Xiaotu Ma, PhD
Xiaotu Ma, PhD

Xiaotu Ma, PhD

Assistant Member, St. Jude Faculty

Departments

Education

PhD - Beijing University, Beijing, China
BS - Beijing Normal University, Beijing, China

Research Interests

  • mathematical modeling
  • early detection of cancers
  • clonal evolution
  • germline mosaicism

Selected Publications

Ma X#, Shao Y, Tian L, Flasch D, Mulder H, Edmonson M, Liu Y, Chen X, Newman S, Nakitandwe J, Li Y, Li B, Shen S, Wang Z, Shurtleff S, Robison L, Levy S, Easton J, Zhang J#. Analysis of error profiles in deep next-generation sequencing data. Genome Biology 20:50, 2019.

Brady S#, Ma X#, Bahrami A, Satas G, Wu G, Newman S, Rusch M, Putnam D, Mulder H, Yergeau D, Edmonson M, Easton J, Alexandrov L, Chen X, Mardis E, Wilson R, Downing J, Pappo A, Raphael B, Dyer M, Zhang J. The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment. Mol Cancer Res 2019. doi: 10.1158/1541-7786. MCR-18-0620

Rusch M, Nakitandwe J, Shurtleff S, Newman S, Zhang Z, Edmonson MN, Parker M, Jiao Y, Ma X, Liu Y, Gu J, Walsh MF, Becksfort J, Thrasher A, Li Y, McMurry J, Hedlund E, Patel A, Easton J, Yergeau D, Vadodaria B, Tatevossian RG, Raimondi S, Hedges D, Chen X, Hagiwara K, McGee R, Robinson GW, Klco JM, Gruber TA, Ellison DW, Downing JR, Zhang J. Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. Nat Commun 9:3962, 2018.

Ma X, Liu Y, Liu Y, Alexandrov LB, Edmonson MN, Gawad C, Zhou X, Li Y, Rusch MC, Easton J, Huether R, Gonzalez-Pena V, Wilkinson MR, Hermida LC, Davis S, Sioson E, Pounds S, Cao X, Ries RE, Wang Z, Chen X, Dong L, Diskin SJ, Smith MA, Guidry Auvil JM, Meltzer PS, Lau CC, Perlman EJ, Maris JM, Meshinchi S, Hunger SP, Gerhard DS, Zhang J. Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. Nature 555:371-376, 2018.

Liu Y, Easton J, Shao Y, Maciaszek J, Wang Z, Wilkinson MR, McCastlain K, Edmonson M, Pounds SB, Shi L, Zhou X, Ma X, Sioson E, Li Y, Rusch M, Gupta P, Pei D, Cheng C, Smith MA, Auvil JG, Gerhard DS, Relling MV, Winick NJ, Carroll AJ, Heerema NA, Raetz E, Devidas M, Willman CL, Harvey RC, Carroll WL, Dunsmore KP, Winter SS, Wood BL, Sorrentino BP, Downing JR, Loh ML, Hunger SP, Zhang J, Mullighan CG. The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia. Nat Genet 49:1211-1218, 2017.

Zhang J, McCastlain K, Yoshihara H, Xu B, Chang Y, Churchman ML, Wu G, Li Y, Wei L, Iacobucci I, Liu Y, Qu C, Wen J, Edmonson M, Payne-Turner D, Kaufmann KB,  Takayanagi SI, Wienholds E, Waanders E, Ntziachristos P, Bakogianni S, Wang J, Aifantis I, Roberts KG, Ma J, Song G, Easton J, Mulder HL, Chen X, Newman S, Ma X, Rusch M, Gupta P, Boggs K, Vadodaria B, Dalton J, Liu Y, Valentine ML, Ding L, Lu C, Fulton RS, Fulton L, Tabib Y, Ochoa K, Devidas M, Pei D, Cheng C, Yang J, Evans WE, Relling MV, Pui CH, Jeha S, Harvey RC, Chen IL, Willman CL, Marcucci G, Bloomfield CD, Kohlschmidt J, Mrózek K, Paietta E, Tallman MS, Stock W, Foster MC, Racevskis J, Rowe JM, Luger S, Kornblau SM, Shurtleff SA, Raimondi SC, Mardis ER, Wilson RK, Dick JE, Hunger SP, Loh ML, Downing JR, Mullighan CG. Deregulation of DUX4 and ERG in acute lymphoblastic leukemia. Nat Genet 48:1481-1489, 2016.

Wang YW, Ma X, Zhang YA, Wang MJ, Yatabe Y, Lam S, Girard L, Chen JY, Gazdar AF. ITPKA Gene Body Methylation Regulates Gene Expression and Serves as an Early Diagnostic Marker in Lung and Other Cancers. J Thorac Oncol 11:1469-81, 2016.

Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba I, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, Kalhor N, Xie Y, Zhang MQ, Minna JD, Gazdar AF. Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. J Thorac Oncol 11:346-360, 2016.

Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, Weaver MS, Ding L, Mardis ER, Wilson RK, Gajjar A, Ellison DW, Pappo AS, Pui CH, Nichols KE, Downing JR. Germline Mutations in Predisposition Genes in Pediatric Cancer. N Engl J Med 373:2336-2346, 2015.

Li B, Li H, Bai Y, Kirschner-Schwabe R, Yang JJ, Chen Y, Lu G, Tzoneva G, Ma X, Wu T, Li W, Lu H, Ding L, Liang H, Huang X, Yang M, Jin L, Kang H, Chen S, Du A, Shen S, Ding J, Chen H, Chen J, von Stackelberg A, Gu L, Zhang J, Ferrando A, Tang J, Wang S, Zhou BB. Negative feedback-defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL. Nat Med 21:563-71, 2015.

Ma X, Edmonson M, Yergeau D, Muzny DM, Hampton OA, Rusch M, Song G, Easton J, Harvey RC, Wheeler DA, Ma J, Doddapaneni H, Vadodaria B, Wu G, Nagahawatte P, Carroll WL, Chen IM, Gastier-Foster JM, Relling MV, Smith MA, Devidas M, Guidry Auvil JM, Downing JR, Loh ML, Willman CL, Gerhard DS, Mullighan CG, Hunger SP, Zhang J. Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia. Nat Commun 6:6604, 2015.

Tirode F, Surdez D, Ma X, Parker M, Le Deley MC, Bahrami A, Zhang Z, Lapouble E, Grossetête-Lalami S, Rusch M, Reynaud S, Rio-Frio T, Hedlund E, Wu G, Chen X, Pierron G, Oberlin O, Zaidi S, Lemmon G, Gupta P, Vadodaria B, Easton J, Gut M, Ding L, Mardis ER, Wilson RK, Shurtleff S, Laurence V, Michon J, Marec-Bérard P, Gut I, Downing J, Dyer M, Zhang J, Delattre O. Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations. Cancer Discov 4:1342-53, 2014.

Ung M, Ma X, Johnson KC, Christensen BC, Cheng C. Effect of estrogen receptor α binding on functional DNA methylation in breast cancer. Epigenetics 9:523-32, 2014.

Ma X, Chen T, Sun F. Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks. Brief Bioinform 15:685-98, 2014.

Ma X, Wang YW, Zhang MQ, Gazdar AF. DNA methylation data analysis and its application to cancer research. Epigenomics 5:301-16, 2013.

Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res 40:e50, 2012.

Wang J, Wang Y, Wang Z, Liu L, Zhu XG, Ma X#. Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment. BMC Evol Biol 11:161, 2011.

Pang K, Cheng C, Xuan Z, Sheng H, Ma X#. Understanding protein evolutionary rate by integrating gene co-expression with protein interactions. BMC Syst Biol 4:179, 2010.

Pang K, Sheng H, Ma X#. Understanding gene essentiality by finely characterizing hubs in the yeast protein interaction network. Biochem Biophys Res Commun 401:112-6, 2010.

Ma X, Zhang K, Li X. Evolution of Drosophila ribosomal protein gene core promoters. Gene 432:54-9, 2009.

Ma X, Tarone AM, Li W. Mapping genetically compensatory pathways from synthetic lethal interactions in yeast. PLoS One 3:e1922, 2008.

Ma X, Lee H, Wang L, Sun F. CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data. Bioinformatics 23:215-21, 2007.

Cheng C, Ma X, Yan X, Sun F, Li LM. MARD: a new method to detect differential gene expression in treatment-control time courses. Bioinformatics 22:2650-7, 2006.

Xu M, Han W, Qian M, Ma X, Ding P, Wang Y, Xia D, Rui M, Wang L, Zhang Y, Ma D. Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene. Biochem Biophys Res Commun 313:135-41, 2004.

#: co-corresponding or corresponding authors
*: equal contributions

Last update: May 2019