KARL J. SMALLEY

Personal Data:
Business Address:Office of Cancer Research Administration / Informatics Shared Resource
Sidney Kimmel Comprehensive Cancer Center
Thomas Jefferson University
Philadelphia, PA 19107
Google VoiceMail: (484) 238-0525
E-Mail: Karl.Smalley@Jefferson.edu
Web: https://ewebapp01pa.jefferson.edu/smalley/
Career Interests:Computer Programming, Database Management, Web Applications, Statistics and Scientific Research.

Experience:

January 2008-  
    Present  		 Database Administrator at the Sidney Kimmel Comprehensive Cancer Center of Thomas Jefferson University. Duties include assisting with management of Linux workstations and Windows File Servers, software/database design and implementation for various scientific and administrative purposes (Oracle, SQL Server, PostgreSQL, MySQL, MS FoxPro, Java, JavaScript, Perl, PHP, & C). Maintain and update multi-user grants accounting and personnel systems that were in use by TJU departments for grants management. Developed 2 types of multi-user web-based automatic billing systems for SKCCC shared resources (one is a reservation type system and the other is a request type system) in PHP/perl with a PostgreSQL database. Developed a web-based Chemotherapy Ordering system for the TJUH Pharmacy to ensure accurate dosing and documentation in perl with a MySQL database. Assisted with the development of a multi-user web based Clinical Trials application (including serious adverse event and unanticipated problem reporting) for the Cancer Center and eventually all of TJU in PHP with a PostgreSQL database. Modified applications to work with OnCore by Forte as a back-end CTMS data source. Continued to assist researchers with statistical analysis and graphics design. Also continued producing several Data Tables in the NCI Cancer Center Support Grant application. Assistance with caBIG projects in the Clinical Trials Management Systems (CTMS), Integrative Cancer Research (ICR) and Tissue Banks and Pathology Tools (TBPT) Workspaces. Developed SMART (SKCCC Member Administrative Reporting Tool - fka CCSGPubs) application to collect and report SKCCC publications and grant funding in CCSG Grant applications. Re-wrote and maintained the Tumor Measurement Request Application for oncology clinical trials that require radiological assessment of tumor progression during trial.

November 1990-  
    December 2007  		 Systems Analyst at the Kimmel Cancer Center of Thomas Jefferson University. Continuation of previous position at Temple. Helped with moving the Center by compiling Personnel & Equipment transfer, Start-Up Equipment & Supply Procurement Reports. Duties included management of Novell File Server, Windows NT Servers, Linux workstations, Silicon Graphics Inc. model 380/GTXB, Indigos, Challenge S servers, Hewlett Packard HP-750's (Unix operating system), ethernet network planning and management, software design and implementation for various scientific and administrative purposes (Oracle, SQL Server, PostgreSQL, MySQL, MS FoxPro, Visual Basic, JavaScript, Perl, PHP, & C). Specifically, developed multi-user grants accounting and personnel systems currently in use by department for grants management. Developed multi-user Mouse Allele Database application in Oracle & C for tracking/recording genetic drift, a multi-user web-based reservation systems for a few KCC resources. Assisted researchers with statistical analysis and graphics design. Also responsible for producing several Summaries in the NCI Cancer Center Support Grant application. Maintenance of Macintosh and Windows based Personal Computers.

August 1989-  
    November 1990  		 Systems programmer/analyst at the Fels Institute for Cancer Research and Molecular Biology of Temple University. Duties included DecStation system management, management of a Silicon Graphics Inc. model 280/GTXB (Unix operating system), ethernet network planning and management, software design and implementation for various scientific (C, Oracle and artificial intelligence-Nexpert Object) and administrative (dBase III+ and Lotus 1-2-3) purposes. Maintenance of Macintosh, IBM and IBM-compatible PCs.

May 1987-
    August 1989		 Systems programmer/analyst at the General Clinical Research Center (GCRC) of Temple University. Duties included routine system management procedures for a MicroVAX II and IBM PC/XTs, as well as assisting physicians/scientists with research study designs, data collection and analysis. Composed many Center specific programs for research and administrative purposes, utilizing Basic and dBase III+. Selected by the National Institutes of Health, GCRC branch to collaborate with other GCRC system managers in the design and implementation of a software package in dBase III+ to automate the annual reporting process. The package was being used on a national scale.

Education Data:
September 1982-  
    January 1988  		 Received BBA from Temple University, School of Business and Management, Philadelphia PA. Graduated Magna Cum Laude. Major concentration areas in Statistics and Computer and Information Sciences(CIS). Studies required the work with the following hardware and software: CDC CYBER 750; MicroVAX II; IBM PC; FORTRAN; COBOL; Basic; Assembly; dBase III; Lotus 1-2-3; word processing software; Minitab; BMDP; and SAS.

Overall GPA (4.0 Scale):3.68
 GPA in Statistics:3.83
 GPA in CIS:3.90

September 1978-  
    June 1982  		 John Bartram High School, Philadelphia, PA

    Class Rank:              1
    GPA (Scale 100):  97.9

Awards, Honors & Professional Associations:
February 2023 SKCC 2023 Retreat - Administration - Lifetime/Career Achievement Award
March 2007 KCC "All Hands" Certificate of Appreciation - Administrative Category
November 1999 Affiliate Membership in the Kimmel Cancer Center.
June 1988 Statistics Award from School of Business and Management of Temple University.
May 1987 Membership in the Association of GCRC Systems Managers (Statistics Committee & Administrative Computing Working Group).
1982-1986 Temple University: Dean's List for 7 of 8 full-time semesters (final 6 semesters).
June 1982 Outstanding Achievement Scholarship (4 years full-tuition) from Temple University.
June 1982 John Bartram High School: Graduated with highest GPA in class.
June 1982 John Bartram High School: Academic awards (Gold Keys) in Math, Science and History.
September 1980 Accepted into the National Honor Society as a High School Junior.
1978-1982 John Bartram High School: Honor Roll for final 13 of 16 quarters.


Publications:
31.   Fong LY, Huebner K, Jing R, Smalley KJ, Brydges CR, Fiehn O, Farber JL, Croce CM. Zinc treatment reverses and anti-Zn-regulated miRs suppress esophageal carcinomas in vivo. Proc Natl Acad Sci U S A. 2023 May 16;120(20):e2220334120. Epub 2023 May 8.

30.   Fong LY, Taccioli C, Palamarchuk A, Tagliazucchi GM, Jing R, Smalley KJ, Fan S, Altemus J, Fiehn O, Huebner K, Farber JL, Croce CM. Abrogation of esophageal carcinoma development in miR-31 knockout rats. Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):6075-6085.

29.   Fong LY, Jing R, Smalley KJ, Wang ZX, Taccioli C, Fan S, Chen H, Alder H, Huebner K, Farber JL, Fiehn O, Croce CM. Human-like hyperplastic prostate with low ZIP1 induced solely by Zn deficiency in rats. Proc Natl Acad Sci U S A. 2018 Nov 20;115(47):E11091-E11100.

28.   Fong LY, Jing R, Smalley KJ, Taccioli C, Fahrmann J, Barupal DK, Alder H, Farber JL, Fiehn O, Croce CM. Integration of metabolomics, transcriptomics, and microRNA expression profiling reveals a miR-143-HK2-glucose network underlying zinc-deficiency-associated esophageal neoplasia. Oncotarget. 2017 Oct 10; 8(47):81910-81925

27.   Fong LY, Taccioli C, Jing R, Smalley KJ, Alder H, Jiang Y, Fadda P, Farber JL, Croce CM. MicroRNA dysregulation and esophageal cancer development depend on the extent of zinc dietary deficiency. Oncotarget. 2016 Mar 8;7(10):10723-38

26.   Taccioli C, Garofalo M, Chen H, Jiang Y, Tagliazucchi GM, Di Leva G, Alder H, Fadda P, Middleton J, Smalley KJ, Selmi T, Naidu S, Farber JL, Croce CM, Fong LY. Repression of Esophageal Neoplasia and Inflammatory Signaling by Anti-miR-31 Delivery In Vivo. J Natl Cancer Inst. 2015 Nov; 107(11):doi:10.1093/jnci/djv220.

25.   Tacioli C, Chen H, Garoalo M, Jiang Y, Di Leva G, Alder H, Middleton J, Smalley KJ, Bottoni A, Costinean S, Farber JL, Croce CM, Fong LYY. Abstract/Poster Presentation: Silencng of miroRNA-31 Prevents Esophageal Neoplasia in Znc-Deficient Rats. American Association for Cancer Research, Washington DC, April 2013.

24.   Alder H, Taccioli C, Chen H, Jiang Y, Smalley KJ, Fadda P, Ozer HG, Huebner K, Farber JL, Croce CM, Fong LY. Dysregulation of miR-31 and miR-21 induced by zinc deficiency promotes esophageal cancer. Carcinogenesis. 2012; 33(9):1736-44.

23.   Taccioli C, Chen H, Jiang Y, Liu XP, Huang K, Smalley KJ, Farber JL, Croce CM, Fong LY. Dietary zinc deficiency fuels esophageal cancer development by inducing a distinct inflammatory signature. Oncogene. 2012 Oct 18;31(42):4550-8.
22.   Fong LY, Jiang Y, Rawahneh ML, Smalley KJ, Croce CM, Farber JL, Huebner K. Zinc supplementation suppresses 4-nitroquinoline 1-oxide-induced rat oral carcinogenesis. Carcinogenesis. 2011; 32(4):554-60.
21.   Wan SG, Taccioli C, Jiang Y, Chen H, Smalley KJ, Huang K, Liu XP, Farber JL, Croce CM, Fong LY. Zinc deficiency activates S100A8 inflammation in the absence of COX-2 and promotes murine oral-esophageal tumor progression. Int J Cancer. 2011; 129(2):331-45.
20.   Fong LY, Jiang Y, Rawahneh ML, Smalley KJ, Croce CM, Farber JL, Huebner K. Abstract/Poster Presentation: Zinc Supplementation Suppresses 4-Nitroquinoline 1-Oxide-Induced Rat Oral Carcinogenesis. American Association for Cancer Research: Frontiers in Cancer Prevention, Philadelphia PA, November 2010.

19.   London JW, Smalley KJ, Chatterjee D, Isikoff JM, Housman D, Palchuk MB. Abstract/Poster Presentation: Integration of caTissue with Clinical Data in an i2b2 Research Data Mart. CaBig Annual Meeting: Building a Collaborative Biomedical Network. Washington DC. September 13-15 2010

18.   London JW, Smalley KJ, Conner K, Smith JB. The automation of clinical trial serious adverse event reporting workflow. Clin Trials. 2009; 6(5):446-54.

17.   Fong LY, Jiang Y, Riley M, Liu X, Smalley KJ, Guttridge DC, Farber JL. Prevention of upper aerodigestive tract cancer in zinc-deficient rodents: Inefficacy of genetic or pharmacological disruption of COX-2. Int J Cancer. 2008; 122(5):978-89.

16.   London JW, Marshall A, Talarico R, Miller C, Conner K, Smalley KJ, Smith JB. Abstract/Poster Presentation: The Design and Implementation of a Fully Automated Adverse Event Reporting System. 2006 Annual Human Research Protection Programs (HRPP) Conference. Washington DC, November 15-18 2006.

15.   Li F, Yang J, Smalley KJ, Warzel D, London JW. Abstract/Poster Presentation: The Challenges of Integrating caGRID in the Cancer Center Environment, NCI caBIG Annual Meeting, Arlington, VA, April 9-11, 2006.

14.   Li F, Smalley KJ, London JW. Abstract/Poster Presentation: Local Cancer Center's Legacy Adoption Strategy For CaBIG Projects, NCI caBIG Annual Meeting, Arlington, VA, April 9-11, 2006.

13.   Li F, Smalley KJ, London JW. Abstract/Poster Presentation: Adapting caArray to a Cancer Center's Workflow, NCI caBIG Annual Meeting, Bethesda, MD. April 12-13, 2005.

12.   Owen OE, Smalley KJ, Jungas RL. Starvation. In: Handbook of Physiology. Section 7: The Endocrine System, Vol. 2: The Endocrine Pancreas and Regulation of Metabolism. Edited by L.S. Jefferson and A.D. Cherrington. Oxford University Press. 2001; Chapter 39,1199-225.

11.   Noé A, Mahoney M, Simpson A, Rodeck U, Jost M, Smalley KJ, Mulholland J. Poster Presentation: Matrilysin and invasiveness of squamous cell carcinoma cell lines. The first symposium of the international society for matrix biology, Jefferson Medical College, Philadelphia, PA. June 14-17, 2000.

10.   Owen OE, Smalley KJ, D'Alessio DA, Mozzoli MA, Dawson EK. Protein, fat, and carbohydrate requirements during starvation: anaplerosis and cataplerosis. Am J Clin Nutr. 1998; 68(1):12-34.

9.   Owen OE, Mozzoli MA, Smalley KJ, D'Alessio DA. Oxidative and nonoxidative macronutrient disposal in lean and obese men following mixed meals. Am J Clin Nutr. 1992; 55:630-6.

8.   Owen OE, Smalley KJ, Mozzoli MA, Polansky M. Urinary nitrogen excretion, body composition, gender, and resting metabolic rate in healthy humans. Clin Res. 1990; 38:338A.

7.   Smalley KJ, Knerr AN, Colliver JA, Owen OE. A reassessment of body mass indices. Am J Clin Nutr. 1990; 52:405-8.

6.   Owen OE, Smalley KJ, D'Alessio DA, Mozzoli MA, Knerr AN, Kendrick ZV, Kavle EC, Donohue M, Tappy L, Boden G. Resting metabolic rate and body composition of achondroplastic dwarfs. Medicine. 1990; 69:56-67.

5.   Comerota AJ, Stewart GJ, Alburger PD, Smalley K, White JV. Operative Venodilation: a previously unsuspected factor in etiology of postoperative deep vein thrombosis. Surgery. 1990; 106:301-9.

4.   Owen OE, Tappy L, Mozzoli MA, Smalley KJ. Acute Starvation. In: The Metabolic and Molecular Basis of Acquired Disease. Edited by R.D. Cohen, K.G.M.M. Alberti, B. Lewis and A.M. Derman. Bailliere Tindall, London. 1990; 550-70.

3.   D'Alessio DA, Kavle EC, Mozzoli MA, Smalley KJ, Polansky M, Kendrick ZV, Owen LR, Bushman MC, Boden G, Owen OE. Thermic effect of food in lean and obese men. J Clin Invest. 1988; 81:1781-9.

2.   Owen OR, Holup JL, D'Alessio DA, Craig ES, Polansky M, Smalley KJ, Kavle EC, Bushman MC, Owen LR, Mozzoli MA, Kendrick ZV, Boden GH. A reappraisal of the caloric requirements of men. Am J Clin Nutr. 1987; 46:875-85.

1.   Owen OE, Holup JL, D'Alessio DA, Craig ES, Polansky M, Smalley KJ, Kavle EC, Bushman MC, Owen LR, Mozzoli MA, Kendrick ZV, Boden GH. Abstract/Poster Presentation: A reappraisal of the caloric requirements of men. Clin Res. 1987; 35:644A.