All Stories

  1. A guide to building the matrisome interactome: from computational predictions to experimental validation

    Article • European Journal of Biochemistry, November 2025, Wiley

    Dr Alexandra Naba

  2. Fibronectin composition and transglutaminase 2 cross-linking cooperatively regulate ovarian cancer cell adhesion in ECM-mimetic constructs

    Article • Acta Biomaterialia, October 2025, Elsevier

    Dr Alexandra Naba

  3. In-depth proteomic profiling of the extracellular matrix of pancreatic ductal adenocarcinomas identifies signatures correlating with lymphocyte infiltration

    Article • August 2025, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  4. Comparative proteomic analysis of the ECM composition of the human omentum and mesentery, the main sites of ovarian cancer metastasis

    Article • July 2025, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  5. MatriCom, a single-cell RNA-sequencing data mining tool to infer cell–extracellular matrix interactions

    Article • Journal of Cell Science, July 2025, The Company of Biologists

    Dr Alexandra Naba

  6. Fibronectin Composition and Transglutaminase 2 Cross-linking Cooperatively Regulate Ovarian Cancer Cell Adhesion in ECM-Mimetic Constructs

    Article • May 2025, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  7. Time-lapse tryptic digestion: a proteomic approach to improve sequence coverage of extracellular matrix proteins

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  8. The novel ECM protein SNED1 mediates cell adhesion via the RGD-binding integrins α5β1 and αvβ3

    Article • Journal of Cell Science, January 2025, The Company of Biologists

    Dr Alexandra Naba

  9. MatriCom: a scRNA-Seq data mining tool to infer ECM-ECM and cell-ECM communication systems

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  10. MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface

    Article • Nucleic Acids Research, November 2024, Oxford University Press (OUP)

    Dr Alexandra Naba

  11. Proteomic insights into the extracellular matrix: a focus on proteoforms and their implications in health and disease

    Article • Expert Review of Proteomics, November 2024, Taylor & Francis

    Dr Alexandra Naba

  12. Mechanisms of assembly and remodelling of the extracellular matrix

    Article • Nature Reviews Molecular Cell Biology, September 2024, Springer Science + Business Media

    Dr Alexandra Naba

  13. The novel ECM protein SNED1 mediates cell adhesion via the RGD-binding integrins α5β1 and αvβ3

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  14. Extracellular matrix dynamics: A key regulator of cell migration across length-scales and systems

    Article • Current Opinion in Cell Biology, February 2024, Elsevier

    Dr Alexandra Naba

  15. Matrisome AnalyzeR – a suite of tools to annotate and quantify ECM molecules in big datasets across organisms

    Article • Journal of Cell Science, September 2023, The Company of Biologists

    Dr Alexandra Naba

  16. Desalting of Peptides to Prepare for Mass Spectrometry Analysis v2

    Article • May 2023, ZappyLab, Inc.

    Dr Alexandra Naba

  17. Matrisome AnalyzeR: A suite of tools to annotate and quantify ECM molecules in big datasets across organisms

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  18. Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives

    Article • Molecular & Cellular Proteomics, April 2023, Elsevier

    Dr Alexandra Naba

  19. Data from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  20. Data from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  21. GSEA gene sets from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  22. Ingenuity Pathway Analysis from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  23. MS data from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  24. Supplementary Figures from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  25. GSEA gene sets from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  26. Marker selection from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  27. Supplementary Tables from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  28. Ingenuity Pathway Analysis from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  29. Supplementary Figures from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  30. MS data from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  31. Supplementary Tables from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  32. Marker selection from Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • March 2023, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  33. Compartmental Protein Extraction to Achieve Enrichment of Extracellular Matrix (ECM) Proteins v1

    Article • March 2023, Springer Science + Business Media

    Dr Alexandra Naba

  34. Reduced SPAG17 Expression in Systemic Sclerosis Triggers Myofibroblast Transition and Drives Fibrosis

    Article • Journal of Investigative Dermatology, February 2023, Elsevier

    Dr Alexandra Naba

  35. Beyond the matrisome: New frontiers in ECM research

    Article • Matrix Biology, January 2023, Elsevier

    Dr Alexandra Naba

  36. MatrisomeDB 2.0: 2023 updates to the ECM-protein knowledge database

    Article • Nucleic Acids Research, November 2022, Oxford University Press (OUP)

    Dr Alexandra Naba

  37. Systematic Analysis of Actively Transcribed Core Matrisome Genes Across Tissues and Cell Phenotypes

    Article • Matrix Biology, August 2022, Elsevier

    Dr Alexandra Naba

  38. New Views of Old Proteins: Clarifying the Enigmatic Proteome

    Article • Molecular & Cellular Proteomics, July 2022, Elsevier

    David Walt, Dr Alexandra Naba

  39. Time-lapsed proteomics reveals a role for the novel protein, SNED1, in modulating ECM composition and protein folding

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  40. The matrix in focus: new directions in extracellular matrix research from the 2021 ASMB hybrid meeting

    Article • Biology Open, January 2022, The Company of Biologists

    Dr Alexandra Naba

  41. A tumor-derived type III collagen-rich ECM niche regulates tumor cell dormancy

    Article • Nature Cancer, December 2021, Springer Science + Business Media

    Dr Alexandra Naba

  42. Multi-modal Profiling of the Extracellular Matrix of Human Fallopian Tubes and Serous Tubal Intraepithelial Carcinomas

    Article • Journal of Histochemistry & Cytochemistry, December 2021, SAGE Publications

    Dr Alexandra Naba

  43. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome

    Article • Biochemical Journal, April 2021, Portland Press Ltd.

    Dr Alexandra Naba

  44. The Burden of Post-Translational Modification (PTM)—Disrupting Mutations in the Tumor Matrisome

    Article • Cancers, March 2021, MDPI AG

    Dr Alexandra Naba

  45. Knockout of the gene encoding the extracellular matrix protein SNED1 results in early neonatal lethality and craniofacial malformations

    Article • Developmental Dynamics, October 2020, Wiley

    Dr Alexandra Naba

  46. Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology

    Article • Matrix Biology, September 2020, Elsevier

    Dr Alexandra Naba

  47. The liver matrisome – looking beyond collagens

    Article • JHEP Reports, August 2020, Elsevier

    Dr Alexandra Naba

  48. Computational and experimental characterization of the novel ECM glycoprotein SNED1 and prediction of its interactome

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  49. Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome

    Article • Cancers, July 2020, MDPI AG

    Dr Alexandra Naba

  50. Proteomic pipeline to identify age-related compositional and structural changes of the human dentin extracellular matrix

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  51. Proteomic Profiling of the ECM of Xenograft Breast Cancer Metastases in Different Organs Reveals Distinct Metastatic Niches

    Article • Cancer Research, April 2020, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  52. The Extracellular Matrix Goes -Omics: Resources and Tools

    Article • January 2020, Springer Science + Business Media

    Dr Alexandra Naba

  53. The Matrisome of Model Organisms: From In-Silico Prediction to Big-Data Annotation

    Article • January 2020, Springer Science + Business Media

    Dr Alexandra Naba

  54. In-silico definition of the Drosophila melanogaster matrisome

    Article • Matrix Biology Plus, November 2019, Elsevier

    Dr Alexandra Naba

  55. MatrisomeDB: the ECM-protein knowledge database

    Article • Nucleic Acids Research, October 2019, Oxford University Press (OUP)

    Dr Alexandra Naba

  56. Exploring the extracellular matrix in health and disease using proteomics

    Article • Essays in Biochemistry, August 2019, Portland Press Ltd.

    Dr Alexandra Naba

  57. The in-silico characterization of the Caenorhabditis elegans matrisome and proposal of a novel collagen classification

    Article • Matrix Biology Plus, February 2019, Elsevier

    Dr Alexandra Naba

  58. MatrixDB: integration of new data with a focus on glycosaminoglycan interactions

    Article • Nucleic Acids Research, October 2018, Oxford University Press (OUP)

    Dr Alexandra Naba

  59. Knockout of the gene encoding the extracellular matrix protein Sned1 results in craniofacial malformations and early neonatal lethality

    Article • October 2018, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  60. The cancer matrisome: From comprehensive characterization to biomarker discovery

    Article • Seminars in Cell and Developmental Biology, July 2018, Elsevier

    Dr Alexandra Naba

  61. Extracellular matrix in lung development, homeostasis and disease

    Article • Matrix Biology, March 2018, Elsevier

    Dr Alexandra Naba, Dr Namasivayam Ambalavanan

  62. The in-silico zebrafish matrisome: A new tool to study extracellular matrix gene and protein functions

    Article • Matrix Biology, January 2018, Elsevier

    Dr Alexandra Naba

  63. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics

    Article • Journal of Proteome Research, July 2017, American Chemical Society (ACS)

    Dr Alexandra Naba

  64. Quantitative proteomics identify Tenascin-C as a promoter of lung cancer progression and contributor to a signature prognostic of patient survival

    Article • Proceedings of the National Academy of Sciences, June 2017, Proceedings of the National Academy of Sciences

    Dr Alexandra Naba

  65. Proteomic characterization of human multiple myeloma bone marrow extracellular matrix

    Article • Leukemia, March 2017, Nature

    Dr Alexandra Naba

  66. Comprehensive proteomic characterization of stem cell-derived extracellular matrices

    Article • Biomaterials, March 2017, Elsevier

    Dr Alexandra Naba

  67. Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression

    Article • Scientific Reports, January 2017, Nature

    Dr Alexandra Naba

  68. Lamellipodin promotes invasive 3D cancer cell migration via regulated interactions with Ena/VASP and SCAR/WAVE

    Article • Oncogene, March 2016, Nature

    Dr Alexandra Naba

  69. The extracellular matrix: Tools and insights for the “omics” era

    Article • Matrix Biology, January 2016, Elsevier

    Dr Alexandra Naba

  70. Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

    Article • Journal of Visualized Experiments, July 2015, MyJove Corporation

    Dr Alexandra Naba

  71. Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver

    Article • BMC Cancer, July 2014, Springer Science + Business Media

    Dr Alexandra Naba

  72. Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters

    Article • eLife, March 2014, eLife

    Dr Alexandra Naba, Dr John Michael Lamar

  73. Towards definition of an ECM parts list: An advance on GO categories

    Article • Matrix Biology, September 2012, Elsevier

    Dr Alexandra Naba

  74. Abstract SY28-01: Multiple changes in tumor extracellular matrices

    Article • Cancer Research, April 2012, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  75. Ezrin phosphorylation on tyrosine 477 regulates invasion and metastasis of breast cancer cells

    Article • BMC Cancer, March 2012, Springer Science + Business Media

    Dr Alexandra Naba

  76. Ezrin regulates microvillus morphogenesis by promoting distinct activities of Eps8 proteins

    Article • Molecular Biology of the Cell, January 2012, American Society for Cell Biology (ASCB)

    Dr Alexandra Naba

  77. The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices

    Article • Molecular & Cellular Proteomics, December 2011, American Society for Biochemistry & Molecular Biology (ASBMB)

    Dr Alexandra Naba

  78. Overview of the Matrisome--An Inventory of Extracellular Matrix Constituents and Functions

    Article • Cold Spring Harbor Perspectives in Biology, September 2011, Cold Spring Harbor Laboratory Press

    Dr Alexandra Naba

  79. Emerging role for ERM proteins in cell adhesion and migration

    Article • Cell Adhesion & Migration, March 2011, Taylor & Francis

    Dr Alexandra Naba

  80. Abstract 2370: A novel Src/Ezrin pathway regulates local invasion and metastasis of breast

    Article • Cancer Research, April 2010, American Association for Cancer Research (AACR)

    Dr Alexandra Naba

  81. Inhibition of endothelial cell chemotaxis toward FGF-2 by gefitinib associates with downregulation of Fes activity

    Article • International Journal of Oncology, October 2009, Spandidos Publications

    Dr Alexandra Naba

  82. Ezrin is a target for oncogenic Kit mutants in murine erythroleukemia

    Article • Blood, March 2008, American Society of Hematology

    Dr Alexandra Naba

  83. Spatial recruitment and activation of the Fes kinase by ezrin promotes HGF-induced cell scattering

    Article • The EMBO Journal, November 2007, Springer Science + Business Media

    Dr Alexandra Naba