Almagro JC, Teplyakov A, Luo J, Sweet RW, Kodangattil S, Hernadez-Guzman F, Stanfield R, Gilliland GL. Second Antibody Modeling Assessment (AMA-II). Proteins. 82: 1553-1562, 2014.

Kodangattil S, Huard C, Ross C, Li J, Gao H, Mascioni A, Hodawadekar S, Naik S, Visintin A, Almagro JC. The functional repertoire of rabbit antibodies and antibody discovery via next-generation sequencing. mAbs. 30: 628-636, 2014.

Raghunathan G, Smart J, Williams JJ and Almagro JC. Antigen-Binding Site Anatomy and Somatic Mutations of Antibodies that Recognize Different Types of Antigens. J. Mol. Recognit. 25: 103-113, 2012.

Almagro JC, Beavers MP, Hernandez-Guzman F, Shaulsky J, Butenhof K, Maier J, Kelly K, Labute P, Thorsteinson N, Teplyakov A, Luo J, Sweet R and Gilliland GL. Antibody Modeling Assessment. Proteins. 79: 3050-3066, 2011.

Fransson J, Teplyakov A, Raghunathan G, Chen J, Cordier W, Dinh T, Lollo B, Nishioka W, Zhou M, Feng Y, Chi E, Swanson R, Gilliland G and Almagro JC. Human Framework Adaptation of a mouse anti-IL13-neutralizing antibody. J. Mol. Biol. 398: 214-231, 2010.

Cobaugh CW, Almagro JC, Pogson M, Iverson B, Georgiou G. Synthetic antibody libraries with a bias towards peptide ligands. J. Mol. Biol. 378: 622-33, 2008.

Almagro JC, Mascioni A. Developability Assessment of Biologic Drugs. 195-220. In: Developability of Biologics: Safe and Cheaper Medicines via Computation. Ed. Sandeep K. CRC press. 2015.

Almagro JC, Kodangattil S. Novel generation of antibody based therapeutics. 147-170. In: Novel Approaches and Strategies for Biologics, Vaccines and Cancer Therapies. Eds Singh M and Salnikova M. Elsevier. 2015.

Almagro JC, Kodangattil S, Li J. Humanized Antibodies. In: Making and Using Antibodies. 395-419. Eds. Howard GC and Matthew R and Kaser MR. 2nd edition. CRC Press. 2013.

Brezski R, Almagro JC. Application of Antibody Engineering in Development of Next Generation Antibody-Based Therapeutics. In: Development of Antibody-Based Therapeutics. 65-93. Eds. Tabrizi MA, Bornstein GG, Klakamp SL. Springer. 2012.

Almagro JC, Strohl WS. Antibody Engineering: Humanization, Affinity Maturation and Selection Methods. 309-334. In: Therapeutic Monoclonal Antibodies: From Bench to Clinic. Ed. Zhiqiang An. John Wiley & Sons, Inc. 2009

Chen J, Fransson J, Fursov N, Hamel D, Malia T, Obmolova G, Ort T, Rycyzyn M, Scully M, Sweet R, Teplyakov A, Wheeler J, Almagro JC. Nucleic acid molecules encoding anti-CD27 antibodies JANSSEN BIOTECH, INC. US Patent: 9,683,046. Issued: 06/20/2017.

Almagro JC, Dubell W, Fransson J, Swanson RV, Pardinas J. Human Oncostatin M antibodies and methods of use. US Patent: 9,163,083. Assignee: JANSSEN BIOTECH, INC. Issued: 10/20/2015.

Chen J, Fransson, J, Fursov N, Hamel D, Malia T, Obmolova G, Ort T, Rycyzyn M, Scully M, Sweet R, Teplyakov A, Wheeler J, Almagro JC. Human anti-CD27 antibodies, methods and uses. US Patent: 9,102,737. Assignee: JANSSEN BIOTECH, INC. Issued: 08/11/2015.

Tsui P, Luo J, Bernard A, Shi L, Jin Lu Wheeler J, Whitaker B, Borozdina-Birch L, Almagro JC, Tornetta M, Reddy R, Knight DM, Sweet SW, Chen Q. Generation of Human De Novo pIX Phage Display Libraries. US Patent: 9,062,305. Assignee: JANSSEN BIOTECH, INC. Issued: 06/23/2015.

Almagro JC, Anderson GM, Chi E, Martinez C, Raghunathan G, Swanson R, Teplyakov A, Tse K-F, Wu S-J, Zhou; Hong M. Human tissue factor antibody and uses thereof. US Patent: 8,999,333 Assignee: JANSSEN BIOTECH, INC. Issued: 04/07/2015.

Almagro JC, Branigan P, Colleen K, Strohl W, Taudte S, Torneta M, Wheelers J. Humanized IL-25 Antibodies. US Patent: 8,785,605. Assignee JANSSEN BIOTECH, INC. Issued: 07/22/2014.

Almagro JC, Fransson J, Raghunathan R. Method of Affinity Maturing Antibodies. US Patent: 8,580,714. Assignee: JANSSEN BIOTECH, INC. Issued: 11/12/2013.

Almagro JC, Della Ducate D, Elloso M, Luo J, Malia T, Naso M, Obmolova G, Rauchenberger R, Rutz M, Wu B, Wu SJ. IL-17A antibodies. US Patent: 8,519,107. Assignee: JANSSEN BIOTECH, INC. Issued: 8/27/2013.

Swanson RV, Chi E, Raghunathan G, Zhao S, Fransson J, Cordier W, Almagro JC, Hyun L, Giles-Komar J, O'Neil KT, Carton JM, Zhou HM, Teplyakov AV, Feng Y. Engineered Anti-IL-13 Antibodies, Compositions, Methods and Uses. US Patent: 8,399,630. Assignee: Centocor Ortho Biotech Inc. Issued: 19/03/2013.

Almagro JC, Daniels-Wells TR, Perez-Tapia SM, Penichet ML. Progress and challenges in the design and clinical development of antibodies for cancer therapy. Frontiers in Immunology 8: 1751, 2017.

Finlay WJJ, Almagro JC. Natural and Man-made V-region repertoires for Antibody Discovery. Frontiers in Immunology. 3: 1-18, 2012.

Gilliland GL, Luo J, Vafa O and Almagro JC. Leveraging SBDD in protein therapeutic development: antibody engineering. Methods in Molecular Biology. 841: 321-349, 2012.

Almagro JC, Fransson J. Humanization of antibodies. Frontier in Biosciences. 13:1619-1633, 2008.