Postdoctoral Research Scientists – Computational Biology - Single Cell/Spatial Transcriptomics on Ageing and Alzheimer’s disease

Columbia University Irving Medical Center
Systems Biology
United States NY New York


The Laboratory of Dr. Chaolin Zhang in Department of Systems Biology, The Laboratory of Maura Boldrini, Columbia University Irving Medical Center (CUIMC) is seeking a Postdoc Research Scientist with computational biology background to conduct research on adult neurogenesis in ageing and Alzheimer’s disease (AD).

Zhang Laboratory:
Taking a multidisciplinary approach that tightly integrates biochemistry, molecular biology, genome engineering and high-throughput data analysis and integrative modeling, the Zhang Laboratory studies how RNA and proteins interact to form regulatory networks in the nervous system at the mechanistic and systems levels, how these networks contribute to intrinsic neuronal functional properties, and how such properties are implicated in health and disease. Given the complexity of the nervous system, an important recent direction of the lab is to understand neuronal subtype-specific regulation, leveraging advance in single cell genomic technologies. We are working to translate fundamental discoveries to RNA-based precision medicine for devastating disorders with unmet medical needs. The Zhang lab consist of a group of inspired and creative scientists from diverse background. Recent lab members have successfully transitioned into prominent academic and pharmaceutical industry positions. More information about the Zhang laboratory can be found at

Boldrini Laboratory:
Maura Boldrini, MD, PhD is an Associate Professor of Psychiatry at Columbia Medical College, Director of the Quantitative Brain Biology Institute (Brain QUANT). The Institute’s mission is to apply cutting edge quantitative neuroscience methods to postmortem human brain tissue to understand how the human brain functions, and the pathogenesis of brain diseases. In her laboratory, Dr. Boldrini is studying brain circuits involved in depression, suicide, aging and other neurodegenerative conditions. The Boldrini lab focuses on understanding cellular and molecular mechanisms of behavioral, cognitive, and emotional changes associated with brain diseases. She has been investigating neurochemical aspects of brain transmission, to find better treatments for brain disorders. She has extensively studied neuron re-growth in the human brain and has shown the potential for adult neurogenesis throughout our lifetime. These new neurons are necessary for learning and copying with stress, for cognitive functions, successful aging, and mental health. Most recently she has been studying how inflammation and COVID affect brain function. Her lab has been fostering a diverse group of motivated and innovative scientists and students, who have gone on to exciting careers in science and academia.

The candidates will participate in and lead exciting collaborative projects that aim to understand molecular mechanisms implicated in aging and neuronal degeneration. The candidates will have the opportunity to work on large scale, multi-modal, single cell and spatial transcriptomic and proteomic datasets generated from high quality, post-mortem healthy and Alzheimer’s Disease brains using cutting-edge technologies. Robust computational analysis pipelines that integrate established and new methods will be developed to perform integrative analysis of these datasets to characterize cell populations and genes impaired in disease and/or ageing. The candidates will work in a dynamic environment and work closely with both computational and experimental biologists in and outside the labs. Strong mentorship will be provided to help them achieve their career goals.

Selected recent publications:
1. Aswathy Ammothumkandy, Kristine Ravina, Victoria Wolseley, Alexandria N Tartt, Pen-Ning Yu, Luis Corona, Naibo Zhang, George Nune, Laura Kalayjian, J. John Mann, Gorazd B. Rosoklija, Victoria Arango, Andrew J. Dwork, Brian Lee, Jason A D Smith, Dong Song, Theodore W Berger, Christianne Heck, Robert H Chow, Maura Boldrini, Charles Y Liu, Jonathan J Russin, and Michael A Bonaguidi. Altered adult neurogenesis and gliogenesis in mesial temporal lobe epilepsy patients. In press, Nature Neuroscience
2. Feng, H., Moakley, D.F., Chen, S., McKenzie, M.G., Menon, V., Zhang, C. 2021. Complexity and graded regulation of neuronal cell type-specific alternative splicing revealed by single-cell RNA sequencing. Proc. Nat. Acad. Sci. USA. 118: e2013056118.
3. Klein R, Soung A, Sissoko C, Nordvig A, Canoll P, Mariani M, Jiang X, Bricker T, Goldman J, Rosoklija G, Arango V, Underwood M, Mann JJ, Boon A, Dowrk A, Boldrini M. COVID-19 induces neuroinflammation and loss of hippocampal neurogenesis. Res Sq. 2021 Oct doi: 10.21203/ Preprint. PMID: 34729556
4. Boldrini M, Peter D. Canoll, Robyn S. Klein. How the novel coronavirus affects the brain. JAMA Psychiatry. 2021 Mar 26. doi: 10.1001/jamapsychiatry.2021.0500. Online ahead of print. PMID: 33769431
5. Feng, H.*, Bao, S.*, Rahman, M.,A., Weyn-Vanhentenryck, S.M., Khan, A., Wong, J., Shah, A., Flynn, E.D., Krainer, A.R., Zhang, C., 2019. Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites. Mol Cell. 74:1189-1204.E6.
6. Boldrini M, Galfalvy H, Dwork AJ, Rosoklija GB, Trencevska-Ivainovska I, Palovski G, Hen R, Arango V, Mann JJ. Resilience Is Associated with Larger Dentate Gyrus while Suicide Decedents with Major Depressive Disorder have Fewer Granule Neurons. Biol Psychiatry. 2019 May 15;85(10):850-862. doi: 10.1016/j.biopsych.2018.12.022. PMID: 30819514
7. Bao, S., Moakley, D.,F., Zhang, C., 2019. The splicing code goes deep. Cell, 176:414-416 (Leading Edge Preview).
8. Ustianenko, D.*, Chiu, H.-S.*, Treiber, T.*, Weyn-Vanhentenryck, S.M., Treiber, N., Meister, G., Sumazin, P. †, Zhang, C. † 2018. LIN28 selectively modulates a subclass of let-7 microRNAs. Mol. Cell. 71: 271-283.e5 (cover story).
9. Boldrini M, Fulmore CA, Tartt AN, Simeon LR, Pavlova I, Poposka V, Rosoklija GB, Stankov A, Arango V, Dwork AJ, Hen R, Mann JJ. Human Hippocampal Neurogenesis Persists Throughout the Eighth Decade of Life. Cell Stem Cell. 2018 Apr 5;22(4):589-599.e5. doi: 10.1016/j.stem.2018.03.015. PMID: 29625071
10. Weyn-Vanhentenryck, S.M.*, Feng, H.*, Ustianenko, D., Duffié, R., Yan, Q., Jacko, M., Martinez, J.C., Goodwin, M., Zhang, X., Hengst, U., Lomvardas, S., Swanson, M.S., Zhang, C. 2018. Precise temporal regulation of alternative splicing during neural development. Nat Commun, 9:2189.
11. Besnard A, Langberg T, Levinson S, Chu D, Vicidomini C, Scobie KN, Dwork AJ, Arango V, Rosoklija GB, Mann JJ, Hen R, Leonardo ED, Boldrini M, Sahay A. Targeting Kruppel-like factor 9 (Klf9) in excitatory forebrain 1 neurons protects against chronic stress-induced dendritic spine enlargement and maladaptive fear responses. Cell Reports, 2018 Jun 12;23(11):3183-3196. doi: 10.1016/j.celrep.2018.05.040. PMID: 29898391
12. Jacko, M., Weyn-Vanhentenryck, S.M., Smerdon, J.W., Yan, R., Feng, H., Williams, D.J., Pai, J., Xu, K., Wichterle, H. †, Zhang, C.† 2018. Rbfox splicing factors promote neuronal maturation and axon initial segment assembly. Neuron, 97: 853-868.e6 (issue highlight).
13. Yan, Q.* , Weyn-Vanhentenrycka, 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. 112:3445-3450.

Required/desired qualifications:

1. A Ph.D. degree in Computational or Systems Biology, Bioinformatics, Computer Sciences, or related fields
2. A genuine interest in solving complex biological problems using quantitative approaches
3. Extensive experience in high-throughput genomic data analysis. Experience working with single cell transcriptomic data is a plus.
4. Solid programing skills (eg., python/perl)
5. Solid statistical and quantitative analysis skills. Experience in statistical modeling and machine learning is a plus.
6. Highly motivated and ability to work independently as well as to collaborate in a team setting
7. Excellent written and verbal communication skills
8. A minimal of one first-author paper published in related peer-reviewed journals


Competitive salaries and full benefits will be provided.

Applicants should send a curriculum vitae and names and contacts of three references by email to:

Dr. Chaolin Zhang, PhD
Associate Professor
Department of Systems Biology
Department of Biochemistry and Molecular Biophysics

Dr. Maura Boldrini
Associate Professor of Psychiatry
Director, Quantitative Brain Biology Institute (Brain QUANT)
Department of Psychiatry

Columbia University is an Equal Opportunity and Affirmative Action Employer. Hiring is contingent upon eligibility to work in the United States. Women and minorities are encouraged to apply.


A Ph.D. degree in Computational or Systems Biology, Bioinformatics, Computer Sciences, or related fields

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