Mark A Watson

Mark A Watson

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Mark A Watson

Mark A Watson

Publications by authors named "Mark A Watson"

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96Publications

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Weighted Averaging Scheme and Local Atomic Descriptor for pK Prediction Based on Density Functional Theory.

J Chem Inf Model 2018 02 5;58(2):271-286. Epub 2018 Feb 5.

Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States.

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February 2018

Identifying biomarkers of breast cancer micrometastatic disease in bone marrow using a patient-derived xenograft mouse model.

Breast Cancer Res 2018 Jan 2;20(1). Epub 2018 Jan 2.

Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.

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January 2018

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

J Chem Theory Comput 2017 Nov 17;13(11):5780-5797. Epub 2017 Oct 17.

Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States.

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November 2017

Enrichment and Molecular Analysis of Breast Cancer Disseminated Tumor Cells from Bone Marrow Using Microfiltration.

PLoS One 2017 27;12(1):e0170761. Epub 2017 Jan 27.

Washington University School of Medicine, Dept. of Surgery, St. Louis, Missouri, United States of America.

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August 2017

Multiconformation, Density Functional Theory-Based pK Prediction in Application to Large, Flexible Organic Molecules with Diverse Functional Groups.

J Chem Theory Comput 2016 Dec 29;12(12):6001-6019. Epub 2016 Nov 29.

Schrödinger, Inc. , 101 SW Main Street, Suite 1300, Portland, Oregon 97204, United States.

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December 2016

caTissue Suite to OpenSpecimen: Developing an extensible, open source, web-based biobanking management system.

J Biomed Inform 2015 Oct 29;57:456-64. Epub 2015 Aug 29.

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.

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October 2015

Paired-like Homeodomain Transcription factor 2 expression by breast cancer bone marrow disseminated tumor cells is associated with early recurrent disease development.

Breast Cancer Res Treat 2015 Oct 23;153(3):507-17. Epub 2015 Sep 23.

Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA.

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October 2015

Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs.

J Chem Theory Comput 2015 May;11(5):2053-62

Department of Chemistry, University of Helsinki , P.O. Box 55, FIN-00014 Helsinki, Finland.

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May 2015

Diffusion Monte Carlo Study of Para-Diiodobenzene Polymorphism Revisited.

J Chem Theory Comput 2015 Mar 2;11(3):907-17. Epub 2015 Mar 2.

School of Information Science, JAIST , Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan.

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March 2015

The Dalton quantum chemistry program system.

Wiley Interdiscip Rev Comput Mol Sci 2014 May;4(3):269-284

Department of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden.

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May 2014

Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.

J Mol Diagn 2013 Sep 26;15(5):623-33. Epub 2013 Jun 26.

Department of Pathology, Washington University School of Medicine, St. Louis, Missouri, USA.

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September 2013

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.

N Engl J Med 2013 05 1;368(22):2059-74. Epub 2013 May 1.

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May 2013

Excited States of Butadiene to Chemical Accuracy: Reconciling Theory and Experiment.

J Chem Theory Comput 2012 Nov 25;8(11):4013-8. Epub 2012 Sep 25.

Department of Chemistry, Princeton University, Princeton, New Jersey, 08544.

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November 2012

Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories.

Am J Clin Pathol 2012 Jul;138(1):31-41

Laboratory for Translational Pathology, Dept of Pathology and Immunology, Washington University School of Medicine, 660 Euclid Ave, Box 8118, St Louis, MO 63110, USA.

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July 2012

Gene expression profiles and differential cytoglobin expression in atrophy and adenocarcinoma of the prostate.

Prostate 2012 Jun 24;72(9):931-7. Epub 2011 Oct 24.

Department of Pathology and Immunology, Washington University, St. Louis, Missouri, USA.

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June 2012

Electronic structure calculations in arbitrary electrostatic environments.

J Chem Phys 2012 Jan;136(2):024101

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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January 2012

A new paradigm for biospecimen banking in the personalized medicine era.

Am J Clin Pathol 2011 Nov;136(5):679-84

Laboratory for Translational Pathology, Dept of Pathology and Immunology, Washington University School of Medicine, 660 Euclid Avenue, St Louis, MO 63110, USA.

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November 2011

Identification of transcriptional regulatory networks specific to pilocytic astrocytoma.

BMC Med Genomics 2011 Jul 11;4:57. Epub 2011 Jul 11.

Department of Pathology and Immunology, Washington University School of Medicine, 660, S, Euclid Ave, St, Louis, MO 63110, USA.

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July 2011

Time-dependent density functional theory of open quantum systems in the linear-response regime.

J Chem Phys 2011 Feb;134(7):074116

Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.

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February 2011

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library.

J Chem Theory Comput 2010 Jan;6(1):135-44

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138 and Q-Chem, Inc., 5001 Baum Boulevard, Suite 690, Pittsburgh, Pennsylvania 15213.

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January 2010

Gene expression profiles of ductal versus acinar adenocarcinoma of the prostate.

Mod Pathol 2009 Oct 24;22(10):1273-9. Epub 2009 Jul 24.

Department of Pathology and Immunology, Division of Anatomic and Molecular Pathology, Washington University School of Medicine, University Medical Center, 660 South Euclid Avenue, St Louis, MO 63110, USA.

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October 2009

An improved long-range corrected hybrid functional with vanishing Hartree-Fock exchange at zero interelectronic distance (LC2gau-BOP).

J Chem Phys 2009 Oct;131(14):144108

Advanced Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

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October 2009

High throughput digital quantification of mRNA abundance in primary human acute myeloid leukemia samples.

J Clin Invest 2009 Jun 18;119(6):1714-26. Epub 2009 May 18.

Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University Medical School, St. Louis, Missouri 63110, USA.

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June 2009

A linear-scaling spectral-element method for computing electrostatic potentials.

J Chem Phys 2008 Nov;129(18):184107

Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan and CREST, Japan Science and Technology Agency, Saitama, 332-0012, Japan.

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November 2008

Core-excitation energy calculations with a long-range corrected hybrid exchange-correlation functional including a short-range Gaussian attenuation (LCgau-BOP).

J Chem Phys 2008 Nov;129(18):184113

Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.

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November 2008

Distal airways in mice exposed to cigarette smoke: Nrf2-regulated genes are increased in Clara cells.

Am J Respir Cell Mol Biol 2008 Oct 25;39(4):400-11. Epub 2008 Apr 25.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.

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October 2008

DNA methylotype analysis in colorectal cancer.

Oncol Rep 2008 Oct;20(4):921-7

Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA.

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October 2008

Copy-number analysis of topoisomerase and thymidylate synthase genes in frozen and FFPE DNAs of colorectal cancers.

Pharmacogenomics 2008 Oct;9(10):1459-66

Washington University School of Medicine, Department of Pathology & Immunology, Saint Louis, MO, USA.

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October 2008

Somatic mutations affect key pathways in lung adenocarcinoma.

Nature 2008 Oct;455(7216):1069-75

The Genome Center at Washington University, Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63108, USA.

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October 2008

Correlating EGFR expression with receptor-binding properties and internalization of 64Cu-DOTA-cetuximab in 5 cervical cancer cell lines.

J Nucl Med 2008 Sep 14;49(9):1472-9. Epub 2008 Aug 14.

Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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September 2008

Celecoxib pre-treatment in human colorectal adenocarcinoma patients is associated with gene expression alterations suggestive of diminished cellular proliferation.

Eur J Cancer 2008 Aug 22;44(12):1754-60. Epub 2008 Jul 22.

UNC Institute for Pharmacogenomics and Individualized Therapy, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599-7360, United States.

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August 2008

Nonlinear optical property calculations of polyynes with long-range corrected hybrid exchange-correlation functionals.

J Chem Phys 2008 Jul;129(2):024117

Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.

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July 2008

Linear-scaling multipole-accelerated Gaussian and finite-element Coulomb method.

J Chem Phys 2008 Feb;128(5):054105

Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.

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February 2008

Patellar taping and bracing for the treatment of chronic knee pain: a systematic review and meta-analysis.

Arthritis Rheum 2008 Jan;59(1):73-83

School of Health and Rehabilitation Sciences, Indiana University, Indianapolis 46202, USA.

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January 2008

An improved long-range corrected hybrid exchange-correlation functional including a short-range Gaussian attenuation (LCgau-BOP).

J Chem Phys 2007 Oct;127(15):154109

Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.

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October 2007

Commonly dysregulated genes in murine APL cells.

Blood 2007 Feb 28;109(3):961-70. Epub 2006 Sep 28.

Department of Medicine, Siteman Cancer Center, and Department of Pathology and Immunology, Washington University, St Louis, MO 63110, USA.

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February 2007

Distinct genetic signatures among pilocytic astrocytomas relate to their brain region origin.

Cancer Res 2007 Feb;67(3):890-900

Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.

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February 2007

DNA repair pathway profiling and microsatellite instability in colorectal cancer.

Clin Cancer Res 2006 Sep;12(17):5104-11

Department of Medicine, Washington University School of Medicine and Siteman Cancer Center, Saint Louis, Missouri 63110-1093, USA.

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September 2006

Gene expression profiling of primary tumor cell populations using laser capture microdissection, RNA transcript amplification, and GeneChip microarrays.

Methods Mol Biol 2005 ;293:187-207

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.

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June 2006

A targeted apoB38.9 mutation in mice is associated with reduced hepatic cholesterol synthesis and enhanced lipid peroxidation.

Am J Physiol Gastrointest Liver Physiol 2006 Jun 2;290(6):G1170-6. Epub 2006 Feb 2.

Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA.

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June 2006

Identification of a unique gene expression signature that differentiates hepatocellular adenoma from well-differentiated hepatocellular carcinoma.

Am J Surg Pathol 2005 Dec;29(12):1600-8

Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110-1093, USA.

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December 2005

RAS pathway activation and an oncogenic RAS mutation in sporadic pilocytic astrocytoma.

Neurology 2005 Oct;65(8):1335-6

Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.

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October 2005

Identification of mammaglobin as a novel serum marker for breast cancer.

Clin Cancer Res 2005 Sep;11(18):6528-35

Departments of Community and Preventive Medicine, Mount Sinai School of Medicine, New York, NY, USA.

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September 2005

Integrative genomic analysis identifies NDRG2 as a candidate tumor suppressor gene frequently inactivated in clinically aggressive meningioma.

Cancer Res 2005 Aug;65(16):7121-6

Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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August 2005

Variance in the expression of 5-Fluorouracil pathway genes in colorectal cancer.

Clin Cancer Res 2005 Apr;11(7):2612-9

Department of Medicine, Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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April 2005

Gene expression profiling of the irinotecan pathway in colorectal cancer.

Clin Cancer Res 2005 Mar;11(5):2053-62

Department of Medicine, Division of Biostatistics, Washington University School of Medicine, 660 South Euclid Avenue, Saint Louis, MO 63110, USA.

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March 2005

PEA3, AP-1, and a unique repetitive sequence all are involved in transcriptional regulation of the breast cancer-associated gene, mammaglobin.

Breast Cancer Res Treat 2005 Feb;89(3):289-96

Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA.

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February 2005

The calculation of indirect nuclear spin-spin coupling constants in large molecules.

Chemistry 2004 Sep;10(18):4627-39

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.

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September 2004

Mammaglobin-based strategies for treatment of breast cancer.

Curr Cancer Drug Targets 2004 Sep;4(6):531-42

Department of Surgery, Washington Univesity School of Medicine, St. Louis, MO 63110, USA.

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September 2004

Density-functional generalized-gradient and hybrid calculations of electromagnetic properties using Slater basis sets.

J Chem Phys 2004 Apr;120(16):7252-61

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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April 2004

Molecular therapeutics: are we making progress?

Curr Opin Mol Ther 2003 Dec;5(6):573-4

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December 2003

Murine cytomegalovirus paralyzes macrophages by blocking IFN gamma-induced promoter assembly.

Proc Natl Acad Sci U S A 2003 Nov 12;100(24):14309-14. Epub 2003 Nov 12.

Department of Pathology, Washington University School of Medicine, St. Louis, MO 63110, USA.

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November 2003

A variable fold change threshold determines significance for expression microarrays.

FASEB J 2003 Feb 3;17(2):321-3. Epub 2002 Dec 3.

Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital at Harvard Medical School, Boston, Massachusetts 02115, USA.

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February 2003

Accurate and reproducible gene expression profiles from laser capture microdissection, transcript amplification, and high density oligonucleotide microarray analysis.

J Mol Diagn 2003 Feb;5(1):9-14

Department of Pathology and Immunology and The Alvin J Siteman Cancer Center, Washington University School of Medicine, St Louis, Missouri 63110, USA.

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February 2003

Plasminogen activator inhibitor-1 gene polymorphism and colorectal cancer risk and prognosis.

Cancer Lett 2003 Jan;189(2):189-96

MRC Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, UK.

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January 2003

Optimized tissue processing and staining for laser capture microdissection and nucleic acid retrieval.

Methods Enzymol 2002 ;356:49-62

Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52246, USA.

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December 2002

Reduced renin expression and altered gene transcript profiles in multicystic dysplastic kidneys.

J Urol 2002 Oct;168(4 Pt 2):1816-20; discussion 1820

Department of Pathology, Washington University School of Medicine, St. Louis, MO, USA.

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October 2002

The Mu three-site synapse: a strained assembly platform in which delivery of the L1 transposase binding site triggers catalytic commitment.

Mol Cell 2002 Sep;10(3):659-69

Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.

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September 2002

Molecular characterization of human meningiomas by gene expression profiling using high-density oligonucleotide microarrays.

Am J Pathol 2002 Aug;161(2):665-72

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110-1093, USA.

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August 2002

Mantel statistics to correlate gene expression levels from microarrays with clinical covariates.

Genet Epidemiol 2002 Jun;23(1):87-96

Department of Medicine, Washington University in St Louis School of Medicine, St Louis, Missouri 63110, USA.

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June 2002

Comparative gene expression profile analysis of neurofibromatosis 1-associated and sporadic pilocytic astrocytomas.

Cancer Res 2002 Apr;62(7):2085-91

Department of Neurology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.

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April 2002

Mouse glioma gene expression profiling identifies novel human glioma-associated genes.

Ann Neurol 2002 Mar;51(3):393-405

Department of Neurology, Washington University School of Medicine, St Louis, MO 63110, USA.

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March 2002