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

• Vaccine-Associated Maintenance of Epithelial Integrity Correlated With Protection Against Virus Entry

  The Journal of Infectious Diseases · 2018-01-29 · 1 citations

  article

  To identify the mechanisms by which human immunodeficiency virus type 1 (HIV-1) might penetrate the epithelial barrier during sexual transmission to women and the mechanisms of vaccine-associated protection against entry, we characterized early epithelial responses to vaginal inoculation of simian immunodeficiency virus strain mac251 (SIVmac251) in naive or SIVmac239Δnef-vaccinated rhesus macaques. Vaginal inoculation induced an early stress response in the cervicovaginal epithelium, which was associated with impaired epithelial integrity, damaged barrier function, and virus and bacterial translocation. In vaccinated animals, early stress responses were suppressed, and the maintenance of epithelial barrier integrity correlated with prevention of virus entry. These vaccine-protective effects were associated with a previously described mucosal system for locally producing and concentrating trimeric gp41 antibodies at the mucosal interface and with formation of SIV-specific immune complexes that block the stress responses via binding to the epithelial receptor FCGR2B and subsequent inhibitory signaling. Thus, blocking virus entry may be one protective mechanism by which locally concentrated non-neutralizing Ab might prevent HIV sexual transmission to women.

  PublisherDOI

• Vaccine-modified NF-kB and GR signaling in cervicovaginal epithelium correlates with protection

  Mucosal Immunology · 2017-08-09 · 8 citations

  articleOpen access
  PublisherOA PDFDOI

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

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

  article
  PublisherDOI

• Mucosal Humoral Immune Response to SIVmac239∆nef Vaccination and Vaginal Challenge

  The Journal of Immunology · 2016-02-11 · 13 citations

  articleOpen access

  Live attenuated vaccines such as SIV with a deleted nef gene have provided the most robust protection against subsequent vaginal challenge with wild-type (WT) SIV in the SIV-rhesus macaque model of HIV-1 transmission to women. Hence, identifying correlates of this protection could enable design of an effective HIV-1 vaccine. One such prechallenge correlate of protection from vaginal challenge has recently been identified as a system with three components: 1) IgG Abs reacting with the viral envelope glycoprotein trimeric gp41; 2) produced by plasma cells in the submucosa and ectopic tertiary lymphoid follicles in the ectocervix and vagina; and 3) concentrated on the path of virus entry by the neonatal FcR in the overlying epithelium. We now examine the mucosal production of the Ab component of this system after vaginal challenge. We show that vaginal challenge immediately elicits striking increases in plasma cells not only in the female reproductive tract but also at other mucosal sites, and that these increases correlate with low but persistent replication at mucosal sites. We describe vaginal ectopic follicles that are structurally and functionally organized similar to follicles in secondary lymphoid organs, and we provide inferential evidence for a key role of the female reproductive tract epithelium in facilitating Ab production, affinity maturation, and class switch recombination. Vaccination thus accesses an epithelial-immune system axis in the female reproductive tract to respond to exposure to mucosal pathogens. Designing strategies to mimic this system could advance development of an effective HIV-1 vaccine.

  PublisherOA PDFDOI

• RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification

  Bioinformatics · 2016-02-18 · 18 citations

  articleOpen access

  UNLABELLED: RIPPER is a framework for mass-spectrometry-based label-free relative quantification for proteomics and metabolomics studies. RIPPER combines a series of previously described algorithms for pre-processing, analyte quantification, retention time alignment, and analyte grouping across runs. It is also the first software framework to implement proximity-based intensity normalization. RIPPER produces lists of analyte signals with their unnormalized and normalized intensities that can serve as input to statistical and directed mass spectrometry (MS) methods for detecting quantitative differences between biological samples using MS. AVAILABILITY AND IMPLEMENTATION: http://www.z.umn.edu/ripper CONTACT: vanr0014@umn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  PublisherOA PDFDOI

• Integration of Hematopoietic Cell Transplantation Outcomes Data

  Lecture notes in computer science · 2015-01-01 · 2 citations

  book-chapter
  PublisherDOI

• Improved Intensity-Based Label-Free Quantification via Proximity-Based Intensity Normalization (PIN)

  Journal of Proteome Research · 2014-02-16 · 5 citations

  article

  Researchers are increasingly turning to label-free MS1 intensity-based quantification strategies within HPLC-ESI-MS/MS workflows to reveal biological variation at the molecule level. Unfortunately, HPLC-ESI-MS/MS workflows using these strategies produce results with poor repeatability and reproducibility, primarily due to systematic bias and complex variability. While current global normalization strategies can mitigate systematic bias, they fail when faced with complex variability stemming from transient stochastic events during HPLC-ESI-MS/MS analysis. To address these problems, we developed a novel local normalization method, proximity-based intensity normalization (PIN), based on the analysis of compositional data. We evaluated PIN against common normalization strategies. PIN outperforms them in dramatically reducing variance and in identifying 20% more proteins with statistically significant abundance differences that other strategies missed. Our results show the PIN enables the discovery of statistically significant biological variation that otherwise is falsely reported or missed.

  PublisherDOI

• 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 gp41 trimers, and these Abs are concentrated on the path of virus entry by the neonatal FcR in cervical reserve epithelium and in vaginal epithelium. This local Ab production and delivery system correlated spatially and temporally with the maturation of local protection against high-dose pathogenic SIV vaginal challenge. Thus, designing vaccines to elicit production and concentration of Abs at mucosal frontlines could aid in the development of an effective vaccine to protect women against HIV-1.

  PublisherOA PDFDOI

• Live SIV vaccine correlate of protection: immune complex-inhibitory Fc receptor interactions that reduce target cellavailability

  Lincoln (University of Nebraska) · 2014-01-01

  articleOpen access

  Principles to guide design of an effective vaccine against HIV are greatly needed, particularly to protect women in the pandemic’s epicentre in Africa. We have been seeking these principles by identifying correlates of the robust protection associated with SIVmac239Δnef vaccination in the SIV-rhesus macaque animal model of HIV-1 transmission to women. We have identified one correlate of SIVmac239Δnef protection against vaginal challenge as a resident mucosal system for SIV-gp41 trimer antibody production and neonatal Fc receptor (FcRn)-mediated concentration of these antibodies on the path of virus entry to inhibit establishment of infected founder populations at the portal of entry. Here we identify as a second protection correlate, blocking CD4+ T cell recruitment to inhibit local expansion of infected founder populations. Virus-specific immune complex interactions with the inhibitory FcγRIIb receptor in the epithelium lining the cervix initiate expression of genes that block recruitment of target cells to fuel local expansion. Immune complex-FcγRIIb receptor interactions at mucosal frontlines to dampen the innate immune response to vaginal challenge could be a potentially general mechanism for the mucosal immune system to sense and modulate the response to a previously encountered pathogen. Designing vaccines to provide protection without eliciting these transmission-promoting innate responses could contribute to developing an effective HIV-1 vaccine.

  Publisher

• Trend-Centric Motion Visualization: Designing and Applying a New Strategy for Analyzing Scientific Motion Collections

  IEEE Transactions on Visualization and Computer Graphics · 2014-08-11 · 16 citations

  articleOpen access

  In biomechanics studies, researchers collect, via experiments or simulations, datasets with hundreds or thousands of trials, each describing the same type of motion (e.g., a neck flexion-extension exercise) but under different conditions (e.g., different patients, different disease states, pre- and post-treatment). Analyzing similarities and differences across all of the trials in these collections is a major challenge. Visualizing a single trial at a time does not work, and the typical alternative of juxtaposing multiple trials in a single visual display leads to complex, difficult-to-interpret visualizations. We address this problem via a new strategy that organizes the analysis around motion trends rather than trials. This new strategy matches the cognitive approach that scientists would like to take when analyzing motion collections. We introduce several technical innovations making trend-centric motion visualization possible. First, an algorithm detects a motion collection's trends via time-dependent clustering. Second, a 2D graphical technique visualizes how trials leave and join trends. Third, a 3D graphical technique, using a median 3D motion plus a visual variance indicator, visualizes the biomechanics of the set of trials within each trend. These innovations are combined to create an interactive exploratory visualization tool, which we designed through an iterative process in collaboration with both domain scientists and a traditionally-trained graphic designer. We report on insights generated during this design process and demonstrate the tool's effectiveness via a validation study with synthetic data and feedback from expert musculoskeletal biomechanics researchers who used the tool to analyze the effects of disc degeneration on human spinal kinematics.

  PublisherOA PDFDOI

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…