Publications

For a complete list of publications see:
Researcher ID
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Gangoda L, Liem M, Ang CS, Keerthikumar S, Adda C, Parker B and Mathivanan S (2017) Proteomic profiling of exosomes secreted by breast cancer cells with varying metastatic potential, Proteomics, 17(23-24), doi: 10.1002/pmic.201600370.

Mathivanan S (2017) Extracellular Matrix and the Extracellular Environment, Proteomics, 17(23-24), doi: 10.1002/pmic.2017700185.

Witwer KW, Soekmadji C, Hill AF, Wauben MH, Buzás EI, Di Vizio D, Falcon-Perez JM, Gardiner C, Hochberg F, Kurochkin IV, Lötvall J, Mathivanan S, Nieuwland R, Sahoo S, Tahara H, Torrecilhas AC, Weaver AM, Yin H, Zheng L, Gho YS, Quesenberry P and Théry C (2017) Updating the MISEV minimal requirements for extracellular vesicle studies: building bridges to reproducibility, J Extracell Vesicles, 6(1): 1396823, doi: 10.1080/20013078.2017.1396823.

Liem M, Ang CS and Mathivanan S (2017) Insulin mediated activation of PI3K/Akt signalling pathway modifies the proteomic cargo of extracellular vesicles, Proteomics, 17(23-24), doi: 10.1002/pmic.201600371.

Samuel M, Chisanga D, Liem M, Keerthikumar S, Anand S, Ang CS, Adda CG, Versteegen E, Jois M and Mathivanan S (2017) Bovine milk-derived exosomes from colostrum are enriched with proteins implicated in immune response and growth, Scientific Reports, 7(1): 5933.

Meeusen E, Lim E and Mathivanan S (2017) Secreted tumor antigens - immune biomarkers for diagnosis and therapy, Proteomics, 17(23-24), doi: 10.1002/pmic.201600442.

Kang Y, Stroud DA, Baker MJ, De Souza DP, Frazier AE, Liem M, Tull D, Mathivanan S, McConville MJ, Thorburn DR, Ryan MT and Stojanovski D (2017) Sengers syndrome associated mitochondrial acylglycerol kinase, is a subunit of the human TIM22 protein import complex, Molecular Cell, 67(3): 457-470.

Vo JL, Martínez Ortiz GC, Subedi P, Keerthikumar S, Mathivanan S, Paxman JJ and Heras B (2017) Autotransporter adhesins in Escherichia coli pathogenesis, Proteomics, 17(23-34), doi:10.1002/pmic.201600431.

EV-TRACK Consortium, Van Deun J, Mestdagh P, Agostinis P, Akay Ö, Anand S, Anckaert J, Martinez ZA, Baetens T, Beghein E, Bertier L, Berx G, Boere J, Boukouris S, Bremer M, Buschmann D, Byrd JB, Casert C, Cheng L, Cmoch A, Daveloose D, De Smedt E, Demirsoy S, Depoorter V, Dhondt B, Driedonks TA, Dudek A, Elsharawy A, Floris I, Foers AD, Gärtner K, Garg AD, Geeurickx E, Gettemans J, Ghazavi F, Giebel B, Kormelink TG, Hancock G, Helsmoortel H, Hill AF, Hyenne V, Kalra H, Kim D, Kowal J, Kraemer S, Leidinger P, Leonelli C, Liang Y, Lippens L, Liu S, Lo Cicero A, Martin S, Mathivanan S, Mathiyalagan P, Matusek T, Milani G, Monguió-Tortajada M, Mus LM, Muth DC, Németh A, Nolte-‘t Hoen EN, O’Driscoll L, Palmulli R, Pfaffl MW, Primdal-Bengtson B, Romano E, Rousseau Q, Sahoo S, Sampaio N, Samuel M, Scicluna B, Soen B, Steels A, Swinnen JV, Takatalo M, Thaminy S, Théry C, Tulkens J, Van Audenhove I, van der Grein S, Van Goethem A, van Herwijnen MJ, Van Niel G, Van Roy N, Van Vliet AR, Vandamme N, Vanhauwaert S, Vergauwen G, Verweij F, Wallaert A, Wauben M, Witwer KW, Zonneveld MI, De Wever O, Vandesompele J and Hendrix A (2017) EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research, Nature Meth.,14(3): 228-32.

Dona M, Prendergast L, Mathivanan S, Keerthikumar S and Salim A (2017) Powerful differential expression analysis incorporating network topology for next-generation sequencing data, Bioinformatics, 33(10): 1505-1513.

Pathan M, Samuel M, Keerthikumar S and Mathivanan S (2017) Unassigned MS/MS Spectra: Who Am I?, Methods in Molecular Biology, 1549: 67-74.

Anand S, Samuel M, Ang CS, Keerthikumar S and Mathivanan S (2017) Label-Based and Label-Free Strategies for Protein Quantitation, Methods in Molecular Biology, 1549: 31-43.

Chisanga D, Keerthikumar S, Mathivanan S and Chilamkurti N (2017) Network Tools for the Analysis of Proteomic Data, Methods in Molecular Biology, 1549: 177-197.

Keerthikumar S and Mathivanan S (2017) Proteotypic Peptides and Their Applications, Methods in Molecular Biology, 1549: 101-107.

Keerthikumar S and Mathivanan S (2017) Proteomic Data Storage and Sharing, Methods in Molecular Biology, 1549: 5-15.

Keerthikumar S, Gangoda L, Gho YS and Mathivanan S (2017) Bioinformatics Tools for Extracellular Vesicles Research, Methods in Molecular Biology, 1545: 189-196.

Pathan M, Keerthikumar S, Chisanga D, Alessandro R, Ang CS, Askenase P, Batagov AO, Benito-Martin A, Camussi G, Clayton A, Collino F, Di Vizio D, Falcon-Perez JM, Fonseca P, Fonseka P, Fontana S, Gho YS, Hendrix A, Nolte-'t Hoen E, Iraci N, Kastaniegaard K, Kislinger T, Kowal J, Kurochkin IV, Leonardi T, Liang Y, Llorente A, Lunavat TR, Maji S, Monteleone F, Overbye A, Panaretakis T, Patel T, Peinado H, Pluchino S, Principe S, Ronquist G, Royo F, Sahoo S, Spinelli C, Stensballe A, Thery C, van Herwijnen M, Wauben M, Welton J, Zhao J and Mathivanan S (2017) A novel community driven software for functional enrichment analysis of extracellular vesicles data, J Extracellular Vesicles, doi: 1321455.

Chisanga D, Keerthikumar S, Pathan M, Ariyaratne D, Kalra H, Boukouris S, Mathew N, Al Saffar H, Gangoda L, Ang CS, Sieber O, Mariadason J, Dasgupta R, Chilamkurti N and Mathivanan S (2016) Colorectal Cancer Atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissue, Nuc Acids Res., 44(D1): D969-74.

Samuel M, Bleackley M, Anderson M and Mathivanan S (2015) Extracellular vesicles including exosomes in cross kingdom regulation: a viewpoint from plant-fungal interactions, Front Plant Sci., doi.org/10.3389/fpls.2015.00766.

Atkin-Smith GK, Tixeira R, Paone S, Mathivanan S, Collins C, Liem M, Goodall KG, Ravichandran KS, Hulett MD and Poon IVH (2015) A novel mechanism of generating extracellular vesicles during apoptosis via a beads-on-a-string membrane structure, Nat Commun., 6: 7439.

Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CMJ, Williamson NJ, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JA, Mariadasson JM, Burgess AW and Mathivanan S (2015) FunRich: a standalone tool for functional enrichment analysis, Proteomics, 15(15): 2597-601.

Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Adda CG, Ang CS and Mathivanan S (2015) Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes, Oncotarget., 17: 15375-96.

Lydic TA, Townsend S, Adda C, Collins C, Mathivanan S and Reid GE (2015) Rapid and comprehensive 'shotgun' lipidome profiling of colorectal cancer cell derived exosomes, Methods, pii: S1046-2023.

Boukouris S and Mathivanan S (2015) Exosomes in bodily fluids are a highly stable resource of disease biomarkers, Proteomics Clin Appl., 9(3-4): 358-67.

Gangoda L, Keerthikumar S, Fonseka P, Edgington LE, Ang CS, Ozcitti C, Bogyo M, Parker BS and Mathivanan S (2015) Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin, Oncotarget., 6:13, 11175-90.

Minciacchi VR, You S, Spinelli C, Morley S, Zandian M, Aspuria PJ, Cavallini L, Ciardiello C, Sobreiro MR, Morello M, Kharmate G, Jang SC, Kim DK, Hosseini-Beheshti E, Guns ET, Gleave M, Gho YS, Mathivanan S, Yang W, Freeman MR and Di Vizio D (2015) Large oncosomes contain distinct protein cargo and represent a separate functional class of tumor-derived extracellular vesicles, Oncotarget., 31: 933-39.

Gangoda L, Boukouris S, Liem M, Kalra H and Mathivanan S (2015) Exosomes are mediators of signal transduction: Are they protective or pathogenic? Proteomics, 15(2-3): 260-71.

Kim DK, Lee J, Kim SR, Choi DS, Yoon YJ, Kim JH, Go G, Nhung D, Hong K, Jang SC, Kim SH, Park KS, Kim OY, Park HT, Seo JH, Aikawa E, Baj-Krzyworzeka M, Van Balkom BW, Belting M, Blanc L, Bond V, Bongiovanni A, Borràs FE, Buée L, Buzás EI, Cheng L, Clayton A, Cocucci E, Dela Cruz CS, Desiderio DM, Di Vizio D, Ekström K, Falcon-Perez JM, Gardiner C, Giebel B, Greening DW, Gross JC, Gupta D, Hendrix A, Hill AF, Hill MM, Hoen EN, Hwang DW, Inal J, Jagannadham MV, Jayachandran M, Jee YK, Jørgensen M, Kim KP, Kim YK, Kislinger T, Lässer C, Lee DS, Lee H, Van Leeuwen J, Lener T, Liu ML, Lötvall J, Marcilla A, Mathivanan S, Möller A, Morhayim J, Mullier F, Nazarenko I, Nieuwland R, Nunes DN, Pang K, Park J, Patel T, Pocsfalvi G, Del Portillo H, Putz U, Ramirez MI, Rodrigues ML, Roh TY, Royo F, Sahoo S, Schiffelers R, Sharma S, Siljander P, Simpson RJ, Soekmadji C, Stahl P, Stensballe A, Stępień E, Tahara H, Trummer A, Valadi H, Vella LJ, Wai SN, Witwer K, Yáñez-Mó M, Youn H, Zeidler R and Gho YS (2015) EVpedia as a resource for extracellular vesicles biology, Bioinformatics, 31(6): 933-39.

Lotvall J, Hill AF, Hochberg F, Buzas EI, Di Vizio D, Gardiner C, Gho YS, Kurochkin IV, Mathivanan S, Quesenberry P, Sahoo S, Tahara H, Wauben MH, Witwer KW and Thery C (2014) Minimal experimental requirements for definition of extracellular vesicles and their functions: a position statement from the International Society for Extracellular Vesicles, J Extracell Vesicles, 3: 26913.

Cossetti C, Iraci N, Mercer TN, Leonardi T, Alpi E, Drago D, Alfaro-Cervello C, Saini HK, Davis MP, Schaeffer J, Vega B, Stefanini M, Zhao C, Muller W, Garcia-Verdugo JM, Mathivanan S, Bachi A, Enright AJ, Mattick JS and Pluchino S (2014) Extracellular vesicles from neural stem Cells transfer IFN-γ via Ifngr1 to activate Stat1 signaling in target cells, Mol Cell., 56(2): 193-204.

Cooke I, Jones D, Bowen J, Denge C, Faou P, Hall N, Jayachandran V, Liem M, Taranto A, Plummer KM and Mathivanan S (2014) Proteogenomic analysis of the Venturia pirina (pear scab fungus) secretome reveals potential effectors, J Proteome Res., 13(8): 3635-44.

Mathivanan S (2014) Integrated bioinformatics analysis of the publicly available protein data shows evidence for 96% of the human proteome, J Proteomics Bioinfo., doi.org/10.4172/jpb.1000301.

Nanjappa V, Thomas JK, Marimuthu A, Muthusamy B, Radhakrishnan A, Sharma R, Khan AA, Balakrishnan L, Sahasrabuddhe N, Kumar S, Jhaveri BN, Sheth KV, Khatana RK, Shaw PG, Srikanth SM, Mathur PP, Shankar S, Nagaraja D, Christopher R, Mathivanan S, Raju R, Sirdeshmukh R, Chatterjee A, Simpson R, Harsha HC, Pandey A and Prasad TSK (2014) Plasma Proteome Database as a resource for proteomics research: 2014 update, Nucleic Acids Res., doi: 10.1093/nar/gkt1251.

Kalra H, Adda CG, Liem M, Ang CS, Mechler A, Simpson RJ, Hulett MD and Mathivanan S (2013) Comparative proteomics evaluation of plasma exosome isolation techniques and assessment of the stability of exosomes in normal human blood plasma, Proteomics, 13(22): 3354-64.

Ji H, Greening DW, Barnes TW, Lim JW, Tauro BJ, Rai A, Xu R, Adda C, Mathivanan S, Zhao W, Xue Y, Xu T, Zhu HJ and Simpson RJ (2013) Proteome profiling of exosomes derived from human primary and metastatic colorectal cells reveal differential expression of key metastatic factors and signal transduction components, Proteomics, 13(10-11): 1672-86.

Tauro BJ, Greening DW, Mathias RA, Mathivanan S, Ji H and Simpson RJ (2013) Two distinct populations of exosomes are released from LIM1863 colon carcinoma cell-derived organoids, Mol Cell Proteomics, 12(3): 587-98.

Mathivanan S (2012) Exosomes and shedding microvesicles are mediators of intercellular communication: how do they communicate with the target cells? J Biotechnol Biomater., doi.org/10.4172/2155-952X.1000e110.

Kalra H, Simpson RJ, Ji H, Aikawa E, Altevogt P, Askenase P, Bond VC, Borràs FE, Breakefield X, Budnik V, Buzas E, Camussi G, Clayton A, Cocucci E, Falcon-Perez JM, Gabrielsson S, Gho YS, Gupta D, Harsha HC, Hendrix A, Hill AF, Inaal JM, Jenster G, Kiang LS, Krämer-Albers E-M, Llorente A, Lötvall J, Mincheva-Nilsson L, Nazarenko I, Nieuwland R, Nolte-'t Hoen ENM, Pandey A, Patel T, Piper MG, Pluchino S, Prasad TSK, Rajendran L, Raposo G, Record M, Reid GE, Sánchez-Madrid F, Schiffelers RM, Siljander P, Stoorvogel W, Taylor D, Thery C, Valadi H, van Balkom BWM, Vázquez J, Vidal M, Yáñez-Mó M, Zoeller M and Mathivanan S (2012) Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation, PLOS Biology, doi: 10.1371/journal.pbio.1001450.

Mathivanan S (2012) Quest for cancer biomarkers: assaying mutant proteins and RNA that provides the much needed specificity, J Proteomics Bioinfo., 5: 13-17.

Mathivanan S, Ji H, Tauro BJ, Chen YS and Simpson RJ (2012) Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry, J Proteomics, 76: 141-49.

Simpson RJ, Kalra H and Mathivanan S (2012) ExoCarta as a resource for exosomal research, J Extracell Vesicles, 1: 18374.

Simpson RJ and Mathivanan S (2012) Extracellular microvesicles: the need for internationally recognized nomenclature and stringent purification criteria, J Proteomics Bioinfo., doi: 10.4172/jpb.10000e10.

Mathivanan S, Patterson C, Reid G and Simpson RJ (2012) ExoCarta for exosomal RNA, proteins and lipids, Nucleic Acids Res., (40): D1241-4.

Tauro BJ, Greening DW, Mathias RA, Ji H, Mathivavan S, Scott AM, and Simpson RJ (2012) Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes, Methods, 56(2): 293-304.