Publications

1. Oshinjo A, Chen D, Petrov PB, Izzi, V*, and Naba A*. MatriSpace: Identification and visualization of spatially resolved ECM gene expression patterns in health and disease. bioRxiv, 2026. Preprint access

2. The Gene Ontology Consortium (incl. Chen D and Naba A). The Gene Ontology knowledgebase in 2026. Nucleic Acids Research, 2025, 54(D1), D1779-D1792. Journal Access | PMC Access

3. 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. Journal Access | PMC Access

4. Lamba R, Paguntalan AM, Petrov PB, Naba A*, Izzi V*. MatriCom, a single-cell RNA-sequencing data mining tool to infer cell-extracellular matrix interactions. Journal of Cell Science, 2025, 138(13), jcs263927. Journal Access | PMC Access

5. Samarasinghe KW, Kotlyar M, Vallet SD, Hayes C, Naba A, Jurisica I, Lisacek F, Ricard-Blum S. MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface. Nucleic Acids Research, 2024, 53(D1), D1677-D1682. Journal Access | PMC Access

6. Petrov PB, Considine JM, Izzi V, 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. Journal Access | PMC Access

7. 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, 2022, 51(D1), D1519-D1530. Journal Access | PMC Access

8. Tellman TV, Dede M, Aggarwal VA, Salmon D, Naba A, Farach-Carson MC. Systematic Analysis of Actively Transcribed Core Matrisome Genes Across Tissues and Cell Phenotypes. Matrix Biology, 2022, 111, 95-107. Journal Access

9. Izzi V, Davis MN, Naba A. Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome. Cancers, 2020, 12(8), 2046. Journal Access | PMC Access

10. Davis MN, Horne-Badovinac S, Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 4, 100015. Journal Access | PMC Access

11. Shao X, Taha IN, Clauser KR, Gao Y, Naba A. MatrisomeDB: the ECM-protein knowledge database. Nucleic Acids Research, 2019, 48(D1), D1136-1144. Journal Access | PMC Access

12. Teuscher AC, Jongsma E, Davis MN, Statzer C, Gebauer JM, Naba A, Ewald CY. The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 1, 100001. Journal Access | PMC Access

13. Clerc O, Deniaud M, Vallet SD, Naba A, Rivet A, Perez S, Thierry-Mieg N, Ricard-Blum S. MatrixDB: integration of new data with a focus on glycosaminoglycan interactions. Nucleic Acids Research, 2018, 47(D1), D376-D381. Journal Access | PMC Access

14. Nauroy P, Hughes S, Naba A, Ruggiero F. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions. Matrix Biology, 2017, 65, 5-13. Journal Access

15. Naba A, Pearce OMT, Del Rosario A, Ma D, Ding H, Rajeeve V, Cutillas PR, Balkwill FR, Hynes RO. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics. Journal of Proteome Research, 2017, 16(8), 3083-3091. Journal Access | PMC Access

16. Naba A, Clauser KR, Hynes RO, Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis. Journal of Visualized Experiments, 2015, 101, e53057. Journal Access | PMC Access

17. Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices. Molecular & Cellular Proteomics, 2011, 11(4), M111.014647. Journal Access | PMC Access | F1000 Recommendation

1. Larrea-Sebal A, Dai C, Brenes A, Korff K, Neely BA, Geyer PE, Dagley L, Unwin RD, Naba A, MacCoss MJ, Guo T, Deutsch EW, Martin C, Schwenk JM, Perez-Riverol Y. Blood Proteomics: Insights from public datasets, accomplishments, and remaining challenges. Genome Biology, 2026, 27, 81. Journal Access | PMC Access

2. Leverton L, Bains AK, Isa I, Ricard-Blum S, Naba A. A guide to building the matrisome interactome: from computational predictions to experimental validation. The FEBS Journal, 2025, 293(1), 42-70. Journal Access | PMC Access

3. Bains AK, Naba A. Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease. Expert Review of Proteomics, 2024, 21(11), 463-481. Journal Access | PMC Access

4. Naba A. Mechanisms of assembly and remodelling of the extracellular matrix. Nature Reviews Molecular Cell Biology, 2024, 25 (11), 865-885. Journal Access | PMC Access

5. Naba A. Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives. Molecular & Cellular Proteomics, 2023, 22(4), 100528. Journal Access | PMC Access

6. 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 View of Old Proteins: Clarifying the Enigmatic Proteome. Molecular & Cellular Proteomics, 2022, 21(7), 100254. Journal Access | PMC Access

7. Gebauer JM, Naba A. The Matrisome of Model Organisms: From In-Silico Prediction to Big-Data Annotation. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, 7, 17-42. Chapter Access

8. Naba A, Ricard-Blum S. The Extracellular Matrix Goes-Omics: Resources and Tools. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, 7, 1-16. Chapter Access

9. Arteel GE, Naba A. The liver matrisome – looking beyond collagens. JHEP Reports, 2020, 2(4), 100115. Journal Access | PMC Access

10. Taha IN, Naba A. Exploring the extracellular matrix in health and disease using proteomics. Essays in Biochemistry, 2019, 63(3), 417-432. Journal Access

11. Socovich AM, Naba A. The cancer matrisome: From comprehensive characterization to biomarker discovery. Seminars in Cell & Developmental Biology, 2019, 89, 157-166. Journal Access

12. 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, 73, 77-104. Journal Access | PMC Access

13. Naba A, Clauser KR, Ding H, Whittaker CA, Carr SA, Hynes RO. The extracellular matrix: Tools and insights for the “omics” era. Matrix Biology, 2015, 49, 10-24. Journal Access | PMC Access

14. Naba A, Hoersch S, Hynes RO. Towards definition of an ECM parts list: An advance on GO categories. Matrix Biology, 2012, 31(7-8), 371-372. Journal Access | PMC Access

15. Hynes RO, Naba A. Overview of the Matrisome – An Inventory of Extracellular Matrix Constituents and Functions. Cold Spring Harbor Perspective in Biology, 2011, 4(1), a004903. Journal Access | PMC Access | Book Review

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).