Michael Waterman

Michael Waterman

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Michael Waterman

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A new statistic for efficient detection of repetitive sequences.

Bioinformatics 2019 Apr 16. Epub 2019 Apr 16.

Department of Automation, MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, BNRist, Tsinghua University, Beijing, China.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz262DOI Listing
April 2019

CYP51 as drug targets for fungi and protozoan parasites: past, present and future.

Parasitology 2018 12 12;145(14):1820-1836. Epub 2018 Apr 12.

Department of Biochemistry,Vanderbilt University School of Medicine,Nashville, Tennessee 37232,USA.

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http://dx.doi.org/10.1017/S0031182018000562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6185833PMC
December 2018

Binding of a physiological substrate causes large-scale conformational reorganization in cytochrome P450 51.

J Biol Chem 2018 12 16;293(50):19344-19353. Epub 2018 Oct 16.

From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232,

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http://dx.doi.org/10.1074/jbc.RA118.005850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302162PMC
December 2018

Optimal choice of word length when comparing two Markov sequences using a χ -statistic.

BMC Genomics 2017 Oct 3;18(Suppl 6):732. Epub 2017 Oct 3.

Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1186/s12864-017-4020-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5629589PMC
October 2017

CAFE: aCcelerated Alignment-FrEe sequence analysis.

Nucleic Acids Res 2017 07;45(W1):W554-W559

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

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https://academic.oup.com/nar/article/45/W1/W554/3791208
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http://dx.doi.org/10.1093/nar/gkx351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793812PMC
July 2017

Functional analysis of human cytochrome P450 21A2 variants involved in congenital adrenal hyperplasia.

J Biol Chem 2017 06 24;292(26):10767-10778. Epub 2017 May 24.

From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146

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http://dx.doi.org/10.1074/jbc.M117.792465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5491764PMC
June 2017

Recent Structural Insights into Cytochrome P450 Function.

Trends Pharmacol Sci 2016 08 4;37(8):625-640. Epub 2016 Jun 4.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA. Electronic address:

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http://www.cell.com/trends/pharmacological-sciences/pdf/S016
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http://linkinghub.elsevier.com/retrieve/pii/S016561471630040
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http://dx.doi.org/10.1016/j.tips.2016.05.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961565PMC
August 2016

Genetic and structural analyses of cytochrome P450 hydroxylases in sex hormone biosynthesis: Sequential origin and subsequent coevolution.

Mol Phylogenet Evol 2016 Jan 3;94(Pt B):676-687. Epub 2015 Oct 3.

Institute of Life Science, Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10557903150027
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http://dx.doi.org/10.1016/j.ympev.2015.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801120PMC
January 2016

Research Resource: Correlating Human Cytochrome P450 21A2 Crystal Structure and Phenotypes of Mutations in Congenital Adrenal Hyperplasia.

Mol Endocrinol 2015 Sep 14;29(9):1375-84. Epub 2015 Jul 14.

Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232-0146.

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http://dx.doi.org/10.1210/ME.2015-1127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552440PMC
September 2015

Structural analysis of cytochrome P450 105N1 involved in the biosynthesis of the zincophore, coelibactin.

Int J Mol Sci 2012 1;13(7):8500-13. Epub 2012 Jun 1.

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA; E-Mails: (L.L.); (M.R.W.).

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http://www.mdpi.com/1422-0067/13/7/8500
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http://dx.doi.org/10.3390/ijms13078500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430247PMC
August 2015

Gene coexpression measures in large heterogeneous samples using count statistics.

Proc Natl Acad Sci U S A 2014 Nov 6;111(46):16371-6. Epub 2014 Oct 6.

Department of Statistics, University of California, Berkeley, CA 94720; and

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http://dx.doi.org/10.1073/pnas.1417128111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246260PMC
November 2014

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.

Brief Bioinform 2014 May 23;15(3):343-53. Epub 2013 Sep 23.

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, USA. or

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http://dx.doi.org/10.1093/bib/bbt067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017329PMC
May 2014

Streptomyces cytochromes P450: applications in drug metabolism.

Expert Opin Drug Metab Toxicol 2013 Oct 6;9(10):1279-94. Epub 2013 Jun 6.

Swansea University, Institute of Life Science, College of Medicine , Singleton Park, Swansea, SA2 8PP , UK.

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http://dx.doi.org/10.1517/17425255.2013.806485DOI Listing
October 2013

VNI cures acute and chronic experimental Chagas disease.

J Infect Dis 2013 Aug 31;208(3):504-11. Epub 2013 Jan 31.

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN, USA.

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http://dx.doi.org/10.1093/infdis/jit042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698996PMC
August 2013

A geometric interpretation for local alignment-free sequence comparison.

J Comput Biol 2013 Jul;20(7):471-85

Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1089/cmb.2012.0280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704055PMC
July 2013

Cytochromes p450: roles in diseases.

J Biol Chem 2013 Jun 30;288(24):17091-8. Epub 2013 Apr 30.

Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA.

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http://dx.doi.org/10.1074/jbc.R112.431916DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682515PMC
June 2013

Unusual properties of the cytochrome P450 superfamily.

Philos Trans R Soc Lond B Biol Sci 2013 Feb 6;368(1612):20120434. Epub 2013 Jan 6.

Institute of Life Science, Medical School, Swansea University, Singleton Park, Swansea SA2 8PP, UK.

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http://dx.doi.org/10.1098/rstb.2012.0434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538423PMC
February 2013

Organocatalytic, enantioselective synthesis of VNI: a robust therapeutic development platform for Chagas, a neglected tropical disease.

Org Lett 2012 Dec 7;14(24):6322-5. Epub 2012 Dec 7.

Department of Chemistry & Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.

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http://dx.doi.org/10.1021/ol303092vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528807PMC
December 2012

Normal and compound poisson approximations for pattern occurrences in NGS reads.

J Comput Biol 2012 Jun;19(6):839-54

School of Mathematics, Shandong University, Jinan, Shandong, China.

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http://dx.doi.org/10.1089/cmb.2012.0029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375642PMC
June 2012

Investigating conservation of the albaflavenone biosynthetic pathway and CYP170 bifunctionality in streptomycetes.

FEBS J 2012 May 27;279(9):1640-9. Epub 2012 Jan 27.

Institute of Life Science, Medical School, Swansea University, Swansea, UK.

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http://dx.doi.org/10.1111/j.1742-4658.2011.08447.xDOI Listing
May 2012

Three-dimensional structure of steroid 21-hydroxylase (cytochrome P450 21A2) with two substrates reveals locations of disease-associated variants.

J Biol Chem 2012 Mar 18;287(13):10613-22. Epub 2012 Jan 18.

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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http://dx.doi.org/10.1074/jbc.M111.323501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323056PMC
March 2012

Structural complex of sterol 14α-demethylase (CYP51) with 14α-methylenecyclopropyl-Delta7-24, 25-dihydrolanosterol.

J Lipid Res 2012 Feb 30;53(2):311-20. Epub 2011 Nov 30.

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.

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http://www.jlr.org/lookup/doi/10.1194/jlr.M021865
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http://dx.doi.org/10.1194/jlr.M021865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269163PMC
February 2012

The role of Ile87 of CYP158A2 in oxidative coupling reaction.

Arch Biochem Biophys 2012 Feb 19;518(2):127-32. Epub 2011 Dec 19.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1016/j.abb.2011.12.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3274592PMC
February 2012

Sterol 14alpha-demethylase (CYP51) as a therapeutic target for human trypanosomiasis and leishmaniasis.

Curr Top Med Chem 2011 ;11(16):2060-71

Department of Biochemistry Vanderbilt University, Nashville, TN 37232, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391166PMC
http://dx.doi.org/10.2174/156802611796575902DOI Listing
December 2011

Targeting Trypanosoma cruzi sterol 14α-demethylase (CYP51).

Adv Parasitol 2011 ;75:65-87

Department of Biochemistry School of Medicine, Vanderbilt University, Nashville, Tennessee, USA.

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http://dx.doi.org/10.1016/B978-0-12-385863-4.00004-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488290PMC
December 2011

New powerful statistics for alignment-free sequence comparison under a pattern transfer model.

J Theor Biol 2011 Sep 25;284(1):106-16. Epub 2011 Jun 25.

School of Physics, South China University of Technology, Guangzhou, PR China.

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http://dx.doi.org/10.1016/j.jtbi.2011.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146591PMC
September 2011

Substrate preferences and catalytic parameters determined by structural characteristics of sterol 14alpha-demethylase (CYP51) from Leishmania infantum.

J Biol Chem 2011 Jul 31;286(30):26838-48. Epub 2011 May 31.

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.

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http://dx.doi.org/10.1074/jbc.M111.237099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143644PMC
July 2011

Moonlighting cytochrome P450 monooxygenases.

IUBMB Life 2011 Jul;63(7):473-7

Department of Biochemistry, Center for Structural Biology, Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1002/iub.501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122146PMC
July 2011

Integrative analysis of many weighted co-expression networks using tensor computation.

PLoS Comput Biol 2011 Jun 16;7(6):e1001106. Epub 2011 Jun 16.

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

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http://dx.plos.org/10.1371/journal.pcbi.1001106
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http://dx.doi.org/10.1371/journal.pcbi.1001106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116899PMC
June 2011

Sequence alignment as hypothesis testing.

J Comput Biol 2011 May;18(5):677-91

MOE Key Lab of Bioinformatics and Bioinformatics Division of TNLIST/Department of Automation, Tsinghua University, Beijing, P.R. China.

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http://dx.doi.org/10.1089/cmb.2010.0328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122928PMC
May 2011

Structural basis for conservation in the CYP51 family.

Biochim Biophys Acta 2011 Jan 11;1814(1):88-93. Epub 2010 Jun 11.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S15709639100016
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http://dx.doi.org/10.1016/j.bbapap.2010.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2962772PMC
January 2011

Alignment-free sequence comparison (II): theoretical power of comparison statistics.

J Comput Biol 2010 Nov 25;17(11):1467-90. Epub 2010 Oct 25.

Molecular and Computational Biology, University of Southern California , Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1089/cmb.2010.0056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3123933PMC
November 2010

Structural insights into inhibition of sterol 14alpha-demethylase in the human pathogen Trypanosoma cruzi.

J Biol Chem 2010 Aug 8;285(33):25582-90. Epub 2010 Jun 8.

Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.

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http://dx.doi.org/10.1074/jbc.M110.133215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2919122PMC
August 2010

High-resolution human genome structure by single-molecule analysis.

Proc Natl Acad Sci U S A 2010 Jun 1;107(24):10848-53. Epub 2010 Jun 1.

The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580, USA.

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http://dx.doi.org/10.1073/pnas.0914638107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890719PMC
June 2010

The power of detecting enriched patterns: an HMM approach.

J Comput Biol 2010 Apr;17(4):581-92

School of Mathematics, Shandong University, Jinan, Shandong, PR China.

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http://dx.doi.org/10.1089/cmb.2009.0218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203519PMC
April 2010

Streptomyces coelicolor A3(2) CYP102 protein, a novel fatty acid hydroxylase encoded as a heme domain without an N-terminal redox partner.

Appl Environ Microbiol 2010 Mar 22;76(6):1975-80. Epub 2010 Jan 22.

Institute of Life Science and Swansea Medical School, Grove Building, Swansea University, Swansea SA2 8PP, United Kingdom.

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http://dx.doi.org/10.1128/AEM.03000-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838009PMC
March 2010

New Generations: Sequencing Machines and Their Computational Challenges.

J Comput Sci Technol 2010 Jan;25(1):3-9

Laboratory for Molecular and Computational Genomics, Department of Chemistry and Laboratory of Genetics, University of Wisconsin-Madison, WI 53706 USA.

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http://dx.doi.org/10.1007/s11390-010-9300-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3222932PMC
January 2010

An integrative modular approach to systematically predict gene-phenotype associations.

BMC Bioinformatics 2010 Jan 18;11 Suppl 1:S62. Epub 2010 Jan 18.

Program in Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S1-S62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3009536PMC
January 2010

Crystal structure of albaflavenone monooxygenase containing a moonlighting terpene synthase active site.

J Biol Chem 2009 Dec 26;284(52):36711-9. Epub 2009 Oct 26.

Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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http://www.jbc.org/lookup/doi/10.1074/jbc.M109.064683
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http://dx.doi.org/10.1074/jbc.M109.064683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794785PMC
December 2009

Alignment-free sequence comparison (I): statistics and power.

J Comput Biol 2009 Dec;16(12):1615-34

Department of Statistics, University of Oxford, Oxford OX1 3TG, UK.

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http://dx.doi.org/10.1089/cmb.2009.0198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818754PMC
December 2009

A single molecule scaffold for the maize genome.

PLoS Genet 2009 Nov 20;5(11):e1000711. Epub 2009 Nov 20.

Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774507PMC
November 2009

The B73 maize genome: complexity, diversity, and dynamics.

Authors:
Patrick S Schnable Doreen Ware Robert S Fulton Joshua C Stein Fusheng Wei Shiran Pasternak Chengzhi Liang Jianwei Zhang Lucinda Fulton Tina A Graves Patrick Minx Amy Denise Reily Laura Courtney Scott S Kruchowski Chad Tomlinson Cindy Strong Kim Delehaunty Catrina Fronick Bill Courtney Susan M Rock Eddie Belter Feiyu Du Kyung Kim Rachel M Abbott Marc Cotton Andy Levy Pamela Marchetto Kerri Ochoa Stephanie M Jackson Barbara Gillam Weizu Chen Le Yan Jamey Higginbotham Marco Cardenas Jason Waligorski Elizabeth Applebaum Lindsey Phelps Jason Falcone Krishna Kanchi Thynn Thane Adam Scimone Nay Thane Jessica Henke Tom Wang Jessica Ruppert Neha Shah Kelsi Rotter Jennifer Hodges Elizabeth Ingenthron Matt Cordes Sara Kohlberg Jennifer Sgro Brandon Delgado Kelly Mead Asif Chinwalla Shawn Leonard Kevin Crouse Kristi Collura Dave Kudrna Jennifer Currie Ruifeng He Angelina Angelova Shanmugam Rajasekar Teri Mueller Rene Lomeli Gabriel Scara Ara Ko Krista Delaney Marina Wissotski Georgina Lopez David Campos Michele Braidotti Elizabeth Ashley Wolfgang Golser HyeRan Kim Seunghee Lee Jinke Lin Zeljko Dujmic Woojin Kim Jayson Talag Andrea Zuccolo Chuanzhu Fan Aswathy Sebastian Melissa Kramer Lori Spiegel Lidia Nascimento Theresa Zutavern Beth Miller Claude Ambroise Stephanie Muller Will Spooner Apurva Narechania Liya Ren Sharon Wei Sunita Kumari Ben Faga Michael J Levy Linda McMahan Peter Van Buren Matthew W Vaughn Kai Ying Cheng-Ting Yeh Scott J Emrich Yi Jia Ananth Kalyanaraman An-Ping Hsia W Brad Barbazuk Regina S Baucom Thomas P Brutnell Nicholas C Carpita Cristian Chaparro Jer-Ming Chia Jean-Marc Deragon James C Estill Yan Fu Jeffrey A Jeddeloh Yujun Han Hyeran Lee Pinghua Li Damon R Lisch Sanzhen Liu Zhijie Liu Dawn Holligan Nagel Maureen C McCann Phillip SanMiguel Alan M Myers Dan Nettleton John Nguyen Bryan W Penning Lalit Ponnala Kevin L Schneider David C Schwartz Anupma Sharma Carol Soderlund Nathan M Springer Qi Sun Hao Wang Michael Waterman Richard Westerman Thomas K Wolfgruber Lixing Yang Yeisoo Yu Lifang Zhang Shiguo Zhou Qihui Zhu Jeffrey L Bennetzen R Kelly Dawe Jiming Jiang Ning Jiang Gernot G Presting Susan R Wessler Srinivas Aluru Robert A Martienssen Sandra W Clifton W Richard McCombie Rod A Wing Richard K Wilson

Science 2009 Nov;326(5956):1112-5

Center for Plant Genomics, Iowa State University, Ames, IA 50011, USA.

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http://www.sciencemag.org/cgi/doi/10.1126/science.1178534
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http://dx.doi.org/10.1126/science.1178534DOI Listing
November 2009

HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome.

Bioinformatics 2009 Sep 27;25(18):2430-1. Epub 2009 Jun 27.

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735662PMC
September 2009

The first virally encoded cytochrome p450.

J Virol 2009 Aug 10;83(16):8266-9. Epub 2009 Jun 10.

Institute of Life Science, Swansea University, United Kingdom.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.00289-09
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http://dx.doi.org/10.1128/JVI.00289-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715754PMC
August 2009

An integrative network approach to map the transcriptome to the phenome.

J Comput Biol 2009 Aug;16(8):1023-34

Program in Computational Biology, Department of Biological Sciences, University of Southern California , Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1089/cmb.2009.0037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154457PMC
August 2009

Structural biology: Anticancer drug target pictured.

Nature 2009 Jan;457(7226):159-60

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http://dx.doi.org/10.1038/457159aDOI Listing
January 2009

The Seventh Asia Pacific Bioinformatics Conference (APBC2009).

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S1. Epub 2009 Jan 30.

Cold Spring Harbor Laboratory, NY, USA.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648764PMC
January 2009

CYP51: A major drug target in the cytochrome P450 superfamily.

Lipids 2008 Dec 4;43(12):1117-25. Epub 2008 Sep 4.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1007/s11745-008-3225-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715142PMC
December 2008

Aromatase is phosphorylated in situ at serine-118.

J Steroid Biochem Mol Biol 2008 Nov 4;112(1-3):95-101. Epub 2008 Sep 4.

Department of Medicine, Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.jsbmb.2008.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2856845PMC
November 2008

Association of a CYP4A11 variant and blood pressure in black men.

J Am Soc Nephrol 2008 Aug 2;19(8):1606-12. Epub 2008 Apr 2.

Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232-6602, USA.

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http://jasn.asnjournals.org/content/early/2008/04/02/ASN.200
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http://www.jasn.org/cgi/doi/10.1681/ASN.2008010063
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http://dx.doi.org/10.1681/ASN.2008010063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488260PMC
August 2008

The ferrous-oxy complex of human aromatase.

Biochem Biophys Res Commun 2008 Jul 13;372(2):379-82. Epub 2008 May 13.

Department of Biochemistry, Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1016/j.bbrc.2008.05.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2478517PMC
July 2008

Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2).

J Biol Chem 2008 Mar 30;283(13):8183-9. Epub 2008 Jan 30.

Department of Biochemistry and the Institute of Chemical Biology, and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1074/jbc.M710421200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2276382PMC
March 2008

Interaction between substrate and oxygen ligand responsible for effective O-O bond cleavage in bovine cytochrome P450 steroid 21-hydroxylase proved by Raman spectroscopy.

J Biol Chem 2008 Feb 21;283(7):3708-17. Epub 2007 Nov 21.

Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan.

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February 2008

Purification and functional characterization of human 11beta hydroxylase expressed in Escherichia coli.

FEBS J 2008 Feb 22;275(4):799-810. Epub 2008 Jan 22.

Department of Biochemistry, Saarland University, Saarbrücken, Germany.

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http://dx.doi.org/10.1111/j.1742-4658.2008.06253.xDOI Listing
February 2008

Cytochromes P450 and drug discovery.

Curr Opin Biotechnol 2007 Dec 19;18(6):504-12. Epub 2007 Nov 19.

Institute of Life Science, Swansea Medical School, Grove Building, Swansea University, Swansea SA2 8PP, UK.

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http://dx.doi.org/10.1016/j.copbio.2007.09.010DOI Listing
December 2007

Novel properties of P450s in Streptomyces coelicolor.

Drug Metab Rev 2007 ;39(2-3):343-52

Biochemistry Department, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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http://dx.doi.org/10.1080/03602530701498836 DOI Listing
October 2007

Conformational dynamics in the F/G segment of CYP51 from Mycobacterium tuberculosis monitored by FRET.

Arch Biochem Biophys 2007 Aug 6;464(2):221-7. Epub 2007 Jun 6.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1016/j.abb.2007.05.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042880PMC
August 2007

Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi.

Genome Res 2007 Jul 13;17(7):1101-10. Epub 2007 Jun 13.

Department of Computer Science, Yonsei University, Seoul, Republic of Korea.

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http://dx.doi.org/10.1101/gr.5894107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899121PMC
July 2007

Different binding modes of two flaviolin substrate molecules in cytochrome P450 158A1 (CYP158A1) compared to CYP158A2.

Biochemistry 2007 Jul 6;46(30):8725-33. Epub 2007 Jul 6.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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http://pubs.acs.org/doi/abs/10.1021/bi7006959
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July 2007

Systematic discovery of functional modules and context-specific functional annotation of human genome.

Bioinformatics 2007 Jul;23(13):i222-9

Molecuolar and Computational Biology, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm222DOI Listing
July 2007

A graph-based approach to systematically reconstruct human transcriptional regulatory modules.

Bioinformatics 2007 Jul;23(13):i577-86

IBM T. J. Watson Research Center, Hawthorne, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm227DOI Listing
July 2007

Electron transport pathway for a Streptomyces cytochrome P450: cytochrome P450 105D5-catalyzed fatty acid hydroxylation in Streptomyces coelicolor A3(2).

J Biol Chem 2007 Jun 19;282(24):17486-500. Epub 2007 Apr 19.

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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http://dx.doi.org/10.1074/jbc.M700863200DOI Listing
June 2007

Accuracy assessment of diploid consensus sequences.

IEEE/ACM Trans Comput Biol Bioinform 2007 Jan-Mar;4(1):88-97

Department of Computer Science, University of Southern California, Los Angeles 90089, USA.

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http://dx.doi.org/10.1109/TCBB.2007.1007DOI Listing
April 2007

On the length of the longest exact position match in a random sequence.

IEEE/ACM Trans Comput Biol Bioinform 2007 Jan-Mar;4(1):153-6

Keble College and Department of Statistics, University of Oxford, UK. reinert@stats ox.ac.uk

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http://dx.doi.org/10.1109/TCBB.2007.1023DOI Listing
April 2007

A quantile method for sizing optical maps.

J Comput Biol 2007 Apr;14(3):255-66

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

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http://dx.doi.org/10.1089/cmb.2006.0006DOI Listing
April 2007

Sterol 14alpha-demethylase cytochrome P450 (CYP51), a P450 in all biological kingdoms.

Biochim Biophys Acta 2007 Mar 2;1770(3):467-77. Epub 2006 Aug 2.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

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http://dx.doi.org/10.1016/j.bbagen.2006.07.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2324071PMC
March 2007

Gene Aging Nexus: a web database and data mining platform for microarray data on aging.

Nucleic Acids Res 2007 Jan 7;35(Database issue):D756-9. Epub 2006 Nov 7.

Department of Biological Sciences, University of Southern California Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/nar/gkl798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669755PMC
January 2007

The cytochrome P450 gene family CYP157 does not contain EXXR in the K-helix reducing the absolute conserved P450 residues to a single cysteine.

FEBS Lett 2006 Nov 30;580(27):6338-42. Epub 2006 Oct 30.

Department of Cell and Developmental Biology, University of Illinois, 1201 W Gregory Dr, Urbana, IL 61801, USA.

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http://dx.doi.org/10.1016/j.febslet.2006.10.043DOI Listing
November 2006

Integrative missing value estimation for microarray data.

BMC Bioinformatics 2006 Oct 12;7:449. Epub 2006 Oct 12.

Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 900089, USA.

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http://dx.doi.org/10.1186/1471-2105-7-449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1622759PMC
October 2006

An algorithm for assembly of ordered restriction maps from single DNA molecules.

Proc Natl Acad Sci U S A 2006 Oct 16;103(43):15770-5. Epub 2006 Oct 16.

Department of Mathematics, University of Southern California, 3620 South Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA.

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http://dx.doi.org/10.1073/pnas.0604040103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635078PMC
October 2006

The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae.

J Biol Chem 2006 Sep 6;281(36):26289-97. Epub 2006 Jul 6.

Life Sciences Institute and Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.

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http://dx.doi.org/10.1074/jbc.M605478200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939096PMC
September 2006

Biophysical characterization of the sterol demethylase P450 from Mycobacterium tuberculosis, its cognate ferredoxin, and their interactions.

Biochemistry 2006 Jul;45(27):8427-43

Manchester Interdisciplinary Biocentre, School of Chemical Engineering and Analytical Sciences, University of Manchester, Jackson's Mill, P.O. Box 88, Sackville Street, Manchester M60 1QD, UK.

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http://dx.doi.org/10.1021/bi0601609DOI Listing
July 2006

Ligand-assisted inhibition in cytochrome P450 158A2 from Streptomyces coelicolor A3(2).

Biochemistry 2006 Jun;45(24):7493-500

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.

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June 2006

Refinement of optical map assemblies.

Bioinformatics 2006 May 24;22(10):1217-24. Epub 2006 Feb 24.

MCB 1050 Childs Way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl063DOI Listing
May 2006

Purification and characterization of bovine steroid 21-hydroxylase (P450c21) efficiently expressed in Escherichia coli.

Biochem Biophys Res Commun 2006 May 20;344(1):400-5. Epub 2006 Mar 20.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1016/j.bbrc.2006.03.067DOI Listing
May 2006

Raman evidence for specific substrate-induced structural changes in the heme pocket of human cytochrome P450 aromatase during the three consecutive oxygen activation steps.

Biochemistry 2006 May;45(17):5631-40

Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki 444-8787, Japan.

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http://dx.doi.org/10.1021/bi060094aDOI Listing
May 2006

Mechanistic analysis of a multiple product sterol methyltransferase implicated in ergosterol biosynthesis in Trypanosoma brucei.

J Biol Chem 2006 Mar 12;281(10):6290-6. Epub 2006 Jan 12.

Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1064, USA.

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http://dx.doi.org/10.1074/jbc.M511749200DOI Listing
March 2006

Alignment of optical maps.

J Comput Biol 2006 Mar;13(2):442-62

Department of Mathematics, University of Southern California, Los Angeles, 90089-1113, USA.

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http://dx.doi.org/10.1089/cmb.2006.13.442DOI Listing
March 2006

CYP51 from Trypanosoma cruzi: a phyla-specific residue in the B' helix defines substrate preferences of sterol 14alpha-demethylase.

J Biol Chem 2006 Feb 30;281(6):3577-85. Epub 2005 Nov 30.

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.

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http://dx.doi.org/10.1074/jbc.M510317200DOI Listing
February 2006

Exploiting Streptomyces coelicolor A3(2) P450s as a model for application in drug discovery.

Expert Opin Drug Metab Toxicol 2006 Feb;2(1):27-40

Swansea Medical School, University of Wales Swansea, Swansea, UK.

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http://dx.doi.org/10.1517/17425255.2.1.27 DOI Listing
February 2006

A second FMN binding site in yeast NADPH-cytochrome P450 reductase suggests a mechanism of electron transfer by diflavin reductases.

Structure 2006 Jan;14(1):51-61

Wolfson Laboratory of P450 Biodiversity, Swansea Medical School University of Wales Swansea, Swansea, Wales SA2 8PP, UK.

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http://dx.doi.org/10.1016/j.str.2005.09.015DOI Listing
January 2006