological and Brain Sciences from Johns Hopkins. He has been working with the Liu Lab and the Center for Functional Cancer Epigenetics for the last decade, and instrumental to the development of many computational algorithms, pipelines, and databases.
Jin Zhao is originally from Xinjiang, China. She graduated from medical school and worked as a radiation oncologist in China before deciding to move to the United States in 2001. Jin joined the Brown lab in 2005, and working as joint lab manager for Brown and Liu lab in 2015. In her spare time she enjoys crocheting and playing with her dog, Buttons Jr.
Nicole Traugh received her B.S. in Biology from Saint Michael's College in Colchester, Vermont. She joined the lab as a research technician in 2016, and is interested in cancer immunology, genetics and infectious disease. Her current work involves set up for the in vivo CRISPR screen platform, performing CRISPR screens in vivo and in vitro, as well as working on the interactions between cancer cells and the immune system. She is currently applying to Ph.D. programs in the Boston area, and enjoys reading and cooking spicy food in her spare time.
Dr. Peng Jiang is a postdoc fellow at Xiaole Liu Lab at the Dana Farber Cancer Institute and Harvard T.H. Chan School of Public Health. His research focused on developing computational models to identify biomarkers and regulators of anticancer drug resistance, with an application focus on cancer immunotherapies. Peng has many first and co-first authored papers in high profile journals, such as Nature Medicine, Science, and PNAS. He is a recipient of the Pathway to Independence Award (K99/R00) of National Cancer Institute. Peng finished his Ph.D. at the department of computer science and Lewis Sigler genomics institute at Princeton University, and his undergraduate study with the highest honor at the department of computer science at Tsinghua University.
Avinash Sahu received PhD in Computer Science (Computation Biology) from University of Maryland in 2016. He is now a Research fellow at Dana-Farber Cancer Institute and Mass General Hospital, with expertise in a niche that lies in an intersection of deep learning/big data and immuno-oncology. He develops machine learning algorithm to analyze high throughput genomic data to model patient response to cancer drugs.
Li Song received Ph.D. in Computer Science from Johns Hopkins University in 2018. His research area is on computational biology. He has designed and implemented algorithms to analyze next-generation sequencing data, mostly RNA-seq data, for various applications, such as transcriptome assembly, error correction, scaffolding, and metagenomics.
Collin Tokheim received his PhD in Biomedical Engineering from Johns Hopkins University in 2018. During his PhD, his research focused on the development and application of novel computational methodologies to statistically implicate mutations underlying the development or progression of human cancers. He has expertise in machine learning, statistical modeling, genomics, and cancer genetics. Collin is now a Research Fellow at the Dana-Farber Cancer Institute. His current research focus is on further dissecting the process of carcinogenesis, examining the response or resistance of tumors to targeted therapeutics, and analyzing cancer immunology.
Chenfei Wang received PhD in Bioinformatics from Tongji University. He is now a Postdoctoral Fellow of Biostatistics and Computational Biology at Harvard University and Dana-Farber Cancer Institute. During his PhD period he studied the epigenetic reprogramming of mammalian early embryos and somatic nuclear transferred (SCNT) embryos utilizing high throughput genomic data. Now he is interested in investigating the mechanism of cancer and immune interactions based on single-cell RNA-seq and epigenomic-seq, and focus on utilizing machine learning algorithms to decipher the regulation of immune diversity and cancer progression.
Zexian Zeng received his master degrees in Computer Science and Industrial and Systems Engineering from University of Wisconsin-Madison. He received his Ph.D. in Biomedical Informatics from Northwestern University. He is now a post-doctoral research fellow in Dr. Shirley Liu’s laboratory at Dana-Farber Cancer Institute. His research interests include machine learning, stochastic modeling, computational genomics, with a focus on developing algorithms to study high-throughput sequencing data.
Shengqing Gu received Ph.D. in Medical Biophysics at University of Toronto, where he performed research across two areas under the supervision of Dr. Benjamin Neel: (1) protein tyrosine phosphatase signaling in hematopoiesis, and (2) computational modeling of ovarian cancer clinical course. Stan is currently a postdoctoral fellow co-supervised by Drs. Shirley Liu and Myles Brown. His research combines computational and experimental approaches to interrogate the interaction between cancer cells and the immune system, including (1) identifying new biomarkers for cancer immunotherapy response; (2) elucidating the epigenetic regulation of key components in cancer-T cell interaction; (3) characterizing the immune repertoire in cancer patients and healthy donors.
Qin joined the group in 2017 under co-mentorship of Dr. Myles Brown and Dr. Shirley Liu to study the intricacies of glucocorticoid signaling its impact on the tumor-immune microenvironment, as well as to utilize CRISPR-mediated gene editing to uncover genetic vulnerabilities in glucocorticoid-refractory pediatric leukemia. In her previous academic career as an (almost) cancer researcher, she trained with David Langenau at Massachusetts General Hospital to develop immune compromised zebrafish models that allow human and mouse cell transplantation. Qin received her Ph.D. in Human Biology and Translational Medicine from Harvard University in 2017, and B.S. in Biological Sciences from Nanjing University in 2012.
Xiaoqing Wang is a postdoc who received his B.Sc. and M.D. in cardiology from Dalian Medical University in China. His current research is focused on identifying new target protein which can affect proliferation and metastasis of breast cancer by using in vivo genome-wide screening. In his free time, Xiaoqing enjoys auto shows and stamp collecting.
Jingxin Fu received a bachelor degree in Biotechnology from the Ocean University of China in 2016. She is now a Ph.D. student of bioinformatics at X. Shirley Liu lab in Tongji University, Shanghai, China. Jingxin is a computational biologist with experiences on data integration, visualization, and Web development. Her current research focuses on biomarkers development and evaluation for immunotherapy response. She is also interested in developing microsatellite instability estimation method from the expression profile.
The overarching goal of Xin Huang's research is to understand the rule of epigenetic regulation at single-cell resolution. Currently, she is developing an imputation algorithm to enhance the resolution of single-cell ATAC-seq profiles by integrating epigenetic big-data resource in public domains. Xin Huang is a Ph.D. candidate of the Beijing Institute of Radiation Medicine with an undergraduate background from electrical engineering.
Jin Wang is a PhD candidate in Bioinformatics from Tongji University, Shanghai, China. Jin is interested in cancer immunology, especially exploring cancer-specific immune characteristics from immune repertoire. Currently, Jin is focused on analyzing BCR repertoire in early lung cancer to identify the relationships between immunoglobulin and cytokines, which helps understand the interaction role of immunoglobulin and cytokines.She is also studying tumor-specific CDR3 motifs which can potentially contribute to early lung cancer prognosis.
Zhangyi Ouyang is a Ph.D candidate from Beijing Institute of Radiation Medicine. She received a bachelor degree in Mathematics and Applied Mathematics from Xi'an Jiaotong University in 2015. Her research focuses on the identification of A-to-I editing using RNA-seq data, allele-specific RNA-seq expression profiling in mouse early embryos. She is interested in post-transcriptional modifications of RNA.
Xiaoman Wang is a Ph.D. candidate from Peking Union Medical College & Chinese Academy of Medical Science, Beijing, China. Her current research focuses on integrating drug perturbation data and clinical cohort data to systematically evaluate potential compounds that boost immunotherapy blockade(ICB) responses. She also helps in developing a deep learning algorithm (DeepImmune) to identify a compressed representation of immunological factors that predict ICB response.
Jijun Yu received a bachelor degree in Electronic Science and Technology from Xi'an Jiaotong University of China in 2015. He is a Ph.D. candidate in Bioinformatics from Beijing Institute of Toxicology and is interested in Cancer Multi-omics Data Analysis, especially studying cancer-specific consensus subtype and Machine Learning algorithm in Bioinformatics. Currently, Jijun focuses on transcription factors imputation with Deep Learning algorithm.
Zhe Zhang received a masters degree in Obstetrics and Gynecology from the Chinese PLA general hospital in 2017. He is now an M.D. & Ph.D. student at X. Shirley Liu lab. His main clinical interests include the surgical and medical treatment of women with all types of gynecologic malignancies. His current research focuses on integrating high dimensional omics data to decipher cancer mechanisms and investigating cancer immunotherapy.
Alumni with at least a 6 month stay
- Jingyu Amy Peng, PhD. (2016-2019), Scientist at Bluebird Bio, Cambridge, MA
- Xihao (Sherlock) Hu, PhD. (2016-2019), Chief Scientist at GV20 Therapeutics LLC, Boston, MA
- Wei Li, Ph.D. (2012-2018), Assistant Professor at Children’s National Medical Center, Washington, D.C.
- Bo Li, Ph.D. (2014-2017), Assistant Professor at UT Southwestern.
- Tengfei Xiao, Ph.D. (2013-2017), Chief Technology Officer at XBH Biotechnology
- Eduardo G. Gusmao, Ph.D. (2016-2017), Research Fellow, University of Cologne, Dr. Argyris Papantonis Lab, Cologne, Germany
- Teng Fei, Ph.D. (2011-2017), Principal Investigator, College of Life and Health Sciences, Northeastern University of China
- Chongzhi Zang (2010-2016), Assistant Professor, Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia.
- Johannes Koster (2015-2016) Group Leader, Institute of Human Genetics, University of Duisburg-Essen in Germany.
- Graham McVicker (2013-2015) Assistant Professor, Salk Institute, La Jolla, California
- Han Xu (2010-2015) Assistant Professor, UT MD Anderson Cancer Center
- Yiwen Chen (2009-2014) Assistant Professor, UT MD Anderson Cancer Center
- H. Hansen He (2008-2013) Assistant Professor, at the University of Toronto
- Tao Liu (2007-2012) Assistant Professor, Department of Biochemistry, SUNY at Buffalo
- Zhenhua Jeremy Wu (2008-2012) Bioinformatics Scientist, H3 Biomedicine
- Shunmin He (2010-2011) Associate Professor, Key Laboratory of Zoological Systematics and Evolution, Chinese Academy of Sciences
- Hyunjin Gene Shin (2007-2011) Scientist, Millennium Pharmaceuticals: The Takeda Oncology Company, Cambridge, MA
- Utz Pape (2009-2010) Statistician, Department of Public Health, Imperial College, United Kingdom
- Xiangfeng Wang (2008-2010) Professor at the Department of Plant Genetics at Chinese Agricultural University
- Yong Zhang (2006-2009) Professor, Department of Bioinformatics, Tongji University, China
- Jun Song (2005-2007) Professor, Institute for Genomic Biology, University of Illinois at Urbana-Champaign
- Wei Li (2004-2007) Professor, Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor School of Medicine
- Evan Johnson, PhD (2004-2007) Associate Professor, Department of Medicine, Boston University
- Kaveh Maghsoudi, MD / PhD (2005-2008) Radiologist at Coastal Radiation Oncology, California
- Ying Lei (2008-2009) PhD candidate, Dept of Bioengineering, Stanford University
- Arjun Kumar Manrai (2006-2008) PhD candidate, Health Sciences and Technology Program, Harvard-MIT
- Rongbin Zheng (2018-2019), PhD Candidate, Tongji University, Shanghai, China.
- Jian Zhang (2016-2018), PhD Candidate, Chinese Institute of Basic Biological Sciences, China
- BinBin Wang (2017-2018), PhD Candidate, Tongji University, Shanghai, China.
- Ziyi Li (2017-2018), PhD Candidate, Tongji University, Shanghai, China.
- Yingbo Cui (2016-2017), PhD candidate, National University of Defense Technology, Changsha, China
- Taiwen Li (2014-2017), Assistant Professor, State Key Laboratory, Sichuan University
- Jingyu Fan (2015-2017), PhD Candidate, Tongji University
- Xiaofang Xing (2016-2017), Associate Professor, M.D. Peking University Cancer Hospital
- Feizhen Wu (2015-2017) Assistant Professor, Fudan University, Institutes of Biomedical Sciences
- Xue Zou (2016-2017) PhD Candidate, Duke University
- Qi Liao (2015-2016) Assistant Professor, Ningbo University
- Ruoxu Dou(2015-2016) Surgeon, Sun Yat-sen University
- Qiu Wu (2014-2015) PhD Candidate, Tongji University
- Jiaxin Wu (2014-2015) PhD Candidate, Tsinghua University
- Shihua Zhang (2014-2015), Associate Professor, Academy of Mathematics and Systems Science, Chinese Academy of Science, Beijing, China
- Shenglin Mei (2013-2014) PhD Candidate, Tongji University
- Haiyun Wang (2012-2014), Associate Professor, Bioinformatics, Tongji University, Shanghai, China
- Xiaoqi Zheng (2012-2014), Associate Professor Department of Mathematics, Shanghai Normal University, Shanghai, China
- Qian Alvin Qin (2014) PhD Candidate, Tongji University
- Yin Liu (2012-2014) PhD, Shanghai Pulmonary Hospital
- Chenfei Wang (2013-2014) PhD Candidate, Tongji University
- Qinghua Jiang, PhD (2012) Associate Professor, Bioinformatics, Harbin Institute of Technology, Harbin, China.
- Hanfei Sun (2012) Graduate Student, Carnegie Mellon University
- Su Wang (2012-2013) Postdoc, Harvard Medical School
- Sheng’en Hu (2012-2013) PhD Candidate, Tongji University
- Zhou Du (2011) Postdoc, Harvard Medical School and Boston Children’s Hospital
- Bo Qin (2011-2012) MS Tongji University; Huarong Investment
- Jian Ma (2010-2011) PhD Candidate, Tongji University
- Qingyi Cao (2008-2009) Assistant Professor, Zhejiang University
- Zhihua Liu (2007-2008) Associate Professor, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, China