1. Schins, R.P.F., McAlinden, A., MacNee, W., Jimenez, L.A,. Ross, J.A., Guy, K., Faux, S & Donaldson, K. Persistent Depletion of I Kappa B alpha (IkBa) and Interleukin-8 Expression in Human Pulmonary Epithelial Cells Exposed to Quartz. Toxicology and. Applied Pharmacology 167(2): 107-117. 2000.
2. McAlinden, A., Dudhia, J., Lorenzo, P., Bolton, M.C., Heinegard, D., & Bayliss M.T.   Age-related Changes in the Expression and Synthesis of Decorin and Aggrecan in Human Meniscus and Articular Cartilage. Osteoarthritis Cartilage 9(1): 33-41, 2001.
3. Zhu, Y., McAlinden, A. & Sandell, L.J.  Type IIA Procollagen in Development of the Human Intervertebral Disc: Regulated Expression of the NH₂-Propeptide by Enzymic Processing Reveals A Unique Developmental Pathway.  Developmental Dynamics  220(4): 350-362, 2001.
4. Zhang, P., McAlinden, A., Schumacher, T., Wang, H., Hu, S., Sandell, L.J. & Crouch, E.C.  The Amino-terminal Heptad Repeats of the Coiled-coil Neck Domain of Pulmonary Surfactant Protein D are Necessary for the Assembly of Trimeric Subunits and Dodecamers.  Journal of Biological Chemistry 27(23): 19862-19870, 2001.
5. McAlinden, A., Crouch, E.C., Bann, J. G., Zhang, P. & Sandell, L.J.  Trimerization of the Amino Propeptide of Type IIA Procollagen Using a 14-Amino Acid Sequence Derived from the Coiled-coil Neck Domain of Surfactant Protein D.  Journal of Biological Chemistry 277(43): 41274-41281, 2002.
6. Fukui, N., McAlinden, A., Zhu, Crouch, E.C., Broekelmann, T.J., Mecham, R.P. & Sandell, L.J.  Processing of Type II Procollagen Amino Propeptide By Matrix Metalloproteinases.  Journal of Biological Chemistry 277(3): 2193-2201, 2002.
7. Sandell, L.J., McAlinden, A., & Sandell, K.S. The vWFC Domain of Type IIA Procollagen Amino-propeptide Functions as an Antagonist of Bone Morphogenetic Proteins.  Journal of  Musculoskeletal and Neuronal Interactions 2(3): 521-523, 2002.
8. McAlinden, A., Zhu, Y., & Sandell, L.J.  Expression of Type II Procollagen During Development of the Human Intervertebral Disc. Biochemical Society Transactions 30(6):831-838, 2002.
9. McAlinden, A., Smith, T.A., Sandell. L.J., Parry, D.A.D. &  Hulmes, D.J.S.  Alpha-helical Coiled-coil Oligomerization Domains are Almost Ubiquitous in the Collagen Superfamily.  Journal of Biological Chemistry 278(43): 42200-42207, 2003.
10. McAlinden, A., Haag, J., Bau, B., Gebhard P.M., and Aigner, T. Quantification of mRNA Expression Levels in Articular Chondrocytes with PCR Technologies.  Methods Molecular Medicine. 100: 79-100, 2004.
11. McAlinden, A., Havlioglu, N., Liang, L., Davies, S. and Sandell L.J. Alternative Splicing of Type II Procollagen Exon 2 is Regulated by the Combination of a Weak 5’ Splice Site and an Adjacent Intronic Stem-Loop Cis Element. Journal of Biological Chemistry. 280: 32700-32711, 2005.
12. McAlinden, A., Liang, L., Mukudai, Y., Imamura, T., and Sandell, LJ. Nuclear Protein TIA-1 Regulates Alternative Splicing of COL2A1 by Interaction with Genomic DNA and Precursor mRNA. Journal of Biological Chemistry, 282(33):24444-54, 2007.
13. McAlinden, A, Majava, M., Bishop, PN., Perveen, R., Black, G., Pierpont, M., Ala-Kokko, L. and Mannikko, M. “Missense and Nonsense Mutations in the Alternatively-Spliced Exon 2 of COL2A1 Cause the Ocular Variant of Stickler Syndrome Human Mutation, 29 (1): 83-90, 2008.
14. McAlinden, A., Johnstone B., Kollar, J., Yoo, J., Kazmi, N., and Hering, TM. Expression of two novel alternatively spliced COL2A1 isoforms during chondrocyte differentiation. Matrix Biology 27(3): 254-66, 2008.
15. Imamura, T., Imamura, C., McAlinden. A., Davies, SR., Iwamoto, Y., and Sandell, LJ. Inactivation of the Tumor Necrosis Factor-Alpha Responsive CCAAT/Enhancer-binding Protein Repressor Site is Permissive for Increased Cartilage Gene Transcription. Arthritis & Rheumatism 58 (5): 1366-76, 2008.
16. Rich, JT., Rosova, I., Nolta, JA., Myckatyn, TM., Sandell, LJ and McAlinden, A. Transcriptional Profiling Reveals Upregulation of Runx2 and Osterix During TGF-ß3 induced in vitro Chondrogenesis of Human Adipose-derived Stromal Cells. Biochemical and Biophysical Research Communications 372(1): 230-235, 2008.

Book Chapters / REVIEWS:

1. McAlinden, A., Fukui, N., & Sandell, L.J.  Type II Procollagen NH₂-Propeptide Functions as an Antagonist of Bone Morphogenetic Proteins.  The Many Faces of Osteoarthritis, Hascall V. & Kuettner, K. (eds.).  Birkhauser Press, Basel Switzerland, pp 5-15, 2002.
2. McAlinden, A., Havlioglu, N. & Sandell, L.J.  Regulation of Protein Diversity by Alternative Pre-mRNA Splicing with Specific Focus on Chondrogenesis.  Birth Defects Research Part C Embryo Today. (Review)  72: 52-68, 2004.
3.  Aigner, T., Soder, S., Gebhard, PM., McAlinden, A. and Haag, J. Role of Chondrocytes in the Pathogenesis of Osteoarthritis – Structure, Chaos and Senescence. Nature Clinical Practical Rheumatology, Jul; 3(7) 391-9, 2007.