John V. Carlis

Professor, University of Minnesota

Computer Science and Engineering

Director of Undergraduate Studies

Associate Director of Biomedical Informatics and Computational Biology

6-225b Keller Hall
200 Union Street SE
University of Minnesota
Minneapolis, MN, USA, 55455
(612) 625-6092
(612) 625-0572 [fax]


Current Teaching

Spring 2014:  CSCI 8725

Spring 2014: BICB 8932

Fall 2014 SENG 5707


Office Hours Spring 2014: 

2:00- 3:00 Mondays and by appointment



Mastering Data Modeling: A User Driven Approach

By   John Carlis and Joseph Maguire

Addison – Wesley, Boston MA, 2001.



Warning!  This page has minimal content.  I am not my internet presence. 



Selected papers

de Jong EP, van Riper SK, Koopmeiners JS, Carlis JV, Griffin TJ, " Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery",  Clin Chim Acta. 2011 Nov 20;412(23-24):2284-8.

Zeng M, Smith AJ, Wietgrefe SW, Southern PJ, Schacker TW, Reilly CS, Estes JD, Burton GF, Silvestri G, Lifson JD, Carlis JV, Haase AT. " Cumulative mechanisms of lymphoid tissue fibrosis and T cell depletion in HIV-1 and SIV infections", J Clin Invest. 2011 Mar 1;121(3):998-1008.

Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions. de Jong EP, Xie H, Onsongo G, Stone MD, Chen XB, Kooren JA, Refsland EW, Griffin RJ, Ondrey FG, Wu B, Le CT, Rhodus NL, Carlis JV, Griffin TJ. PLoS One. 2010 Jun 17;5(6):e11148.

Hexapeptide libraries for enhanced protein PTM identification and relative abundance profiling in whole human saliva. Bandhakavi S, Van Riper SK, Tawfik PN, Stone MD, Haddad T, Rhodus NL, Carlis JV, Griffin TJ.J Proteome Res. 2011 Mar 4;10(3):1052-61. Epub 2011 Jan 14.

Fluorodeoxyglucose positron emission tomography of mild cognitive impairment with clinical follow-up at 3 years. Pardo JV, Lee JT, Kuskowski MA, Munch KR, Carlis JV, Sheikh SA, Surerus C, Lewis SM, McCarten JR, Fink H, McPherson S, Shah HH, Rottunda S, Dysken MW. Alzheimers Dement. 2010 Jul;6(4):326-33. Epub 2010 May 6.

Qingsheng Li, Pamela J. Skinner, Sang-Jun Ha, Lijie Duan, Teresa L. Mattila, Aaron Hage, Cara White, Daniel L. Barber, Leigh O’Mara, Peter J. Southern, Cavan S. Reilly, Christopher J. Miller, Rafi Ahmed, John V. Carlis and Ashley T. Haase, “Visualizing antigen specific and infected cells in situ predicts outcome in early viral infection,” Science, e-pub, March 26, 2009.

Qingsheng Li, Jacob D. Estes, Patrick M. Schlievert, Lijie Duan, Amanda J. Brosnahan, Peter J. Southern, Cavan S. Reilly, Marnie L. Peterson, Nancy Schultz-Darken, Kevin G. Brunner, Karla R. Nephew, Stefan Pambuccian, Jeffrey D. Lifson, John V. Carlis & Ashley T. Haase, “Glycerol monolaurate prevents mucosal SIV transmission”  Nature, e-pub March 4,2009. (A “newsworthy” article).

Griffin TJ, Xie H, Bandhakavi S, Popko J, Mohan A, Carlis JV, Higgins L, “ iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer,” Journal of Proteome Research. 7(3): 486-98, March, 2008.

Munch K.R., J.V. Carlis, J.V. Pardo, JT Lee, “Bringing functional brain image analysis to the clinician: Initial assessment of an online interactive diagnostic aide,” Computers in Biology and Medicine, 38(2), 155-164, May, 2008.

Qingsheng Li, Lijie Duan, Jacob D. Estes, Zhong-Min Ma, Tracy Rourke, Yichuan Wang, Cavan Reilly, John Carlis, Christopher J. Miller & Ashley T. Haase , “Peak SIV replication in resting memory CD4+ T cells depletes gut lamina propria CD4+ T cells”, Nature, April 28, 2005 [plus a news item about this article].

John Carlis, “Pathways to Success and Pitfalls in Interdisciplinary Scientific Database Research”, IEEE EMB, Nov., 2002.

Joel T. Lee, Kristin R. Munch, John V. Carlis and Jose' V. Pardo, “Internet Image Viewer (iiV)”,  BMC Medical Imaging, forthcoming, 2008

Estes JD, Wietgrefe S, Schacker T, Southern P, Beilman G, Reilly C, Milush JM, Lifson JD, Sodora DL, Carlis JV, Haase AT. “Simian immunodeficiency virus-induced lymphatic tissue fibrosis is mediated by transforming growth factor Beta 1-positive regulatory T cells and begins in early infection.” J Infect Dis. 2007 Feb 15;195(4):551-61. [cover article]

Estes JD, Li Q, Reynolds MR, Wietgrefe S, Duan L, Schacker T, Picker LJ, Watkins DI, Lifson JD, Reilly C, Carlis J, Haase AT. “Premature induction of an immunosuppressive regulatory T cell response during acute simian immunodeficiency virus infection.” J Infect Dis. 2006 Mar 1;193(5):703-12. [cover article]

J. Williams, A. Pusey, J. Carlis, J. Goodall and B. Farm, “Female Competition and Male Territorial Behavior Influence Female Chimpanzee’s Ranging Patterns”, Animal Behavior, January, 2002.

Chen, Jake Yue and John Carlis, “Genomic Data Modeling”. Information Systems, January, 2003.


[Other papers can be found via pubmed and other web resources.]

“Design: The Key to Writing (and Advising) aOne-Draft PhD Thesis” by John Carlis.   

Thinking about Abstracts


Useful Links

A list of good books

notes from my talk on how to give a talk


Upward Links

University of Minnesota

Computer Science Dept.



The views and opinions expressed in this page are strictly those of the page author.
The contents of this page have not been reviewed or approved by the University of Minnesota.