Allen, Matthew R., PhD


  • Alma College, Exercise & Health Science, BS, 1994-1998
  • Texas A&M University, Department of Health & Kinesiology, PhD, 1998-2003
  • Indiana University School of Medicine, Department of Anatomy & Cell Biology, Postdoctoral fellow, 2003-2005
  • Indiana University School of Medicine, Department of Anatomy & Cell Biology, Assistant Research Professor, 2005-2008
  • Indiana University School of Medicine, Department of Anatomy & Cell Biology, Assistant Professor


Academic Appointments

  • 2003:  Postdoctoral Fellow.  Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis IN.
  • 2006:  Assistant Research Professor.  Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis IN.
  • 2008:  Assistant Professor.  Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis IN.


Professional Societies

  • American Association of Anatomists
  • International Bone and Mineral Society
  • American Society for Bone and Mineral Research



  • 2001:  Sun Valley Hard Tissue Workshop Young Investigator Travel Award
  • 2001:  Texas American College of Sports Medicine Manuscript Award
  • 2002:  Texas American College of Sports Medicine Doctoral Poster Award
  • 2005:  American Society of Bone and Mineral Research Young Investigator Award
  • 2006:  International Bone and Mineral Society Travel Award, Davos Bisphosphonate Meeting
  • 2006:  Sun Valley Hard Tissue Workshop Young Investigator Travel Award
  • 2006:  American Society of Bone and Mineral Research media worthy abstract designation
  • 2009:  American Association of Anatomists' Morphological Sciences Award



CV in PDF format

My long-term research goal is to understand the principle factors responsible for bone fragility and determine how interventions can be maximized to strengthen the skeleton. Currently, the main focus of my research is to better understand the effects of bisphosphonates on bone remodeling, osteocyte viability, and matrix necrosis in bones of the oral cavity.


  • Alterations in would healing with anti-remodeling treatment
  • Bisphosphonates for treatment and prevention of bone loss associated with kidney disease
  • Alterations in osteocyte apoptosis with bisphosphonate treatment
  • Effects of aging and microdamage accumulation


Laboratory website:

A) Peer-reviewed journal publications in Research

1.        SA Bloomfield, MR Allen, HA Hogan, and MD Delp.  Site- and compartment-specific changes in bone with hindlimb unloading in mature adult rats.  Bone 31:149-157, 2002.

2.        XD Chen, MR Allen, S Bloomfield T Xu, and M Young.  Biglycan deficient mice have delayed osteogenesis after marrow ablation.  Calcif Tissue Int 72: 577-582, 2003.

3.        KL Nielsen, MR Allen, SA Bloomfield, TL Andersen, XD Chen, T Xu, HS Poulsen, MF Young, and AM Heegaard.  Biglycan deficiency interferes with ovariectomy-induced bone loss.  J Bone Miner Res 18: 2152-2158, 2003.

4.        MR Allen and SA Bloomfield.  Hindlimb unloading has a greater effect on cortical compared to cancellous bone in mature female rats.   J Appl Physiol 94: 642-650, 2003.

5.        R Naryanan, MR Allen, D Gaddy S, SA Bloomfield, CL Smith, and NL Weigel.  Differential skeletal responses of hindlimb unloaded rats on a vitamin D deficient diet to 1,25-dihydroxyvitamin D3 and its analog, EB1089.  Bone 35:135-143, 2004.

6.        GL Warren, JL Stallone, MR Allen, and SA Bloomfield.  Functional recovery of the plantarflexor muscle group after hindlimb unloading in the rat.  Eur J Appl Physiol 93:130-138, 2004.

7.        M.Miura, XD Chen, MR Allen, Y Bi, S Gronthos, BM Seo, S Lakhani, RA Flavell, XH Feng, PG Robey, M Young, and S Shi. A crucial role of Caspase-3 in osteogenic differentiation of bone marrow stromal stem cells J Clin Invest 114: 1704-1713, 2004.

8.        MJ Hubal, CP Ingalls, MR Allen, JC Wenke, HA Hogan, and SA Bloomfield.  Effects of eccentric exercise training on cortical bone and muscle strength in the estrogen-deficient mouse.  J Appl Physiol  98: 1674-1681, 2005.

9.        MR Allen and DB Burr.  Periosteum at the femoral neck: A histological analysis in humans.  Bone 36: 311-316, 2005.

10.      Y Miura, M Miura, S Gronthos, MR Allen, C Cao, TE Uveges, Y Bi, D Ehirchiou, A Kortesidis, S Shi, and L Zhang. Defective osteogenesis of the stromal stem cells predisposes CD18-null mice to osteoporosis. Proc Natl Acad Sci 102:14022-14027, 2005.

11.      JM Wallace, RM Rajachar, XD Chen, S Shi, MR Allen, SA Bloomfield, CM Les, PG Robey, MF Young, and DH Kohn.  The mechanical phenotype of biglycan deficient mice is bone- and gender-specific.  Bone 39: 106-116, 2006.

12.      MR Allen, HA Hogan, and SA Bloomfield.  Mismatch of bone and muscle recovery following long-term hindlimb unloading.  J Musculoskelet Neuronal Interact 6:217-225, 2006. 

13.      MR Allen, K Iwata, R Phipps, and DB Burr. Alterations in canine vertebral bone turnover, microdamage accumulation, and biomechanical properties following 1-year treatment with clinical treatment doses of risedronate or alendronate. Bone 39:872-879, 2006.

14.      MR Allen, K Iwata, M Sato, and DB Burr. Raloxifene enhances vertebral mechanical properties independent of bone density.  Bone 39: 1130-1135, 2006.

15.      MR Allen, H Folett, M Khurana, M Sato, and DB Burr. Anti-remodeling agents influence osteoblast activity differently in modeling- and remodeling-sites of canine ribCalcif Tissue Int.  79:255-261, 2006.

16.      JM Wallace, RM Rajachar, MR Allen, SA Bloomfield, PG Robey, MF Young, and DH Kohn.  Exercise-induced changes in the cortical bone of growing mice are bone- and gender-specific.  Bone 40: 1120-1127, 2007.

17.      SK Eswaran, MR Allen, DB Burr, and TM Keaveny.  Mechanical consequences of changes in canine trabecular bone volume fraction and microarchitecture after 1-year of risedronate treatment.  J Biomechanics 40: 3424-3431, 2007.

18.      R Prisby, M Ramsey, B Behnke, J Dominguez, A Donato, MR Allen, and M Delp.  Aging reduces skeletal blood flow, endothelium-dependent vasodilation and nitric oxide bioavailability in rats.  J Bone Miner Res 22: 1280-1288, 2007.

19.      MR Allen, HA Hogan, WA Hobbs, AS Koivuniemi, MC Koivuniemi, and DB Burr.  Raloxifene enhances material-level mechanical properties of femoral cortical and trabecular bone.  Endocrinology 148: 3908-3913, 2007.

20.      MR Allen and DB Burr.  Three years of alendronate treatment results in similar levels of vertebral microdamage as after one year of treatment.  J Bone Miner Res 22:1759-1765, 2007.

21.      MR Allen.  Animal models of osteonecrosis of the jaw.  J Musculoskelet Neuronal Interact  7: 358-360, 2007.

22.      MR Allen and DB Burr.  Strength-density and energy absorption-density relationships demonstrate that bisphosphonates have different effects on vertebral bone strength and energy to fracture.  Osteo Int 19: 95-99, 2008.

23.      RK Fuchs, MR Allen, ME Ruppel, T Diab, RJ Phipps, LM Miller, and DB Burr.  In situ examination of the time-course for secondary mineralization of haversian bone using synchrotron Fourier transformed infrared microspectroscopy.  Matrix Biology 27: 34-41, 2008.

24.      RK Fuchs, MR Allen, KW Condon, S Reinwald, LM Miller, D McClenatahan, B Keck, RJ Phipps, and DB Burr. Strontium ranelate at clinical dose levels does not stimulate bone formation in ovariectomized rats.  Osteo Int 19:1331-1341, 2008.

25.      AG Robling, PJ Niziolek, LA Baldridge, KW Condon, MR Allen, I Alam, SM Mantila, J Gluhak-Heinrich, TM Bellido, SE Harris, and CH Turner.  Mechanical stimulation of bone in vivo reduces osteocyte expression of Sost/sclerostin.  J Biol Chem 283:5866-5875, 2008.

26.      T Siegmund, MR Allen, and DB Burr.  Failure of mineralized collagen fibrils:  Modeling the role of collagen cross-linking. Journal of Biomechanics 41:1427-1435, 2008.

27.      K Baek, AA Barlow, MR Allen, and SA Bloomfield.  Food restriction and simulated microgravity: effects on bone and serum leptin. J Appl Physiol  104: 1086-1093, 2008.

28.      MR Allen, E Gineyts, DJ Leeming, DB Burr, and PD Delmas.  Bisphosphonates alter trabecular bone collagen cross-linking and isomerization in beagle dog vertebra.  Osteo Int 19:329-337, 2008.

29.      MR Allen and DB Burr.  Mandible necrosis in beagle dogs following 3-years of daily oral bisphosphonate treatment.  J Oral Maxillofac Surg 66:987-994, 2008.

30.      MR Allen, S Reinwald, and DB Burr.  Alendronate reduces bone toughness of ribs without significantly increasing microdamage accumulation in dogs following three years of daily treatment.  Calcif Tissue Int  82:354-360, 2008.

31.      CA O’Brien, LI Plotkin, C Galli, JJ Goellner, AR Gortazar, MR Allen, A Robling, M Bouxsein, E Schipani, CH Turner, RL Jilka, RS Weinstein, SC Manolagas, and T Bellido.  Control of bone mass and remodeling by PTH receptor signaling in osteocytes.  PLoS ONE  2008 Aug 13;3(8):e2942, 2008.

32.      X Wang, MR Allen, DB Burr, EJ Lavernia, B Jeremic, and DP Fyhrie.  Identification of material parameters based on Mohr-Coulomb failure criterion for bisphosphonate treated canine vertebral cancellous bone.  Bone 43:775-780, 2008.

*33.    SK Eswaran, G Bevill, P Nagarathnam, MR Allen, DB Burr, and TM Keaveny.  Effects of suppression of bone turnover on cortical and trabecular load sharing in the canine vertebral body.  J Biomechanics 42:517-523, 2009.

*34.    X Wang, A Erickson, MR Allen, DB Burr, RB Martin, and SJ Hazelwood.  Theoretical analysis of alendronate and risedronate effects on canine vertebral remodeling and microdamage.  J Biomechanics 42: 938-944, 2009.

*35.    T Diab, MR Allen, and DB Burr.  Alendronate treatment results in similar levels of trabecular bone remodeling in the femoral neck and vertebra.  Osteo Int 20: 647-652, 2009.

36.      S Reinwald R Peterson, MR Allen, and DB Burr. Skeletal changes associated with the onset of type 2 diabetes in the ZDF and ZDSD rodent models.  AJP Endocrinology 296: E765-774, 2009

*37.    SY Tang, MR Allen, R Phipps, DB Burr, and D Vashishth.  Changes in non-enzymatic glycation and its association with altered mechanical properties following 1-year treatment with risedronate or alendronate.  Osteo Int 20: 887-894, 2009

*38.    MR Allen and SL Ruggiero.  Higher bone matrix density exists in only a subset of patients with bisphosphonate-related osteonecrosis of the jaw.   J Oral Maxillofac Surg 67: 1373-1377, 2009.

*39.    DB Burr, T Diab, A Koivunemi, M Koivunemi, and MR Allen.  Effects of one to three years treatment with alendronate on mechanical properties of the femoral shaft in a canine model:  Implications for subtrochantaric femoral fracture risk.  J Ortho Res 27: 1288-1292, 2009

*40.    MR Allen, DJ Kubek, and DB Burr.  Cancer treatment dosing regimens of zoledronic acid result in near complete suppression of mandible intra-cortical bone remodeling in beagle dogs.  J Bone Miner Res 25: 98-105, 2010.

*†41.  DJ Kubek, Gattone VH 2nd, and MR Allen.  Methodological assessment of acid-etching for visualizing the osteocyte lacunar-canalicular networks using scanning electron microscopy.  Micros Res Tech 73: 182-186, 2010.

*†42.   A Feher, A Koivuniemi, M Koivuniemi, RK Fuchs, DB Burr, RJ Phipps, SR Reinwald, and MR Allen.  Bisphosphonates do not inhibit periosteal bone formation in estrogen deficient animals and allow enhanced bone modeling in response to mechanical loading. Bone 46: 203-207, 2010.

*43.      MR Allen, AM Erickson, X Wang, DB Burr, RB Martin, and S Hazelwood.  Morphological assessment of basic multicellular unit resorption parameters in dogs shows additional mechanisms of bisphosphonate effects on bone. Calcif Tissue Int 86: 67-71, 2010.

*44.    JM Dominguez, RD Prisby, JM Muller-Delp, MR Allen, and MD Delp.  Increased nitric oxide-mediated vasodilation of bone resistance arteries is associated with increased trabecular bone volume after endurance training in rats. Bone 46:813-819, 2010.

*45.      LM Havill, MR Allen, TL Bredbenner, DB Burr, DP Nicolella, CH Turner, DM Warren, and MC Mahaney.  Heritability of lumbar trabecular bone mechanical properties in baboons.  Bone  46:835-840, 2010.

*46.    S Gourion-Arsiquaud, MR Allen, DB Burr, D Vashishth, SY Tang, and AL Boskey.  Bisphosphonate treatment modifies canine bone mineral and matrix properties and their heterogeneity.  Bone 46:666-672, 2010.

*47.      MR Allen, TG Chu, D Kubek, and D Burr. Compromised osseous healing of dental extraction sites in zoledronic acid-treated dogs.  Osteo Int (Accepted)

*48.      T Siegmund, MR Allen, and DB Burr.  Can deterministic mechanical size effects contribute to fracture and microdamage accumulation in trabecular bone? J Theor Biol 21: 202-210, 2010.

*49.      J O’Neal, T Diab, MR Allen, DB Burr, and R Goldberg.  One year of alendronate treatment lowers microstructural stresses associated with trabecular microdamage initiation.  Bone 47: 241-247, 2010.

*50.      MR Allen, B Pandya, and SL Ruggiero.  Lack of correlation between duration of ONJ and sequestra morphology:  What it tells us about disease progression and what it means for data interpretation.  J Oral Maxillo Surg 68: 2730-2734, 2010.

*51.      E Allam, MR Allen, TMG Chu, A Ghoneima,and  LJ Windsor. In vivo effects of zoledronic acid on oral mucosa epithelial cell proliferation, apoptosis, and matrix metalloproteinase expression.  Oral Dis (Accepted).

*†52.    D Kubek, DB Burr, and MR Allen. Ovariectomy stimulates and zoledronic acid inhibits intra-cortical remodeling in the mouse mandible. Orthod Craniofac Res 13: 214-222, 2010. 

*53.      MR Allen, J Turek, RJ Phipps, and DB Burr.  Risedronate has a more rapid onset of remodeling suppression than alendronate in rabbit vertebral trabecular bone.  Bone (Accepted). 

*54.    Y Rhee, MR Allen, K Condon, V Lezcano, AC Ronda, C Galli, N Oliovos, G Passeri, CA O’Brien, N Bivi, LI Plotkin, and T Bellido.  PTH receptor signaling in osteocytes governs periosteal bone formation and intra-cortical remodeling.  J Bone and Mineral Res (Accepted).

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