Keith A Baggerly

Keith A Baggerly

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Keith A Baggerly

Publications by authors named "Keith A Baggerly"

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Refining statistics clarifies leukaemic stem cell genomics.

Authors:
Shelley M Herbrich Keith A Baggerly Marina Konopleva

Br J Haematol 2019 Jun 26;185(5):1005-1007. Epub 2018 Nov 26.

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1111/bjh.15697DOI Listing
June 2019

Pan-cancer genomic analysis links 3'UTR DNA methylation with increased gene expression in T cells.

Authors:
Michael H McGuire Shelley M Herbrich Santosh K Dasari Sherry Y Wu Ying Wang Rajesha Rupaimoole Gabriel Lopez-Berestein Keith A Baggerly Anil K Sood

EBioMedicine 2019 May 2;43:127-137. Epub 2019 May 2.

Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2019.04.045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558231PMC
May 2019

Proteomic Profiling of Signaling Networks Modulated by G-CSF/Plerixafor/Busulfan-Fludarabine Conditioning in Acute Myeloid Leukemia Patients in Remission or with Active Disease prior to Allogeneic Stem Cell Transplantation.

Authors:
Zhihong Zeng Wenbin Liu Christopher B Benton Sergej Konoplev Hongbo Lu Rui-Yu Wang Julianne Chen Elizabeth Shpall Keith A Baggerly Richard Champlin Marina Konopleva

Acta Haematol 2019 21;142(3):176-184. Epub 2019 May 21.

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,

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http://dx.doi.org/10.1159/000495456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6792289PMC
May 2019

Defining Survivorship Trajectories Across Patients With Solid Tumors: An Evidence-Based Approach.

Authors:
Robert L Dood Yang Zhao Shannon D Armbruster Robert L Coleman Shelley Tworoger Anil K Sood Keith A Baggerly

JAMA Oncol 2018 11;4(11):1519-1526

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston.

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http://dx.doi.org/10.1001/jamaoncol.2018.2761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6248088PMC
November 2018

A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.

Authors:
Ashton C Berger Anil Korkut Rupa S Kanchi Apurva M Hegde Walter Lenoir Wenbin Liu Yuexin Liu Huihui Fan Hui Shen Visweswaran Ravikumar Arvind Rao Andre Schultz Xubin Li Pavel Sumazin Cecilia Williams Pieter Mestdagh Preethi H Gunaratne Christina Yau Reanne Bowlby A Gordon Robertson Daniel G Tiezzi Chen Wang Andrew D Cherniack Andrew K Godwin Nicole M Kuderer Janet S Rader Rosemary E Zuna Anil K Sood Alexander J Lazar Akinyemi I Ojesina Clement Adebamowo Sally N Adebamowo Keith A Baggerly Ting-Wen Chen Hua-Sheng Chiu Steve Lefever Liang Liu Karen MacKenzie Sandra Orsulic Jason Roszik Carl Simon Shelley Qianqian Song Christopher P Vellano Nicolas Wentzensen John N Weinstein Gordon B Mills Douglas A Levine Rehan Akbani

Cancer Cell 2018 04 2;33(4):690-705.e9. Epub 2018 Apr 2.

Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2018.03.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5959730PMC
April 2018

Genetic Polymorphisms of CFH and ARMS2 Do Not Predict Response to Antioxidants and Zinc in Patients with Age-Related Macular Degeneration: Independent Statistical Evaluations of Data from the Age-Related Eye Disease Study.

Authors:
Melissa J Assel Fan Li Ying Wang Andrew S Allen Keith A Baggerly Andrew J Vickers

Ophthalmology 2018 03 9;125(3):391-397. Epub 2017 Oct 9.

Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York. Electronic address:

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http://dx.doi.org/10.1016/j.ophtha.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820191PMC
March 2018

Macrophage depletion through colony stimulating factor 1 receptor pathway blockade overcomes adaptive resistance to anti-VEGF therapy.

Authors:
Yasmin A Lyons Sunila Pradeep Sherry Y Wu Monika Haemmerle Jean M Hansen Michael J Wagner Alejandro Villar-Prados Archana S Nagaraja Robert L Dood Rebecca A Previs Wei Hu Yang Zhao Duncan H Mak Zhilan Xiao Brenda D Melendez Gregory A Lizee Imelda Mercado-Uribe Keith A Baggerly Patrick Hwu Jinsong Liu Willem W Overwijk Robert L Coleman Anil K Sood

Oncotarget 2017 Nov 24;8(57):96496-96505. Epub 2017 Aug 24.

Departments of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.18632/oncotarget.20410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5722500PMC
November 2017

Elevation of TP53 Autoantibody Before CA125 in Preclinical Invasive Epithelial Ovarian Cancer.

Authors:
Wei-Lei Yang Aleksandra Gentry-Maharaj Archana Simmons Andy Ryan Evangelia Ourania Fourkala Zhen Lu Keith A Baggerly Yang Zhao Karen H Lu David Bowtell Ian Jacobs Steven J Skates Wei-Wu He Usha Menon Robert C Bast

Clin Cancer Res 2017 Oct 21;23(19):5912-5922. Epub 2017 Jun 21.

University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/1078-0432.CCR-17-0284DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626590PMC
October 2017

High-throughput profiling of signaling networks identifies mechanism-based combination therapy to eliminate microenvironmental resistance in acute myeloid leukemia.

Authors:
Zhihong Zeng Wenbin Liu Twee Tsao YiHua Qiu Yang Zhao Ismael Samudio Dos D Sarbassov Steven M Kornblau Keith A Baggerly Hagop M Kantarjian Marina Konopleva Michael Andreeff

Haematologica 2017 09 28;102(9):1537-1548. Epub 2017 Jun 28.

Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

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http://dx.doi.org/10.3324/haematol.2016.162230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5685227PMC
September 2017

Maternal 25(OH)D concentrations ≥40 ng/mL associated with 60% lower preterm birth risk among general obstetrical patients at an urban medical center.

Authors:
Sharon L McDonnell Keith A Baggerly Carole A Baggerly Jennifer L Aliano Christine B French Leo L Baggerly Myla D Ebeling Charles S Rittenberg Christopher G Goodier Julio F Mateus Niño Rebecca J Wineland Roger B Newman Bruce W Hollis Carol L Wagner

PLoS One 2017 24;12(7):e0180483. Epub 2017 Jul 24.

Medical University of South Carolina Children's Hospital, Charleston, South Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180483PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5524288PMC
September 2017

Surface PD-L1, E-cadherin, CD24, and VEGFR2 as markers of epithelial cancer stem cells associated with rapid tumorigenesis.

Authors:
Goodwin G Jinesh Ganiraju C Manyam Chinedu O Mmeje Keith A Baggerly Ashish M Kamat

Sci Rep 2017 08 29;7(1):9602. Epub 2017 Aug 29.

Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.

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http://dx.doi.org/10.1038/s41598-017-08796-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5575243PMC
August 2017

Immune cell profiling in cancer: molecular approaches to cell-specific identification.

Authors:
Yasmin A Lyons Sherry Y Wu Willem W Overwijk Keith A Baggerly Anil K Sood

NPJ Precis Oncol 2017 15;1(1):26. Epub 2017 Aug 15.

1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA.

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http://dx.doi.org/10.1038/s41698-017-0031-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871917PMC
August 2017

Integrated MicroRNA-mRNA Profiling Identifies Oncostatin M as a Marker of Mesenchymal-Like ER-Negative/HER2-Negative Breast Cancer.

Authors:
Giulia Bottai Lixia Diao Keith A Baggerly Laura Paladini Balázs Győrffy Carlotta Raschioni Lajos Pusztai George A Calin Libero Santarpia

Int J Mol Sci 2017 Jan 19;18(1). Epub 2017 Jan 19.

Oncology Experimental Therapeutics, Humanitas Clinical and Research Institute, 20089 Rozzano-Milan, Italy.

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http://www.mdpi.com/1422-0067/18/1/194
Publisher Site
http://dx.doi.org/10.3390/ijms18010194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5297825PMC
January 2017

Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer.

Authors:
Charles Chuanhai Guo Vipulkumar Dadhania Li Zhang Tadeusz Majewski Jolanta Bondaruk Maciej Sykulski Weronika Wronowska Anna Gambin Yan Wang Shizhen Zhang Enrique Fuentes-Mattei Ashish Madhav Kamat Colin Dinney Arlene Siefker-Radtke Woonyoung Choi Keith A Baggerly David McConkey John N Weinstein Bogdan Czerniak

Eur Urol 2016 10 15;70(4):611-620. Epub 2016 Mar 15.

Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2016.02.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5804336PMC
October 2016

Functional CAR models for large spatially correlated functional datasets.

Authors:
Lin Zhang Veerabhadran Baladandayuthapani Hongxiao Zhu Keith A Baggerly Tadeusz Majewski Bogdan A Czerniak Jeffrey S Morris

J Am Stat Assoc 2016 18;111(514):772-786. Epub 2016 Aug 18.

The University of Texas M.D. Anderson Cancer Center, Houston, Texas, U.S.A.

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http://dx.doi.org/10.1080/01621459.2015.1042581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176110PMC
August 2016

Optimized Prediction of Extreme Treatment Outcomes in Ovarian Cancer.

Authors:
Burook Misganaw Eren Ahsen Nitin Singh Keith A Baggerly Anna Unruh Michael A White M Vidyasagar

Cancer Inform 2015 21;14(Suppl 5):45-55. Epub 2016 Mar 21.

Cecil and Ida Green Chair in Systems Biology Science, Erik Jonsson School of Engineering and Computer Science, University of Texas at Dallas, Richardson, TX, USA.

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http://dx.doi.org/10.4137/CIN.S30803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806766PMC
April 2016

A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer.

Authors:
Sherry Y Wu Rajesha Rupaimoole Fangrong Shen Sunila Pradeep Chad V Pecot Cristina Ivan Archana S Nagaraja Kshipra M Gharpure Elizabeth Pham Hiroto Hatakeyama Michael H McGuire Monika Haemmerle Viviana Vidal-Anaya Courtney Olsen Cristian Rodriguez-Aguayo Justyna Filant Ehsan A Ehsanipour Shelley M Herbrich Sourindra N Maiti Li Huang Ji Hoon Kim Xinna Zhang Hee-Dong Han Guillermo N Armaiz-Pena Elena G Seviour Sue Tucker Min Zhang Da Yang Laurence J N Cooper Rouba Ali-Fehmi Menashe Bar-Eli Ju-Seog Lee Prahlad T Ram Keith A Baggerly Gabriel Lopez-Berestein Mien-Chie Hung Anil K Sood

Nat Commun 2016 Apr 4;7:11169. Epub 2016 Apr 4.

Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms11169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822037PMC
April 2016

Role of Increased n-acetylaspartate Levels in Cancer.

Authors:
Behrouz Zand Rebecca A Previs Niki M Zacharias Rajesha Rupaimoole Takashi Mitamura Archana Sidalaghatta Nagaraja Michele Guindani Heather J Dalton Lifeng Yang Joelle Baddour Abhinav Achreja Wei Hu Chad V Pecot Cristina Ivan Sherry Y Wu Christopher R McCullough Kshipra M Gharpure Einav Shoshan Sunila Pradeep Lingegowda S Mangala Cristian Rodriguez-Aguayo Ying Wang Alpa M Nick Michael A Davies Guillermo Armaiz-Pena Jinsong Liu Susan K Lutgendorf Keith A Baggerly Menashe Bar Eli Gabriel Lopez-Berestein Deepak Nagrath Pratip K Bhattacharya Anil K Sood

J Natl Cancer Inst 2016 Jan 26;108(6):djv426. Epub 2016 Jan 26.

Departments of Gynecologic Oncology and Reproductive Medicine (BZ, RAP, RR, TM, ASN, HJD, WH, CI, SYW, KMG, SP, LSM, AMN, GAP, AKS), Cancer Systems Imaging (NMZ, CRM, PKB), Biostatistics (MG), Cancer Medicine (CVP), Center for RNA Interference and Non-Coding RNA (CI, LSM, CRA, GLB, AKS), Cancer Biology (YS, MBE, GLB, AKS), Experimental Therapeutics (CRA, GLB), Bioinformatics and Computational Biology (YW, KAB), Melanoma Medical Oncology (MAD), and Pathology (JL), University of Texas M. D. Anderson Cancer Center, Houston, TX; Department of Nanomedicine and Bioengineering, UT Health, Houston, TX (GLB, AKS); Departments of Psychology, Urology, and Obstetrics and Gynecology, the University of Iowa, Iowa City, IA (SKL); Laboratory for Systems Biology of Human Diseases (LY, JB, AA, DN), Department of Chemical and Biomolecular Engineering (LY, JB, AA, DN), and Department of Bioengineering (DN), Rice University, Houston, TX.

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http://dx.doi.org/10.1093/jnci/djv426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849357PMC
January 2016

A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression.

Authors:
Benjamin B Shields Chad V Pecot Hua Gao Elizabeth McMillan Malia Potts Christa Nagel Scott Purinton Ying Wang Cristina Ivan Hyun Seok Kim Robert J Borkowski Shaheen Khan Cristian Rodriguez-Aguayo Gabriel Lopez-Berestein Jayanthi Lea Adi Gazdar Keith A Baggerly Anil K Sood Michael A White

Mol Syst Biol 2015 Dec 11;11(12):842. Epub 2015 Dec 11.

Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704493PMC
http://dx.doi.org/10.15252/msb.20156308DOI Listing
December 2015

Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas.

Authors:
Kanishka Sircar Suk-Young Yoo Tadeusz Majewski Khalida Wani Lalit R Patel Horatiu Voicu Wandaliz Torres-Garcia Roel G W Verhaak Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak

J Pathol Clin Res 2015 Oct 7;1(4):212-24. Epub 2015 Jul 7.

Department of Pathology The University of Texas MD Anderson Cancer Center Houston Texas USA.

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http://dx.doi.org/10.1002/cjp2.23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939892PMC
October 2015

Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy.

Authors:
Rajesh R Singh Paari Murugan Lalit R Patel Horatiu Voicu Suk-Young Yoo Tadeusz Majewski Meenakshi Mehrotra Khalida Wani Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Chad J Creighton L Jeffrey Medeiros Russell R Broaddus Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak Rajyalakshmi Luthra Kanishka Sircar

Mod Pathol 2015 Sep 26;28(9):1225-35. Epub 2015 Jun 26.

Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1038/modpathol.2015.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4556533PMC
September 2015

A Phase I/II Study of the mTOR Inhibitor Everolimus in Combination with HyperCVAD Chemotherapy in Patients with Relapsed/Refractory Acute Lymphoblastic Leukemia.

Authors:
Naval Daver Yanis Boumber Hagop Kantarjian Farhad Ravandi Jorge Cortes Michael E Rytting Jitesh D Kawedia Jordan Basnett Kirk S Culotta Zhihong Zeng Hongbo Lu Mary Ann Richie Rebecca Garris Lianchun Xiao Wenbin Liu Keith A Baggerly Elias Jabbour Susan O'Brien Jan Burger Linda J Bendall Deborah Thomas Marina Konopleva

Clin Cancer Res 2015 Jun 27;21(12):2704-14. Epub 2015 Feb 27.

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

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http://dx.doi.org/10.1158/1078-0432.CCR-14-2888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4470787PMC
June 2015

Clinically relevant microRNAs in ovarian cancer.

Authors:
Shu Zhang Zhen Lu Anna K Unruh Cristina Ivan Keith A Baggerly George A Calin Zongfang Li Robert C Bast Xiao-Feng Le

Mol Cancer Res 2015 Mar 10;13(3):393-401. Epub 2014 Oct 10.

Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.

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http://dx.doi.org/10.1158/1541-7786.MCR-14-0424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4369176PMC
March 2015

Expression of sulfotransferase SULT1A1 in cancer cells predicts susceptibility to the novel anticancer agent NSC-743380.

Authors:
Xiao Huang Mengru Cao Li Wang Shuhong Wu Xiaoying Liu Hongyu Li Hui Zhang Rui-Yu Wang Xiaoping Sun Caimiao Wei Keith A Baggerly Jack A Roth Michael Wang Stephen G Swisher Bingliang Fang

Oncotarget 2015 Jan;6(1):345-54

Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.

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http://www.oncotarget.com/fulltext/2814
Publisher Site
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381599PMC
http://dx.doi.org/10.18632/oncotarget.2814DOI Listing
January 2015

BRCA2 inhibition enhances cisplatin-mediated alterations in tumor cell proliferation, metabolism, and metastasis.

Authors:
Mateusz Rytelewski Jessica G Tong Adrian Buensuceso Hon S Leong Saman Maleki Vareki Rene Figueredo Christine Di Cresce Sherry Y Wu Shelley M Herbrich Keith A Baggerly Larissa Romanow Trevor Shepherd Bonnie J Deroo Anil K Sood Ann F Chambers Mark Vincent Peter J Ferguson James Koropatnick

Mol Oncol 2014 Dec 6;8(8):1429-40. Epub 2014 Jun 6.

Department of Microbiology and Immunology, Western University, London, Ontario, Canada; Department of Oncology, Western University, London, Ontario, Canada; Department of Pathology, Western University, London, Ontario, Canada; Department of Physiology and Pharmacology, Western University, London, Ontario, Canada; Lawson Health Research Institute, London Health Sciences Centre, London, Ontario, Canada. Electronic address:

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http://dx.doi.org/10.1016/j.molonc.2014.05.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528603PMC
December 2014

Reverse-phase protein array for prediction of patients at low risk of developing bone metastasis from breast cancer.

Authors:
Naoki Hayashi Ganiraju C Manyam Ana M Gonzalez-Angulo Naoki Niikura Hideko Yamauchi Seigo Nakamura Gabriel N Hortobágyi Keith A Baggerly Naoto T Ueno

Oncologist 2014 Sep 12;19(9):909-14. Epub 2014 Aug 12.

Departments of Breast Medical Oncology, Bioinformatics and Computational Biology, and Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Department of Breast Surgical Oncology, St. Luke's International Hospital, Tokyo, Japan; Department of Surgery, Division of Breast Surgical Oncology, The Showa University School of Medicine, Tokyo, Japan

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http://dx.doi.org/10.1634/theoncologist.2014-0099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4153464PMC
September 2014

Focal adhesion kinase: an alternative focus for anti-angiogenesis therapy in ovarian cancer.

Authors:
Rebecca L Stone Keith A Baggerly Guillermo N Armaiz-Pena Yu Kang Angela M Sanguino Duangmani Thanapprapasr Heather J Dalton Justin Bottsford-Miller Behrouz Zand Rehan Akbani Lixia Diao Alpa M Nick Koen DeGeest Gabriel Lopez-Berestein Robert L Coleman Susan Lutgendorf Anil K Sood

Cancer Biol Ther 2014 Jul 23;15(7):919-29. Epub 2014 Apr 23.

Department of Gynecologic Oncology; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA; Department of Cancer Biology; The University of Texas M.D. Anderson Cancer Center; Houston, TX USA.

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http://dx.doi.org/10.4161/cbt.28882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100993PMC
July 2014

Notch3 pathway alterations in ovarian cancer.

Authors:
Wei Hu Tao Liu Cristina Ivan Yunjie Sun Jie Huang Lingegowda S Mangala Takahito Miyake Heather J Dalton Sunila Pradeep Rajesh Rupaimoole Rebecca A Previs Hee Dong Han Justin Bottsford-Miller Behrouz Zand Yu Kang Chad V Pecot Alpa M Nick Sherry Y Wu Ju-Seog Lee Vasudha Sehgal Prahlad Ram Jinsong Liu Susan L Tucker Gabriel Lopez-Berestein Keith A Baggerly Robert L Coleman Anil K Sood

Cancer Res 2014 Jun 17;74(12):3282-93. Epub 2014 Apr 17.

Authors' Affiliations: Departments of Gynecologic Oncology and Reproductive Medicine, Systems Biology, Pathology, Experimental Therapeutics, Bioinformatics and Computational Biology, Cancer Biology, Thoracic/Head and Neck Medical Oncology, and The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TexasAuthors' Affiliations: Departments of Gynecologic Oncology and Reproductive Medicine, Systems Biology, Pathology, Experimental Therapeutics, Bioinformatics and Computational Biology, Cancer Biology, Thoracic/Head and Neck Medical Oncology, and The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TexasAuthors' Affiliations: Departments of Gynecologic Oncology and Reproductive Medicine, Systems Biology, Pathology, Experimental Therapeutics, Bioinformatics and Computational Biology, Cancer Biology, Thoracic/Head and Neck Medical Oncology, and The Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas

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http://dx.doi.org/10.1158/0008-5472.CAN-13-2066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058356PMC
June 2014

Molecular biomarkers of residual disease after surgical debulking of high-grade serous ovarian cancer.

Authors:
Susan L Tucker Kshipra Gharpure Shelley M Herbrich Anna K Unruh Alpa M Nick Erin K Crane Robert L Coleman Jamie Guenthoer Heather J Dalton Sherry Y Wu Rajesha Rupaimoole Gabriel Lopez-Berestein Bulent Ozpolat Cristina Ivan Wei Hu Keith A Baggerly Anil K Sood

Clin Cancer Res 2014 Jun 22;20(12):3280-8. Epub 2014 Apr 22.

Authors' Affiliations: Departments of Bioinformatics and Computational Biology, Gynecologic Oncology and Reproductive Medicine, Experimental Therapeutics, Cancer Biology, and Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Fred Hutchinson Cancer Research Center, Seattle, WashingtonAuthors' Affiliations: Departments of Bioinformatics and Computational Biology, Gynecologic Oncology and Reproductive Medicine, Experimental Therapeutics, Cancer Biology, and Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Fred Hutchinson Cancer Research Center, Seattle, WashingtonAuthors' Affiliations: Departments of Bioinformatics and Computational Biology, Gynecologic Oncology and Reproductive Medicine, Experimental Therapeutics, Cancer Biology, and Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Fred Hutchinson Cancer Research Center, Seattle, Washington

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http://clincancerres.aacrjournals.org/cgi/doi/10.1158/1078-0
Publisher Site
http://dx.doi.org/10.1158/1078-0432.CCR-14-0445DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4062703PMC
June 2014

illuminaio: An open source IDAT parsing tool for Illumina microarrays.

Authors:
Mike L Smith Keith A Baggerly Henrik Bengtsson Matthew E Ritchie Kasper D Hansen

F1000Res 2013 4;2:264. Epub 2013 Dec 4.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA ; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.

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http://dx.doi.org/10.12688/f1000research.2-264.v1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968891PMC
April 2014

Tumour angiogenesis regulation by the miR-200 family.

Authors:
Chad V Pecot Rajesha Rupaimoole Da Yang Rehan Akbani Cristina Ivan Chunhua Lu Sherry Wu Hee-Dong Han Maitri Y Shah Cristian Rodriguez-Aguayo Justin Bottsford-Miller Yuexin Liu Sang Bae Kim Anna Unruh Vianey Gonzalez-Villasana Li Huang Behrouz Zand Myrthala Moreno-Smith Lingegowda S Mangala Morgan Taylor Heather J Dalton Vasudha Sehgal Yunfei Wen Yu Kang Keith A Baggerly Ju-Seog Lee Prahlad T Ram Murali K Ravoori Vikas Kundra Xinna Zhang Rouba Ali-Fehmi Ana-Maria Gonzalez-Angulo Pierre P Massion George A Calin Gabriel Lopez-Berestein Wei Zhang Anil K Sood

Nat Commun 2013 ;4:2427

Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 950, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/ncomms3427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904438PMC
April 2014

Preclinical and early clinical evaluation of the oral AKT inhibitor, MK-2206, for the treatment of acute myelogenous leukemia.

Authors:
Marina Y Konopleva Roland B Walter Stefan H Faderl Elias J Jabbour Zhihong Zeng Gautam Borthakur Xuelin Huang Tapan M Kadia Peter P Ruvolo Jennie B Feliu Hongbo Lu Lakiesha Debose Jan A Burger Michael Andreeff Wenbin Liu Keith A Baggerly Steven M Kornblau L Austin Doyle Elihu H Estey Hagop M Kantarjian

Clin Cancer Res 2014 Apr 28;20(8):2226-35. Epub 2014 Feb 28.

Authors' Affiliations: Department of Leukemia; Division of Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Hematology/Department of Medicine; Department of Epidemiology, University of Washington, Seattle, Washington; and National Cancer Institute, Rockville, Maryland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989412PMC
April 2014

Most expression and splicing changes in myotonic dystrophy type 1 and type 2 skeletal muscle are shared with other muscular dystrophies.

Authors:
Linda L Bachinski Keith A Baggerly Valerie L Neubauer Tamara J Nixon Olayinka Raheem Mario Sirito Anna K Unruh Jiexin Zhang Lalitha Nagarajan Lubov T Timchenko Guillaume Bassez Bruno Eymard Josep Gamez Tetsuo Ashizawa Jerry R Mendell Bjarne Udd Ralf Krahe

Neuromuscul Disord 2014 Mar 15;24(3):227-40. Epub 2013 Nov 15.

Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Graduate Programs in Human & Molecular Genetics, University of Texas at Houston Graduate School in Biomedical Sciences, Houston, TX, USA; Graduate Programs in Genes & Development, University of Texas at Houston Graduate School in Biomedical Sciences, Houston, TX, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943873PMC
March 2014

2'-OMe-phosphorodithioate-modified siRNAs show increased loading into the RISC complex and enhanced anti-tumour activity.

Authors:
Sherry Y Wu Xianbin Yang Kshipra M Gharpure Hiroto Hatakeyama Martin Egli Michael H McGuire Archana S Nagaraja Takahito M Miyake Rajesha Rupaimoole Chad V Pecot Morgan Taylor Sunila Pradeep Malgorzata Sierant Cristian Rodriguez-Aguayo Hyun J Choi Rebecca A Previs Guillermo N Armaiz-Pena Li Huang Carlos Martinez Tom Hassell Cristina Ivan Vasudha Sehgal Richa Singhania Hee-Dong Han Chang Su Ji Hoon Kim Heather J Dalton Chandra Kovvali Khandan Keyomarsi Nigel A J McMillan Willem W Overwijk Jinsong Liu Ju-Seog Lee Keith A Baggerly Gabriel Lopez-Berestein Prahlad T Ram Barbara Nawrot Anil K Sood

Nat Commun 2014 Mar 12;5:3459. Epub 2014 Mar 12.

1] Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas 77054, USA [2] Center for RNA Interference and Non-Coding RNA, MDACC, Houston, Texas 77054, USA [3] Department of Cancer Biology, MDACC, Houston, Texas 77054, USA.

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http://dx.doi.org/10.1038/ncomms4459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112501PMC
March 2014

Targeting SRC and tubulin in mucinous ovarian carcinoma.

Authors:
Tao Liu Wei Hu Heather J Dalton Hyun Jin Choi Jie Huang Yu Kang Sunila Pradeep Takahito Miyake Jian H Song Yunfei Wen Chunhua Lu Chad V Pecot Justin Bottsford-Miller Behrouz Zand Nicholas B Jennings Cristina Ivan Gary E Gallick Keith A Baggerly David G Hangauer Robert L Coleman Michael Frumovitz Anil K Sood

Clin Cancer Res 2013 Dec 7;19(23):6532-43. Epub 2013 Oct 7.

Authors' Affiliations: Departments of Gynecologic Oncology and Reproductive Medicine, Genitourinary Medical Oncology, Bioinformatics and Computational Biology, and Cancer Biology; Division of Cancer Medicine; Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas; Kinex Pharmaceuticals LLC, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York; Department of General Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei; Department of Gynecology, Obstetrics and Gynecology, Hospital of Fudan University, Shanghai, P.R. China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852199PMC
December 2013

Comparison of molecular subtype distribution in triple-negative inflammatory and non-inflammatory breast cancers.

Authors:
Hiroko Masuda Keith A Baggerly Ying Wang Takayuki Iwamoto Takae Brewer Lajos Pusztai Kazuharu Kai Takahiro Kogawa Pascal Finetti Daniel Birnbaum Luc Dirix Wendy A Woodward James M Reuben Savitri Krishnamurthy W Symmans Steven J Van Laere François Bertucci Gabriel N Hortobagyi Naoto T Ueno

Breast Cancer Res 2013 Nov 25;15(6):R112. Epub 2013 Nov 25.

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November 2013

Differential response to neoadjuvant chemotherapy among 7 triple-negative breast cancer molecular subtypes.

Authors:
Hiroko Masuda Keith A Baggerly Ying Wang Ya Zhang Ana Maria Gonzalez-Angulo Funda Meric-Bernstam Vicente Valero Brian D Lehmann Jennifer A Pietenpol Gabriel N Hortobagyi W Fraser Symmans Naoto T Ueno

Clin Cancer Res 2013 Oct 15;19(19):5533-40. Epub 2013 Aug 15.

Authors' Affiliations: Morgan Welch Inflammatory Breast Cancer Research Program and Clinic; Departments of Breast Medical Oncology, Bioinformatics and Computational Biology, Pathology, and Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; and Department of Biochemistry, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813597PMC
October 2013

Independent validation of a model using cell line chemosensitivity to predict response to therapy.

Authors:
Wenting Wang Keith A Baggerly Steen Knudsen Jon Askaa Wiktor Mazin Kevin R Coombes

J Natl Cancer Inst 2013 Sep 20;105(17):1284-91. Epub 2013 Aug 20.

Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA.

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http://dx.doi.org/10.1093/jnci/djt202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955959PMC
September 2013

Bisphosphorylated PEA-15 sensitizes ovarian cancer cells to paclitaxel by impairing the microtubule-destabilizing effect of SCLIP.

Authors:
Xuemei Xie Chandra Bartholomeusz Ahmed A Ahmed Anna Kazansky Lixia Diao Keith A Baggerly Gabriel N Hortobagyi Naoto T Ueno

Mol Cancer Ther 2013 Jun 29;12(6):1099-111. Epub 2013 Mar 29.

Section of Translational Breast Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1158/1535-7163.MCT-12-0737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681833PMC
June 2013

Metabolic shifts induced by fatty acid synthase inhibitor orlistat in non-small cell lung carcinoma cells provide novel pharmacodynamic biomarkers for positron emission tomography and magnetic resonance spectroscopy.

Authors:
Madhuri Sankaranarayanapillai Nianxiang Zhang Keith A Baggerly Juri G Gelovani

Mol Imaging Biol 2013 Apr;15(2):136-47

Department of Experimental Diagnostic Imaging, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1007/s11307-012-0587-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3591534PMC
April 2013

Epigenetic analysis of the Notch superfamily in high-grade serous ovarian cancer.

Authors:
Cristina Ivan Wei Hu Justin Bottsford-Miller Behrouz Zand Heather J Dalton Tao Liu Jie Huang Alpa M Nick Gabriel Lopez-Berestein Robert L Coleman Keith A Baggerly Anil K Sood

Gynecol Oncol 2013 Mar 28;128(3):506-11. Epub 2012 Nov 28.

Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.

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http://dx.doi.org/10.1016/j.ygyno.2012.11.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645276PMC
March 2013

Targeting of mTORC1/2 by the mTOR kinase inhibitor PP242 induces apoptosis in AML cells under conditions mimicking the bone marrow microenvironment.

Authors:
Zhihong Zeng Yue Xi Shi Twee Tsao YiHua Qiu Steven M Kornblau Keith A Baggerly Wenbin Liu Katti Jessen Yi Liu Hagop Kantarjian Christian Rommel David A Fruman Michael Andreeff Marina Konopleva

Blood 2012 Sep 23;120(13):2679-89. Epub 2012 Jul 23.

Departments of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1182/blood-2011-11-393934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460689PMC
September 2012

Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots.

Authors:
E Shannon Neeley Keith A Baggerly Steven M Kornblau

Cancer Inform 2012 11;11:77-86. Epub 2012 Apr 11.

Brigham Young University, Department of Statistics, Provo, UT, USA.

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http://dx.doi.org/10.4137/CIN.S9055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329188PMC
August 2012

Protein and phosphoprotein levels in glioma and adenocarcinoma cell lines grown in normoxia and hypoxia in monolayer and three-dimensional cultures.

Authors:
Victor A Levin Sonali Panchabhai Li Shen Keith A Baggerly

Proteome Sci 2012 Jan 25;10(1). Epub 2012 Jan 25.

Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317865PMC
January 2012

Silencing of p130cas in ovarian carcinoma: a novel mechanism for tumor cell death.

Authors:
Alpa M Nick Rebecca L Stone Guillermo Armaiz-Pena Bulent Ozpolat Ibrahim Tekedereli Whitney S Graybill Charles N Landen Gabriel Villares Pablo Vivas-Mejia Justin Bottsford-Miller Hye Sun Kim Ju-Seog Lee Soo Mi Kim Keith A Baggerly Prahlad T Ram Michael T Deavers Robert L Coleman Gabriel Lopez-Berestein Anil K Sood

J Natl Cancer Inst 2011 Nov 28;103(21):1596-612. Epub 2011 Sep 28.

Department of Gynecologic Oncology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77230-1439, USA.

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http://dx.doi.org/10.1093/jnci/djr372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3206039PMC
November 2011

Bias, randomization, and ovarian proteomic data: a reply to "producers and consumers".

Authors:
Keith A Baggerly Kevin R Coombes Jeffrey S Morris

Cancer Inform 2005 ;1:9-14

Department of Biostatistics, U.T. M.D. Anderson Cancer Center, Houston, Texas, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657654PMC
July 2011

Understanding the characteristics of mass spectrometry data through the use of simulation.

Authors:
Kevin R Coombes John M Koomen Keith A Baggerly Jeffrey S Morris Ryuji Kobayashi

Cancer Inform 2005 ;1:41-52

Departments of Biostatistics and Applied Mathematics, University of Texas M.D. Anderson Cancer Center, Houston TX 77030 USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657656PMC
July 2011

Population frequency of myotonic dystrophy: higher than expected frequency of myotonic dystrophy type 2 (DM2) mutation in Finland.

Authors:
Tiina Suominen Linda L Bachinski Satu Auvinen Peter Hackman Keith A Baggerly Corrado Angelini Leena Peltonen Ralf Krahe Bjarne Udd

Eur J Hum Genet 2011 Jul 2;19(7):776-82. Epub 2011 Mar 2.

Neuromuscular Research Unit, Medical School, University of Tampere, Tampere, Finland.

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http://dx.doi.org/10.1038/ejhg.2011.23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137497PMC
July 2011

What information should be required to support clinical "omics" publications?

Authors:
Keith A Baggerly Kevin R Coombes

Clin Chem 2011 May;57(5):688-90

Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1373/clinchem.2010.158618DOI Listing
May 2011

Reproducibility of SELDI Spectra Across Time and Laboratories.

Authors:
Lixia Diao Charlotte H Clarke Kevin R Coombes Stanley R Hamilton Jack Roth Li Mao Bogdan Czerniak Keith A Baggerly Jeffrey S Morris Eric T Fung Robert C Bast

Cancer Inform 2011 Mar 14;10:45-64. Epub 2011 Mar 14.

Departments of Bioinformatics and Computational Biology.

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http://dx.doi.org/10.4137/CIN.S6438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3085423PMC
March 2011

Methylation of the candidate biomarker TCF21 is very frequent across a spectrum of early-stage nonsmall cell lung cancers.

Authors:
Kristy L Richards Baili Zhang Menghong Sun Wenli Dong Jennifer Churchill Linda L Bachinski Charmaine D Wilson Keith A Baggerly Guosheng Yin D Neil Hayes Ignacio I Wistuba Ralf Krahe

Cancer 2011 Feb 13;117(3):606-17. Epub 2010 Oct 13.

Department of Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1002/cncr.25472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023841PMC
February 2011

Altered MEF2 isoforms in myotonic dystrophy and other neuromuscular disorders.

Authors:
Linda L Bachinski Mario Sirito Maria Böhme Keith A Baggerly Bjarne Udd Ralf Krahe

Muscle Nerve 2010 Dec;42(6):856-63

Department of Genetics, M.D. Anderson Cancer Center, Unit 1010, University of Texas, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, USA.

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http://doi.wiley.com/10.1002/mus.21789
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136472PMC
December 2010

Blasted cell line names.

Authors:
Jing Wang Lauren A Byers John S Yordy Wenbin Liu Li Shen Keith A Baggerly Uma Giri Jeffrey N Myers K Kian Ang Michael D Story Luc Girard John D Minna John V Heymach Kevin R Coombes

Cancer Inform 2010 Oct 14;9:251-5. Epub 2010 Oct 14.

Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978931PMC
October 2010

Statistical contributions to proteomic research.

Authors:
Jeffrey S Morris Keith A Baggerly Howard B Gutstein Kevin R Coombes

Methods Mol Biol 2010 ;641:143-66

Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1007/978-1-60761-711-2_9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889133PMC
August 2010

Clinical evaluation of chemotherapy response predictors developed from breast cancer cell lines.

Authors:
Cornelia Liedtke Jing Wang Attila Tordai William F Symmans Gabriel N Hortobagyi Ludwig Kiesel Kenneth Hess Keith A Baggerly Kevin R Coombes Lajos Pusztai

Breast Cancer Res Treat 2010 Jun 15;121(2):301-9. Epub 2009 Jul 15.

Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, BO Box 301439, Houston, TX 77030-1439, USA.

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http://dx.doi.org/10.1007/s10549-009-0445-7DOI Listing
June 2010

Differences in aberrant expression and splicing of sarcomeric proteins in the myotonic dystrophies DM1 and DM2.

Authors:
Anna Vihola Linda L Bachinski Mario Sirito Shodimu-Emmanuel Olufemi Shohrae Hajibashi Keith A Baggerly Olayinka Raheem Hannu Haapasalo Tiina Suominen Jeanette Holmlund-Hampf Anders Paetau Rosanna Cardani Giovanni Meola Hannu Kalimo Lars Edström Ralf Krahe Bjarne Udd

Acta Neuropathol 2010 Apr 12;119(4):465-79. Epub 2010 Jan 12.

Department of Medical Genetics, Folkhälsan Institute of Genetics, University of Helsinki, 00014 Helsinki, Finland.

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http://dx.doi.org/10.1007/s00401-010-0637-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199327PMC
April 2010

Different changes in protein and phosphoprotein levels result from serum starvation of high-grade glioma and adenocarcinoma cell lines.

Authors:
Victor A Levin Sonali C Panchabhai Li Shen Steven M Kornblau Yihua Qiu Keith A Baggerly

J Proteome Res 2010 Jan;9(1):179-91

Departments of Neuro-Oncology, Bioinformatics and Computational Biology, and Blood and Marrow Transplantation, Section of Molecular Hematology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA.

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http://dx.doi.org/10.1021/pr900392bDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3386607PMC
January 2010

Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines.

Authors:
Hannah C Cheung Tao Hai Wen Zhu Keith A Baggerly Spiridon Tsavachidis Ralf Krahe Gilbert J Cote

Brain 2009 Aug 8;132(Pt 8):2277-88. Epub 2009 Jun 8.

Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/brain/awp153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2724917PMC
August 2009

Genome-wide hypomethylation in head and neck cancer is more pronounced in HPV-negative tumors and is associated with genomic instability.

Authors:
Kristy L Richards Baili Zhang Keith A Baggerly Stefano Colella James C Lang David E Schuller Ralf Krahe

PLoS One 2009 18;4(3):e4941. Epub 2009 Mar 18.

Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654169PMC
July 2009

Variable slope normalization of reverse phase protein arrays.

Authors:
E Shannon Neeley Steven M Kornblau Kevin R Coombes Keith A Baggerly

Bioinformatics 2009 Jun 31;25(11):1384-9. Epub 2009 Mar 31.

Department of Statistics, Rice University, Houston, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968550PMC
June 2009

Dual targeting of EphA2 and FAK in ovarian carcinoma.

Authors:
Mian M K Shahzad Chunhua Lu Jeong-Won Lee Rebecca L Stone Rahul Mitra Lingegowda S Mangala Yiling Lu Keith A Baggerly Christopher G Danes Alpa M Nick Jyotsnabaran Halder Hye-Sun Kim Pablo Vivas-Mejia Charles N Landen Gabriel Lopez-Berestein Robert L Coleman Anil K Sood

Cancer Biol Ther 2009 Jun 24;8(11):1027-34. Epub 2009 Jun 24.

Department of Gynecologic Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748749PMC
http://dx.doi.org/10.4161/cbt.8.11.8523DOI Listing
June 2009

Molecular signatures of metastasis in head and neck cancer.

Authors:
Stefano Colella Kristy L Richards Linda L Bachinski Keith A Baggerly Spiridon Tsavachidis James C Lang David E Schuller Ralf Krahe

Head Neck 2008 Oct;30(10):1273-83

Department of Cancer Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1002/hed.20871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136479PMC
October 2008

Bayesian analysis of mass spectrometry proteomic data using wavelet-based functional mixed models.

Authors:
Jeffrey S Morris Philip J Brown Richard C Herrick Keith A Baggerly Kevin R Coombes

Biometrics 2008 Jun 20;64(2):479-89. Epub 2007 Sep 20.

The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030-4009, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2007.00895.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2659628PMC
June 2008

Global analysis of aberrant pre-mRNA splicing in glioblastoma using exon expression arrays.

Authors:
Hannah C Cheung Keith A Baggerly Spiridon Tsavachidis Linda L Bachinski Valerie L Neubauer Tamara J Nixon Kenneth D Aldape Gilbert J Cote Ralf Krahe

BMC Genomics 2008 May 12;9:216. Epub 2008 May 12.

Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas M, D, Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1186/1471-2164-9-216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2410136PMC
May 2008

Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer.

Authors:
Keith A Baggerly Kevin R Coombes E Shannon Neeley

J Clin Oncol 2008 Mar;26(7):1186-7; author reply 1187-8

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http://dx.doi.org/10.1200/JCO.2007.15.1951DOI Listing
March 2008

Microarrays: retracing steps.

Authors:
Kevin R Coombes Jing Wang Keith A Baggerly

Nat Med 2007 Nov;13(11):1276-7; author reply 1277-8

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http://dx.doi.org/10.1038/nm1107-1276bDOI Listing
November 2007

Non-parametric quantification of protein lysate arrays.

Authors:
Jianhua Hu Xuming He Keith A Baggerly Kevin R Coombes Bryan T J Hennessy Gordon B Mills

Bioinformatics 2007 Aug 28;23(15):1986-94. Epub 2007 Jun 28.

Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, TX, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm283DOI Listing
August 2007

PrepMS: TOF MS data graphical preprocessing tool.

Authors:
Yuliya V Karpievitch Elizabeth G Hill Adam J Smolka Jeffrey S Morris Kevin R Coombes Keith A Baggerly Jonas S Almeida

Bioinformatics 2007 Jan 22;23(2):264-5. Epub 2006 Nov 22.

Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633108PMC
January 2007

Synchronous selection of homing peptides for multiple tissues by in vivo phage display.

Authors:
Mikhail G Kolonin Jessica Sun Kim-Anh Do Claudia I Vidal Yuan Ji Keith A Baggerly Renata Pasqualini Wadih Arap

FASEB J 2006 May 31;20(7):979-81. Epub 2006 Mar 31.

Department of Genitourinary Medical Oncology, The University of Texas M. D. Anderson Cancer, Houston, Texas, USA.

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http://dx.doi.org/10.1096/fj.05-5186fjeDOI Listing
May 2006

Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform.

Authors:
Kevin R Coombes Spiridon Tsavachidis Jeffrey S Morris Keith A Baggerly Mien-Chie Hung Henry M Kuerer

Proteomics 2005 Nov;5(16):4107-17

Department of Biostatistics and Applied Mathematics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://doi.wiley.com/10.1002/pmic.200401261
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November 2005

Patterns of gene expression in different histotypes of epithelial ovarian cancer correlate with those in normal fallopian tube, endometrium, and colon.

Authors:
Rebecca T Marquez Keith A Baggerly Andrea P Patterson Jinsong Liu Russell Broaddus Michael Frumovitz Edward N Atkinson David I Smith Lynn Hartmann David Fishman Andrew Berchuck Regina Whitaker David M Gershenson Gordon B Mills Robert C Bast Karen H Lu

Clin Cancer Res 2005 Sep;11(17):6116-26

Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-04-2509DOI Listing
September 2005

Diagnostic protein discovery using liquid chromatography/mass spectrometry for proteolytic peptide targeting.

Authors:
John M Koomen Haitao Zhao Donghui Li Waleed Nasser David H Hawke James L Abbruzzese Keith A Baggerly Ryuji Kobayashi

Rapid Commun Mass Spectrom 2005 ;19(12):1624-36

Molecular Pathology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.

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http://dx.doi.org/10.1002/rcm.1963DOI Listing
July 2005

Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum.

Authors:
Jeffrey S Morris Kevin R Coombes John Koomen Keith A Baggerly Ryuji Kobayashi

Bioinformatics 2005 May 26;21(9):1764-75. Epub 2005 Jan 26.

Department of Biostatistics and Applied Mathematics, The University of Texas MD Anderson Cancer Center, Houston, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti254DOI Listing
May 2005

Serum proteomics profiling--a young technology begins to mature.

Authors:
Kevin R Coombes Jeffrey S Morris Jianhua Hu Sarah R Edmonson Keith A Baggerly

Nat Biotechnol 2005 Mar;23(3):291-2

Section of Bioinformatics, Department of Biostatistics and Applied Mathematics, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 447, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1038/nbt0305-291DOI Listing
March 2005

Signal in noise: evaluating reported reproducibility of serum proteomic tests for ovarian cancer.

Authors:
Keith A Baggerly Jeffrey S Morris Sarah R Edmonson Kevin R Coombes

J Natl Cancer Inst 2005 Feb;97(4):307-9

Department of Biostatistics, M.D. Anderson Cancer Center, Houston, TX, USA.

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https://academic.oup.com/jnci/article-lookup/doi/10.1093/jnc
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http://dx.doi.org/10.1093/jnci/dji008DOI Listing
February 2005

The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales.

Authors:
Jianhua Hu Kevin R Coombes Jeffrey S Morris Keith A Baggerly

Brief Funct Genomic Proteomic 2005 Feb;3(4):322-31

Department of Biostatistics and Applied Mathematics, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 447, Houston, TX 77030-4009, USA.

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http://dx.doi.org/10.1093/bfgp/3.4.322DOI Listing
February 2005

Overdispersed logistic regression for SAGE: modelling multiple groups and covariates.

Authors:
Keith A Baggerly Li Deng Jeffrey S Morris C Marcelo Aldaz

BMC Bioinformatics 2004 Oct 6;5:144. Epub 2004 Oct 6.

Department of Biostatistics and Applied Mathematics, UT M. D. Anderson Cancer Center, Houston, TX, USA.

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http://dx.doi.org/10.1186/1471-2105-5-144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC524524PMC
October 2004

Pharmacoproteomic analysis of prechemotherapy and postchemotherapy plasma samples from patients receiving neoadjuvant or adjuvant chemotherapy for breast carcinoma.

Authors:
Lajos Pusztai Betsy W Gregory Keith A Baggerly Bo Peng John Koomen Henry M Kuerer Francisco J Esteva W Fraser Symmans Peter Wagner Gabriel N Hortobagyi Christine Laronga O John Semmes George L Wright Richard R Drake Antonia Vlahou

Cancer 2004 May;100(9):1814-22

Department of Breast Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030-4009, USA.

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http://dx.doi.org/10.1002/cncr.20203DOI Listing
May 2004

Selection of potential markers for epithelial ovarian cancer with gene expression arrays and recursive descent partition analysis.

Authors:
Karen H Lu Andrea P Patterson Lin Wang Rebecca T Marquez Edward N Atkinson Keith A Baggerly Lance R Ramoth Daniel G Rosen Jinsong Liu Ingegerd Hellstrom David Smith Lynn Hartmann David Fishman Andrew Berchuck Rosemarie Schmandt Regina Whitaker David M Gershenson Gordon B Mills Robert C Bast

Clin Cancer Res 2004 May;10(10):3291-300

Ovarian Cancer Research Laboratory, Department of Experimental Therapeutics, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-03-0409DOI Listing
May 2004

Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments.

Authors:
Keith A Baggerly Jeffrey S Morris Kevin R Coombes

Bioinformatics 2004 Mar 29;20(5):777-85. Epub 2004 Jan 29.

Department of Biostatistics, U.T. M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Box 447, Houston, TX 77030-4009, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg484DOI Listing
March 2004

Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization.

Authors:
Kevin R Coombes Herbert A Fritsche Charlotte Clarke Jeng-Neng Chen Keith A Baggerly Jeffrey S Morris Lian-Chun Xiao Mien-Chie Hung Henry M Kuerer

Clin Chem 2003 Oct;49(10):1615-23

Department of Biostatistics, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 447, Houston TX 77030, USA.

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http://dx.doi.org/10.1373/49.10.1615DOI Listing
October 2003

A comprehensive approach to the analysis of matrix-assisted laser desorption/ionization-time of flight proteomics spectra from serum samples.

Authors:
Keith A Baggerly Jeffrey S Morris Jing Wang David Gold Lian-Chun Xiao Kevin R Coombes

Proteomics 2003 Sep;3(9):1667-72

Department of Biostatistics, UT M.D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://doi.wiley.com/10.1002/pmic.200300522
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http://dx.doi.org/10.1002/pmic.200300522DOI Listing
September 2003

Bayesian shrinkage estimation of the relative abundance of mRNA transcripts using SAGE.

Authors:
Jeffrey S Morris Keith A Baggerly Kevin R Coombes

Biometrics 2003 Sep;59(3):476-86

Department of Biostatistics, University of Texas, M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Box 447, Houston, Texas 77030-4009, USA.

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http://dx.doi.org/10.1111/1541-0420.00057DOI Listing
September 2003

Differential expression in SAGE: accounting for normal between-library variation.

Authors:
Keith A Baggerly Li Deng Jeffrey S Morris C Marcelo Aldaz

Bioinformatics 2003 Aug;19(12):1477-83

Department of Biostatistics, UT M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Box 447, Houston, TX 77030-4009, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg173DOI Listing
August 2003

Identifying and quantifying sources of variation in microarray data using high-density cDNA membrane arrays.

Authors:
Kevin R Coombes W Edward Highsmith Tammy A Krogmann Keith A Baggerly David N Stivers Lynne V Abruzzo

J Comput Biol 2002 ;9(4):655-69

Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1089/106652702760277372DOI Listing
April 2003

Steps toward mapping the human vasculature by phage display.

Authors:
Wadih Arap Mikhail G Kolonin Martin Trepel Johanna Lahdenranta Marina Cardó-Vila Ricardo J Giordano Paul J Mintz Peter U Ardelt Virginia J Yao Claudia I Vidal Limor Chen Anne Flamm Heli Valtanen Lisa M Weavind Marshall E Hicks Raphael E Pollock Gregory H Botz Corazon D Bucana Erkki Koivunen Dolores Cahill Patricia Troncoso Keith A Baggerly Rebecca D Pentz Kim-Anh Do Christopher J Logothetis Renata Pasqualini

Nat Med 2002 Feb;8(2):121-7

Department of Genito-Urinary Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA.

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http://dx.doi.org/10.1038/nm0202-121DOI Listing
February 2002