Massachusetts General Hospital
Harvard Medical School
Broad Institute of MIT and Harvard
Ragon Institute of Mass General Brigham, MIT and Harvard

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• Li S, Agudelo Garcia PA, Aliferis C, Becich MJ, Calyeca J, Cosgrove BD, Elisseeff J, Farzad N, Fertig EJ, Glass C, Gu L, Hu Q, Ji Z, Königshoff M, LeBrasseur NK, Li D, Ma A, Ma Q, Menon V, Mitchell JT, Mora AL, Nagaraj S, Nelson AC, Niedernhofer LJ, Rojas M, Taha HB, Wang J, Wang S, Wu P-H, Xie J, Xu M, Yu M, Zhang X, Zhao Y, Adams PD, Aguayo-Mazzucato C, Baker DJ, Benz C, Bernlohr DA, Bueno M, Chen J, Childs BG, Chuang JH, Chung D, Dileepan M, Ding L, Dong M, Duncan F, Enninful A, Flynn WF, Franco AC, Furman D, Garovic V, Halene S, Herman AB, Hertzel AV, Iwasaki K, Jeon H, Kang JW, Karmakar S, Kirkland JL, Korstanje R, Kummerfeld E, Lee JH, Liu Y, Lu Y, Lugo-Martinez J, Martini H, Melov S, Musi N, Passos JF, Peters ST, Rahman I, Ramasamy R, Rindone AN, Robbins PD, Robson P, Rodriguez-Lopez J, Rosas L, Rosenthal N, Schafer MJ, Schilling B, Schmidt EL, Schneider K, Sengupta K, Shu J, So PTC, Sun L, Tchkonia T, Teneche MG, Vanegas N, Wang J, Xie J, Yin S, Zhang K, Zhu Q, Fan R; SenNet Consortium. Advancing biological understanding of cellular senescence with computational multiomics. Nature Genetics. 2025. doi:10.1038/s41588-025-02314-y. 

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• Wamaitha SE, Rojas EJ, Monticolo F, Hsu F-M, Sosa E, Mackie AM, Oyama K, Custer M, Murphy M, Laird DJ, Shu J, Hennebold JD, Clark AT. Defining the cell and molecular origins of the primate ovarian reserve. Nature Communications 2025;16:1–17.

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• Gupta N, Zhang K, Sabbisetti V, Shu J, Morizane R. AAV for gene therapy drives a nephrotoxic response via NFκB in kidney organoids. Signal Transduction Targeted Therapy. 2025;10(1):252.

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• Jin K, Zhang Z, Zhang K, Viggiani F, Callahan C, Tang J, Aronow BJ, Shu J. Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings. Nature Communications 2025;16:6618.

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• Shu J. When cellular reprogramming meets AI: towards de novo cell design. Nature Reviews Genetics 2025:1–1.

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• Comiter C, Chen X, Vaishnav ED, Kobayashi‑Kirschvink KJ, Ciampricotti M, Zhang K, Murray J, Monticolo F, Qi J, Tanaka R, Brodowska SE, Li B, Yang Y, Rodig SJ, Karatza A, Quintanal Villalonga A, Turner M, Pfaff KL, Jané‑Valbuena J, Slyper M, Waldman J, Vigneau S, Wu J, Blosser TR, Segerstolpe Å, Abravanel DL, Wagle N, Demehri S, Zhuang X, Rudin CM, Klughammer J, Rozenblatt‑Rosen O, Stultz CM+, Shu J+, Regev A+. Inference of single cell profiles from histology stains with the Single Cell omics from Histology Analysis Framework (SCHAF). bioRxiv. 2023 https://www.biorxiv.org/content/10.1101/2023.03.21.533680v2 (+Co-corresponding authors)

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• Wang HY, Taher H, Kreklywich CN, Schmidt KA, Scheef EA, Barfield R, Otero CE, Valencia SM, Zhang K, Callahan C, Monticolo F, Qiao Y, Gilbride RM, Crooks CM, Mirza A, Knight K, Moström MJ, Manuel TD, Sprehe L, Kendall S, Burgt NV, Kowalik TF, Barry PA, Hansen SG, Shu J, Tarantal AF, Chan C, Streblow DN, Picker LJ, Kaur A, Früh K, Permar SR, Malouli D. The pentameric complex is not required for congenital CMV transmission in seronegative rhesus macaques. Science Translational Medicine. 2025;17(789):eadm8961.

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• ​Wamaitha SE, Rojas EJ, Monticolo F, Hsu Fm, Sosa E, Mackie AM, Oyama K, Custer M, Murphy M, Laird DJ, Shu J, Hennebold JD, Clark AT. Defining the cell and molecular origins of the primate ovarian reserve. bioRxiv 2025.01.21.634052; doi: https://doi.org/10.1101/2025.01.21.634052

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• Haider S, Shu J. High-resolution spatial multiomic census of the human placenta. Nature Medicine 2024. https://doi.org/10.1038/s41591-024-03353-4.

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• Ounadjela JR, Zhang K, Kobayashi-Kirschvink K, Jin K, Russel A, Lackner AI, Callahan C, Viggiani F, Dey KK, Jagadeesh K, Maxian T, Prandstetter AM, Nadal N, Gong Q, Raichur R, Zvezdov ML, Hui M, Simpson M, Liu X, Min W, Knöfler M, Chen F, Haider S, Shu J. Spatial multiomic landscape of the human placenta at molecular resolution. Nature Medicine 2024. https://doi.org/10.1038/s41591-024-03073-9

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• Shao S, Zhang N, Specht GP, You S, Song L, Fu Q, Huang D, You H, Shu J, Domissy A, Li S, Nguyen-Tran V, Joseph SB, Chatterjee AK, Chen JJ, Schultz PG, Bollong MJ. Pharmacological expansion of type 2 alveolar epithelial cells promotes regenerative lower airway repair. Proc Natl Acad Sci U S A 2024;121:. https://doi.org/10.1073/pnas.2400077121.

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• Liu X, Shi L, Zhao Z, Shu J, Min W. VIBRANT: spectral profiling for single-cell drug responses. Nat Methods 2024. https://doi.org/10.1038/s41592-024-02185-x.

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• 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+. Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA. Nat Biotechnol 2024:1–9. (+Co-corresponding authors)

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• Wang M, Ran X, Leung W, Kawale A, Saxena S, Ouyang J, Patel PS, Dong Y, Yin T, Shu J, Manguso RT, Lan L, Wang XF, Lawrence MS, Zou L. ATR inhibition induces synthetic lethality in mismatch repair-deficient cells and augments immunotherapy. Genes Dev. 2023 Oct 1;37(19-20):929-943. doi: 10.1101/gad.351084.123. Epub 2023 Nov 6. 

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• Jin K, Zhang ZB, Zhang K, Viggiani F, Callahan C, Tang J, Aronow B, Shu J. Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings. bioRxiv 2023. https://doi.org/10.1101/2023.09.19.558548

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• Comiter C, Vaishnav E, Ciapmricotti M, Li B, Yang Y, Rodig S, Turner M, Pfaff K, Valbuena JJ, Slyper M, Waldman J, Vigneau S, Wu J, Blosser T, Segerstolpe A, Abravanel D, Wagle N, Zhuang X, Rudin CM, Klughammer J, Rozenblatt-Rosen O, Kobayash-Kirschvink K, Shu J, Regev A. Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF). bioRxiv 2023. https://doi.org/10.1101/2023.03.21.533680

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• Kobayashi-Kirschvink 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 2021. https://doi.org/10.1101/2021.11.30.470655 (+Corresponding authors)

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• He Y, Tang X, Huang J, Ren J, Zhou H, Chen K, Liu A, Shi H, Lin Z, Li Q, Aditham A, Ounadjela J, Grody E, Shu J, Liu J, Wang X. ClusterMap for multi-scale clustering analysis of spatial gene expression. Nature Communications. 2021 Oct 8;12(1):1-3.

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• 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 2; PubMed PMID: 33654293. (*Co-first authors.)

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• 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. bioRxiv 2021 January 01; :2021.02.18.431337. Available from: http://biorxiv.org/content/early/2021/02/19/2021.02.18.431337.abstract DOI: 10.1101/2021.02.18.431337

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• Muus C*, Luecken M*, Eraslan G*, Waghray A*, Heimberg G*, Sikkema L*, Kobayashi Y*, Vaishnav E*, Subramanian A*, Smilie C*, Jagadeesh K*, Duong E*, Fiskin E*, Triglia E*, Ansari M*, Cai P*, Lin B*, Buchanan J*, Chen S*, Shu J*, Haber A*, Chung H*, Montoro D*, Adams T, Aliee H, Samuel J., Andrusivova A, Angelidis L, Ashenberg O, Bassler K, Becavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui L, Chaffin M, Chichelnitskiy E, Chiou J, Conlon T, Cuoco M, Deprez M, Fischer D, Gillich A, Gould J, Guo M, Gutierrez A, Habermann A, Harvey T, He P, Hou X, Hu L, Jaiswal A, Jiang P, Kapellos T, Kuo C, Larsson L, Michael A. Lim L, Litviňuková M, Lu J, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Marquette C, Mbano I, McAdams A, Metzger R, Nabhan A, Nyquist S, Ordovas-Montanes J, Penland L, Poirion O, Poli S, Qi C, Reichart D, Rosas I, Schupp J, Sinha R, Sit R, Slowikowski K, Slyper M, Smith N, Sountoulidis A, Strunz M, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini K, Tucker N, Vernon K, Wadsworth M, Waldmann J, Wang X, Yan W, Zhao W, Ziegler C, The NHLBI LungMAP Consortium, and The Human Cell Atlas Lung Biological Network. Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells. bioRxiv (2020). https://www.biorxiv.org/content/10.1101/2020.04.19.049254v2 (*Co-first Authors.)

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• Svobada D, Barrasa I, Shu J, Zhang S, Mitalipova M, Berube P, Fu D, Shultz L, Bell G, Jaenisch R. Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain. Proceedings of the National Academy of Sciences. 116.50 (2019): 25293-25303

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• 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. doi: 10.1016/j.cell.2019.01.006. Epub 2019 Jan 31. PubMed PMID: 30712874; PubMed Central PMCID: PMC6402800. (*Co-first Authors. +Corresponding authors.)

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• Schiebinger G*, Shu J*+, Tabaka M*, Cleary B*, Subramanian V, Solomon A, Liu S, Lin S, Berube P, Lee L, Chen J, Brumbaugh J, Rigollet P, Hochedlinger K, Jaenisch R, Regev A+, Lander E+. Reconstruction of developmental landscapes by optimal-transport analysis of single-cell gene expression sheds light on cellular reprogramming. bioRxiv.org : the preprint server for biology. 2017 September; (*Co-first Authors. +Corresponding authors.)

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• 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. doi: 10.1016/j.cell.2016.08.056. PubMed PMID: 27662091; PubMed Central PMCID: PMC5062609.

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• 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. doi: 10.1038/cr.2015.6. Epub 2015 Jan 16. PubMed PMID: 25591928; PubMed Central PMCID: PMC4650575.

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• 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. doi: 10.1016/j.stem.2014.01.008. Epub 2014 Feb 27. PubMed PMID: 24582926.

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• Shu J, Deng H. Lineage specifiers: new players in the induction of pluripotency. Genomics Proteomics Bioinformatics. 2013 Oct;11(5):259-63. doi: 10.1016/j.gpb.2013.09.005. Epub 2013 Oct 4. Review. PubMed PMID: 24095709; PubMed Central PMCID: PMC4357841.

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• 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 153(5):963-75. doi: 10.1016/j.cell.2013.05.001. PubMed PMID: 23706735.