Photo of Mike Klymkowsky

Mike Klymkowsky

Porter room B425
Visit the Klymkowsky Lab website.
Explore Mike Klymkowsky's areas of research and more in Vivo


BS, The Pennsylvania State University (1971-1974)
Ph.D., California Institute of Technology, 1980
Post-doctoral positions:
University College London with Martin Raff
The Rockefeller University with Lee Rubin


Research Interests:
Embryonic patterning, gene regulatory networks, effective teacher education, coherent biology course and curricular design and delivery, improving student learning.

Research Profile:

Xenopus as a model for cell biology in situ: We originally turned to the Xenopus (African clawed frog) oocyte and embryo as more realistic system (as compared to cultured cells) in which to characterize organization and functional roles of intermediate filaments (described here). Beginning with the description of the asymmetrically organized and remarkably dynamics oocyte/early embryonic keratin system and ending with the characterization of keratin (in morphogenic epithelial) and desmin (in skeletal muscle), these studies largely fulfilled their original goals.

Subsequently, our studies on IFs led us in a number of directions, from the role of plakoglobin (γ-catenin) as a modulator of Wnt signaling to the identification of HMG-domain containing SOX proteins as antagonists of β-catenin-mediated Wnt signaling.

In part because of the dramatic changes in IF expression, we turned to studies of the induction and behavior of neural crest. We found roles of the Zn-finger transcription factor Slug (Snail2) in both mesoderm formation and induction of neural crest (Shi et al., 2011 and references therein).

One of the apparent targets of Slug/Snail2 regulation in the early embryo is Chibby, a protein involved in both ciliary formation and the regulation of Wnt signaling. In a close collaboration with Mark Winey's lab, we have been actively exploring the roles of ciliary proteins in both ciliogenesis and other developmental processes. These studies, currently in preparation, revealing previously unexpected roles in the regulation of gene expression, cell migration, and neural patterning (stay tuned).

Course & curriculum design and teacher preparation: We have learned much about the conceptual obstacles students face through the development and use of the NSF-funded Biology Concept Inventory (BCI) and, through a collaboration with Annie Champaign, Katje Kohler and Ernst Hafen (ETH, Zurich) we continued to improve and make the BCI more interactive through integration into the beSocratic system (see below).

Thinking about the conceptual foundations of biology (Klymkowsky, 2010) has influenced the design of a dramatically revised and interactive introductory molecular and evolutionary biology course (Biofundamentals). Together with my collaborator Melanie Cooper (Michigan State) we are turning bFun into a book (ready for the Fall 2014 semester) to accompany our NSF-supported revised general chemistry text Chemistry, Life, the Universe and Everything (Cooper & Klymkowsky, 2013). Both courses rely heavily on a rather revolutionary graphics based formative assessment system, beSocratic (Bryfcyzinski et al. 2013). With Erin Furtak (School of Education, UC Boulder) we have developed a capstone course MCDB 4811/5811 on Teaching and Learning Biology that also serves as part of our CU Teach teacher certification program. I am currently working on a new course, MCDB 3391 Systems Biology for Biologists which should be ready by Spring semester 2014.

Thinking about biology education: That education in the biological sciences is currently ineffective (not to mention incoherent) is suggested by the wide-spread support among high school teachers for the teaching of creationism and the popularity of ineffective "alternative therapies" among the general public. Students are commonly taught to believe in evolutionary processes, rather than understand them.

We have learned much about the conceptual obstacles students face through the development and use of the Biology Concept Inventory (BCI). The have built the BCI and the tools used to develop it can be accessed at

We are also exploring a number of approaches to generate more interactive learning experiences. These include variations on conventional testing strategies: tutorials and virtual laboratories. We are currently working on tutorials that address phylogenetic relationships (the tree of life project) and the effects of mutations on phenotype.

We are part of a vibrant science education community at UC Boulder that includes the Learning Assistant (LA) program, whose goal is to recruit the best students into K-12 teaching and CU Teach, the recruitment and training program for Science and Math teacher certification.

Selected Publications

Cooper, M.M. & M.W. Klymkowsky. 2013.
Chemistry, Life, the Universe and Everything: a new approach to general chemisry and a model for curriculum reform,
J. Amer.Chem. Soc., in press.

Cooper, M.M. & M.W. Klymkowsky. 2013.
The trouble with chemical energy: why understanding bond energies requires an interdisciplinary systems approach.
CBE Life Sci. Education,12:306-12. doi: 10.1187/cbe.12-10-0170..

Cooper, M.M, S.M. Underwood, C. Hilley & M.W Klymkowsky. 2012.
Development and assessment of a molecular structure and properties learning progression.
J. Chem. Educ., 89: 1351-1357.

Bryfcyzinski, S., R.O. Pargas, M.M. Cooper & M.W. Klymkowsky. 2012. Analyzing and visualizing student work with BeSocratic.

ACM-SE '12 Proceedings of the 50th Annual Southeast Regional Conference. P: 349-350 (doi: 10.1145/2184512.2184599)

Klymkowsky, M.W. & M.M. Cooper. 2012.
Now for the hard part: the path to coherent curricular design.
BAMBED, 40: 271-272. (PMID: 22807431)

Henson, K., M.M. Cooper, & M.W. Klymkowsky. 2012.
Turning randomness into meaning at the molecular level using Mullers morphs.
Biology Open 1:405-10. (PMID: 23213431)

Cattell, M., A. Garnett, M.W. Klymkowsky & D.M.Medioros. 2012.
A maternally established soxB1/soxF axis is a conserved feature of chordate germ layer.
Evo. & Devo., 14:104-115.

Shi, J., H. Zheng, R.D. Dowell & M.W. Klymkowsky. 2012.
sizzled function and secreted network interactions in the dorsolateral mesoderm.
Biol. Open., 1: 286-294 (PMID: 23213419)

Trujillo, C*. M.M. Cooper & M.W. Klymkowsky. 2012.
Using graph-based assessments within Socratic tutorials to reveal and refine students analytical thinking about molecular networks.
BAMBED 40:100-107. doi: 10.1002/bmb.20585

Klymkowsky, M.W. 2011.
Mitochondrial activity, embryogenesis, and the dialogue between the big and little brains of the cell.
Mitochondrion, 11:814-819.

Shi, J., C. Severson, J. Yang, D. Wedlich & M.W. Klymkowsky. 2011.
Snail2-specific, BMP- and Wnt- dependent mesodermal induction of neural crest.
Development 138: 3135-45.

Klymkowsky, M.W. 2011.
Teaching disconcerting scientific ideas.
ASBMB Today ,June

Klymkowsky, M.W. 2011.
Why is understanding evolution hard?
ASBMB Today, March.

Klymkowsky, M.W. 2011.
Getting serious about science education.
ASBMB Today, February.

Shi, J., J. Power & M.W. Klymkowsky. 2011.
Revealing student thinking about experimental design and control experiments.
Int. J. Sci. Ed. 5:in press.

Klymkowsky. M.W. 2011.
Review of "Why evolution works (and creationism fails). by M. Young & P.K. Strode.
Reports of the National Center for Science Education.

Klymkowsky, M.W., S. Underwood, & R.K. Garvin-Doxas. 2010.
The Biological Concepts Instrument (BCI), a diagnostic tool to reveal student thinking.

Klymkowsky, M.W., C. Cortez-Rossi, & K.B. Artinger. 2010
Mechanisms driving neural crest induction and migration in the zebrafish and Xenopus laevis.
Cell Adhesion & Migration, 4: 595-608.

Hikasa, H.. J. Ezan, X. Li, M.W. Klymkowsky & S. Sokol. 2010.
Wnt-dependent phosphorylation of TCF3 leads to transcriptional derepression during vertebrate anteroposterior axis specification.
Dev. Cell, 9:521-32.

Klymkowsky, M.W. 2010.
Thinking about the conceptual foundations of the biological sciences.
CBE Life Science Educ. 9: 405-7.

Cooper, M.M., N. Grove, S. Underwood & M.W. Klymkowsky. 2010
Lost in Lewis Structures: an investigation of student difficulties in developing representational competence.
J. Chem Ed.,DOI: 10.1021/ed900004y.

Klymkowsky M.W. 2009.
Make room for computing.
Science. 2009 Oct 9;326(5950):227. (letter)

Klymkowsky, M.W. 2009.
A guide to the productive poking, prodding and injection of cells, a review of 'Microinjection: Methods and Applications'"Microinjection: Methods and Applications" by David Carroll,
ed. Development 136:4070-4072.

Zhang, C. & M.W. Klymkowsky. 2009.
Unexpected functional redundancy between Twist and Slug (Snail2) and their feedback regulation of NF-kB via Nodal and Cerberus.
Developmental Biology, 331:340-9.

Klymkowsky, M.W. & P. Savagner. 2009.
Epithelial-mesenchymal transition (EMT): a cancer researcher's conceptual friend and foe.
American Journal of Pathology. 174:1588-93.

Klymkowsky, M.K. & E.M. Furtak. 2009.
How the incoherent state of science and mathematics education undermines biological (and scientific) literacy.
Colorado Higher Education News.

Schlosser,G., T. Awtry, S.A. Brugmann, E.D. Jensen, K. Neilson, G. Ruan, A. Stammler, D. Volker, B. Yan, C. Zhang, M.W. Klymkowsky, & Sally A. Moody. 2008.
Eya1 and Six1 promote neurogenesis in the cranial placodes in a SoxB1-dependent fashion.
Devel. Biol. 320:199-214.

Garvin-Doxas, K. & M.W. Klymkowsky. 2008.
Understanding Randomness and its impact on Student Learning: Lessons from the Biology Concept Inventory (BCI).
CBE Life Sci Educ 7: 227-233.

Cortez-Rossi, C., L. Hernandez-Lagunas, C. Zhang, I.F. Choi, L. Kwok, M.W. Klymkowsky & K.B. Artinger. 2008.
Rohon-Beard sensory neurons are induced by BMP4 expressing non-neuronal ectoderm in Xenopus laevis,
Devel. Biol., 314:351-61.

Klymkowsky, M.W. & K. Garvin-Doxas. 2008. R
ecognizing Student Misconceptions through Ed's Tool and the Biology Concept Inventory.
PLoS Biology, 6: e3.

Garvin-Doxas, K., I. Doxas & M.W. Klymkowsky. 2007.
Ed's Tools: A web-based software tooset for accelerated concept inventory construction.
Proceedings of the National STEM Assessment of Student Achievement conference.

Klymkowsky, M.W. 2007.
Teaching without a textbook: a strategy to focus learning.
CBE Life Sci Educ 6: 190-193.

Garvin-Doxas, K., M.W. Klymkowsky & S. Elrod. 2007.
Building, using, and maximizing the impact of concept inventories in the biology education: a meeting report.
CBE Life Science Educ, 6: 277-282.

Zhang, C, & M.W. Klymkowsky, 2007.
The Sox Axis, Nodal Signaling, & Germ Layer Specification.
Differentiation 75: 536-545. (in memory of Larry Etkin).

Klymkowsky, M.W. 2007.
Conceptual interference in biology education: How jigsaw puzzle/lock and key models of molecular interactions impact understanding evolutionary change.
National Association for Research in Science Education (NARST) meeting proceedings.

Klymkowsky, M.W., R. Gheen*, & K. Garvin-Doxas. 2007.
Avoiding reflex responses: Strategies for revealing students' conceptual understanding in biology. Physics Education Research.
2006 Physics Education Research Conference. L. McCullough, J. Hsu & P. Heron, eds. pp.3-6

Zhang, C., Timothy F. Carl, E. Trudeau, Thomas Simmet & M.W. Klymkowsky. 2006.
An NF-kB and Slug regulatory loop active in early vertebrate mesoderm.
PLoS ONE, 1:e106 (1-14)

Klymkowsky, M.W. 2007.
Cell Adhesion.
McGraw-Hill Encyclopedia of Science & Technolog. ( I think this was published, at least they paid me to write it!).

Klymkowsky, M.W., Taylor, L.B.*, S.R. Spindler *, & K. Garvin-Doxas. 2006.
Two-dimensional, implicit confidence tests as a tool for recognizing student misconceptions.
J. College Science Teaching 36:44-48.

Klymkowsky, M.W., R. Gheen, I. Doxas & K. Garvin-Doxas. 2006.
Mapping student misconceptions using Ed's Tools, an on-line analysis system.
Dev. Biol. 295:349-350. doi:10.1016/j.ydbio.2006.04.074 .

Grow, M.W.& M.W. Klymkowsky. 2006.
Xenopus as a Model Organism for Functional Genomics: Rich History, Promising Future.
in Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine.

Wang, T.W., G.P. Stromberg, J.T.Whitney, N.W. Brower, M.W.Klymkowsky & J.M. Parent. 2006.
SOX3 expression identifies neural progenitors in persistent neonatal and adult mouse forebrain germinative zones.
J. Comp. Neurol., 497:88-100.

Member of the writing team for "Doing Science: The process of scientific inquiry".
2005. an NIH Curriculum Supplement for Grades 7-8. BSCS.

Zhang, C., T. Basta, & M.W. Klymkowsky. 2005.
SOX7 and SOX18 are essential for cardiogenesis in Xenopus.
Developmental Dynamics, 234:878-891.

Klymkowsky, M.W. 2005.
Can non-majors courses lead to biological literacy? Do majors courses do any better?
Cell Biology Education 4:196-198.