columbia systems biology phd

Skip to content

Chaolin Zhang, PhD

• Associate Professor of Systems Biology and Biochemistry and Molecular Biophysics (in the Motor Neuron Center)

Profile Navigation

Dr. Chaolin Zhang is an Associate Professor in the Department of Systems Biology, Department of Biochemistry and Molecular Biophysics, and Motor Neuron Center at Columbia University.

Academic Appointments

Dr. Chaolin Zhang's lab takes a multidisciplinary approach to studying mechanisms and functions of post-transcriptional gene regulation, in particular alternative splicing in both normal and disease contexts. On the mechanistic side, the Zhang lab focuses on fundamental understanding of the targeting specificity of RNA-binding proteins (RBPs), how they regulate alternative splicing in various cellular contexts, especially in the nervous system, and how such regulation can be disrupted by mutations and genetic variations. On the functional side, the lab aims to uncover the roles of RBPs in determining the neuronal cell fate, morphological and functional properties during neural differentiation and maturation. More recently, the lab has also been working on translating fundamental knowledge on RNA regulation to precision genetic medicine, with a particular focus on multiple devastating monogenic diseases affecting the central nervous system.

Dr. Zhang and his lab have pioneered RNA Systems Biology approaches to investigating splicing-regulatory networks. Dr. Zhang’s work has led to breakthroughs in mapping protein-RNA interactions at single-nucleotide resolution on a genome-wide scale (e.g., Zhang & Darnell, Nat Biotech, 2011; Weyn-Vanhentenryck, Cell Rep. 2014). Building on this unprecedented resolution, his lab has developed innovative statistical models to better define the binding specificity of RBPs, which led to discoveries of novel binding modes of old RBPs under decades of investigations, with implications in development and cancer (e.g., Ustianenko, Mol Cell, 2018 (cover story); Feng, Mol Cell, 2019). Dr. Zhang also developed an integrative modeling strategy to define splicing-regulatory networks by combining multiple modalities of genomic data and evolutionary signatures (Zhang, Science 2010). The lab has leveraged these networks to elucidate RBPs driving molecular diversity underlying neurodevelopment (e.g., Weyn-Vanhentenryck, Nat Commun, 2018; Jacko, Neuron, 2018) and neuronal cell type diversity (Feng, PNAS, 2021).

To approach the research goals, Dr. Zhang and his lab regularly use a variety of experimental and computational approaches and techniques, including CRISPR-based genome engineering, high-throughput screening, deep sequencing, probabilistic modeling and machine learning (e.g., Bayesian networks and deep learning). The lab uses both cell-based (e.g., mouse ESCs and human iPSCs and directed neuronal differentiation) and mouse models. Work in his lab has been funded by multiple Institutes at NIH, Simons Foundation, and Columbia Precision Medicine Initiative.

Research Interests

• Computational and Systems Biology
• RNA-based Medicine
• RNA Biology

Selected Publications

Feng, H., Zhang, X., Zhang, C., 2015. mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA sequencing data. Nat Comm. 6:7816. doi: 10.1038/ncomms8816.

Yan, Q., Weyn-Vanhentenryck, S.M.,Wu, J., Sloan, S.A., Zhang, Y., Chen, K., Wu, J.-Q., Barres, B.A., Zhang, C., 2015. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc. Nat. Acad. Sci. USA. Mar 3. pii: 201502849.

Weyn-Vanhentenryck, S.M., Mele,A., Yan,Q., Sun,S., Farny,N., Zhang,Z., Xue,C., Herre,M., Silver,P.A., Zhang, M.Q., Krainer,A.R., Darnell,R.B. , Zhang,C. 2014. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 10.1016/j.celrep.2014.02.005.

Moore, M., Zhang, C., Gantman, E.C., Mele, A., Darnell, J.C., Darnell, R.B. 2014. Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protocols, 9:263-293.

Zhang, C., Lee, K.-Y., Swanson, M.S., Darnell, R.B. 2013. Prediction of clustered RNA-binding protein motif sites in the mammalian genome. Nucleic Acids Res. 41:6793-6807.

Wu,J., Anczukow, O., Krainer, A.R., Zhang,M.Q. , Zhang,C. , 2013. OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res. 41:5149-5163.

Darnell, J.C., Van Driesche, S.J., Zhang,C., Hung, K.Y.S., Mele, A., Fraser, C.E., Stone, E.F., Chen, C., Fak, J.J., Chi, S.W., Licatalosi, D.D., Richter, J.D., Darnell, R.B., 2011. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell, 146:247-261.

Zhang,C., Darnell, R.B. 2011. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat. Biotech. 29:607-614.

Zhang,C., Frias, M.A., Mele, A., Ruggiu, M., Eom, T., Marney, C.B., Wang, H., Licatalosi, D.D., Fak, J.J., Darnell, R.B. 2010. Integrative modeling defines the Nova splicing-regulatory network and its combinatorial controls. Science. 329: 439-443.

Zhang,C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A.R. and Zhang, M.Q. 2008. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev. 22:2550-2563.

Wu Lab @ Columbia

Decoding and targeting the central dogma.

We study the fundamental principles of how genetic information is coded and decoded in health and disease and how to target these processes in cancer, heart disease, aging, and neurodegeneration. To achieve these goals, we utilize cutting edge technologies, including CRISPR, genomics, and machine learning.

Decoding the central dogma

How do cells accurately synthesize a complex proteome from a genome with 98% noncoding DNA?

CRISPR technology & therapy

We use CRISPR to control RNAs and proteins for therapeutic applications.

Computational biology

We are currently developing interpretable deep learning models for alternative splicing and CRISPR targeting.

1 ) A web server called kpLogo for position-specific short motif analysis. See Wu & Bartel 2017 Nucleic Acids Research 2 ) Network-based global prediction of human disease genes. See Wu et al. 2008 Molecular Systems Biology 3 ) Network alignment-based identification of disease families and associated gene modules. See Wu et al. 2009 Bioinformatics

PUBLICATIONS

Peiguo Shi, Xuebing Wu Programmable RNA targeting with CRISPR-Cas13. RNA Biology , 2024, 21:1–9

Imdadul Haq, Jason C. Ngo, Nainika Roy, Richard L. Pan, Nawsheen Nadiya, Rebecca Chiu, Ya Zhang, Masashi Fujita, Rajesh K. Soni, Xuebing Wu, David A Bennett, Vilas Menon, Marta Olah, Falak Sher An integrated toolkit for human microglia functional genomics. Stem Cell Research & Therapy , 2024, 15:104

Jian Ge, Hongxu Ding, Hongxia Shao, Yuefeng Huang, Xuebing Wu, Jie Sun, Jianwen Que Single cell analysis of lung lymphatic endothelial cells and lymphatic responses during influenza infection. Journal of Respiratory Biology and Translational Medicine , 2024, 1:10003

Yingyu Zhang, Wanwei Zhang, Jingyao Zhao, Takamasa Ito, Jiacheng Jin, Alexis O. Aparicio, Junsong Zhou, Vincent Guichard, Yinshan Fang, Jianwen Que, Joseph F. Urban Jr, Jacob H. Hanna, Sankar Ghosh, Xuebing Wu, Lei Ding, Uttiya Basu & Yuefeng Huang m6A RNA modification regulates innate lymphoid cell responses in a lineage-specific manner. Nature Immunology , 2023, 24:1256–1264

Jordan S Kesner*, Ziheng Chen*, Peiguo Shi, Alexis O Aparicio, Michael R. Murphy, Yang Guo, Aditi Trehan, Jessica E. Lipponen, Yocelyn Recinos, Natura Myeku, Xuebing Wu Noncoding translation mitigation. Nature , 2023, 617:395–402 See related preprint

Peiguo Shi^, Michael R Murphy, Alexis O Aparicio, Jordan S Kesner, Zhou Fang, Ziheng Chen, Aditi Trehan, Yang Guo, Xuebing Wu^ Collateral activity of the CRISPR/RfxCas13d system in human cells. Communications Biology , 2023 6:334 See related preprint

Jordan S Kesner*, Ziheng Chen*, Alexis A Aparicio, Xuebing Wu A unified model for the surveillance of translation in diverse noncoding sequences. bioRxiv , 2022.07.20.500724; doi: https://doi.org/10.1101/2022.07.20.500724

Peiguo Shi^, Michael R Murphy, Alexis O Aparicio, Jordan S Kesner, Zhou Fang, Ziheng Chen, Aditi Trehan, Xuebing Wu^ RNA-guided cell targeting with CRISPR/RfxCas13d collateral activity in human cells. bioRxiv , 2021, 2021.11.30.470032; doi: https://doi.org/10.1101/2021.11.30.470032

Cheng Zhang, Silvana Konermann, Nicholas J. Brideau, Peter Lotfy, Xuebing Wu , Scott J. Novick, Timothy Strutzenberg, Patrick R. Griffin, Patrick D. Hsu, Dmitry Lyumkis Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d. Cell , 2018, 175:212-223

Josh Tycko, Luis A Barrera, Nicholas Huston, Ari E Friedland, Xuebing Wu , Jonathan S Gootenberg, Omar O Abudayyeh, Vic E Myer, Christopher J Wilson, Patrick D Hsu Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells. Nature Communications , 2018, 9:2962

Wei Jiang*, Yuehua Wei*, Yong Long*, Arthur Owen, Bingying Wang, Xuebing Wu , Shuo Luo, Yongjun Dang, Dengke K. Ma A genetic program mediates cold-warming response and promotes stress-induced phenoptosis in C. elegans eLife , 2018, 7:e35037

X Shawn Liu, Hao Wu, Marine Krzisch, Xuebing Wu , John Graef, Julien Muffat, Denes Hnisz, Charles H. Li, Bingbing Yuan, Chuanyun Xu, Yun Li, Dan Vershkov, Angela Cacace, Richard A. Young, Rudolf Jaenisch Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene Cell , 2018, 172:979–992

Anthony C. Chiu*, Hiroshi I. Suzuki*, Xuebing Wu , Dig B. Mahat, Andrea J. Kriz, Phillip A. Sharp Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP Molecular Cell , 2018, 69:648–663

Xuebing Wu , David P. Bartel Widespread influence of 3′-end structures on mammalian mRNA processing and stability Cell , 2017, 169: 905–917

Xuebing Wu ^, David P. Bartel^ (^co-corresponding author) k pLogo: positional k -mer analysis reveals hidden specificity in biological sequences Nucleic Acids Research , gkx323 http://kplogo.wi.mit.edu

Xiaochang Zhang, Ming Hui Chen, Xuebing Wu , Andrew Kodani, Jean Fan, Ryan Doan, Manabu Ozawa, Jacqueline Ma, Nobuaki Yoshida, Jeremy F Reiter, Douglas L. Black, Peter V Kharchenko, Phillip A. Sharp, Christopher A. Walsh Cell type-specific alternative splicing governs cell fate in the developing cerebral cortex Cell , 2016, 166:1147-1162

F. Ann Ran*, Le Cong*, Winston X. Yan*, David A. Scott, Jonathan S. Gootenberg, Andrea J. Kriz, Bernd Zetsche, Ophir Shalem, Xuebing Wu , Kira S. Makarova, Eugene V. Koonin, Phillip A. Sharp, Feng Zhang In vivo genome editing using Staphylococcus aureus Cas9 Nature , 2015, 520:186-191

Xuebing Wu , Andrea J. Kriz, Phillip A. Sharp Target specificity of the CRISPR-Cas9 system Quantitative Biology , 2014, 2:59-70

Xuebing Wu , David A. Scott, Andrea J. Kriz, Anthony C. Chiu, Patrick D. Hsu, Daniel B. Dadon, Albert W. Cheng, Alexandro E. Trevino, Silvana Konermann, Sidi Chen, Rudolf Jaenisch, Feng Zhang, Phillip A. Sharp Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells Nature Biotechnology , 2014, 32:670-676

Sidi Chen, Yuan Xue, Xuebing Wu , Le Cong, Arjun Bhutkar, Eric Bell, Feng Zhang, Robert Langer, Phillip A. Sharp Global microRNA depletion suppresses tumor angiogenesis Genes & Development , 2014, 28:1054-1067

Xuebing Wu , Phillip A. Sharp Divergent transcription: a driving force for new gene origination? Cell , 2013, 155:990-996

Albert E. Almada*, Xuebing Wu *, Andrea J. Kriz, Christopher B. Burge, Phillip A. Sharp (*equal contribution) Promoter directionality is controlled by U1 snRNP and polyadenylation signals Nature , 2013, 499:360–363

Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu , Wenyan Jiang, Luciano A Marraffini, Feng Zhang Multiplex genome engineering using CRISPR/Cas systems Science , 2013, 339 (6121):819-823.

Patrick D. Hsu, David A. Scott, Joshua A. Weinstein, F. Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J. Fine, Xuebing Wu , Ophir Shalem, Thomas J. Cradick, Luciano A. Marraffini, Gang Bao, and Feng Zhang DNA Targeting Specificity of the RNA-guided Cas9 Nuclease Nature Biotechnology , 2013, 31:827-832

Anna Lyubimova, Shalev Itzkovitz, Jan Philipp Junker, Zi Peng Fan, Xuebing Wu , Alexander van Oudenaarden Single-molecule mRNA detection and counting in mammalian tissue Nature Protocols , 2013, 8:1743–1758 (download software)

Yong Chen, Xuebing Wu , Rui Jiang Integrating human omics data to prioritize candidate genes BMC Medical Genomics , 2013, 6:57

Xuebing Wu , Qifang Liu, Rui Jiang Align human interactome with phenome to identify causative genes and networks underlying disease families Bioinformatics , 2009, 25 (1): 98-104 [ Data ]

Wanwan Tang, Xuebing Wu , Rui Jiang, Yanda Li Epistatic module detection for case-control studies: A Bayesian model with a Gibbs sampling strategy PLoS Genetics , 2009, (5):e1000464

Rui Jiang, Wanwan Tang, Xuebing Wu , Wenhui Fu A random forest approach to the detection of epistatic interactions in case-control studies BMC Bioinformatics , 2009, 10 (Suppl 1):S65

Xuebing Wu , Rui Jiang, Michael Q. Zhang, Shao Li Network-based global inference of human disease genes Molecular Systems Biology , 2008, 4:189.

Xuebing's undergraduate publications

Xuebing Wu , Zhirong Sun, Rui Jiang Logic motif of combinatorial control in transcriptional networks Nature Precedings , 2008, https://doi.org/10.1038/npre.2008.2227.1

Zhirong Sun, Xuebing Wu Systems biology: new interdisciplinary science Communication of China Computer Society , 2006, 2 (3):56-65 (Cover story, review, in Chinese)

Xuebing Wu , Yuanjie Li, Huaiyu Wang An intelligent transportation system based on virtual force Physics and Engineering , 2005, 2 (in Chinese)

Lab members

--> --> --> --> -->

2024/07/12
[email protected]
	[email protected]

Jordan Kesner 8/1/2020-10/1/2023, PhD student -> Postdoc

Katherine Da 9/1/2023-11/30/2023, Visiting undergraduate student, Dartmouth College

Yue Yin 11/01/2021-07/01/2022, Barnard Summer Research Institute, undergraduate student

Alexis Aparicio 02/19/19-08/19/2022, Technician B

Jonathan Algoo 9/20/21-12/14/2021, Rotation student, integrated program

Zhou "Zanis" Fang 11/01/19-12/06/2021, DSI Scholar -> Postdoc

Ziheng "Calvin" Chen 1/15/19-8/10/2020, Master's student, Columbia BME

Qijin Yin 11/25/19-5/10/2020, Visiting PhD student from Tsinghua University

Ellen Alt 5/28/19-8/1/19, Barnard Summer Research Institute, undergraduate student

,

, which stands for Correlating interactome and phenome networks to predict disease genes, is a computational framework we proposed to prioritize human disease genes. It was one of the first studies to explore interactome-phenome wide gene-disease relationships, and generated the first comprehensive genetic landscape of human disease, connecting 5080 human disease phenotypes with 14433 human genes. Click here to or (try ) Wu X, Jiang R, Zhang MQ, Li S (2008) Network-based global inference of human disease genes. Molecular Systems Biology, 4:189

is the abbreviation of "Align Phenome & Interactome." We have performed the first alignment of human phenome and interactome network, and identified 39 bi-modules and made predictions of candidate genes for 70 diseases. Bi-module consists of two inter-connected modules: a network of diseases and a network of genes.  : The website provides a search interface for all identified bi-modules and candidate gene predictions, and corresponding functional enrichment analysis.  : Wu X, Liu Q, Jiang R (2009) Align human interactome with phenome to identify causative genes and networks underlying disease families. Bioinformatics, 25 (1): 98-104

4sU-2P-Seq and DIM-2P-seq protocol (Mar 2017) (PDF)

8/15/24 Xuebing gave an invited seminar at Tsinghua University, Beijing

7/26/24 Xuebing speaks at the 2024 International Conference on Life Sciences, Guiyang, China

7/18/24 Xuebing is invited to present in 2024 STXBP1 Summit

7/8/24 Colin and Feiyue join the lab as PhD studnet #3 and #4!

7/8/24 Wesley Huang joins the lab for his summer research rotation

6/24/24 Xuebing speaks at the 50th Sharp lab reunion symposium “Half A Century of Sharp Minds”

6/10/24 Caroline Ugoaru joins the lab for her T35 summer research as an MD student

6/7/24 Xuebing speaks at the 2024 High-Risk, High-Reward Research (HRHR) Symposium at Bethesda

5/19/24 Peiguo's Cas13 review was published online

5/13/24 Xuebing was selected as a 2024 Schaefer Research Scholar

4/19/24 Xuebing speaks at the first Healthspan Extension Summit at Columbia

4/3/24 Xuebing is invited to speak at the inaugural RNADay@Penn 2024

3/26/24 We received the MIND Prize to test a new idea for treating neurodegeneration

2/1/24 We received our first R01 grant from NHLBI!

1/8/24 We welcomed rotation students Feiyue Yang (Systems Biology) and Sebastian Ho (Nutritional & Metabolic Bio)

12/20/23 We received a grant from the Million Dollar Bike Ride (MDBR) Grant Program to dissect STXBP1 3’ UTR regulation for therapeutic development

12/19/23 We received a grant from the Ines Mandl Research Foundation (IMRF) to develop an off-the-shelf gene editing therapy for Marfan Syndrome

11/17/23 We received a grant from the Cure Alzheimer’s Fund to study noncoding translation and feedback loops in Alzheimer's disease!

11/10/23 Xuebing is invited to give a seminar at Duke Biology and RNA Center @ Durham

11/9/23 Xuebing is invited to give a seminar at NIEHS @ Durham

10/17/23 Xuebing is invited to give a seminar at Koch Institute/MIT

10/14/23 Xuebing gave a talk at EMBL@Heidelberg, Germany, during the 2023 non-coding genome symposium

10/13/23 Xuebing is invited to give a seminar at Heidelberg University Hospital @ Heidelberg, Germany

10/11/23 Xuebing is invited to give a seminar at Max Planck Institute for Molecular Genetics @ Berlin, Germany

9/20/23 We received the inaugural Glenn Foundation Discovery Award !

9/18/23 Our NCI admin supplement grant with Que lab has been funded!

9/13/23 We welcome visiting student Katherine Da, Biology and CS @ Dartmouth College

9/4/23 We receive a 2nd grant from Longevity Impetus Grants !

8/28/23 We welcome graduate student Colin Kalicki for his 1st rotation

7/31/23 Xuebing gave a talk in the Basic Cardiovascular Sciences (BCVS) conference in Boston

7/3/23 Our collaborative work with Yuefeng Huang lab was published at Nature Immunology

7/1/23 We receive a grant from HICCC/Inter/Intra-Programmatic Pilot Program (IPPP) to target lung cancer using CRISPR/Cas13

5/30-6/4/23 Xuebing, Michael, and Jordan attended 2023 annual RNA meeting at Singapore. Michael won a poster award. Xuebing gave a talk on RPL3L ribosomes.

4/19/23 Xuebing was invited to visit U of Chicago by postdocs at the Department of Human Genetics

4/12/23 Our paper titled noncoding translation mitigation has been published online at Nature. See CUIMC news release Illuminating tumor cells with dark proteins

3/28/23 Our paper on Cas13 collateral activity has been published online at Communications Biology

3/21/23 Jordan has been selected as one of the two recipients of the 2023 Dean’s Award for Excellence in Research! Congratulations, Jordan!

10/14/22 Xuebing and Michael each gave an invited virtual talk to the Toronto RNA Club

9/29/22 Xuebing gave an invited virtual seminar at the University of Texas at Dallas

9/6-9/22 Xuebing and Michael each gave a talk at the 18th translational control conference at CSHL

8/31/22 Xuebing gave an invited talk at the first FASEB conference on RNA and immunity .

8/25/22 Congrats Dr. Jordan Kesner! First PhD from the lab!

7/21/22 Lab releases the 2nd bioRxiv preprint , led by Jordan, Ziheng, and Alex

6/4/22 Jordan gave a talk at RNA society meeting 2022

5/25/22 Congrats to Aditi for passing her qualifying exam!

5/4/22 Xuebing gave an invited talk at Weill Cornell and MSKCC

5/3/22 Xuebing gave an invited virtual talk at Prevail Therapeutics / Eli Lilly and Company

4/18/22 Lab welcomes Yang Guo as a postdoctoral research scientist !

11/30/21 First preprint from the lab, led by Peiguo: RNA-guided cell targeting with CRISPR/RfxCas13d collateral activity in human cells

11/16/21 Lab welcomes Barnard/Columbia undergraduate student Yue Yin!

10/14/21 Lab receives Longevity Impetus Grants to study aging!

9/20/21 Lab welcomes Jonathan Algoo as a rotation student in the Fall!

6/21/21 Lab receives 2021 Paul A. Marks Scholars Award , which provides unrestricted fund for 3 years

6/3/21 Lab receives Columbia Precision Medicine Pilot Grant , which supports our study on specialized ribosomes in the heart

5/27/21 Aditi Trehan became PhD student #2 of the Wu lab!

5/18/21 Lab receives the 2021 Pershing Square Sohn Prize for Young Investigators in Cancer Research , which supports our study on cancer-targeting using CRISPR/Cas13 and machine learning. Also see CUIMC News

4/12/21 Aditi Trehan started her rotation in the lab!

10/6/20 Lab receives NIH Director's New Innovator Award (DP2) for genome-scale study of mRNA noncoding functions using CRISPR/Cas13. Also see CUIMC News

9/1/20 Zanis joined the lab as a Postdoc!

8/3/20 The Wu lab welcomes our first PhD student Jordan Kesner!

6/15/20 Xuebing is named a 2020 Pew-Stewart Scholar for Cancer Research , which will support our study of how cancer cells reprogram mRNA structures on a genome-scale. Also see Columbia HICCC News

4/1/20 Lab's COVID-19 research highlighted in HICCC news article Columbia University Cancer Researchers in the Fight Against COVID-19

2/21/20 Xuebing's faculty profile/interview article at Dept. Systems Biology and Cancer Center / HICCC

2/10/20 Shruti Verma joined the lab from Columbia Engineering

12/17/19 Xuebing is named Highly Cited Researcher in 2019 by Web of Science

12/03/19 Michael's AHA postdoc fellowship application was funded. Congratulations!

11/25/19 Qijin Yin started as a visiting scholar. Welcome Qijin!

11/01/19 Welcome four new members to the lab: Peiguo Shi (postdoc), Zanis Fang (MS/DSI Scholar), Katherine Liu and Yixuan Li (undergrad)

10/24/19 Lab moves to our permanent space in P&S

06/28/19 Xuebing gave a talk at the RNA therapeutics conference at UMass Med School.

06/14/19 Xuebing gave a video-taped talk at the RNA Society Annual Meeting in Krakow, Poland.

05/28/19 Ellen Alt joined the lab as a summer research student. Welcome Ellen!

03/01/19 Michael Murphy joined the lab as a staff associate. Welcome Michael!

02/19/19 Alexis Aparicio joined the lab as our first Technician. Welcome Alex!

01/15/19 Ziheng (Calvin) Chen, a graduate student in the BME Master of Science program joined the lab. Welcome Calvin!

12/07/18 Xuebing won the The RNA Society/Scaringe Young Scientist Award 2019

11/01/18 Lab officially started!

We are seeking passionate researchers of all stages (postdocs, graduate students, undergraduates, and research associates) to join our team.

Graduate student looking for rotation or postdoc opportunity : please email me ([email protected]) directly.

Graduate programs we are affiliated with : Integrated Program in Cellular, Molecular, and Biomedical Studies (CMBS) ; Systems Biology (also a track in the CMBS program); Nutritional and Metabolic Biology .

Skip to content

Explore CUIMC

Diversity, equity, and inclusion.

At CUIMC, we are committed to continuous improvement in providing culturally inclusive medical education and clinical care.

Columbia Vagelos College of Physicians and Surgeons is dedicated to developing the next generation of leaders in medicine

Patient Care

• Find a Doctor

Search for a provider by specialty, expertise, location and insurance. Schedule an appointment online.

Read the latest news stories about CUIMC faculty, research, and events

Update on the Department of Systems Biology

Share this page.

• Share on Facebook
• Share on X (formerly Twitter)
• Share on LinkedIn
• Share by email

Dear Colleagues:

I am writing with news that Andrea Califano, Dr, the founding chair of the Department of Systems Biology, will be leaving the chair role this fall to launch an exciting new program in collaboration with multiple universities in the tri-state area. We look forward to sharing further details on this new endeavor soon. In the meantime, I am pleased to share that Harris Wang, PhD, another founding member of the department, has agreed to serve as the interim chair.

While Dr. Califano is leaving his post as chair, his lab will remain at Columbia and he will continue to be a full-time faculty member in systems biology, biochemistry & molecular biophysics, medicine, and biomedical informatics, as well as a member of the Herbert Irving Comprehensive Cancer Center. As Dr. Wang steps into his role as interim chair, Dr. Califano will work closely with him to ensure continuity during the leadership transition.

Dr. Wang is well respected within the department and widely acknowledged as a pioneer in the field of synthetic biology. He holds dual bachelor’s degrees in physics and applied mathematics from the Massachusetts Institute of Technology and a PhD in biophysics & medical engineering from Harvard University, where he served as an instructor in systems biology before joining the Columbia faculty in 2013. Dr. Wang's research focuses on advancing next-generation microbiome and cellular therapeutics using systems and synthetic biology approaches. His development of Multiplex Automated Genome Engineering (MAGE), a technique allowing rapid genome editing of microbial cells, was celebrated as a breakthrough in the field of synthetic biology in 2009. More recently, Dr. Wang has been recognized for his pioneering work in spatial mapping and precision editing of the gut microbiome and using CRISPR technologies to track and record transient cellular processes. He was named a Schaefer Research Scholar at VP&S in 2018, one of many honors he has received. He received the 2022 Vilcek Prize for Creative Promise in Biomedical Science, the Presidential Early Career Award for Scientists and Engineers (PECASE) from the White House, and the NIH Director’s Early Independence award.  

The Department of Systems Biology has made exceptional strides since its inception in 2013. Under Dr. Califano’s leadership as founding chair, the department has grown to more than 30 faculty members and is now funded by multiple center grants. Over the past 10 years, it has grown to become one of the top three departments of its kind in the country and is characterized by the quality of its interdisciplinary and collaborative science. It has been funded by all three of the NCI Cancer Systems Biology multi-investigator programs: the Physical Sciences in Oncology Network (PS-ON), the Cancer Systems Biology Centers (CSBC), and the Cancer Target Discovery and Development (CTD2). The department has generated over 50 patent applications and multiple startup companies. It counts three members of the National Academies and five recipients of Outstanding Investigator Awards (R35 OIA) among its faculty.

Please join me in thanking Dr. Califano for his role in the growth of the department and welcoming Dr. Wang as he begins his interim role during a search for Dr. Califano’s permanent successor.  

All my best,

Katrina Armstrong, MD Dean of the Faculties of Health Sciences and the Vagelos College of Physicians and Surgeons Executive Vice President for Health and Biomedical Sciences

Genetics, Molecular & Cellular Biology Admissions

Students seeking admission to the Genetics, Molecular and Cell Biology (GMCB) program apply to the Graduate School of Biomedical Sciences and select the GMCB program. Students interested in the Mammalian Genetics at JAX track must select this track when they apply to GMCB.

Prospective applicants are evaluated based on prior grades, three letters of recommendation, and responses to the short essays that are part of the application. Prior research experience is strongly valued but is not required.

The essay prompts for our program are:

• Academic Statement of Purpose (750 words maximum): tell us about your development as a scientist, your research experience, your vision for your professional trajectory, and why this particular program, in this particular location, is the right step for you now.
• Personal Statement (750 works maximum): Anything that can give reviewers a sense of you as a person, and your promise as a member of the Tufts community, belongs here.
• More Information (Optional, 250 words maximum): Our students have many different backgrounds, experiences, identities, interests, and talents that meaningfully inspired them to pursue a career in science. What inspired you?

A personal interview is an important part of our evaluation process and may be conducted in person or virtually. An undergraduate major in the biological or life sciences is recommended, but not required.

The GRE is not required but can be submitted with the application.

The application is completed online on the GSBS Application Portal .

Information about application deadlines and the application process can be found in the Admissions section of this website.

Our graduate student community is comprised of students who received their undergraduate degrees from both large and small universities with various scientific backgrounds and who hail from around the world. Graduate students doing work in DSB labs are part of the broad  Morningside Graduate School of Biomedical Sciences with different subspecialized programs of study. Projects in the different labs encompass topics such as genome structure and function, antibiotic function and resistance, mechanisms of cell death, metabolism, gene expression regulation, host-microbial interaction and pathogenesis, chromosomal aberrations, cancer etiology and cellular survival and adaptation under harsh conditions all studied at the systems level. Since research in most DSB labs involve a combination of both experimental (molecular biology, genomics, imaging…) and computational sciences (quantitative modeling, AI, bioinformatics…), graduate students in the DSB have the opportunity to obtain training in both aspects. Students engage in research that is often highly collaborative among the DSB labs and vibrant discussions often take place both within the labs and in the departmental break areas. In addition to attending meetings and presenting their work at offsite meetings within their field, students are encouraged to present their research in our weekly Science on Tap seminar series. For information about the graduate student application process please see our Education homepage .