Skip to main content
Jiyang Yu, PhD
Jiyang Yu, PhD


PhD - Columbia University, New York, NY
 - Zhejiang University, Hangzhou, China

Research Interests

  • Systems biology
  • Systems immunology
  • Single-cell systems biology
  • Immuno-oncology
  • Translational oncology
  • Functional genomics

Lab members      

Selected Publications

Huang H, Zhou P, Wei J, Long L, Shi H, Dhungana Y, Chapman NM, Fu G, Saravia J, Raynor JL, Liu S, Palacios G, Wang Y-D, Qian C, Yu J, Chi H. In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8 T cell fate decisions. Cell (in press).

Gocho Y, Liu J, Hu J, Yang W, Dharia NV, Zhang J, Du G, John A, Lin T-N, Hunt J, Rowland L, Shi L, Maxwell D, Smart B, Crews K, Yang W, Hagiwara K, Zhang Y, Roberts K, Wang H, Jabbour E, Stock W, Eisfelder B, Paietta E, Newman S, Roti G, Litzow M, Zhang J, Peng J, Chi H, Pounds S, Relling MV, Inaba H, Zhu X, Kornblau S, Pui C-H, Konopleva M, Teachey D, Mullighan CG, Stegmaier K, Evans WE, Yu J#, Yang JJ#. Network-based systems pharmacology identifies heterogeneity in LCK and BCL2 signaling and differential vulnerability of T-cell acute lymphoblastic leukemia to targeted therapy. Nat Cancer. #Co-corresponding authors. (Clinical trials are being initiated based on this study).

Shi H, Yan K-K, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience. 23(8):101354, 2020. PMID: 32717640; PMCID: PMC7390880.

Tosello V, Bongiovanni D, Liu J, Pan Q, Yan KK, Saccomani V, Van Trimpont M, Pizzi M, Mazzoni M, Dei Tos AP, Amadori A, Zanovello P, Van Vlierberghe P, Yu J, Piovan E. Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination. Leukemia. 2020. PMID: 32733009.

Marks DK, Gartrell RD, El Asmar M, Boboila S, Hart T, Lu Y, Pan Q, Yu J, Hibshoosh H, Guo H, Andreopoulou E, Wiechmann L, Crew K, Sparano J, Hershman D, Connolly E, Saenger Y, Kalinsky K. Akt Inhibition Is Associated With Favorable Immune Profile Changes Within the Tumor Microenvironment of Hormone Receptor Positive, HER2 Negative Breast Cancer. Front Oncol. 10:968,m 2020. Epub 07/03/2020. doi: 10.3389/fonc.2020.00968. PubMed PMID: 32612958; PMCID: PMC7308467.

Autry R, Paugh S, Carter R, Shi L, Liu J, Ferguson D, Lau C, Bonten E, Yang W, McCorkle J, Beard J, Panetta J, Diedrich J, Crews K, Pei D, Coke C, Natarajan S, Khatamian A, Karol S, Lopez-Lopez E, Diouf B, Smith C, Roberts K, Pounds S, Kornblau S, Mullighan C, Jeha S, Pui C, Cheng C, Yang J, Savic D, Yu J, Gawad C, Relling M, Evans WE. Integrative genomic analyses reveal known and novel mechanisms of glucocorticoid resistance in acute lymphoblastic leukemia. Nat Cancer 1(3):329-44, 2020. PMID: 32885175; PMCID: PMC7467080.

Yang P, Mathieu C, Kolaitis RM, Zhang P, Messing J, Yurtsever U, Yang Z, Wu J, Li Y, Pan Q, Yu J, Martin EW, Mittag T, Kim HJ, Taylor JP. G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules. Cell. 181(2):325-45 e28, 2020. PMID: 32302571; PMCID: PMC7448383.

Wijaya J, Vo BT, Liu J, Xu B, Wu G, Wang Y, Peng J, Zhang J, Janke LJ, Orr BA, Yu J, Roussel MF, Schuetz JD. An ABC transporter drives the Sonic Hedgehog pathway contributing to medulloblastoma pathogenesis. Cancer research. 80(7):1524-37, 2020. doi: 10.1158/0008-5472.CAN-19-2054. PubMed PMID: 31948942.

Wei J, Long L, Zheng W, Dhungana Y, Lim SA, Guy C, Wang Y, Wang YD, Qian C, Xu B, Kc A, Saravia J, Huang H, Yu J, Doench JG, Geiger TL, Chi H. Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy. Nature 576(7787):471-6., 2019 doi: 10.1038/s41586-019-1821-z. PubMed PMID: 31827283; PMCID: PMC6937596.

Wang Y, Du X, Wei J, Long L, Tan H, Guy C, Dhungana Y, Qian C, Neale G, Fu YX, Yu J, Peng J, Chi H. LKB1 orchestrates dendritic cell metabolic quiescence and anti-tumor immunity. Cell Research 29:391-405; 2019. doi: 10.1038/s41422-019-0157-4. PMID: 30911060

Yu J#, Peng J#, Chi H#. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity. Current Opinion in Systems Biology. 15:19-29; 2019. doi: 10.1016/j.coisb.2019.03.003. #Co-corresponding authors.

Khatamian A, Paull EO, Califano A#, Yu J#. SJARACNe: a scalable software tool for gene network reverse engineering from big data. Bioinformatics 35(12);2165-2166, 2019. PMID: 30388204. #Corresponding authors. [GitHub:]

Boboila S, Lopez G, Yu J, Banerjee D, Kadenhe-Chiweshe A, Connolly EP, Kandel JJ, Rajbhandari P, Silva JM, Califano A, Yamashiro DJ. Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma. Oncogene 2018. PMID: 29880876.

Du X, Wen J, Wang Y, Karmaus PWF, Khatamian A, Tan H, Li Y, Guy C, Nguyen TM, Dhungana Y, Neale G, Peng J, Yu J#, Chi H#. Hippo/Mst signalling couples metabolic state and immune function of CD8α+ dendritic cells. Nature 558(7708):141-145, 2018. PMID: 29849151. #Corresponding authors. [NetBID GitHub:]

Rajbhandari P, Lopez G, Capdevila C, Salvatori B, Yu J, Rodriguez-Barrueco R, Martinez D, Yarmarkovich M, Weichert-Leahey N, Abraham BJ, Alvarez MJ, Iyer A, Harenza JL, Oldridge D, De Preter K, Koster J, Asgharzadeh S, Seeger RC, Wei JS,  Khan J, Vandesompele J, Mestdagh P, Versteeg R, Look AT, Young RA, Iavarone A, Lasorella A, Silva JM, Maris JM, Califano A. Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer discovery 8(5):582-599, 2018. PMID: 29510988.

Yu J#, Silva JM. Bayesian Network to Infer Drug-Induced Apoptosis Circuits from Connectivity Map Data. Methods in molecular biology (Clifton, N.J.) 1783:361-378, 2018. PMID: 29767372. #Corresponding authors.

Rodriguez-Barrueco R, Nekritz EA, Bertucci F, Yu J, Sanchez-Garcia F, Zeleke TZ, Gorbatenko A, Birnbaum D, Ezhkova E, Cordon-Cardo C, Finetti P, Llobet-Navas D, Silva JM. miR-424(322)/503 is a breast cancer tumor suppressor whose loss promotes resistance to chemotherapy. Genes & development 31(6):553-566, 2017. PMID: 28404630.

Tosello V, Bordin F, Yu J, Agnusdei V, Indraccolo S, Basso G, Amadori A, Piovan E. Calcineurin and GSK-3 inhibition sensitizes T-cell acute lymphoblastic leukemia cells to apoptosis through X-linked inhibitor of apoptosis protein degradation. Leukemia 30(4):812-22, 2016. PMID: 26648536.

Yu J#, Silva J#, Califano A#. ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. Bioinformatics (Oxford, England) 32(2):260-7, 2016. PMID: 26415723. #Corresponding authors.

Putcha P*, Yu J*, Rodriguez-Barrueco R, Saucedo-Cuevas L, Villagrasa P, Murga-Penas E, Quayle SN, Yang M, Castro V, Llobet-Navas D, Birnbaum D, Finetti P, Woodward WA, Bertucci F, Alpaugh ML, Califano A, Silva J. HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers. Breast cancer research: BCR 17(1):149, 2015. PMID: 26643555. (Clinical trial NCT02632071 was initiated and a biomarker patent is being evaluated in the trial) *Equal contributions.

O'Brien SK, Chen L, Zhong W, Armellino D, Yu J, Loreth C, Follettie M, Damelin M. Breast cancer cells respond differentially to modulation of TGFβ2 signaling after exposure to chemotherapy or hypoxia. Cancer research 75(21):4605-16, 2015. PMID: 26340918.

Rodriguez-Barrueco R*, Yu J*, Saucedo-Cuevas LP, Olivan M, Llobet-Navas D, Putcha P, Castro V, Murga-Penas EM, Collazo-Lorduy A, Castillo-Martin M, Alvarez M, Cordon-Cardo C, Kalinsky K, Maurer M, Califano A, Silva JM. Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers. Genes & development 29(15):1631-48, 2015. PMID: 26227964. (Clinical trial NCT02066532 was initiated based on this work; featured at Science Signaling, 25 Aug 2015) *Equal contributions.

Yu J#, Putcha P, Silva JM#. Recovering drug-induced apoptosis subnetwork from Connectivity Map data. BioMed research international 2015:708563, 2015. PMID: 25883971. #Corresponding authors.

Piovan E*, Yu J*, Tosello V, Herranz D, Ambesi-Impiombato A, Da Silva AC, Sanchez-Martin M, Perez-Garcia A, Rigo I, Castillo M, Indraccolo S, Cross JR, de Stanchina E, Paietta E, Racevskis J, Rowe JM, Tallman MS, Basso G, Meijerink JP, Cordon-Cardo C, Califano A, Ferrando AA. Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia. Cancer cell 24(6):766-76, 2013. PMID: 24291004. *Equal contributions.

Yu J, Putcha P, Califano A, Silva JM. Pooled shRNA screenings: computational analysis. Methods in molecular biology (Clifton, N.J.) 980:371-84, 2013. PMID: 23359167.

Lü B*, Yu J*, Xu J, Chen J, Lai M. A novel approach to detect differentially expressed genes from count-based digital databases by normalizing with housekeeping genes. Genomics 94(3):211-6, 2009. PMID: 19446020. *Equal contributions.

Last update: January 2021