Alan P. Hoyle
115 Autumn Lane
Chapel Hill, NC 27516-1101
(919) 593-0885
alan@alanhoyle.com
http://www.alanhoyle.com/

Career Objective: Full-time permanent position as a computer programmer.
Education: University of North Carolina at Chapel Hill
B.S. Mathematical Sciences - Computer Science Option, Minor in Physics.
May 1996.
Experience:

Bioinformatics Scientist: Bioinfomatics Core, UNC Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC, October 2016 to present.
Developed applications in Perl, Python, Bash, R, and Javascript in distributed compute cluster environment. Developed and troubleshot bioinformatics workflows for DNA and RNA analyses. Used cloud computing resources from multiple vendors. Contributed to large projects including TCGA. Developed and maintained databases in Oracle. Administered workstations and servers running Linux and Mac OS X. Created documentation of internal processes.

Application Specialist: Bioinfomatics Core, UNC Lineberger Comprehensive Cancer Center, UNC-CH, Chapel Hill, NC, July 2009 to September 2016.
Developed applications in Perl, Python, Bash, and Javascript in distributed compute cluster environment. Developed and troubleshot bioinformatics workflows for DNA and RNA analyses. Used cloud computing resources from multiple vendors. Contributed to large projects including TCGA. Developed and maintained databases in Oracle. Administered workstations and servers running Linux, Mac OS X, and Windows. Developed clinical databases for researchers. Created documentation of internal processes.

Application Analyst: ITS Teaching and Learning, Teaching and Learning Interactive, UNC-CH, Chapel Hill, NC, August 2006 to July 2009.
Developed applications in Perl, PHP, and Java in distributed environment. Maintained and developed databases in Oracle and MySQL. Administered workstations and servers running Linux, Mac OS X, and Windows XP. Supported and developed for distributed learning applications Blackboard and Sakai. Taught training classes for users and support staff. Created user documentation for applications, administration, and other miscellaneous subjects.

Application Programmer: ITS Enterprise Applications, Student Information Services, UNC-CH, Chapel Hill, NC, September 2004 to August 2006.
Developed applications in Perl, Java, and JSP in distributed environment. Maintained and developed databases in Oracle. Administered workstations and servers running Linux and Windows XP. Supported and developed for distributed learning application Blackboard. Taught training classes for users and support staff. Created user documentation for applications, administration, and other miscellaneous subjects.

Application Programmer: AIS Student Information Services, UNC-CH, Chapel Hill, NC, November 2001 to September 2004.
Developed applications in Perl and JSP in distributed environment. Maintained and developed databases in Oracle and MySQL. Administered workstations and servers running Linux, Solaris, Windows 2000 and Windows XP. Supported and developed for distributed learning application Blackboard. Created user documentation for applications, administration, and other miscellaneous subjects.

Application Programmer: ATN Instructional Technology Development, UNC-CH, Chapel Hill, NC, March 1998 to November 2001.
Developed applications in Perl and Cold Fusion in distributed environment. Maintained and developed databases in Oracle, MySQL, and Microsoft Access. Administered Linux, Windows NT, and Solaris workstations. Supported distributed learning applications Blackboard and WebCT. Developed user documentation for applications and other miscellaneous subjects.

Consultant: OIT Technical Assistance Center, UNC-CH, Chapel Hill, NC, October 1994 to March 1998.
Supported DOS, Windows, Mac and Unix operating systems and gave assistance for numerous software applications. Developed user documentation for Windows, DOS, Macintosh, and Unix operating systems and applications.

Demonstrator: Magic Shop, Busch Gardens, Williamsburg, VA, June to August 1993.
Performed magic tricks; trained customers and other demonstrators.

Skills: Languages: Perl, Python, SQL, Unix shell scripts, R, HTML, Javascript, Java, PL/SQL.

Server Operating Systems: Centos, RHEL.

Server Applications: SunGridEngine, Docker, Oracle.

Desktop Operating Systems: Mac OSX, GNU/Linux (Ubuntu, RHEL, Centos), Windows.

Desktop Applications: Emacs, vi, SQLDeveloper, SVN, git.

Cloud Platforms: Google Compute Platform, Amazon, Curoverse/Arvados.

Publications: Authorship noted in bold, "Publication Titles" are underlined

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. "Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas." Nat Genet. 2016 Jun;48(6):607-16. doi: 10.1038/ng.3564. Epub 2016 May 9.

Seifert BA, O'Daniel JM, Amin K, Marchuk DS, Patel NM, Parker JS, Hoyle AP, Mose LE, Marron A, Hayward MC, Bizon C, Wilhelmsen KC, Evans JP, Earp HS, Sharpless N, Hayes DN, Berg JS. "Germline Analysis from Tumor-Germline Sequencing Dyads to identify clinically actionable secondary findings." Clin Cancer Res. 2016 Apr 15. pii: clincanres.0015.2016. [Epub ahead of print]

Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG. "Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma." Cell. 2016 Jan 28;164(3):550-63. doi: 10.1016/j.cell.2015.12.028.

Cancer Genome Atlas Research Network. "The Molecular Taxonomy of Primary Prostate Cancer." Cell. 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025.

Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. "Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma." N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. Epub 2015 Nov 4.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. "Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer." Cell. 2015 Oct 8;163(2):506-19. doi: 10.1016/j.cell.2015.09.033.

Cancer Genome Atlas Network. "Genomic Classification of Cutaneous Melanoma." Cell. 2015 Jun 18;161(7):1681-96. doi: 10.1016/j.cell.2015.05.044.

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. "Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas." N Engl J Med. 2015 Jun 25;372(26):2481-98. doi: 10.1056/NEJMoa1402121. Epub 2015 Jun 10.

Cancer Genome Atlas Network. "Comprehensive genomic characterization of head and neck squamous cell carcinomas." Nature. 2015 Jan 29;517(7536):576-82. doi: 10.1038/nature14129.

Cancer Genome Atlas Research Network. "Integrated genomic characterization of papillary thyroid carcinoma." Cell. 2014 Oct 23;159(3):676-90. doi: 10.1016/j.cell.2014.09.050.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. "Characterization of HPV and host genome interactions in primary head and neck cancers." Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ. "The somatic genomic landscape of chromophobe renal cell carcinoma." Cancer Cell. 2014 Sep 8;26(3):319-30. doi: 10.1016/j.ccr.2014.07.014. Epub 2014 Aug 21.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. "Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin." Cell. 2014 Aug 14;158(4):929-44. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7.

Cancer Genome Atlas Research Network. "Comprehensive molecular profiling of lung adenocarcinoma." Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. Erratum in: Nature. 2014 Oct 9;514(7521):262. Rogers, K [corrected to Rodgers, K].

Cancer Genome Atlas Research Network. "Comprehensive molecular characterization of urothelial bladder carcinoma." Nature. 2014 Mar 20;507(7492):315-22. doi: 10.1038/nature12965. Epub 2014 Jan 29.

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. "The Cancer Genome Atlas Pan-Cancer analysis project." Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764.

Cancer Genome Atlas Research Network. "Comprehensive molecular characterization of clear cell renal cell carcinoma." Nature. 2013 Jul 4;499(7456):43-9. doi: 10.1038/nature12222. Epub 2013 Jun 23.

Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. "Integrated genomic characterization of endometrial carcinoma." Nature. 2013 May 2;497(7447):67-73. doi: 10.1038/nature12113. Erratum in: Nature. 2013 Aug 8;500(7461):242.

Cancer Genome Atlas Network. "Comprehensive molecular portraits of human breast tumours." Nature. 2012 Oct 4;490(7418):61-70. doi: 10.1038/nature11412. Epub 2012 Sep 23.

Cancer Genome Atlas Research Network. "Comprehensive genomic characterization of squamous cell lung cancers." Nature. 2012 Sep 27;489(7417):519-25. doi: 10.1038/nature11404. Epub 2012 Sep 9. Erratum in: Nature. 2012 Nov 8;491(7423):288. Rogers, Kristen [corrected to Rodgers, Kristen].

Cancer Genome Atlas Network. "Comprehensive molecular characterization of human colon and rectal cancer." Nature. 2012 Jul 18;487(7407):330-7. doi: 10.1038/nature11252.
Activities: Ultimate Frisbee:
Boneyard: Masters division team. 2016 World Ultimate Champions (as US Men's Masters National Team); 2014 World Ultimate Club Champions; 2015 US National Champions; 2010, 2012, 2013 National silver medalists, 2009 Spirit of the Game award winners.
Ring of Fire: Open division team, Silver medalists at 2002 UPA Championships, third place at 1998 US Nationals, fifth place at 1999 World Club Championships;
Spear: Mixed-gender team, Champions at 2000 Co-ed Nationals;
Blue Ridge Ultimate: Mixed-gender team finished fourth at 2002 World Club Championships;
Gorilla Foot: Mixed-gender team won Spirit of the Game Award at 2005 National Championships;
Alchemy: Grandmasters division team, 2015 Beach Ultimate National Champions;
UNC-Chapel Hill Darkside: co-founded and captained during college, 1993-1996;
USA Ultimate: 501.(c)(3) Standing Rules Committee 2000-present; officiated at 1999 and 2000 College National Championships and other tournaments;
Triangle Ultimate: 501.(c)(3) Board member, 2009-present.

Other: NC State Employee Credit Union: Advisory board member for Pittsboro Street, Chapel Hill location.



References available on request.

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© Alan Hoyle
Last update: 2016 July 6