Publications by authors named "Xiaotu Ma"

66Publications

Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint.

Authors:
Xin Zhou Jian Wang Jaimin Patel Marc Valentine Ying Shao Scott Newman Edgar Sioson Liqing Tian Yu Liu Samuel W Brady Diane Flasch Xiaotu Ma Yanling Liu Robin Paul Michael N Edmonson Michael C Rusch Chunliang Li Suzanne J Baker John Easton Jinghui Zhang

Cancer Cell 2021 Jan;39(1):83-95.e4

Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. Electronic address:

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January 2021

St. Jude Cloud-a Pediatric Cancer Genomic Data Sharing Ecosystem.

Authors:
Clay McLeod Alexander M Gout Xin Zhou Andrew Thrasher Delaram Rahbarinia Samuel Warren Brady Michael Macias Kirby Birch David Finkelstein Jobin Sunny Rahul Mudunuri Brent A Orr Madison Treadway Bob Davidson Tracy K Ard Arthur Chiao Andrew Swistak Stephanie Wiggins Scott Foy Jian Wang Edgar Sioson Shuoguo Wang J Robert Michael Yu Liu Xiaotu Ma Aman Patel Michael N Edmonson Mark R Wilkinson Andrew M Frantz Ti-Cheng Chang Liqing Tian Shaohua Lei S M Ashiqul Islam Christopher Meyer Naina Thangaraj Pamella Tater Vijay Kandali Singer Ma Tuan Nguyen Omar Abdulgafoor Serang Irina McGuire Nedra Robison Darrell Gentry Xing Tang Lance E Palmer Gang Wu Ed Suh Leigh Tanner James McMurry Matthew Lear Alberto S Pappo Zhaoming Wang Carmen L Wilson Yong Cheng Soheil Meshinchi Ludmil B Alexandrov Mitchell J Weiss Gregory T Armstrong Leslie L Robison Yutaka Yasui Kim E Nichols David W Ellison Chaitanya Bangur Charles G Mullighan Suzanne J Baker Michael A Dyer Geralyn Miller Scott Newman Michael Rusch Richard Daly Keith Perry James R Downing Jinghui Zhang

Cancer Discov 2021 Jan 6. Epub 2021 Jan 6.

Department of Computational Biology, St. Jude Children's Research Hospital

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January 2021

High Intensity Focused Ultrasound-Responsive and Ultrastable Cerasomal Perfluorocarbon Nanodroplets for Alleviating Tumor Multidrug Resistance and Epithelial-Mesenchymal Transition.

Authors:
Xiaotu Ma Meinan Yao Jiyun Shi Xiaoda Li Yu Gao Qi Luo Rui Hou Xiaolong Liang Fan Wang

ACS Nano 2020 11 11;14(11):15904-15918. Epub 2020 Nov 11.

Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China.

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November 2020

Evolution of the Epigenetic Landscape in Childhood B Acute Lymphoblastic Leukemia and Its Role in Drug Resistance.

Authors:
Shella Saint Fleur-Lominy Nikki A Evensen Teena Bhatla Gunjan Sethia Sonali Narang Jun H Choi Xiaotu Ma Jun J Yang Stephen Kelly Elizabeth Raetz Richard C Harvey Cheryl Willman Mignon L Loh Stephen P Hunger Patrick A Brown Kylie M Getz Cem Meydan Christopher E Mason Aristotelis Tsirigos William L Carroll

Cancer Res 2020 Dec 16;80(23):5189-5202. Epub 2020 Oct 16.

Perlmutter Cancer Center, NYU Langone Health, New York, New York.

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December 2020

Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations.

Authors:
Samuel W Brady Yanling Liu Xiaotu Ma Alexander M Gout Kohei Hagiwara Xin Zhou Jian Wang Michael Macias Xiaolong Chen John Easton Heather L Mulder Michael Rusch Lu Wang Joy Nakitandwe Shaohua Lei Eric M Davis Arlene Naranjo Cheng Cheng John M Maris James R Downing Nai-Kong V Cheung Michael D Hogarty Michael A Dyer Jinghui Zhang

Nat Commun 2020 10 14;11(1):5183. Epub 2020 Oct 14.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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October 2020

Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia.

Authors:
Esmé Waanders Zhaohui Gu Stephanie M Dobson Željko Antić Jeremy Chase Crawford Xiaotu Ma Michael N Edmonson Debbie Payne-Turner Maartje van der Vorst Marjolijn C J Jongmans Irina McGuire Xin Zhou Jian Wang Lei Shi Stanley Pounds Deqing Pei Cheng Cheng Guangchun Song Yiping Fan Ying Shao Michael Rusch Kelly McCastlain Jiangyan Yu Ruben van Boxtel Francis Blokzijl Ilaria Iacobucci Kathryn G Roberts Ji Wen Gang Wu Jing Ma John Easton Geoffrey Neale Scott R Olsen Kim E Nichols Ching-Hon Pui Jinghui Zhang William E Evans Mary V Relling Jun J Yang Paul G Thomas John E Dick Roland P Kuiper Charles G Mullighan

Blood Cancer Discov 2020 Jul;1(1):96-111

Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

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July 2020

FPGS relapse-specific mutations in relapsed childhood acute lymphoblastic leukemia.

Authors:
Sung-Liang Yu Hui Zhang Bing-Ching Ho Chih-Hsiang Yu Chia-Ching Chang Yin-Chen Hsu Yu-Ling Ni Kai-Hsin Lin Shiann-Tarng Jou Meng-Yao Lu Shu-Huey Chen Kang-Hsi Wu Shih-Chung Wang Hsiu-Hao Chang Ching-Hon Pui Jun J Yang Jinghui Zhang Dong-Tsamn Lin Shu-Wha Lin Xiaotu Ma Yung-Li Yang

Sci Rep 2020 07 21;10(1):12074. Epub 2020 Jul 21.

Department of Laboratory Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, No. 7, Chung Shan S. Rd, Zhongshan S. Rd, Zhongzheng Dist, Taipei, 100, Taiwan, ROC.

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July 2020

Therapy-induced mutagenesis in relapsed ALL is supported by mutational signature analysis.

Authors:
Samuel W Brady Xiaotu Ma Bin-Bing S Zhou Ching-Hon Pui Jun J Yang Jinghui Zhang

Blood 2020 Nov;136(19):2235-2237

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN.

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November 2020

Developing PEGylated Reversed D-Peptide as a Novel HER2-Targeted SPECT Imaging Probe for Breast Cancer Detection.

Authors:
Shuaifan Du Chuangwei Luo Guangjie Yang Hannan Gao Yanpu Wang Xiaoda Li Huiyun Zhao Qi Luo Xiaotu Ma Jiyun Shi Fan Wang

Bioconjug Chem 2020 08 24;31(8):1971-1980. Epub 2020 Jul 24.

Medical Isotopes Research Center and Department of Radiation Medicine, State Key Laboratory of Natural and Biomimetic Drugs, School of Basic Medical Sciences, Peking University, Beijing 100191, China.

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August 2020

Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X.

Authors:
Yu Liu Chunliang Li Shuhong Shen Xiaolong Chen Karol Szlachta Michael N Edmonson Ying Shao Xiaotu Ma Judith Hyle Shaela Wright Bensheng Ju Michael C Rusch Yanling Liu Benshang Li Michael Macias Liqing Tian John Easton Maoxiang Qian Jun J Yang Shaoyan Hu A Thomas Look Jinghui Zhang

Nat Genet 2020 08 6;52(8):811-818. Epub 2020 Jul 6.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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August 2020

Feasibility of monitoring peripheral blood to detect emerging clones in children with acute lymphoblastic leukemia.

Authors:
Jason Saliba Nikki A Evensen Julia A Meyer Daniel Newman Jacob Nersting Sonali Narang Xiaotu Ma Kjeld Schmiegelow William L Carroll

Pediatr Blood Cancer 2020 07 11;67(7):e28306. Epub 2020 May 11.

Department of Pediatrics, Perlmutter Cancer Center, NYU Langone Health, New York.

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July 2020

An Integrin Alpha 6-Targeted Radiotracer with Improved Receptor Binding Affinity and Tumor Uptake.

Authors:
Qi Luo Guangjie Yang Hannan Gao Yanpu Wang Chuangwei Luo Xiaotu Ma Yu Gao Xiaoda Li Huiyun Zhao Bing Jia Jiyun Shi Fan Wang

Bioconjug Chem 2020 05 7;31(5):1510-1521. Epub 2020 May 7.

Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

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May 2020

The NSD2 p.E1099K Mutation Is Enriched at Relapse and Confers Drug Resistance in a Cell Context-Dependent Manner in Pediatric Acute Lymphoblastic Leukemia.

Authors:
Joanna Pierro Jason Saliba Sonali Narang Gunjan Sethia Shella Saint Fleur-Lominy Ashfiyah Chowdhury Anita Qualls Hannah Fay Harrison L Kilberg Takaya Moriyama Tori J Fuller David T Teachey Kjeld Schmiegelow Jun J Yang Mignon L Loh Patrick A Brown Jinghui Zhang Xiaotu Ma Aristotelis Tsirigos Nikki A Evensen William L Carroll

Mol Cancer Res 2020 08 24;18(8):1153-1165. Epub 2020 Apr 24.

Departments of Pediatrics and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, New York.

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August 2020

In situ conversion of rose bengal microbubbles into nanoparticles for ultrasound imaging guided sonodynamic therapy with enhanced antitumor efficacy.

Authors:
Rui Hou Xiaolong Liang Xiaoda Li Xu Zhang Xiaotu Ma Fan Wang

Biomater Sci 2020 May;8(9):2526-2536

Medical Isotopes Research Center and Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing, China. and Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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May 2020

Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs.

Authors:
Stephanie M Dobson Laura García-Prat Robert J Vanner Jeffrey Wintersinger Esmé Waanders Zhaohui Gu Jessica McLeod Olga I Gan Ildiko Grandal Debbie Payne-Turner Michael N Edmonson Xiaotu Ma Yiping Fan Veronique Voisin Michelle Chan-Seng-Yue Stephanie Z Xie Mohsen Hosseini Sagi Abelson Pankaj Gupta Michael Rusch Ying Shao Scott R Olsen Geoffrey Neale Steven M Chan Gary Bader John Easton Cynthia J Guidos Jayne S Danska Jinghui Zhang Mark D Minden Quaid Morris Charles G Mullighan John E Dick

Cancer Discov 2020 Apr 21;10(4):568-587. Epub 2020 Feb 21.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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April 2020

Therapy-induced mutations drive the genomic landscape of relapsed acute lymphoblastic leukemia.

Authors:
Benshang Li Samuel W Brady Xiaotu Ma Shuhong Shen Yingchi Zhang Yongjin Li Karol Szlachta Li Dong Yu Liu Fan Yang Ningling Wang Diane A Flasch Matthew A Myers Heather L Mulder Lixia Ding Yanling Liu Liqing Tian Kohei Hagiwara Ke Xu Xin Zhou Edgar Sioson Tianyi Wang Liu Yang Jie Zhao Hui Zhang Ying Shao Hongye Sun Lele Sun Jiaoyang Cai Hui-Ying Sun Ting-Nien Lin Lijuan Du Hui Li Michael Rusch Michael N Edmonson John Easton Xiaofan Zhu Jingliao Zhang Cheng Cheng Benjamin J Raphael Jingyan Tang James R Downing Ludmil B Alexandrov Bin-Bing S Zhou Ching-Hon Pui Jun J Yang Jinghui Zhang

Blood 2020 01;135(1):41-55

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN.

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January 2020

Host-Guest Polypyrrole Nanocomplex for Three-Stimuli-Responsive Drug Delivery and Imaging-Guided Chemo-Photothermal Synergetic Therapy of Refractory Thyroid Cancer.

Authors:
Xiaotu Ma Xiaoda Li Jiyun Shi Meinan Yao Xu Zhang Rui Hou Nan Shao Qi Luo Yu Gao Shuaifan Du Xiaolong Liang Fan Wang

Adv Healthc Mater 2019 09 7;8(17):e1900661. Epub 2019 Aug 7.

Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P. R. China.

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September 2019

VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity.

Authors:
Daniel K Putnam Xiaotu Ma Stephen V Rice Yu Liu Scott Newman Jinghui Zhang Xiang Chen

Sci Rep 2019 07 17;9(1):10357. Epub 2019 Jul 17.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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July 2019

Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia.

Authors:
Liqing Tian Ying Shao Stephanie Nance Jinjun Dang Beisi Xu Xiaotu Ma Yongjin Li Bensheng Ju Li Dong Scott Newman Xin Zhou Patrick Schreiner Elizabeth Tseng Ting Hon Meredith Ashby Chunliang Li John Easton Tanja A Gruber Jinghui Zhang

Nat Commun 2019 06 26;10(1):2789. Epub 2019 Jun 26.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

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June 2019

Highly stable near-infrared dye conjugated cerasomes for fluorescence imaging-guided synergistic chemo-photothermal therapy of colorectal cancer.

Authors:
Xu Zhang Xiaolong Liang Xiaotu Ma Rui Hou Xiaoda Li Fan Wang

Biomater Sci 2019 Jul 9;7(7):2873-2888. Epub 2019 May 9.

Medical Isotopes Research Center and Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China and Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

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July 2019

Genomic subtyping and therapeutic targeting of acute erythroleukemia.

Authors:
Ilaria Iacobucci Ji Wen Manja Meggendorfer John K Choi Lei Shi Stanley B Pounds Catherine L Carmichael Katherine E Masih Sarah M Morris R Coleman Lindsley Laura J Janke Thomas B Alexander Guangchun Song Chunxu Qu Yongjin Li Debbie Payne-Turner Daisuke Tomizawa Nobutaka Kiyokawa Marcus Valentine Virginia Valentine Giuseppe Basso Franco Locatelli Eric J Enemark Shirley K Y Kham Allen E J Yeoh Xiaotu Ma Xin Zhou Edgar Sioson Michael Rusch Rhonda E Ries Elliot Stieglitz Stephen P Hunger Andrew H Wei L Bik To Ian D Lewis Richard J D'Andrea Benjamin T Kile Anna L Brown Hamish S Scott Christopher N Hahn Paula Marlton Deqing Pei Cheng Cheng Mignon L Loh Benjamin L Ebert Soheil Meshinchi Torsten Haferlach Charles G Mullighan

Nat Genet 2019 04 29;51(4):694-704. Epub 2019 Mar 29.

Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.

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April 2019

Analysis of error profiles in deep next-generation sequencing data.

Authors:
Xiaotu Ma Ying Shao Liqing Tian Diane A Flasch Heather L Mulder Michael N Edmonson Yu Liu Xiang Chen Scott Newman Joy Nakitandwe Yongjin Li Benshang Li Shuhong Shen Zhaoming Wang Sheila Shurtleff Leslie L Robison Shawn Levy John Easton Jinghui Zhang

Genome Biol 2019 03 14;20(1):50. Epub 2019 Mar 14.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

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March 2019

Lectin-Mediated pH-Sensitive Doxorubicin Prodrug for Pre-Targeted Chemotherapy of Colorectal Cancer with Enhanced Efficacy and Reduced Side Effects.

Authors:
Meinan Yao Xiaotu Ma Xin Zhang Linqing Shi Tianyu Liu Xiaolong Liang Huiyun Zhao Xiaoda Li Liqiang Li Hannan Gao Bing Jia Fan Wang

Theranostics 2019 24;9(3):747-760. Epub 2019 Jan 24.

Medical Isotopes Research Center and Department of Radiation Medicine, School of Basic Medical Sciences, Peking University, Beijing 100191, P. R. China.

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January 2020

Closed Loop Recycling of Electric Vehicle Batteries to Enable Ultra-high Quality Cathode Powder.

Authors:
Mengyuan Chen Zhangfeng Zheng Qiang Wang Yubin Zhang Xiaotu Ma Chao Shen Dapeng Xu Jin Liu Yangtao Liu Paul Gionet Ian O'Connor Leslie Pinnell Jun Wang Eric Gratz Renata Arsenault Yan Wang

Sci Rep 2019 Feb 7;9(1):1654. Epub 2019 Feb 7.

Department of Mechanical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609, USA.

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February 2019

Publisher Correction: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.

Authors:
Hamid Bolouri Jason E Farrar Timothy Triche Rhonda E Ries Emilia L Lim Todd A Alonzo Yussanne Ma Richard Moore Andrew J Mungall Marco A Marra Jinghui Zhang Xiaotu Ma Yu Liu Yanling Liu Jaime M Guidry Auvil Tanja M Davidsen Patee Gesuwan Leandro C Hermida Bodour Salhia Stephen Capone Giridharan Ramsingh Christian Michel Zwaan Sanne Noort Stephen R Piccolo E Anders Kolb Alan S Gamis Malcolm A Smith Daniela S Gerhard Soheil Meshinchi

Nat Med 2019 Mar;25(3):530

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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March 2019

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment.

Authors:
Samuel W Brady Xiaotu Ma Armita Bahrami Gryte Satas Gang Wu Scott Newman Michael Rusch Daniel K Putnam Heather L Mulder Donald A Yergeau Michael N Edmonson John Easton Ludmil B Alexandrov Xiang Chen Elaine R Mardis Richard K Wilson James R Downing Alberto S Pappo Benjamin J Raphael Michael A Dyer Jinghui Zhang

Mol Cancer Res 2019 04 16;17(4):895-906. Epub 2019 Jan 16.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.

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April 2019

Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome.

Authors:
Michael Rusch Joy Nakitandwe Sheila Shurtleff Scott Newman Zhaojie Zhang Michael N Edmonson Matthew Parker Yuannian Jiao Xiaotu Ma Yanling Liu Jiali Gu Michael F Walsh Jared Becksfort Andrew Thrasher Yongjin Li James McMurry Erin Hedlund Aman Patel John Easton Donald Yergeau Bhavin Vadodaria Ruth G Tatevossian Susana Raimondi Dale Hedges Xiang Chen Kohei Hagiwara Rose McGee Giles W Robinson Jeffery M Klco Tanja A Gruber David W Ellison James R Downing Jinghui Zhang

Nat Commun 2018 09 27;9(1):3962. Epub 2018 Sep 27.

Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.

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September 2018

Genetic Risk for Subsequent Neoplasms Among Long-Term Survivors of Childhood Cancer.

Authors:
Zhaoming Wang Carmen L Wilson John Easton Andrew Thrasher Heather Mulder Qi Liu Dale J Hedges Shuoguo Wang Michael C Rusch Michael N Edmonson Shawn Levy Jennifer Q Lanctot Eric Caron Kyla Shelton Kelsey Currie Matthew Lear Aman Patel Celeste Rosencrance Ying Shao Bhavin Vadodaria Donald Yergeau Yadav Sapkota Russell J Brooke Wonjong Moon Evadnie Rampersaud Xiaotu Ma Ti-Cheng Chang Stephen V Rice Cynthia Pepper Xin Zhou Xiang Chen Wenan Chen Angela Jones Braden Boone Matthew J Ehrhardt Matthew J Krasin Rebecca M Howell Nicholas S Phillips Courtney Lewis Deokumar Srivastava Ching-Hon Pui Chimene A Kesserwan Gang Wu Kim E Nichols James R Downing Melissa M Hudson Yutaka Yasui Leslie L Robison Jinghui Zhang

J Clin Oncol 2018 07 30;36(20):2078-2087. Epub 2018 May 30.

Zhaoming Wang, Carmen L. Wilson, John Easton, Andrew Thrasher, Heather Mulder, Dale J. Hedges, Shuoguo Wang, Michael C. Rusch, Michael N. Edmonson, Jennifer Q. Lanctot, Eric Caron, Kyla Shelton, Kelsey Currie, Matthew Lear, Aman Patel, Celeste Rosencrance, Ying Shao, Bhavin Vadodaria, Donald Yergeau, Yadav Sapkota, Russell J. Brooke, Wonjong Moon, Evadnie Rampersaud, Xiaotu Ma, Ti-Cheng Chang, Stephen V. Rice, Cynthia Pepper, Xin Zhou, Xiang Chen, Wenan Chen, Matthew J. Ehrhardt, Matthew J. Krasin, Rebecca M. Howell, Nicholas S. Phillips, Courtney Lewis, Deokumar Srivastava, Ching-Hon Pui, Chimene A. Kesserwan, Gang Wu, Kim E. Nichols, James R. Downing, Melissa M. Hudson, Yutaka Yasui, Leslie L. Robison, and Jinghui Zhang, St Jude Children's Research Hospital, Memphis, TN; Qi Liu, University of Alberta, Edmonton, Alberta, Canada; Shawn Levy, Angela Jones, and Braden Boone, HudsonAlpha Institute for Biotechnology, Huntsville, AL; and Rebecca M. Howell, The University of Texas MD Anderson Cancer Center, Houston, TX.

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July 2018

Erratum: The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.

Authors:
Hamid Bolouri Jason E Farrar Timothy Triche Rhonda E Ries Emilia L Lim Todd A Alonzo Yussanne Ma Richard Moore Andrew J Mungall Marco A Marra Jinghui Zhang Xiaotu Ma Yu Liu Yanling Liu Jaime M Guidry Auvil Tanja M Davidsen Patee Gesuwan Leandro C Hermida Bodour Salhia Stephen Capone Giridharan Ramsingh Christian Michel Zwaan Sanne Noort Stephen R Piccolo E Anders Kolb Alan S Gamis Malcolm A Smith Daniela S Gerhard Soheil Meshinchi

Nat Med 2018 Apr;24(4):526

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April 2018

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours.

Authors:
Xiaotu Ma Yu Liu Yanling Liu Ludmil B Alexandrov Michael N Edmonson Charles Gawad Xin Zhou Yongjin Li Michael C Rusch John Easton Robert Huether Veronica Gonzalez-Pena Mark R Wilkinson Leandro C Hermida Sean Davis Edgar Sioson Stanley Pounds Xueyuan Cao Rhonda E Ries Zhaoming Wang Xiang Chen Li Dong Sharon J Diskin Malcolm A Smith Jaime M Guidry Auvil Paul S Meltzer Ching C Lau Elizabeth J Perlman John M Maris Soheil Meshinchi Stephen P Hunger Daniela S Gerhard Jinghui Zhang

Nature 2018 03 28;555(7696):371-376. Epub 2018 Feb 28.

Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.

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March 2018

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions.

Authors:
Hamid Bolouri Jason E Farrar Timothy Triche Rhonda E Ries Emilia L Lim Todd A Alonzo Yussanne Ma Richard Moore Andrew J Mungall Marco A Marra Jinghui Zhang Xiaotu Ma Yu Liu Yanling Liu Jaime M Guidry Auvil Tanja M Davidsen Patee Gesuwan Leandro C Hermida Bodour Salhia Stephen Capone Giridharan Ramsingh Christian Michel Zwaan Sanne Noort Stephen R Piccolo E Anders Kolb Alan S Gamis Malcolm A Smith Daniela S Gerhard Soheil Meshinchi

Nat Med 2018 01 11;24(1):103-112. Epub 2017 Dec 11.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.

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January 2018

Genome-wide segregation of single nucleotide and structural variants into single cancer cells.

Authors:
John Easton Veronica Gonzalez-Pena Donald Yergeau Xiaotu Ma Charles Gawad

BMC Genomics 2017 Nov 25;18(1):906. Epub 2017 Nov 25.

Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.

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November 2017

The genomic landscape of pediatric and young adult T-lineage acute lymphoblastic leukemia.

Authors:
Yu Liu John Easton Ying Shao Jamie Maciaszek Zhaoming Wang Mark R Wilkinson Kelly McCastlain Michael Edmonson Stanley B Pounds Lei Shi Xin Zhou Xiaotu Ma Edgar Sioson Yongjin Li Michael Rusch Pankaj Gupta Deqing Pei Cheng Cheng Malcolm A Smith Jaime Guidry Auvil Daniela S Gerhard Mary V Relling Naomi J Winick Andrew J Carroll Nyla A Heerema Elizabeth Raetz Meenakshi Devidas Cheryl L Willman Richard C Harvey William L Carroll Kimberly P Dunsmore Stuart S Winter Brent L Wood Brian P Sorrentino James R Downing Mignon L Loh Stephen P Hunger Jinghui Zhang Charles G Mullighan

Nat Genet 2017 Aug 3;49(8):1211-1218. Epub 2017 Jul 3.

Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

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August 2017

SHOX2 is a Potent Independent Biomarker to Predict Survival of WHO Grade II-III Diffuse Gliomas.

Authors:
Yu-An Zhang Yunyun Zhou Xin Luo Kai Song Xiaotu Ma Adwait Sathe Luc Girard Guanghua Xiao Adi F Gazdar

EBioMedicine 2016 Nov 28;13:80-89. Epub 2016 Oct 28.

The Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; The Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address:

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November 2016

Deregulation of DUX4 and ERG in acute lymphoblastic leukemia.

Authors:
Jinghui Zhang Kelly McCastlain Hiroki Yoshihara Beisi Xu Yunchao Chang Michelle L Churchman Gang Wu Yongjin Li Lei Wei Ilaria Iacobucci Yu Liu Chunxu Qu Ji Wen Michael Edmonson Debbie Payne-Turner Kerstin B Kaufmann Shin-Ichiro Takayanagi Erno Wienholds Esmé Waanders Panagiotis Ntziachristos Sofia Bakogianni Jingjing Wang Iannis Aifantis Kathryn G Roberts Jing Ma Guangchun Song John Easton Heather L Mulder Xiang Chen Scott Newman Xiaotu Ma Michael Rusch Pankaj Gupta Kristy Boggs Bhavin Vadodaria James Dalton Yanling Liu Marcus L Valentine Li Ding Charles Lu Robert S Fulton Lucinda Fulton Yashodhan Tabib Kerri Ochoa Meenakshi Devidas Deqing Pei Cheng Cheng Jun Yang William E Evans Mary V Relling Ching-Hon Pui Sima Jeha Richard C Harvey I-Ming L Chen Cheryl L Willman Guido Marcucci Clara D Bloomfield Jessica Kohlschmidt Krzysztof Mrózek Elisabeth Paietta Martin S Tallman Wendy Stock Matthew C Foster Janis Racevskis Jacob M Rowe Selina Luger Steven M Kornblau Sheila A Shurtleff Susana C Raimondi Elaine R Mardis Richard K Wilson John E Dick Stephen P Hunger Mignon L Loh James R Downing Charles G Mullighan

Nat Genet 2016 12 24;48(12):1481-1489. Epub 2016 Oct 24.

Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

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December 2016

ITPKA Gene Body Methylation Regulates Gene Expression and Serves as an Early Diagnostic Marker in Lung and Other Cancers.

Authors:
Yi-Wei Wang Xiaotu Ma Yu-An Zhang Mei-Jung Wang Yasushi Yatabe Stephen Lam Luc Girard Jeou-Yuan Chen Adi F Gazdar

J Thorac Oncol 2016 09 24;11(9):1469-81. Epub 2016 May 24.

Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas; Department of Pathology and Harold Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas. Electronic address:

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September 2016

Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers.

Authors:
Yu-An Zhang Xiaotu Ma Adwait Sathe Junya Fujimoto Ignacio Wistuba Stephen Lam Yasushi Yatabe Yi-Wei Wang Victor Stastny Boning Gao Jill E Larsen Luc Girard Xiaoyun Liu Kai Song Carmen Behrens Neda Kalhor Yang Xie Michael Q Zhang John D Minna Adi F Gazdar

J Thorac Oncol 2016 Mar 25;11(3):346-360. Epub 2015 Dec 25.

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March 2016

Germline Mutations in Predisposition Genes in Pediatric Cancer.

Authors:
Jinghui Zhang Michael F Walsh Gang Wu Michael N Edmonson Tanja A Gruber John Easton Dale Hedges Xiaotu Ma Xin Zhou Donald A Yergeau Mark R Wilkinson Bhavin Vadodaria Xiang Chen Rose B McGee Stacy Hines-Dowell Regina Nuccio Emily Quinn Sheila A Shurtleff Michael Rusch Aman Patel Jared B Becksfort Shuoguo Wang Meaghann S Weaver Li Ding Elaine R Mardis Richard K Wilson Amar Gajjar David W Ellison Alberto S Pappo Ching-Hon Pui Kim E Nichols James R Downing

N Engl J Med 2015 Dec 18;373(24):2336-2346. Epub 2015 Nov 18.

Departments of Computational Biology (J.Z., G.W., M.N.E., D.H., X.M., X.Z., M.R.W., X.C., M.R., A.P., J.B.B., S.W.), Oncology (M.F.W., T.A.G., R.B.M., S.H.-D., R.N., E.Q., A.G., A.S.P., C.-H.P., K.E.N.), and Pathology (T.A.G., M.R.W., S.A.S., D.W.E., C.-H.P., J.R.D.) and the Pediatric Cancer Genome Project (J.Z., M.F.W., G.W., M.N.E., T.A.G., J.E., X.M., D.A.Y., B.V., X.C., R.B.M., S.H.-D., R.N., E.Q., S.A.S., M.R., A.P., J.B.B., S.W., M.S.W., A.G., D.W.E., A.S.P., C.-H.P., K.E.N., J.R.D.), St. Jude Children's Research Hospital, Memphis, TN; and the Department of Genetics and McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis (L.D., E.R.M., R.K.W.).

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December 2015

Outcome of children with hypodiploid ALL treated with risk-directed therapy based on MRD levels.

Authors:
Charles G Mullighan Sima Jeha Deqing Pei Debbie Payne-Turner Elaine Coustan-Smith Kathryn G Roberts Esmé Waanders John K Choi Xiaotu Ma Susana C Raimondi Yiping Fan Wenjian Yang Guangchun Song Jun J Yang Hiroto Inaba James R Downing Wing H Leung W Paul Bowman Mary V Relling William E Evans Jinghui Zhang Dario Campana Ching-Hon Pui

Blood 2015 Dec 2;126(26):2896-9. Epub 2015 Nov 2.

Departments of Oncology and Pathology, St. Jude Children's Research Hospital, Memphis, TN.

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December 2015

Cancer-Specific Production of N-Acetylaspartate via NAT8L Overexpression in Non-Small Cell Lung Cancer and Its Potential as a Circulating Biomarker.

Authors:
Tzu-Fang Lou Deepa Sethuraman Patrick Dospoy Pallevi Srivastva Hyun Seok Kim Joongsoo Kim Xiaotu Ma Pei-Hsuan Chen Kenneth E Huffman Robin E Frink Jill E Larsen Cheryl Lewis Sang-Won Um Duk-Hwan Kim Jung-Mo Ahn Ralph J DeBerardinis Michael A White John D Minna Hyuntae Yoo

Cancer Prev Res (Phila) 2016 Jan 28;9(1):43-52. Epub 2015 Oct 28.

Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas. Center for Systems Biology, University of Texas at Dallas, Richardson, Texas. Department of Bioengineering, University of Texas at Dallas, Richardson, Texas.

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January 2016

Regulation of AURKC expression by CpG island methylation in human cancer cells.

Authors:
Satoshi Fujii Vibhuti Srivastava Apurva Hegde Yutaka Kondo Lanlan Shen Koyu Hoshino Yvette Gonzalez Jin Wang Kaori Sasai Xiaotu Ma Hiroshi Katayama Marcos R Estecio Stanley R Hamilton Ignacio Wistuba Jean-Pierre J Issa Subrata Sen

Tumour Biol 2015 Sep 20;36(10):8147-58. Epub 2015 May 20.

Department of Translational Molecular Pathology, UT MD Anderson Cancer Center, Unit 2951, Life Science Plaza Building, 2130 W. Holcombe Blvd., Houston, TX, 77030, USA.

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September 2015

Cross-Species Genomics Identifies TAF12, NFYC, and RAD54L as Choroid Plexus Carcinoma Oncogenes.

Authors:
Yiai Tong Diana Merino Birgit Nimmervoll Kirti Gupta Yong-Dong Wang David Finkelstein James Dalton David W Ellison Xiaotu Ma Jinghui Zhang David Malkin Richard J Gilbertson

Cancer Cell 2015 May;27(5):712-27

Department of Developmental Neurobiology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA; Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. Electronic address:

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May 2015

Negative feedback-defective PRPS1 mutants drive thiopurine resistance in relapsed childhood ALL.

Authors:
Benshang Li Hui Li Yun Bai Renate Kirschner-Schwabe Jun J Yang Yao Chen Gang Lu Gannie Tzoneva Xiaotu Ma Tongmin Wu Wenjing Li Haisong Lu Lixia Ding Huanhuan Liang Xiaohang Huang Minjun Yang Lei Jin Hui Kang Shuting Chen Alicia Du Shuhong Shen Jianping Ding Hongzhuan Chen Jing Chen Arend von Stackelberg Longjun Gu Jinghui Zhang Adolfo Ferrando Jingyan Tang Shengyue Wang Bin-Bing S Zhou

Nat Med 2015 Jun 11;21(6):563-71. Epub 2015 May 11.

1] Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [2] Pediatric Translational Medicine Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [3] Department of Pharmacology, School of Basic Medicine and Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China. [4] Collaborative Innovation Center of Systems Biomedicine, National Research Center for Translational Medicine, Shanghai, China.

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June 2015

Rise and fall of subclones from diagnosis to relapse in pediatric B-acute lymphoblastic leukaemia.

Authors:
Xiaotu Ma Michael Edmonson Donald Yergeau Donna M Muzny Oliver A Hampton Michael Rusch Guangchun Song John Easton Richard C Harvey David A Wheeler Jing Ma HarshaVardhan Doddapaneni Bhavin Vadodaria Gang Wu Panduka Nagahawatte William L Carroll I-Ming Chen Julie M Gastier-Foster Mary V Relling Malcolm A Smith Meenakshi Devidas Jaime M Guidry Auvil James R Downing Mignon L Loh Cheryl L Willman Daniela S Gerhard Charles G Mullighan Stephen P Hunger Jinghui Zhang

Nat Commun 2015 Mar 19;6:6604. Epub 2015 Mar 19.

Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.

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March 2015

Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations.

Authors:
Franck Tirode Didier Surdez Xiaotu Ma Matthew Parker Marie Cécile Le Deley Armita Bahrami Zhaojie Zhang Eve Lapouble Sandrine Grossetête-Lalami Michael Rusch Stéphanie Reynaud Thomas Rio-Frio Erin Hedlund Gang Wu Xiang Chen Gaelle Pierron Odile Oberlin Sakina Zaidi Gordon Lemmon Pankaj Gupta Bhavin Vadodaria John Easton Marta Gut Li Ding Elaine R Mardis Richard K Wilson Sheila Shurtleff Valérie Laurence Jean Michon Perrine Marec-Bérard Ivo Gut James Downing Michael Dyer Jinghui Zhang Olivier Delattre

Cancer Discov 2014 Nov 15;4(11):1342-53. Epub 2014 Sep 15.

INSERM U830, Laboratory of Genetics and Cancer Biology, Institut Curie, Paris, France. Centre de Recherche, Institut Curie, Paris, France.

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November 2014

A search for novel cancer/testis antigens in lung cancer identifies VCX/Y genes, expanding the repertoire of potential immunotherapeutic targets.

Authors:
Ayumu Taguchi Allen D Taylor Jaime Rodriguez Müge Celiktaş Hui Liu Xiaotu Ma Qing Zhang Chee-Hong Wong Alice Chin Luc Girard Carmen Behrens Wan L Lam Stephen Lam John D Minna Ignacio I Wistuba Adi F Gazdar Samir M Hanash

Cancer Res 2014 Sep 26;74(17):4694-705. Epub 2014 Jun 26.

Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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September 2014

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma.

Authors:
Gang Wu Alexander K Diaz Barbara S Paugh Sherri L Rankin Bensheng Ju Yongjin Li Xiaoyan Zhu Chunxu Qu Xiang Chen Junyuan Zhang John Easton Michael Edmonson Xiaotu Ma Charles Lu Panduka Nagahawatte Erin Hedlund Michael Rusch Stanley Pounds Tong Lin Arzu Onar-Thomas Robert Huether Richard Kriwacki Matthew Parker Pankaj Gupta Jared Becksfort Lei Wei Heather L Mulder Kristy Boggs Bhavin Vadodaria Donald Yergeau Jake C Russell Kerri Ochoa Robert S Fulton Lucinda L Fulton Chris Jones Frederick A Boop Alberto Broniscer Cynthia Wetmore Amar Gajjar Li Ding Elaine R Mardis Richard K Wilson Michael R Taylor James R Downing David W Ellison Jinghui Zhang Suzanne J Baker

Nat Genet 2014 May 6;46(5):444-450. Epub 2014 Apr 6.

Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105.

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May 2014

Effect of estrogen receptor α binding on functional DNA methylation in breast cancer.

Authors:
Matthew Ung Xiaotu Ma Kevin C Johnson Brock C Christensen Chao Cheng

Epigenetics 2014 Apr 16;9(4):523-32. Epub 2014 Jan 16.

Department of Genetics; Geisel School of Medicine at Dartmouth; Hanover, NH USA; Institute for Quantitative Biomedical Sciences; Geisel School of Medicine at Dartmouth; Lebanon, NH USA; Norris Cotton Cancer Center; Geisel School of Medicine at Dartmouth; Lebanon, NH USA.

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April 2014

Identification of breast cancer DNA methylation markers optimized for fine-needle aspiration samples.

Authors:
Dawei Bu Cheryl M Lewis Venetia Sarode Min Chen Xiaotu Ma Aaron M Lazorwitz Roshni Rao Marilyn Leitch Amy Moldrem Valerie Andrews Adi Gazdar David Euhus

Cancer Epidemiol Biomarkers Prev 2013 Dec 2;22(12):2212-21. Epub 2013 Oct 2.

Authors' Affiliations: Departments of Surgery, Pathology, Clinical Sciences, and Pathology, Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center; and Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas, Dallas, Texas.

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December 2013

CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer.

Authors:
Kit W Tam Wei Zhang Junichi Soh Victor Stastny Min Chen Han Sun Kelsie Thu Jonathan J Rios Chenchen Yang Crystal N Marconett Suhaida A Selamat Ite A Laird-Offringa Ayumu Taguchi Samir Hanash David Shames Xiaotu Ma Michael Q Zhang Wan L Lam Adi Gazdar

J Thorac Oncol 2013 Nov;8(11):1378-88

*Hamon Center for Therapeutic Oncology Research and †Division of Biostatistics, University of Texas Southwestern Medical Center, Dallas, Texas; ‡Department of Integrative Oncology, British Columbia Cancer Agency Research Centre, Vancouver, B.C., Canada; §Texas Scottish Rite Hospital for Children, Dallas, Texas; ‖Department of Surgery, Biochemistry, and Molecular Biology, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, Los Angeles, California; ¶Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; #Oncology Biomarker Development, Genentech Inc., South San Francisco, California; **Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Dallas, Texas; and ††Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas.

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November 2013

Integrative approaches for predicting protein function and prioritizing genes for complex phenotypes using protein interaction networks.

Authors:
Xiaotu Ma Ting Chen Fengzhu Sun

Brief Bioinform 2014 Sep 19;15(5):685-98. Epub 2013 Jun 19.

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September 2014

DNA methylation data analysis and its application to cancer research.

Authors:
Xiaotu Ma Yi-Wei Wang Michael Q Zhang Adi F Gazdar

Epigenomics 2013 Jun;5(3):301-16

Department of Molecular & Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX 75080, USA.

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June 2013

Bivalent-like chromatin markers are predictive for transcription start site distribution in human.

Authors:
Zhihua Zhang Xiaotu Ma Michael Q Zhang

PLoS One 2012 29;7(6):e38112. Epub 2012 Jun 29.

Department of Molecular Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, Texas, United States of America.

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November 2012

Altered expression profiles of microRNAs upon arsenic exposure of human umbilical vein endothelial cells.

Authors:
Xinna Li Yanfen Shi Yudan Wei Xiaotu Ma Yulin Li Ronggui Li

Environ Toxicol Pharmacol 2012 Sep 19;34(2):381-387. Epub 2012 May 19.

Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun 130021, China. Electronic address:

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September 2012

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Authors:
Xiaotu Ma Ashwinikumar Kulkarni Zhihua Zhang Zhenyu Xuan Robert Serfling Michael Q Zhang

Nucleic Acids Res 2012 Apr 6;40(7):e50. Epub 2012 Jan 6.

Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA.

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April 2012

Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment.

Authors:
Jie Wang Yu Wang Zhuo Wang Lei Liu Xin-Guang Zhu Xiaotu Ma

BMC Evol Biol 2011 Jun 13;11:161. Epub 2011 Jun 13.

Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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June 2011

Understanding protein evolutionary rate by integrating gene co-expression with protein interactions.

Authors:
Kaifang Pang Chao Cheng Zhenyu Xuan Huanye Sheng Xiaotu Ma

BMC Syst Biol 2010 Dec 30;4:179. Epub 2010 Dec 30.

Department of Computer Science and Engineering, Shanghai Jiao Tong University, China.

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December 2010

Understanding gene essentiality by finely characterizing hubs in the yeast protein interaction network.

Authors:
Kaifang Pang Huanye Sheng Xiaotu Ma

Biochem Biophys Res Commun 2010 Oct 15;401(1):112-6. Epub 2010 Sep 15.

Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.

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October 2010

Chromatin regulation and gene centrality are essential for controlling fitness pleiotropy in yeast.

Authors:
Linqi Zhou Xiaotu Ma Michelle N Arbeitman Fengzhu Sun

PLoS One 2009 Nov 30;4(11):e8086. Epub 2009 Nov 30.

Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

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November 2009

Evolution of Drosophila ribosomal protein gene core promoters.

Authors:
Xiaotu Ma Kangyu Zhang Xiaoman Li

Gene 2009 Mar 7;432(1-2):54-9. Epub 2008 Nov 7.

Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China.

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March 2009

The effects of protein interactions, gene essentiality and regulatory regions on expression variation.

Authors:
Linqi Zhou Xiaotu Ma Fengzhu Sun

BMC Syst Biol 2008 Jun 26;2:54. Epub 2008 Jun 26.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2913, USA.

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June 2008

Mapping genetically compensatory pathways from synthetic lethal interactions in yeast.

Authors:
Xiaotu Ma Aaron M Tarone Wenyuan Li

PLoS One 2008 Apr 9;3(4):e1922. Epub 2008 Apr 9.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.

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April 2008

CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data.

Authors:
Xiaotu Ma Hyunju Lee Li Wang Fengzhu Sun

Bioinformatics 2007 Jan 10;23(2):215-21. Epub 2006 Nov 10.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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January 2007

Removed: Integrative differential gene expression analysis for cross-platform microarray datasets.

Authors:
Fei Pan Xiaotu Ma Xianghong Jasmine Zhou

J Biomed Inform 2006 Aug 22. Epub 2006 Aug 22.

Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

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August 2006

MARD: a new method to detect differential gene expression in treatment-control time courses.

Authors:
Chao Cheng Xiaotu Ma Xiting Yan Fengzhu Sun Lei M Li

Bioinformatics 2006 Nov 23;22(21):2650-7. Epub 2006 Aug 23.

Molecular and Computational Biology Program, Department of Biological Sciences, Computational Biology, University of Southern California Los Angeles, CA, USA.

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November 2006

Last intron of the chemokine-like factor gene contains a putative promoter for the downstream CKLF super family member 1 gene.

Authors:
Mingxu Xu Wenling Han Mingping Qian Xiaotu Ma Peiguo Ding Ying Wang Donglan Xia Min Rui Lu Wang Yinmei Zhang Dalong Ma

Biochem Biophys Res Commun 2004 Jan;313(1):135-41

Laboratory of Medical Immunology, School of Basic Medical Science, Peking University, 38 Xueyuan Road, Beijing 100083, PR China.

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January 2004