Publications

• 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

• Leverton L^#, Pally D^#, Jones A, Therol C, Ricard-Blum S, Naba A. SNED1 fibrillar assembly in the extracellular matrix requires fibronectin and collagen I. bioRxiv, 2026. bioRxiv Access
• Pally D^#, Leverton L^#, Jones A, Naba A. SNED1 modulates ECM architecture and cell alignment via LDV-binding integrins. bioRxiv, 2026. bioRxiv Access

• The Gene Ontology Consortium (incl. Chen D and Naba A). The Gene Ontology knowledgebase in 2026. Nucleic Acids Research, 2025, gkaf1292. Journal Access | PMC Access
• Considine JM, Gomez C, Pally D, Yang N, Taha IN, Sorenson J, Brooks EG, Kreeger PK^*, Naba A^*. Comparative proteomic analysis of the ECM composition of the human omentum and mesentery, the main sites of ovarian cancer metastasis. iScience, 2025, 29(1):114461. Journal Access | PMC Access
• Yang N, Abbaspour A, Considine JM, McGregor S, Brooks EG, Naba A, Masters KS, Kreeger PK. Fibronectin composition and transglutaminase 2 cross-linking cooperatively regulate ovarian cancer cell adhesion in ECM-mimetic constructs. Acta Biomaterialia, 2025. Journal Access | PMC Access
• Lamba R, Paguntalan AM, Petrov PB, Naba A^*, Izzi V^*. MatriCom: a scRNA-Seq data mining tool to infer cell-extracellular matrix interactions. Journal of Cell Science, 2025, 138(13): jcs263927. Journal Access | PMC Access
• Pally D, Kapoor N, Naba A. The novel ECM protein SNED1 mediates cell adhesion via the RGD-binding integrins α5β1 and αvβ3. Journal of Cell Science, 2025, 138(2): JCS263479. Journal Access | PMC Access
• Samarasinghe KW, Kotlyar M, Vallet SD, 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, 53(D1):D1677–D1682. Journal Access | PMC Access

• Leverton L, Bains AK, Isa I, Ricard-Blum S, Naba A. A guide to building the matrisome interactome: From computational prediction to experimental validation. FEBS Journal, 2025. Journal Access | PMC Access

• Considine JM, Pally D, O’Brien SA, Potts, J, Feng D, Pignatelli J, Kashyap AS, Sharma N, Naba A. In-depth proteomic profiling of the extracellular matrix of pancreatic ductal adenocarcinomas identifies signatures correlating with lymphocyte infiltration. bioRxiv, 2025. bioRxiv Access
• 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. bioRxiv Access

• 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, 21(11):463–481. Journal Access | PMC Access
• Naba A. Mechanisms of assembly and remodeling of the extracellular matrix. Nature Reviews Molecular Cell Biology, 2024, 25(11):865-885. Journal Access | PMC Access
• Pally D and Naba A. Extracellular matrix dynamics: a key regulator of cell migration across length-scales and systems. Current Opinion in Cell Biology, 2024, 86:102309. Journal Access | PMC Access

• 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. Journal Access | PMC Access
• Desert R, Chen W, Ge X, Viel R, Han H, Athavale D, Das S, Song Z, Lantvit D, Cano L, Naba A, Musso O, Nieto N. Hepatocellular carcinomas, exhibiting intratumor fibrosis, express cancer-specific extracellular matrix remodeling and WNT/TGFb signatures, associated with poor outcome. Hepatology, 2023, 78(3):741-757. Journal Access
• 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, 51(D1):D1519–D1530. Journal Access | PMC Access

• Jain S, Pei L, Spraggins JM, Börner K, Snyder MP, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nature Cell Biology, 2023, 25(8):1089-1100. Journal Access | PMC Access
• Naba A. 10 years of extracellular matrix proteomics: Accomplishments, challenges, and future perspectives. Molecular and Cellular Proteomics, 2023, 22(4):100528. Journal Access | PMC Access
• Apte SS and Naba A. Editorial Beyond the matrisome: New frontiers in ECM research. Matrix Biology, 2023, 115:133-138. Journal Access

• Sapao P, Roberson E, Shi B, Shervin Assassi S, Skaug B, Lee F, Naba A, Perez White B, Cordova Fletes C, Tsou PS, Sawalha AH, Gudjonsson JE, Ma F, Verma P, Bhattacharyya D, Carns M, Strauss III JF, Sicard D, Tschumperlin D, Champer M, Campagnola P, Teves ME, and Varga J. Reduced SPAG17 expression in systemic sclerosis triggers myofibroblast transition and drives fibrosis. Journal of Investigative Dermatology, 2022, 143(2):284-293. Journal Access | PMC Access
•  Mondal C, Larkin K, Gacha Garcia M, Adikes R, Di Martino JS_, Chien C, Fraser M, Eni-aganga I, Agullo-Pascual E, Ozbek U, Naba A, Gaitas A, Fu T, Upadhyayula S, Betzig E, Martin B, Matus DQ, and Bravo-Cordero JJ. A proliferative to invasive switch is mediated by srGAP1 downregulation through the activation of TGFβ2 signaling. Cell Reports, 2022, 40(12):111358. Journal Access | PMC Access
• 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. Journal Access

• 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, 21(7):100254. Journal Access | PMC Access
• Nerger BA, Jones TM, Rose KWJ, Barqué A, Weinbaum JS, Petrie RJ, Chang J, Vanhoutte D, Kendra LaDuca K, Hubmacher D*, Naba A*. The Matrix in Focus: New Directions in Extracellular Matrix Research from the 2021 ASMB Hybrid Meeting. Biology Open, 2022, 11(1): bio059156. Journal Access | PMC Access

• Di Martino J, Nobre AR, Mondal C, Taha IN, Farias E, Fertig E, Naba A, Aguirre-Ghiso J, and Bravo-Cordero JJ. A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy. Nature Cancer, 2021, 3(1):90-107. Journal Access | PMC Access
• Renner C, Gomez CD, Visetsouk MR, Taha IN, Khan A, McGregor S, Weisman P, Naba A*, Masters KS*, Kreeger PK*. Multi-modal profiling of the extracellular matrix of human fallopian tubes and serous tubal intraepithelial carcinomas. Journal of Histochemistry and Cytochemistry, 2021, 70(2):151-168. Journal Access | PMC Access
• Yazdanpanah G, Jiang Y, Rabiee B, Omidi M, Rosenblatt MI, Shokuhfar T, Pan Y, Naba A*, Djalilian A*. Fabrication, Rheological and Compositional Characterization of Thermoresponsive Hydrogel from Cornea. Tissue Eng Part C Methods, 2021, 27(5):307-321. Journal Access | PMC Access
• Vallet SD, Davis MN, Barqué A, Thahab AH, Ricard-Blum S, and Naba A. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome. Biochemical Journal, 2021, 478(7):1413–1434. Journal Access
• Pokhilko A, Brezzo G, Handunnetthi L, Heilig R, Lennon R, Smith C, Allan SM, Granata A, Sinha S, Wang T, Markus HS, Naba A, Fischer R, Van Agtmael T, Horsburgh K, and Cader MZ. Global proteomic analysis of extracellular matrix in mouse and human brain highlights relevance to cerebrovascular disease. J Cereb Blood Flow Metab. 2021, 41(9):2423-2438. Journal Access | PMC Access
• Holstein E, Dittmann A, Kääriäinen, Pesola V, Koivunen J, Pihlajaniemi T, Naba A, and Izzi V. The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome. Cancers, 2021, 13(5): 1081. Journal Access | PMC Access

• Barqué A, Jan K, De La Fuente E, Nicholas CL, and Hynes RO*, and Naba A*. Knockout of the gene encoding the extracellular matrix protein Sned1 results in craniofacial malformations and early neonatal lethality. Developmental Dynamics, 2020, 250(2):274-294. Journal Access | PMC Access
• Izzi V, Davis MN, and Naba A. Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome. Cancers, 2020, 12(8), 2046 Journal Access | PMC Access
• Hebert JA, Myers SA, Naba A, Abbruzzese G, Lamar JM, Carr SA, and Hynes RO. Proteomic profiling of the ECM of xenograft breast cancer metastases in different organs reveals distinct metastatic niches. Cancer Research, 2020, 80(7):1475-1485 Journal Access | PMC Access

• 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, 7: 17-42, Springer. Journal Access
• Naba A* and Ricard-Blum S*. The Extracellular Matrix Goes -Omics: Resources and Tools. In: Extracellular Matrix Omics. Biology of Extracellular Matrix, 2020, 7: 1-16, Springer. Journal Access
• Bingham GC, Lee F, Naba A, Barker TH. Spatial-omics: Novel Approaches to Probe Cell Heterogeneity and Extracellular Matrix Biology. Matrix Biology, 2020, 91-92:152-166. Journal Access | PMC Access
• Arteel GE^* and Naba A*. The liver matrisome: looking beyond collagens. JHEP Reports, 2020, 2(4):100115. Journal Access | PMC Access

• Davis MN, Horne-Badovinac S, and Naba A. In-silico definition of the Drosophila melanogaster matrisome. Matrix Biology Plus, 2019, 100015. Journal Access | PMC Access
• Shao X, Taha IN, Clauser KR, Gao YT*, Naba A*. MatrisomeDB: the ECM-protein knowledge database. Nucleic Acids Research, 2019, pii: gkz849. Journal Access | PMC Access
• Teuscher A, Jongsma E, Davis MN, Statzer C, Gebauer JM^*, Naba A*, and Ewald CY^*. The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification. Matrix Biology Plus, 2019, 100001. Journal Access | PMC Access

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

• 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 Acid Research, 2018, 47(D1):D376–D381. Journal Access | PMC Access
• 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. Journal Access

• Socovich AM and Naba A. The cancer matrisome: from comprehensive characterization to biomarker discovery. Seminars in Cell & Developmental Biology, 2018, 89:157-166. Journal Access
• 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

• 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. Journal Access | PMC Access
• Gocheva V, Naba A*, Bhutkar A, Guardia T, Miller KM, Li CM, Dayton TL, Sanchez-Rivera FJ, Kim-Kiselak C, Jailkhani N, Winslow MW, Del Rosario A, Hynes RO, and Jacks T*. Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival. Proceedings of the National Academy of Sciences, 2017, 114(28):E5625-E5634. Journal Access | PMC Access
• Glavey S.V^#, Naba A^#, Manier S^#, Clauser K.R, Tahri S, Park J, Reagan MR, Moschetta M, Mishima Y, Gambella M, Rocci A, Sacco A, O’Dwyer M.E, Asara JM, Palumbo A, Roccaro AM, Hynes RO, and Ghobrial IM. Proteomic characterization of human multiple myeloma bone marrow extracellular matrix. Leukemia, 2017, (11):2426-2434 Journal Access
• Ragelle H^#, Naba A^#, Larson BL, Zhou F, Prijic M, Whittaker CA, Del Rosario A, Langer R, Hynes RO, and Anderson DG. Comprehensive proteomic characterization of stem-cell-derived extracellular matrices. Biomaterials, 2017, 128:147-159. Journal Access | PMC Access
• Naba A*, Clauser KR, Mani DR, Carr SA, and Hynes RO*. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression. Scientific Reports, 2017, 7:40495. Journal Access | PMC Access
• Carmona G^#, Perera U^#, Gillett C, Naba A, Law A.L, Sharma V.P, Wang J, Wyckoff J, Balsamo M, Mosis F, De Piano M, Monypenny J, Woodman N, McConnell R.E, Mouneimne G, Van Hemelrijck M, Cao Y, Condeelis J, Hynes RO, Gertler FB, and Krause M. Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE. Oncogene, 2016, 35:5155-69. Journal Access | PMC Access
• 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. Video | Journal Access | PMC Access
• Naba A*, Clauser KR, Whittaker CA, Carr SA, Tanabe KK, and Hynes RO*. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver. BMC Cancer, 2014, 14(1):518. Journal Access | PMC Access
• Naba A*, Clauser KR, Lamar JM, Carr SA, and Hynes RO*. Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters. eLife, 2014, 3:e01308. Journal Access | PMC Access
• 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. Journal Access | PMC Access
• Mak H^#, Naba A^#, Varma S^#, Meens J, Arpin M, SenGupta S, and Elliott BE. Ezrin phosphorylation on tyrosine 477 regulates invasion and metastasis of breast cancer cells. BMC Cancer, 2012, 12(1):82-95. Journal Access | PMC Access
• Zwaenepoel I^#, Naba A^#, da Cunha MML^#, Del Maestro L, Formstecher E, Louvard D, and Arpin M. Ezrin regulates microvillus morphogenesis by promoting distinct activities of Eps8 proteins. Molecular Biology of the Cell, 2012, 23(6):1080-95. Cover Journal Access | PMC Access
• Kanda S, Naba A, and Miyata Y. Inhibition of endothelial cell chemotaxis toward FGF-2 by Gefitinib associates with downregulation of Fes activity. International Journal of Oncology, 2009, 35:1305-1312. Journal Access
• Monni R, Haddaoui L, Naba A, Arpin M, Mayeux P, and Moreau-Gachelin F. Ezrin is a target for oncogenic Kit mutants in murine erythroleukemia. Blood, 2008, 6:3163-3172. Journal Access
• Naba A, Reverdy C, Louvard D, and Arpin M. Spatial recruitment and activation of the Fes kinase by ezrin promotes HGF-induced cell scattering. EMBO Journal, 2008, 27:38-50. Journal Access | PMC Access

• Naba A^*, Clauser K.R, Ding H, Whittaker C.A, Carr S.A, and Hynes R.O^*. The extracellular matrix: tools and insights for the “omics” era. Matrix Biology, 2016, pii: S0945-053X(15)00121-3. Journal Access | PMC Access
• 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. Journal Access | PMC Access
• 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. Journal Access | PMC Access
• Arpin M, Chirivino D, Naba A, and Zwaenepoel I. Emerging role for ERM proteins in cell adhesion and migration. Cell Adhesion and Migration, 2011, 5:199-206. Journal Access | PMC Access

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).