Shu Laboratory: Jian Shu, PhD

Biological Question Driven + Technological Innovation. 

Central theme: Decoding and Engineering Cell Fates, Circuits, and Multicellular Systems

Research Laboratory Website: https://jianshulab.org

Principal Investigator
Jian Shu, PhD
Assistant Professor
Massachusetts General Hospital
Harvard Medical School
Associate Member
Broad Institute of MIT and Harvard

Overview

Our research focuses on 1) developing novel experimental and computational technologies by integrating genomic, epigenomic, spatial, and imaging data, along with CRISPR perturbations and lineage tracing, to decode complex multicellular systems in time and space at single-cell resolution; 2) applying these single-cell and engineering toolboxes to study stem cell biology, immunology, and development in health and disease.

Publications

Complete List of Publications: 

Google Scholar Profile

Selected Publications

1. Kobayashi-Kirshvink K, Gaddam S, James-Sorenson T, Grody E, Ounadjela JR, Ge BL, Zhang K, Kang JW, Xavier R, So PTC, Biancalani T⁺, Shu J⁺, Regev A⁺. Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy. BioRxiv https://doi.org/10.1101/2021.11.30.470655 (⁺Co-corresponding authors)
2. Muus C*, Luecken MD*, Eraslan G*, Sikkema L*, Waghray A*, Heimberg G*, Kobayashi Y*, Vaishnav ED*, Subramanian A*, Smillie C*, Jagadeesh KA*, Duong ET*, Fiskin E*, Triglia ET*, Ansari M*, Cai P*, Lin B*, Buchanan J*, Chen S*, Shu J*, Haber AL*, Chung H*, Montoro DT*, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine. 2021 Mar;27(3):546-559. PubMed PMID: 33654293. (*These authors contributed equally)
3. He Y, Tang X, Huang J, Zhou H, Chen K, Liu A, Ren J, Shi H, Lin Z, Li Q, Aditham A, Shu J, Liu J, Wang X. ClusterMap: multi-scale clustering analysis of spatial gene expression. Nature Communications. 12.1 (2021): 1-13
4. Svoboda DS, Barrasa MI, Shu J, Rietjens R, Zhang S, Mitalipova M, Berube P, Fu D, Shultz LD, Bell GW, Jaenisch R. Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain. PNAS U S A. 2019 Dec 10;116(50):25293-25303. PubMed Central PMCID: PMC6911218.
5. Schiebinger G*, Shu J*⁺, Tabaka M*, Cleary B*, Subramanian V, Solomon A, Gould J, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A, Lander ES. Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming. Cell. 2019 Feb 7;176(4):928-943.e22. PubMed Central PMCID: PMC6402800. (*These authors contributed equally; ⁺Co-corresponding authors)
6. Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R. Editing DNA Methylation in the Mammalian Genome. Cell. 2016 Sep 22;167(1):233-247.e17. PubMed Central PMCID: PMC5062609.
7. Shu J, Zhang K, Zhang M, Yao A, Shao S, Du F, Yang C, Chen W, Wu C, Yang W, Sun Y, Deng H. GATA family members as inducers for cellular reprogramming to pluripotency. Cell Research. 2015 Feb;25(2):169-80. PubMed Central PMCID: PMC4650575.
8. Du Y, Wang J, Jia J, Song N, Xiang C, Xu J, Hou Z, Su X, Liu B, Jiang T, Zhao D, Sun Y, Shu J, Guo Q, Yin M, Sun D, Lu S, Shi Y, Deng H. Human hepatocytes with drug metabolic function induced from fibroblasts by lineage reprogramming. Cell Stem Cell. 2014 Mar 6;14(3):394-403. PubMed PMID: 24582926.
9. Shu J, Wu C, Wu Y, Li Z, Shao S, Zhao W, Tang X, Yang H, Shen L, Zuo X, Yang W, Shi Y, Chi X, Zhang H, Gao G, Shu Y, Yuan K, He W, Tang C, Zhao Y, Deng H. Induction of pluripotency in mouse somatic cells with lineage specifiers. Cell. 2013 May 23;153(5):963-75. PubMed Central PMCID: PMC4640445