John R. Jungck, Ph.D.


  • BISC 195 - Evolution

Research Interests

I am a theoretical biologist who specializes in molecular evolution, evolutionary bioinformatics, image analysis, and mathematical biology education. My interests are deeply involved with various aspects of promoting interdisciplinary work: science, technology, and society; history, philosophy, and social studies of biology; art and science (STEAM – putting art in Science, Technology, Engineering, and Mathematics); numeracy (quantitative reasoning); Citizen Science and Participatory Democracy; international collaboration (International Union of Biological Sciences); mathematics and science education (PBL, collaborative learning, open ended investigations, strategic simulations for learning long-term strategies of research, problem solving, interdisciplinary education, progressive cyberlearning); and, promoting diversity and student retention. I was the co-founder of the BioQUEST Curriculum Consortium (<>). Many of the computer software packages that I have co-developed are available through that website. Much of my career has included serving the community as an editor of journals that range from the Bulletin of Mathematical Biology, Evolutionary Bioinformatics, and BioSystems to Biology International, Bioscene: Journal of College Biology Teaching, the American Biology Teacher, and the American Journal of Undergraduate Research.

Current Projects

In 2018-2019, Professor Jungck is on sabbatical where he is focusing on completing two books: “A BioGraphy of Life: Modeling Biology with Dots and Lines” and “Math Saves Lives: Cancer and Evolution.” He is spending part of his sabbatical at the National Institute for Mathematical Biology Synthesis Center.

Image analysis of cell division of Drosophila melaganaster and Arabidopsis thaliana with computational geometry (Voronoi tessellations), graph theory (Delaunay triangulations, Pitteway violoations, minimal spanning trees, nearest neighbor networks, Ulam trees, Eulerian circuits, Hamiltonian pathways, DeBruijn graphs), and spatial statistics. We are also looking at polygonal tessellations on polyherdral radiolarians. Much of this work involves scientific visualization via 3D microscopy, 3D scanning, 3D and 4D printing, and 3D projection.

Phylogenetic tree and network analysis of the evolution of protein targets of anti-cancer drugs and the general problem of the evolution of resistance to cancer chemotherapy. Much of this work involves bioinformatics data mining of large complex data bases and developing software for testing evolutionary hypotheses (split decomposition, new metrics for scoring multiple sequence alignments based on Hamiltonian distances of 4D hypercube representations  of genetic coding, matrix algebra analyses of gene expression data, interval graph analyses for motif detection and transitivity ordering in systems biology, combinatorics of genome rearrangements, and network visualization).

Graph theoretic analysis of food webs via community ecology analysis of niche space, trophic levels, and energy flux.

Development of computer simulations called strategic simulations for learning long-term strategies of research (primarily in genetics, evolution, biochemistry, and bioinformatics) and complex databases of original research data (most famously BIRDD: Beagle Investigations Return with Darwinian Data – on the Galapagos Finches) that are more easily probed by students with multivariate statistics and multidimensional visualization.

Research Group

  • Rama Viswanathan, Beloit College (graph theory, computer science)
  • Noppadon Khiripet, NECTEC (Bangkok, Thailand) (graph theory, computer science) 
  • Roger Wagner, University of Delaware (histologist, microscopist)
  • Anton Weinstein, Truman State University (population genetics, bioinformatics)
  • Vince Streif, University of Wisconsin Madison (graph theory, computer science)
  • Sijia Liang and Yang Yang, University of Minnesota (statistics)
  • Peter Lockhart, Massey University (New Zealand) (molecular evolution)
  • Peter Biro, Centre for Ecological Research, Balaton Limnological Institute, Hungarian Academy of Sciences (community ecology)
  • Kristin Jenkins, University of Wisconsin Madison; Stacey Kiser, Lane Community College (Oregon); Ethel Stanley, Three Rivers Community College (Missouri); and Sam Donovan (University of Pittsbugh) (BioQUEST Curriculum Consortium)

Selected Publications

  • John R. Jungck, Debra Knisley, Jeff Randell Knisley, Greta Pangborn, Manda Riehl, and Emilie Wiesner. (2019). “Multi-scale graph-theoretic modeling of bimolecular structures.” In Raina Robeva and Matthew Macauley, Editors. Algebraic and Combinatorial Computational Biology Mathematics in Science and Engineering), 1st Edition. Academic Press: pages 1-34.
  • Wilson Sayres, Melissa A., Charles Hauser, Michael Sierk, Srebrenka Robic, Anne G. Rosenwald, Todd M. Smith, Eric W. Triplett, Jason J. Williams, Elizabeth Dinsdale, William R. Morgan, James M. Burnette III, Samuel S. Donovan, Jennifer C. Drew, Sarah C. R. Elgin, Edison R. Fowlks, Sebastian Galindo-Gonzalez, Anya L. Goodman, Nealy F. Grandgenett, Carlos C. Goller, John R. Jungck, Jeffrey D. Newman, William Pearson, Elizabeth F. Ryder, Rafael Tosado-Acevedo, William Tapprich, Tammy C. Tobin, Arlín Toro-Martínez, Lonnie R. Welch, Robin Wright, Lindsay Barone, David Ebenbach, Mindy McWilliams, Kimberly C. Olney, Mark A. Pauley. (2018) Bioinformatics core competencies for undergraduate life sciences education. PLoS ONE 13(6): e0196878.
  • John R. Jungck. (In press). Why Fractal Features Flourish: Measurement, Modeling, and Morphogenesis. Fractal Geometry and Nonlinear Analysis in Medicine and Biology.
  • Viswanathan, Rama, Sijia Liang, Yang Yang, and John R. Jungck. (2016). Biographer: Visualization of Graph Theoretical Patterns, Measurements, and Analysis in Mathematical Biology. In Rubem P Mondaini, Editor.  BIOMAT 2015. World Scientific: Singapore, pp. 118-140.
  • Jungck, John R., and Rama Viswanathan. (2015). Graph Theory for Systems Biology: Interval Graphs, Motifs, and Pattern Recognition. In Raina Robeva, editor. Algebraic and Discrete Mathematical Methods for Modern Biology. Elsevier, Inc., pages 1-27.
  • Wagner, Roger, John R. Jungck, and Denis van Loo. (2015). Sub-Micron X-ray Tomography of Radiolarians: Computer Modeling and Skeletonization. Microscopy Today 23 (5): 18-22 and cover photo.
  • Waldrop, Lindsay D., Stephen C. Adolph, Cecilia G. Diniz Behn, Emily Braley, Joshua A. Drew, Robert J. Full, Louis J. Gross, John A. Jungck, Brynja Kohler, Jennifer C. Prairie, Blerta Shtylla and Laura A. Miller. (2015). Using Active Learning to Teach Concepts and Methods in Quantitative Biology. Integrative and Comparative Biology 55 (5): 933-948.
  • Jungck, John R., and Ranjan Roy. (2014). "3P’s union MMM in Finite Mathematics: A Union of the BioQUEST Curriculum Consortium’s Problem Posing, Problem Solving, Peer Review/Publication Pedagogy with the Modified Moore Method." In Proceedings of the Symposium on BEER 1 (1): 13 pages.  
  • Jungck, John R., and Anton E. Weisstein, (2013). Mathematics and evolutionary biology make bioinformatics education comprehensible. Briefings in Bioinformatics 14 (5): 599-609.
  • Schneider, Maria Victoria , and John R. Jungck. (2013). International, interdisciplinary, multi-level bioinformatics training and education. Briefings in Bioinformatics 14 (5): 527.
  • Jungck, John R. (2013). Artful Science: From STEM to STEAM. Biology International 53: 3-6.
  • Jungck, John R. (2013). Genesis of What Is Life?: A Paradigm Shift in Genetics History. CBE Life Science Education 9: 201–211  (Fall). Reprinted in “Highlights of 2013” hardcopy printed issue: pages 31-32.
  • Jungck, John R. (2012). Mathematics Make Microbes Beautiful, Beneficial, and Bountiful. In Sima Sariaslani and Geoffrey M. Gadd, Editors.  Advances in Applied Microbiology, Volume 80, Pages 37-80. ISBN: 978-0-12-394381-1
  • Khiripet, Noppadon, Wongarnet Khantuwan, and John R. Jungck. (2012). Ka-me: a Voronoi image analyzer. Bioinformatics 28 (13): 1802-1804.
  • Jungck, John R. (2012). Global Conservation Education: Participatory, Open, and Place-Based Approaches to Outreach. Biology International 50: 3-4.
  • Jungck, John R. (2012). If Life is Analog, Why Be Discrete? Middle-Out Modelling in Mathematical Biology. In Rubem P Mondaini, Editor. BIOMAT 2011 World Scientific: Singapore, pages 376-391. ISBN-13: 9789814397704
  • Jungck, John R. (2012). “Incorporating Quantitative Reasoning in Common Core Courses: Mathematics for The Ghost Map.” Numeracy: Advancing Education in Quantitative Literacy, Volume 5, Issue 1, Article 7, pages 1-32.
  • Khiripet, Noppadon, R. Viruchpintu, Jutarat Maneewattanapluk, Jenifer Spangenberg. and John R. Jungck. Morphospace: Measurement, Modeling, Mathematics, and Meaning. Mathematical Modeling of Natural Phenomena 6 (6):  54-81.
  • Jungck, John R. (2011). “Mathematical Biology Education: Modeling Makes Meaning.” Mathematical Modeling of Natural Phenomena 6 (6):  1-21.
  • Jungck, John R., Samuel S. Donovan, Anton E.Weisstein, Noppadon Khiripet, and Stephen J. Everse. (2010). “Bioinformatics education dissemination with an evolutionary problem solving perspective.” Briefings in Bioinformatics 11 (6): 570-581.
  • Robic, Srebrenka, and John R. Jungck. (2010). “Unraveling the Tangled Complexity of DNA: Combining Mathematical Modeling and Experimental Biology to Understand Replication, Recombination and Repair.” Mathematical Modeling of Natural Phenomena 6 (2):  108-135.
  • Jungck, John R., Holly Gaff, and Anton E. Weisstein. (2009). “Mathematical Manipulative Models: In Defense of Beanbag Biology.”  CBE—Life Sciences Education Vol. 9, 201–211, Fall 2010
  • Jungck, John R., Holly D. Gaff, Adam P. Fagen, and Jay B. Labov. (2010). “Beyond BIO2010: Celebration and Opportunities” at the Intersection of Mathematics and Biology.” CBE Life Sci Educ 2010 9:143-14.
  • Jungck, John R. (2009). Genetic Codes as Codes: Towards a Theoretical Basis for Bioinformatics. In Rubem Mondani, ed., BIOMAT 2008. World Scientific: Singapore, pages 300-337.
  • Jungck, John R. (2009), But is it mathematics or biology or education? Mathematical Biology Newsletter  23 (1): 10-11 (Winter).

Joint Appointment, Department of Mathematical Sciences
Affiliated Faculty, Computational Biology and Bioinformatics

Phone: (302) 831-4041


Office: 118 ISE Lab

Lab: 409 ISE Lab

221 Academy Street ISE Lab 402
University of Delaware
Newark, DE 19716


  • B.S. - University of Minnesota: Biochemistry and Mathematics
  • M.S. - University of Minnesota: Genetics, Microbiology
  • Ph.D. - University of Miami: Evolution, Molecular and Cellular Biology
  • D.Sc. honoris causa - University of Minnesota