Publications

1. Lee F, Shao X, Considine JM, Gao Y*, and Naba A*. Time-lapse tryptic digestion: a proteomic approach to improve sequence coverage of extracellular matrix proteins. bioRxiv, 2025. https://doi.org/10.1101/2025.03.26.645502v1

2. Lamba R, Paguntalan AM, Petrov PB, Naba A*, Izzi V*. MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems. Journal of Cell Science, 2025, 138 (13): jcs263927. https://doi.org/10.1242/jcs.263927

3. Samarasinghe KW, Kotlyar M, Vallet SD, Naba A, Jurisica I, Lisacek F, Ricard-Blum S. MatrixDB 2024: an expanded interaction dataset and a new network explorer interface. Nucleic Acids Research, 2025 Database Issue. https://doi.org/10.1093/nar/gkae1088

4. Petrov PB, Considine JM, Izzi, V, and Naba A. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms. Journal of Cell Science, 2023, 136 (17): jcs261255. https://doi.org/10.1242/jcs.261255 

5. Shao X, Gomez CD, Kapoor N, Considine JM, Grams C, Gao Y, Naba A. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database. Nucleic Acids Research, 2023, gkac1009. https://doi.org/10.1093/nar/gkac1009 

6. Tellman TV, Dede M, Aggarwal VA, Salmon DR, Naba A, and Farach-Carson MC. Systematic analysis of actively transcribed core matrisome genes across tissues and cell phenotypes. Matrix Biology, 2022, 111:95-107. https://doi.org/10.1016/j.matbio.2022.06.003

7. Izzi V, Davis MN, and Naba A. Pan-cancer analysis of the genomic alterations and mutations of the matrisome. Cancers, 2020, 12(8), 2046 https://doi.org/10.3390/cancers12082046

8. Davis MN, Horne-Badovinac S, and Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 100015. https://doi.org/10.1016/j.mbplus.2019.100015 

> Press coverage: https://www.chicagobiomedicalconsortium.org/news/success-stories/august-2-2019/

9. Shao X, Taha IN, Clauser KR, Gao YT, Naba A. MatrisomeDB: the ECM-protein knowledge database. Nucleic Acids Research, 2019, gkz849. https://doi.org/10.1093/nar/gkz849

10. Teuscher A, Jongsma E, Davis MN, Statzer C, Gebauer JM, Naba A, and Ewald CY. In-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 100001. https://doi.org/10.1016/j.mbplus.2018.11.001

11. Clerc O, Deniaud M, Vallet S.D, Naba A, Rivet A, Perez S, Thierry-Mieg N, and Ricard-Blum S. MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. Nucleic Acids Research, 2018, gky1035.  https://doi.org/10.1093/nar/gky1035

12. Nauroy P, Hughes S, Naba A, and Ruggiero F. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions. Matrix Biology, 2018, 65:5-13. https://doi.org/10.1016/j.matbio.2017.07.001

13. Naba A, Pearce OMT, Del Rosario A, Ma D, Ding H, Rajeeve V, Cutillas PR, Balkwill FR, and Hynes RO. Characterization of the extracellular matrix of normal and diseased tissues using proteomics. Journal of Proteome Research, 2017, 16(8):3083-3091. https://doi.org/10.1021/acs.jproteome.7b00191

14. Naba A, Clauser KR, and Hynes RO. Enrichment of extracellular matrix proteins from tissues and digestion into peptides for mass spectrometry analysis. Journal of Visualized Experiments, 2015, 101:e53057. https://doi.org/10.3791/53057 [Video]

15. Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, and Hynes RO. The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices. Molecular and Cellular Proteomics, 2012, 11(4):M111.014647. https://doi.org/10.1074/mcp.M111.014647

> Read the F1000 recommendation of this article.

1. Bains AK and Naba A. Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease. Expert Review of Proteomics, 2024. https://doi.org/10.1080/14789450.2024.2427136

2. Naba A. Mechanisms of assembly and remodeling of the extracellular matrix. Nature Reviews Molecular Cell Biology, 2024. https://doi.org/10.1038/s41580-024-00767-3

3. Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Molecular and Cellular Proteomics, 2023, 22(4):100528. https://doi.org/10.1016/j.mcpro.2023.100528

4. Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Rodriguez H, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, and Kelleher NL. New views of old proteins: clarifying the enigmatic proteome. Molecular and Cellular Proteomics, 2022, S1535-9476(22)00062-7. https://doi.org/10.1016/j.mcpro.2022.100254

5. Gebauer J.M and Naba A. The Matrisome of Model Organisms: From in-silico prediction to big-data annotation. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, vol 7: 17-42, Springer. https://doi.org/10.1007/978-3-030-58330-9_2

6. Naba A and Ricard-Blum S. The extracellular matrix goes -omics: resources and tools. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, vol 7: 1-16, Springer. https://doi.org/10.1007/978-3-030-58330-9_1

7. Arteel GE and Naba A. The liver matrisome: looking beyond collagens. JHEP Reports, 2020, pii: S2589-5559(20)30049-5. https://doi.org/10.1016/j.jhepr.2020.100115 

8. Taha IN and Naba A. Exploring the extracellular matrix in health and disease using proteomics. Essays in Biochemistry, 2019, EBC20190001 [Full Text]

> Press coverage: https://www.chicagobiomedicalconsortium.org/news/success-stories/2019-09-12-ecm-in-health-and-disease/

9. Socovich AM and Naba A. The cancer matrisome: from comprehensive characterization to biomarker discovery. Seminars in Cell & Developmental Biology, 2018, pii: S1084-9521(17)30580-3. https://doi.org/10.1016/j.semcdb.2018.06.005

10. Zhou Y, Horowitz JC, Naba A, Ambalavanan N, Atabai K, Balestrini J, Bitterman PB, Corley RA, Ding BS, Engler AJ, Hansen KC, Hagood JS, Kheradmand F, Lin QS, Neptune E, Niklason L, Ortiz LA, Parks WC, Tschumperlin DJ, White ES, Chapman HA, Thannickal VJ. Extracellular matrix in lung development, homeostasis and disease. Matrix Biology, 2018, pii: S0945-053X(17)30434-1. https://doi.org/10.1016/j.matbio.2018.03.005

11. Naba A, Clauser K.R, Ding H, Whittaker C.A, Carr S.A, and Hynes R.O. The extracellular matrix in the “omics” era. Matrix Biology, 2016, pii: S0945-053X(15)00121-3. https://doi.org/10.1016/j.matbio.2015.06.003

12. Naba A, Hoersch S, and Hynes R.O. Towards Definition of an ECM Parts List: an Advance on GO Categories. Matrix Biology, 2012, 31(7/8):371-372. https://doi.org/10.1016/j.matbio.2012.11.008

13. Hynes R.O and Naba A. Overview of the matrisome – an Inventory of ECM constituents and functions. In Extracellular Matrix Biology (eds. R.O. Hynes and K.M. Yamada), Cold Spring Harbor Perspectives in Biology, 2012, 4(1):a004903. https://doi.org/10.1101/cshperspect.a004903

> Read the review of the book "Extracellular Matrix Biology" by Dr. Charles Streuli in Development.

Cancer-related extracellular matrix signatures and related methods and products. Hynes R.O, Naba A, Carr S.A, Clauser K.R and Tanabe K.K. Issued December 27, 2016 under the U.S. Patent No. 9,526,800 (colorectal cancer). Divisional application issued July 17, 2018 under the U.S. Patent No. 10,024,860 (breast cancer).