Dr. Hanigan’s formal education includes post-doctoral work in Biochemistry at UC-Davis; a Ph.D. in Nutrition, and an M.S. in Animal Science from UC-Davis; and a B.S. in Dairy Science from Iowa State University.  Prior to undergraduate work, he operated a dairy farm in Iowa.


In 1993, he joined Purina Mills, Inc. as a research scientist where he worked on modeling metabolism in the lactating animal with emphasis on nitrogen metabolism.  In support of that effort, he collaborated with a number of individuals both within Purina Mills and externally to develop metabolic and isotopic models of mammary, liver, and portal drained viscera tissues.


Dr. Hanigan joined Virginia Tech as an Associate Professor in the Dept. of Dairy Science in 2005 where he continues to work on nitrogen metabolism and modelling problems.  His current research is focused in 3 areas: 1) experimentally characterizing responses of cellular signaling pathways regulating protein synthesis to individual amino acids, hormonal signals, and cellular energy supply and building a model of that system with the goal of refining amino acid requirements for lactating cattle; 2) improving models of nitrogen recycling to the digestive tract with the goal of better defining ruminally degradable protein requirements; and 3) improving our understanding of the regulation of volatile fatty acid production in the rumen with the goal of improving prediction accuracy within our current rumen models and better understanding the relationship between ruminal function and methane production.  The long-term objective of the work is to improve animal efficiency and reduce the impact of food animal production on the environment.


Experimental models include the use of intact animals, abomasal and jugular infusions, omasal and ileal sampling, tissue arterio-venous difference studies, tissue slices, and cell lines.  Stable isotopes are used extensively to trace metabolism.  The laboratory is equipped with 3 gas chromatographs with mass spectrometers allowing extensive analyses of isotope movement through the animal.


Dr. Hanigan’s laboratory group consists of a technician, post-doctoroal students, graduate students working on M. S. and Ph. D. degrees, visiting scientists, and undergraduate students assisting with projects and conducting their own work.

Our group's primary interest is the regulation of energy and nitrogen metabolism in the ruminant and the resulting impact on the environment. Efforts to better understand regulation of metabolism should lead to improvements in feed efficiency which reduce the impact of the animals on the environment.


We are currently working on 4 projects: 1) quantification of the mechanisms controlling amino acid metabolism and protein synthesis in lactating mammary tissue, 2) identification of animals with improved feed efficiency, 3) improvement of models of energy and amino acid metabolism and associated predictions of greenhouse gas production, 4) identification of mechanisms regulating volatile fatty acid production and absorption.


Experimental approaches include in vitro and in vivo studies. Data collected are integrated using models of pathway, tissue, and whole animal metabolism.  These models provide a means to interpret and extend the experimental observations. Pathway or cellular models provide a quantitative understanding of the processes of interest. Tissue and whole animal models can be used to explore the effects of various dietary treatments and identify key components defining metabolic responses. These components can then be distilled and incorporated into software to be used by industry for balancing rations on farm. We hope to use data collected from our experimental efforts to improve current metabolic models and use those to define new nutrient supply and requirement equations for industry use.

*Visit PubMed for Dr. Hanigan's peer reviewed articles.*



Mathematical Modeling in Nutrition and Agriculture, Proceedings of the Ninth International Conference on Mathematical Modeling In Nutrition, Roanoke, VA, August 14-17 2006.  Bassingthwaighte, James B., Raymond C. Boston, Christina Chan, Andrew J. Clifford, Dr. C.M.B. Dematawewa, James France, Michael Green, James Hargrove, Mark Hanigan, Rick Kohn, Janet A.Novotny, Kimberly O'Brien, Jim Oltjen, Chris Palliser, Blossom Patterson, Candido Pomar, Ganesh Sriram, Normand St-Pierre, Meryl Wastney.  Virginia Polytechnic Institute and State University, Blacksburg, VA.


  1. Crompton, L. A., J. France, R. S. Dias, E. Kebreab, and M. D. Hanigan. 2008. Compartmental models of protein turnover to resolve isotope dilution data.  In: J. France and E. Kebreab (Eds.) Mathematical modeling in animal nutrition.  CABI Publishing, Wallingford.
  2. Hanigan, M. D., A. G. Rius*, and C. C. Palliser. 2008. Modeling lactation potential in a whole animal model.  In: Mathematical modeling in animal nutrition (J. France and E. Kebreab, Eds.).  pp. 485-506. CABI Publishing, Wallingford.
  3. France, J., L. A. Crompton, M. D. Hanigan, R. S. Dias, and J. Dijkstra. 2007.  Using static balance models to analyze and extend observations.  In: Mathematical modeling in nutrition and agriculture (M. D. Hanigan, J. A. Novotny, and C. L. Marstaller, Eds.). pp. 15-38. Virginia Tech, Blacksburg.
  4. Bequette, B. J., M. D. Hanigan, and H. Lapierre.  2003.  Mammary uptake and metabolism of amino acids by lactating ruminants. IN: Amino Acids in Farm Animal Nutrition. 2nd Edition. (J. P. F. D’Mello ed.). pp. 347-365. CABI Publishing.  Wallingford, Oxon, U.K.
  5. Hanigan, M. D., and R. L. Baldwin. 1995.  Dynamic models of ruminant mammary metabolism. In: Modeling Ruminant Digestion and Metabolism.  pp. 370-412. New York: Chapman and Hall.
  6. Baldwin, R. L., C. C. Calvert, M. D. Hanigan, and J. Beckett. 1994.  Modelling amino acid metabolism in ruminants.  IN: Amino Acids in Farm Animal Nutrition (J. P. F. D’Mello ed.). pp281-306.  CAB International.  Wallingford, Oxon, UK.
  7. Baldwin, R. L., and M. D. Hanigan. 1990. Biological and physiological systems: Animal Sciences. In: Systems Theory Applied to Agriculture and the Food Chain. pp.1-22. Elsevier Sci. Publ. LTD



  1. R. R. White, and M. D. Hanigan. 2015. Modeling cross-species feed intake responses to environmental stress. J. Agric. Sci.,available on CJO2015. doi:10.1017/S0021859615001033.
  2. White, R. R., and M. D. Hanigan. 2015.  Evaluating equations estimating change in swine feed intake during heat and cold stress.  J. Anim. Sci. 93:5395–5410.
  3. Feng, X., K. F. Knowlton, and M. D. Hanigan. 2015.  Parameterization of a Ruminant Model of Phosphorus Digestion and Metabolism. J. Dairy Sci. 98: 7194–7208.
  4. Feng, X.,  E. Ronk, M. D. Hanigan, K. F. Knowlton, H. Schramm, and M. McCann. 2015. Effect of dietary phosphorus on intestinal P absorption in growing Holstein steers. J. Dairy Sci. 98: 3410–3416.
  5. Gregorini, P., P. C. Beukes, G. C. Waghorn, D. Pacheco, and M. D. Hanigan.. 2015.  Development of an improved representation of rumen digesta outflow in a mechanistic and dynamic model of a dairy cow, Molly. Ecological Modeling. 313: 293–306.
  6. Li, M. M., M. L. Ponder, R. R. Rhoads, K. Seelenbinder, and M. D. Hanigan. 2015.  Effects of porcine respiratory and reproductive virus syndrome on growing swine performance, manure output, and greenhouse gas production from stored manure. J. Anim. Sci. 93: 4424-4435
  7. Vetharaniam, I., R. Vibart, M. D. Hanigan, P.H. Janssen, M. H. Tavendale, and D. Pacheco. 2015. Conversion of the Molly cow rumen model to an independent representation of the sheep rumen. J. Anim. Sci.  93: 3551-3563
  8. Nayananjalie, W. A. D., T. R. Wiles, D. E. Gerrard, M. A. McCann, and M. D. Hanigan. 2015. Acetate and glucose incorporation into subcutaneous, intramuscular, and visceral fat of finishing steers. J. Anim Sci. 93: 2451-2459.     
  9. Nayananjalie, W. A. D., K. L. Pike, T. R. Wiles, J. M. Scheffler, H. Jiang, D. E. Gerrard, M. A. McCann, and M. D. Hanigan. 2015. Effect of early grain feeding of steers on postabsorptive capacity to utilize acetate. J. Anim Sci. 93: 2439-2450.
  10. Kim, W. Y., M. D. Hanigan, S. J. Lee, S. M. Lee, D. H. Kim, J. H. Hyun, J. M. Yeo, and S. S. Lee. 2014. Effects of Cordyceps militaris on the growth of rumen microorganisms and in vitro rumen fermentation with respect to methane emissions. J. Dairy Sci. 97: 7065-7075.
  11. Arriola Apelo, S. I., A. L. Bell, K. Estes, J. Ropelewski, M. J. de Veth, and M. D. Hanigan. 2014. Effects of reduced dietary protein and supplemental rumen protected essential amino acids on the nitrogen efficiency of dairy cows. J. Dairy Sci. 97: 5688–5699.
  12. Crompton, L. A., J. France, C. K. Reynolds, J. A. N. Mills, M. D. Hanigan, J. L. Ellis, A. Bannink, B. J. Bequette, and J. Dijkstra. 2014. An isotope dilution model for partitioning phenylalanine and tyrosine uptake by the mammary gland of lactating dairy cows. J. Theor. Biol. 359: 54-60.
  13. Arriola Apelo, S. I., L. M. Singer, W.K. Ray, R.F. Helm, X. Y. Lin, M. L. McGilliard, N. R. St-Pierre, and M. D. Hanigan. 2014.  Casein synthesis is independently and additively related to individual essential amino acid supply. J. Dairy Sci. 97:2998-3005. 
  14. Arriola Apelo, S. I., L. M. Singer, X. Y. Lin, M. L. McGilliard, N. R. St-Pierre, and M. D. Hanigan. 2014. Isoleucine, leucine, methionine and threonine effects on mTOR signaling in mammary tissue. J. Dairy Sci. 97: 1047-1056.
  15. Appuhamy, J. A. D. R. N., W. A. Nayananjalie, E. M. England, D. E. Gerrard, R. M. Akers, and M. D. Hanigan. 2014. Effects of AMP-activated protein kinase (AMPK) signaling and essential amino acids on mammalian target of rapamycin (mTOR) signaling and protein synthesis rates in mammary cells. J. Dairy Sci. 97:419-429.
  16. Scheffler, J. M., M. A. McCann, S. P. Greiner, H. Jiang, M. D. Hanigan, G. A. Bridges, S. L. Lake and D. E. Gerrard. 2014. Early metabolic imprinting events increase marbling scores in fed cattle. J Anim. Sci. 92:320-324.
  17. Ghimire, S., P. Gregorini, and M. D. Hanigan. 2014. Evaluation of predictions of volatile fatty acid production rates by the Molly cow model. J. Dairy Sci. 97:354–362.
  18. Gregorini, P., P. C. Beukes, M. D. Hanigan, G. Waghorn, S. Muetzel, and J. P. McNamara. 2013. Comparison of updates to the Molly cow model to predict methane production from dairy cows fed pasture. J. Dairy Sci. 96:5046-5052.
  19. Hanigan. M. D., J. A. D. R. N. Appuhamy, and P. Gregorini. 2013. Revised digestive parameter estimates for the Molly cow model. J. Dairy Sci. 96:3867-3885.
  20. Harrison, J., K. F. Knowlton, R. E. James, M. D. Hanigan, C. C. Stallings. 2012. Case Study:  National survey of barriers related to precision phosphorus feeding.  Prof. Anim. Scientist  28:564-568.
  21. Aguilar, M., M. D. Hanigan, H. A. Tucker, B. L. Jones, S. K. Garbade, M. L. McGilliard, C. C. Stallings, K. F. Knowlton, and R. E. James. 2012 Cow and herd variation in milk urea nitrogen concentrations in lactating dairy cattle. J. Dairy Sci. 95 :7261–7268.
  22. Storm, A. C., N. B. Kristensen, and M. D. Hanigan. 2012.  A model of ruminal VFA absorption kinetics and rumen epithelial blood flow in lactating Holstein cows. J. Dairy Sci. 95: 2919-2934.
  23. Rius, A.G. , H.A. Weeks, J. Cyriac, R.M. Akers, B.J. Bequette, and M.D. Hanigan. 2012.  Protein and energy intakes affected amino acid concentrations in plasma, muscle, and liver, and cell signaling in the liver of growing dairy calves. J Dairy Sci 95(4):1983-1991.
  24. Urschel, K. L., R. J. Geor, M. D. Hanigan, and P. A. Harris. 2012. Amino acid supplementation does not alter whole-body phenylalanine kinetics in Arabian geldings. J. Nutr. 142(3):461-469.
  25. Brown, K. L., B. G. Cassell, M. L. McGilliard, M. D. Hanigan, and F. C. Gwazdauskas. 2012.  Hormones, metabolites, and reproduction in Holsteins, Jerseys, and their crosses. J. Dairy Sci. 95(2):698-707.
  26. Appuhamy, J. A. D. R. N., N. Knoebel, J. Escobar, and M. D. Hanigan. 2012. Isoleucine and leucine independently regulate mTOR signaling and protein synthesis in MAC-T cells and bovine mammary tissue slices. J. Nutr. 142:483-91.
  27. Stewart, B. A., R. E. James, M. D. Hanigan, and K. F. Knowlton. 2012. Cost of reducing protein and phosphorus content of dairy rations.  Prof. Anim. Sci. 28(1):115-11



  1. Appuhamy, J. A. D. R. N.*.and M. D. Hanigan. 2010. Modeling the effects of insulin and amino acids on the phosphorylation of mTOR, Akt, and 4EBP1 in mammary cells. IN Nutrient digestion and utilization in farm animals: modeling approaches. D. Sauvant, ed. Wageningen Academic Publishers, Wageningen.
  2. Boston, R. C. and M. D. Hanigan. 2006. Segmented, constrained, nonlinear, multi-objective, dynamic optimization methodology applied to the dairy cow ration formulation problem in a situation where some of the constraints may be discontinuous. In: Nutrient digestion and utilization in farm animals: modeling approaches (E. Kebreab et al., Eds.). CABI Publishing, Wallingford.
  3. Hanigan, M. D., J. G. Fadel, H. G. Bateman, J.P. McNamara, and N. E. Smith. 2006.  An ingredient-based input scheme for Molly.  In: Nutrient digestion and utilization in farm animals: modeling approaches (E. Kebreab et al., Eds.). CABI Publishing, Wallingford.
  4. Crompton, L.A., J. France, B. J. Bequette, J. A. Maas, M. D. Hanigan, M. A. Lomax, and J. Dijkstra,  2000.  Isotope dilution models for partitioning amino acid uptake by the liver, mammary gland and hindlimb tissues of ruminants. IN: Modelling Nutrient Utilization in Farm Animals (J. P. McNamara, J. France and D.E. Beever eds.). pp.353-360.  CABI Publishing. Wallingford, Oxon, U.K.
  5. Hanigan, M. D., J. France, L. A. Crompton, and B. J. Bequette. 2000.  Evaluation of a representation of the limiting amino acid theory for milk protein synthesis.  IN: Modelling Nutrient Utilization in Farm Animals (J. P. McNamara, J. France & D.E. Beever eds.).  pp.127-144.  CAB International.  Wallingford, Oxon, U.K.
  6. Hanigan, M. D., J. Dijkstra, W. J. J. Gerrits, and J. France. 1997.  Modelling postabsorptive protein and amino acid metabolism in the ruminant.  Proc. Nutr. Soc. 56:631-643.
  7. Baldwin, R. L., P. S. Miller, H. C. Freetly, M. D. Hanigan, J. Fadel, M. K. Bowers, and C. C. Calvert. 1989. Future of tissue level models. In: Modelling Ruminant Digestion and Metabolism. Proceedings of the Third International Workshop on Modelling Digestion and Metabolism in Farm Animals. pp.345-357.



  1. Stallings, C. C., M. D. Hanigan, and R. E. James. 2007.  Feeding protein to meet dairy cow nutrient requirements can result in cheaper, environmentally friendly rations. Virginia Cooperative Extension Pub. 404-354.



  1. What We Are Learning about Phosphorus Feeding in Virginia?  2008. C. C. Stallings, K. F. Knowlton, R. E. James, M. D. Hanigan, and B. Cox. Penn State Dairy Cattle Nutrition Workshop Proceedings p. 121-126.



  1. Hristov, A. N. , M. Hanigan, A. Cole, R. Todd, T. A. McAllister, P. M. Ndegwa, and A. Rotz. 2011. Ammonia emissions from dairy farms and beef feedlots. Can. J. Anim. Sci. 91:1-35.
  2. Hanigan, M. D., H. G. Bateman, J. G. Fadel, and J.P. McNamara. 2006. Metabolic models of ruminant metabolism: recent improvements and current status.  J. Dairy Sci. 89: E53-64. (Impact Factor: 2.240).
  3. Hanigan, M. D.  2005. Quantitative aspects of splanchnic metabolism in the ruminant. Anim Sci. 80:23-32. (Impact Factor: 1.021).
  4. Hanigan, M. D., and B. J. Bequette, 2001.  Modelling mammary amino acid metabolism. Live. Prod. Sci. 70:63-78. (Impact Factor: 1.131).
  5. Hanigan, M. D., J. Cant, D. C. Weakley, and J. Beckett.  1998. An evaluation of postabsorptive protein and amino acid metabolism in the lactating dairy cow. J. Dairy Sci. 81:3385-401. (Impact Factor: 2.240).



  1. Mathematical modeling in nutrition and agriculture. M. D. Hanigan, J. A. Novotny, and C. L. Marstaller, eds.  2007. Virginia Tech. Blacksburg.

David R. and Margaret Lincicome Professor, Virginia Tech

Associate Professor, Virginia Tech

Research Scientist, Dairy, Purina Mills and Land O' Lakes
St. Louis, MO

Post-doctoral Research, Dept. of Biochem. Biophys.

Graduate Research Assistant, Depts. of Animal Science and  Physiological Chemistry, UC-Davis

Dairy Farm Owner
Denison, Iowa


1991  PhD   University of California, Davis--Nutrition, minor Physiological Chemistry

1989   MS    University of California, Davis--Animal Science

1987    BS    Iowa State University--Dairy Science

Tara Wiles


Michelle Aguilar, PhD

Laura Harthan, PhD

Xinbei Huang, PhD

Meng Meng Li, PhD

Adelyn Myers, MS

Peter Yoder, PhD


Xin Feng


Visiting Scientist
Hyuck Choi

American Dairy Science Association

American Society for Nutrition

Professional photo of Dr. Mark Hanigan

Dr. Mark Hanigan

David R. & Margaret Lincicome Professor
Department of Dairy Science
3310 Litton-Reaves Hall
175 West Campus Drive
Blacksburg, VA 24061

(540) 231-0967

Areas of Expertise

Animal Nutrition

Nutrient Metabolism

Metabolic Modeling