John V. Carlis

Professor, University of Minnesota

Computer Science and Engineering

Director of Undergraduate Studies


Biomedical Informatics and Computational Biology

Associate Director of Graduate Studies

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


Current Teaching

Fall 2014 SENG 5707

Spring 2015 BICB 8932

Spring 2015 CSCI 1133


Office Hours Fall 2014: 

2:00- 3:00 Thursdays [but not 10/2] 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

“Live Simian Immunodeficiency Virus Vaccine Correlate of Protection: Immune Complex-Inhibitory Fc Receptor Interactions That Reduce Target Cell Availability”, Smith AJ, Wietgrefe SW, Shang L, Reilly CS, Southern PJ, Perkey KE, Duan L, Kohler H, Müller S, Robinson J, Carlis JV, Li Q, Johnson RP, Haase AT., Journal of Immunology, August , 2014.

“Live Simian Immunodeficiency Virus Vaccine Correlate of Protection: Local Antibody Production and Concentration on the Path of Virus Entry”, Li Q, Zeng M, Duan L, Voss JE, Smith AJ, Pambuccian S, Shang L, Wietgrefe S, Southern PJ, Reilly CS, Skinner PJ, Zupancic ML, Carlis JV, Piatak M Jr, Waterman D, Reeves RK, Masek-Hammerman K, Derdeyn CA, Alpert MD, Evans DT, Kohler H, Müller S, Robinson J, Lifson JD, Burton DR, Johnson RP, Haase AT.Journal of Immunology, August, 2014. 

Improved intensity-based label-free quantification via proximity-based intensity normalization (PIN)”, Van Riper SK, de Jong EP, Higgins L, Carlis JV, Griffin TJ, J Proteome Res. 2014 Mar 7;13(3):1281-92.

“Mass spectrometry-based proteomics: basic principles and emerging technologies and directions”, Van Riper SK, de Jong EP, Carlis JV, Griffin TJ. Adv Exp Med Biol. 2013.

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

" Cumulative mechanisms of lymphoid tissue fibrosis and T cell depletion in HIV-1 and SIV infections", Zeng M, Smith AJ, Wietgrefe SW, Southern PJ, Schacker TW, Reilly CS, Estes JD, Burton GF, Silvestri G, Lifson JD, Carlis JV, Haase AT. 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.