Publications by authors named "Xiaotu Ma"

66Publications

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

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

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

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.

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.

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

Germline Mutations in Predisposition Genes in Pediatric Cancer.

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

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

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.

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.

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.

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

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

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.

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.

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

DNA methylation data analysis and its application to cancer research.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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