John Carlis

About

Professor John Carlis was a member of the Department of Computer Science & Engineering at the University of Minnesota Twin Cities since 1981. He was known for his tireless mentoring, coaching, and humor, benefitting generations of students, colleagues, and staff. Carlis received multiple awards including the Gordon Starr Service Award, the Department’s Outstanding Instructor Award, and was a finalist for the Morse-Alumni Teaching Award. He served as the Director of Undergraduate Studies for over a decade, leading curriculum revisions and developing resources to enhance student advising and graduation rates. He was instrumental in creating the Master of Science Program in Software Engineering (MSSE) in 1996, where he became a beloved advisor and professor, ensuring high-quality courses and outstanding adjunct faculty. Carlis also contributed significantly to interdisciplinary research and teaching at the intersection of computer science and biology, serving as Director of Graduate Studies for the Bioinformatics Graduate Minor and as Associate Director of Graduate Studies for the Biomedical Informatics and Computations Biology Program (BICB). His work was driven by a passion for preparing the next generation of biological science researchers with computational expertise. Carlis’s positive attitude, mentorship, and scholarly contributions left a lasting impact on the department and its community.

Research topics

• Computer science
• Biology
• Database
• Immunology
• Virology

Selected publications

• Cumulative mechanisms of lymphoid tissue fibrosis and T cell depletion in HIV-1 and SIV infections

  Journal of Clinical Investigation · 2011-02-18 · 303 citations

  articleOpen access

  The hallmark of HIV-1 and SIV infections is CD4(+) T cell depletion. Both direct cell killing and indirect mechanisms related to immune activation have been suggested to cause the depletion of T cells. We have now identified a mechanism by which immune activation-induced fibrosis of lymphoid tissues leads to depletion of naive T cells in HIV-1 infected patients and SIV-infected rhesus macaques. The T regulatory cell response to immune activation increased procollagen production and subsequent de…

  PublisherOA PDFDOI

• Quantitative Proteomics Reveals Myosin and Actin as Promising Saliva Biomarkers for Distinguishing Pre-Malignant and Malignant Oral Lesions

  PLoS ONE · 2010-06-17 · 110 citations

  articleOpen access

  BACKGROUND: Oral cancer survival rates increase significantly when it is detected and treated early. Unfortunately, clinicians now lack tests which easily and reliably distinguish pre-malignant oral lesions from those already transitioned to malignancy. A test for proteins, ones found in non-invasively-collected whole saliva and whose abundances distinguish these lesion types, would meet this critical need. METHODOLOGY/PRINCIPAL FINDINGS: To discover such proteins, in a first-of-its-kind study w…

  PublisherOA PDFDOI

• Live Simian Immunodeficiency Virus Vaccine Correlate of Protection: Local Antibody Production and Concentration on the Path of Virus Entry

  The Journal of Immunology · 2014-08-19 · 62 citations

  articleOpen access

  We sought design principles for a vaccine to prevent HIV transmission to women by identifying correlates of protection conferred by a highly effective live attenuated SIV vaccine in the rhesus macaque animal model. We show that SIVmac239Δnef vaccination recruits plasma cells and induces ectopic lymphoid follicle formation beneath the mucosal epithelium in the rhesus macaque female reproductive tract. The plasma cells and ectopic follicles produce IgG Abs reactive with viral envelope glycoprotein…

  PublisherOA PDFDOI

• Hexapeptide Libraries for Enhanced Protein PTM Identification and Relative Abundance Profiling in Whole Human Saliva

  Journal of Proteome Research · 2010-12-13 · 49 citations

  article

  Dynamic range compression (DRC) by hexapeptide libraries increases MS/MS-based identification of lower-abundance proteins in complex mixtures. However, two unanswered questions impede fully realizing DRC's potential in shotgun proteomics. First, does DRC enhance identification of post-translationally modified proteins? Second, can DRC be incorporated into a workflow enabling relative protein abundance profiling? We sought to answer both questions analyzing human whole saliva. Addressing question…

  PublisherDOI

• Comparison techniques utilized in spatial 3D and 4D data visualizations: A survey and future directions

  Computers & Graphics · 2017-06-20 · 41 citations

  article
  PublisherDOI

Frequent coauthors

• Ashley T. Haase

  University of Minnesota

  38 shared

• Lijie Duan

  35 shared

• Cavan Reilly

  University of Minnesota

  33 shared

• Qingsheng Li

  University of Nebraska–Lincoln

  32 shared

• Peter J. Southern

  University of Minnesota

  25 shared

• Christopher J. Miller

  Hospital of the University of Pennsylvania

  22 shared

• Joseph A. Konstan

  University of Minnesota

  22 shared

• Pamela J. Skinner

  18 shared

Awards & honors

• Gordon Starr Service Award
• Department’s Outstanding Instructor Award
• Morse-Alumni Teaching Award (finalist)
• John V. Carlis Memorial Fund (supporting excellence in teach…

Similar researchers at University of Minnesota

• Dan Knightsh-97
• Yousef Saadh-81