Exosomes

Role of extracellular matrix in cancer


PUBLICATIONS  

 

Full list of Mathivanan's publications in




Word cloud of Journals in this page


1. Chisanga, D., Keerthikumar, S., Pathan, M., Ariyaratne, D., Kalra, H., Boukouris, S., Mathew, N., Al Saffar, H., Gangoda, L., Ang, C.S., 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. Nucleic Acids Research. 44(D1), D969-74.

2. Keerthikumar, S., Gangoda, L., Liem, M., Fonseka, P., Atukorala, I., Ozcitti, C., Mechler, A., Adda, C.G., Ang, C.S. and Mathivanan, S. (2015) Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes. Oncotarget. 17, 15375-15396.

3. Pathan, M., Keerthikumar, S., Ang, C.S., Gangoda, L., Quek, C.M.J., Williamson, N.J., Mouradov, D., Sieber, O.M., Simpson, R.J., Salim, A., Bacic, A., Hill, A.F., Stroud, D.A., Ryan, M.T., Agbinya, J.A., Mariadasson, J.M., Burgess, A.W. and Mathivanan, S. (2015) FunRich: a standalone tool for functional enrichment analysis. Proteomics. 15, 2597-2601.

4. Gangoda, L., Keerthikumar, S., Fonseka, P., Edgington, L.E., Ang, C.S., Ozcitti, C., Bogyo, M., Parker, B.S. and Mathivanan, S. (2015) Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. Oncotarget. 6:13, 11175-11190.

5. Kalra, H., Adda, C.G., Liem, M., Ang, C.S., Mechler, A., Simpson, R.J., Hulett, M.D. 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. 22, 3354-64.

6. Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inaal, J.M., Jenster, G., Kiang, L.S., Kramer-Albers, E-M., Llorente, A., Lotvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A., Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S.K., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Yanez-Mo, M., Zoeller, M. and Mathivanan, S. (2012) Vesiclepedia: A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 12, e1001450.

7. Mathivanan, S., Lim, J. W. E., Taro, B., Hong, J., Moritz, R. L. and Simpson, R. J. (2010). Proteomic analysis of A33-immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. Mol Cell Proteomics. 2, 197-208.

8. Mathivanan, S., Ahmed, M. et al. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-7.

9. Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286.

10. Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293.


2017

 


67. Pathan, M., Keerthikumar, S., Chisanga, D., Alessandro, R., Ang, C.S., Askenase, P., Batagov, A.O., Benito-Martin, A., Camussi, G., Clayton, A., Collino, F., Di Vizio, D., Falcon-Perez, J.M., Fonseca, P., Fonseka, P., Fontana, S., Gho, Y.S., Hendrix, A., Nolte-'t Hoen, E., Iraci, N., Kastaniegaard, K., Kislinger, T., Kowal, J., Kurochkin, I.V., Leonardi, T., Liang, Y., Llorente, A., Lunavat, T.R., 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. In press (accepted on 18/04/17)

66. Jan Van Deun, Pieter Mestdagh, Patricia Agostinis, Geert Berx, Jan Gettemans, Bernd Giebel, Andrew Hill, Mathivanan, S., Esther Nolte-t-Hoen, Michael Pfaffl, Susmita Sahoo, Johan Swinnen, Clotilde Thery, Guillaume Van Niel, Marca Wauben, Kenneth Witwer, Olivier De Wever, Jo Vandesompele, An Hendrix. (2017) EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nature Methods. 14(3):228-232.

65. 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. In press.

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

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

62. 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.

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

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

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


2016

 


58. Lasser, C., Thery, C., Buzas, E. I., Mathivanan, S., Zhao, W., Gho, Y. S., Lotvall, J. (2016) The International Society for Extracellular Vesicles launches the first massive open online course on extracellular vesicles. Journal of Extracellular Vesicles. 16;5: 34299.

57. Kang, Y., Baker, M.J., Liem, M., Louber, J., McKenzie, M., Atukorala, I., Ang, C.S., Keerthikumar, S., Mathivanan, S. and Stojanovski, D. (2016) Tim29 is a novel subunit of the human TIM22 translocase and is involved in complex assembly and stability. eLife. Aug 24;5. pii: e17463.

56. Gangoda, L. and Mathivanan, S. (2016) Cortactin enhances exosome secretion without altering cargo. Journal of Cell Biology. 214 (2): 129.

55. Cheung, KH., Keerthikumar, S., Roncaglia, P., Subramanian, SL., Roth, ME., Gould, S., Alexander, R., Galas, D., Gerstein, MB., Hill, AF., Kitchen, RR., Lotvall, J., Patel, T., Procaccini, DC., Queensberry, P., Rozowsky, J., Raffai, RL., Shypitsyn, A., Su, AI., Thery, C., Vickers, K., Wauben, M., Mathivanan, S., Milosavljevic, A. and Laurent, L. (2016). Extending Gene Ontology in the Context of Extracellular RNA and Vesicle Communication. Journal of Biomedical Semantics. 7:19.

54. Mackenzie, K.D., Foot, N.J., Anand, S., Dalton, H.E., Chaudhary, N., Collins, B.M., Mathivanan, S. and Kumar, S. (2016) Regulation of the divalent metal ion transporter via membrane budding. Cell Discovery. 2, 16011.

53. Chisanga, D., Keerthikumar, S., Pathan, M., Ariyaratne, D., Kalra, H., Boukouris, S., Mathew, N., Al Saffar, H., Gangoda, L., Ang, C.S., 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. Nucleic Acids Research. 44(D1), D969-74.

52. Kalra, H., Drummen, G.P.C. and Mathivanan, S. (2016) Focus on Extracellular Vesicles: Introducing the Next Small Big Thing. International Journal of Molecular Sciences. 6;17(2).

51. Keerthikumar, S., Chisanga, D., Ariyaratne, D., Al Saffar, H., Anand, S., Zhao, K., Samuel, M., Pathan, M., Jois, M., Chilamkurti, N., Gangoda, L. and Mathivanan, S. (2016) ExoCarta: A web-based compendium of exosomal cargo. Journal of Molecular Biology. 428, 688-692


2015

 


50. Lowe, R., McCorkelle, O., Bleackley, M., Collins, C., Faou, P., Mathivanan, S. and Anderson, M. (2015) Extracellular peptidases of the cereal pathogen Fusarium graminearum. Frontiers in Plant Science. 6, 962.

49. Samuel, M., Bleackley, M., Anderson, M. and Mathivanan, S. (2015) Extracellular vesicles including exosomes in cross kingdom regulation: a viewpoint from plant-fungal interactions. Frontiers in Plant Science. 6, 766.

48. Atkin-Smith, G.K., Tixeira, R., Paone, S., Mathivanan, S., Collins, C., Liem, M., Goodall, K.G., Ravichandran, K.S., Hulett, M.D. and Poon, I.V.H. (2015) A novel mechanism of generating extracellular vesicles during apoptosis via a beads-on-a-string membrane structure. Nature Communications. 6, 7439.

47. Pathan, M., Keerthikumar, S., Ang, C.S., Gangoda, L., Quek, C.M.J., Williamson, N.J., Mouradov, D., Sieber, O.M., Simpson, R.J., Salim, A., Bacic, A., Hill, A.F., Stroud, D.A., Ryan, M.T., Agbinya, J.A., Mariadasson, J.M., Burgess, A.W. and Mathivanan, S. (2015) FunRich: a standalone tool for functional enrichment analysis. Proteomics. 15, 2597-2601.

46. Keerthikumar, S., Gangoda, L., Liem, M., Fonseka, P., Atukorala, I., Ozcitti, C., Mechler, A., Adda, C.G., Ang, C.S. and Mathivanan, S. (2015) Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes. Oncotarget. 17, 15375-15396.

45. Lydic, T.A., Townsend, S., Adda, C., Collins, C., Mathivanan, S. and Reid, G.E. (2015) Rapid and comprehensive 'shotgun' lipidome profiling of colorectal cancer cell derived exosomes Methods. pii: S1046-2023.

44. Gangoda, L., Keerthikumar, S., Fonseka, P., Edgington, L.E., Ang, C.S., Ozcitti, C., Bogyo, M., Parker, B.S. and Mathivanan, S. (2015) Inhibition of cathepsin proteases attenuates migration and sensitizes aggressive N-Myc amplified human neuroblastoma cells to doxorubicin. Oncotarget. 6:13, 11175-11190.

43. Boukoris, S. and Mathivanan, S. (2015) Exosomes in bodily fluids are a highly stable resource of disease biomarkers. Proteomics clinical applications. 9, 358-67.

42. 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, Borras FE, Buee L, Buzas EI, Cheng L, Clayton A, Cocucci E, Dela Cruz CS, Desiderio DM, Di Vizio D, Ekstrom 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, Jorgensen M, Kim KP, Kim YK, Kislinger T, Lasser C, Lee DS, Lee H, Van Leeuwen J, Lener T, Liu ML, Lotvall J, Marcilla A, Mathivanan S, Moller 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, Stepien E, Tahara H, Trummer A, Valadi H, Vella LJ, Wai SN, Witwer K, Yanez-Mo M, Youn H, Zeidler R, Gho YS (2015) EVpedia: A Community Web Portal for Extracellular Vesicles Research. Bioinformatics. 31, 933-939.

41. Minciacchi, V.R., You, S., Spinelli, C., Morley, S., Zandian, M., Aspuria, P.J., Cavallini, L., Ciardiello, C., Sobreiro, M.R., Morello, M., Kharmate, G., Jang, S.C., Kim, D.K., Hosseini-Beheshti, E., Guns, E.T., Gleave, M., Gho, Y.S., Mathivanan, S., Yang, W., Freeman, M.R. and Di Vizio, D. (2015) Large oncosomes contain distinct protein cargo and represent a separate functional class of tumor-derived extracellular vesicles. Oncotarget. 6:13, 11327-11341.

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


2014

 


39. Lotvall, J., Hill, A.F., Hochberg, F., Buzas, E.I., Di Vizio, D., Gardiner, C., Gho, Y.S., Kurochkin, I.V., Mathivanan, S., Quesenberry, P., Sahoo, S., Tahara, H., Wauben, M.H., Witwer, K.W. 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. Journal of Extracellular Vesicles. 3:26913.

38. Cossetti, C., Iraci, N., Mercer, T.N., Leonardi, T., Alpi, E., Drago, D., Alfaro-Cervello, C., Saini, H.K., Davis, M.P., Schaeffer, J., Vega, B., Stefanini, M., Zhao, C., Muller, W., Garcia-Verdugo, J.M., Mathivanan, S., Bachi, A., Enright, A.J., Mattick, J.S. and Pluchino, S. (2014) Extracellular Vesicles from Neural Stem Cells Transfer IFN-γ via Ifngr1 to Activate Stat1 Signaling in Target Cells. Molecular Cell. 56 (2), 193-204.

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

36. Mathivanan, S. (2014) Integrated bioinformatics analysis of the publicly available protein data shows evidence for 96% of the human proteome. Journal of Proteomics and Bioinformatics 7, 41-49.

35. Nanjappa, V., Thomas, J.K., Marimuthu, A., Muthusamy, B., Radhakrishnan, A., Sharma, R., Khan, A. A., Balakrishnan, L., Sahasrabuddhe, N., Kumar, S., Jhaveri, B.N., Sheth, K.V., Khatana, R.K., Shaw, P.G., Srikanth, S.M., Mathur, P.P., Shankar, S., Nagaraja, D., Christopher, R., Mathivanan, S., Raju, R., Sirdeshmukh, R., Chatterjee, A., Simpson, R., Harsha, H.C., Pandey, A. and Prasad, T.S.K. (2014) Plasma Proteome Database as a resource for proteomics research: 2014 update. Nucleic Acids Research. 1, D959-65.


2013

 


34. Kalra, H., Adda, C.G., Liem, M., Ang, C.S., Mechler, A., Simpson, R.J., Hulett, M.D. 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. 22, 3354-64.

33. Ji, H., Greening, D.W., Barnes, T.W., Lim, J.W., Tauro, B.J., Rai, A., Xu, R., Adda, C., Mathivanan, S., Zhao, W., Xue, Y., Xu, T., Zhu, H.J. and Simpson, R.J. (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, 1672-86.

32. Tauro, B.J., Greening, D.W., Mathias, R.A., Mathivanan, S., Ji, H. and Simpson, R.J. (2013) Two distinct populations of exosomes are released from LIM1863 colon carcinoma cell-derived organoids. Mol Cell Proteomics. 12, 587-98.


2012

 


31. Kalra, H., Simpson, R.J., Ji, H., Aikawa, E., Altevogt, P., Askenase, P., Bond, V.C., Borras, F.E., Breakefield, X., Budnik, V., Buzas, E., Camussi, G., Clayton, A., Cocucci, E., Falcon-Perez, J.M., Gabrielsson, S., Gho, Y.S., Gupta, D., Harsha, H.C., Hendrix, A., Hill, A.F., Inaal, J.M., Jenster, G., Kiang, L.S., Kramer-Albers, E-M., Llorente, A., Lotvall, J., Mincheva-Nilsson, L., Nazarenko, I., Nieuwland, R., Nolte-'t Hoen, E.N.M., Pandey, A., Patel, T., Piper, M.G., Pluchino, S., Prasad, T.S.K., Rajendran, L., Raposo, G., Record, M., Reid, G.E., Sanchez-Madrid, F., Schiffelers, R.M., Siljander, P., Stoorvogel, W., Taylor, D., Thery, C., Valadi, H., van Balkom, B.W.M., Vazquez, J., Vidal, M., Yanez-Mo, M., Zoeller, M. and Mathivanan, S. (2012) Vesiclepedia: A compendium for extracellular vesicles with continuous community annotation. PLoS Biology. 12, e1001450.

      --- Nature Methods: Tools in brief - Introducing Vesiclepedia
      --- Journal of Extracellular Vesicles: Launch of Vesiclepedia

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

29. Mathivanan, S., Ji, H., Tauro, B.J., Chen, Y.S. and Simpson, R.J. (2012) Identifying mutated proteins secreted by colon cancer cell lines using mass spectrometry. Journal of Proteomics. 76, 141-9.

28. Simpson, R.J., Kalra, H. and Mathivanan, S. (2012) ExoCarta as a resource for exosomal research. Journal of Extracellular Vesicles. 1, 18374.

27. Simpson, R.J. and Mathivanan, S. (2012) Extracellular microvesicles: the need for internationally recognized nomenclature and stringent purification criteria. Journal of Proteomics and Bioinformatics. 5:2.

26. Mathivanan, S.*, Patterson, C., Reid, G. and Simpson, R.J.* (2012). ExoCarta for exosomal RNA, proteins and lipids. Nucleic Acids Research. 1, D1241-4.
*corresponding author

25. Mathivanan, S. (2012) Exosomes and shedding microvesicles are mediators of intercellular communication: how do they communicate with the target cells? Journal of Biotechnology & Biomaterials. 2:e110.

24. Tauro, B.J., Greening, D.W., Mathias, R.A., Ji, H., Mathivanan, S., Scott, A.M., Simpson, R.J. (2012). Comparison of ultracentrifugation, density gradient separation, and immunoaffinity capture methods for isolating human colon cancer cell line LIM1863-derived exosomes. Methods. 56, 293-304.


2011

 


23. Ji, H., Goode, R.J.A., Vaillant, F., Mathivanan, S., Kapp, E.A., Mathias, R.A., Linderman, G.J., Visvader, J.E., Simpson, R.J. (2011). Proteomic profiling of secretome and adherent plasma membranes from distinct mammary epithelial cell subpopulations. Proteomics. 20, 4029-39.

22. Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W.H., Joore, J., Beer, M.A., Cope, L. and Pandey, A. (2011). Identification of novel phosphorylation motifs through integrative computational and experimental analysis of human phosphoproteome. Journal of Proteomics and Bioinformatics. 4, 22-35.

21. Mathias, R.A., Chen, Y., Kapp, E.A., Greening, D.W., Mathivanan, S. and Simpson, R.J. (2011). Triton X-114 phase separation in the isolation and purification of mouse liver microsomal membrane proteins. Methods. 4, 396-406.

20. Mathias, R.A., Chen, Y., Kapp, E.A., Mathivanan, S., Zhu, H. and Simpson, R.J. (2011). Tandem application of cationic colloidal silica and Triton-X 114 for plasma membrane isolation and purification. Proteomics. 11, 1238-53.

19. Chen, Y., Mathias, R.A., Mathivanan, S., Kapp, E.A., Moritz, R.L., Zhu, H. and Simpson, R.J. (2011). Proteomic profiling of MDCK plasma membranes reveals Wnt-5a involvement during oncogenic H-Ras/TGF-β-mediated epithelial-mesenchymal transition. Mol Cell Proteomics. 10, M110.001131.


2010

 


18. Mathivanan, S., Hong, J. and Simpson, R.J. (2010). Exosomes: extracellular organelles important in intercellular communication. J Proteomics. 10, 1907-20.

17. Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugopal, A. K., Telikicherla, D., Navarro, D. J., Mathivanan, S. et al. (2010). NetPath: A public resource of curated signal transduction pathways. Genome Biology. 1, R3.

16. Mathivanan, S., Lim, J. W. E., Taro, B., Hong, J., Moritz, R. L. and Simpson, R. J. (2010). Proteomic analysis of A33-immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. Mol Cell Proteomics. 2, 197-208.


2009

 


15. Simpson, R. J., Lim, J. W. E., Moritz, R. L. and Mathivanan, S. (2009). Exosomes: proteomic insights and diagnostic potential. Expert reviews in proteomics. 6, 267-83.

14. Mathivanan, S. and Simpson, R. J. (2009). ExoCarta: A compendium of exosomal proteins and RNA. Proteomics. 9, 4997-5000.

13. Kandasamy, K., Keerthikumar, S., Mathivanan, S., Patankar, N., Shafreen, B., Renuse, S., Pawar, H., Ramachandra, Y. L., Prasad, T. S. K., Acharya, P. K., Ranganathan, P., Chaerkady, R. and Pandey A. (2009). Human Proteinpedia: A unified discovery resource for proteomics research. Nucleic Acids Research. 37, D773-D781.

12. Harsha, H. C., Kandasamy, K., Ranganathan, P., Rani, S., Ramabadran, S., Gollapudi, S., Balakrishnan, L., Dwivedi, S. B., Telikicherla, D., Selvan, L. D. N., Goel, R., Mathivanan, S., Marimuthu, A., Kashyap, M. K., Vizza, R. F., Mayer, R. J., DeCaprio, J. A., Srivastava, S., Hanash, S. M., Hruban, R. H. and Pandey, A. (2009). A compendium of potential biomarkers of pancreatic cancer. PLoS Medicine. 6, e1000046.

11. Prasad, T. S. K., Goel, R., Kandasamy, K., Keerthikumar, S., Mathivanan, S. et al. (2009). Human Protein Reference Database 2009 update. Nucleic Acids Research. 37, D767-D772.


2008

 


10. Mathivanan, S. and Pandey, A. (2008). Human Proteinpedia as a resource for clinical proteomics. Mol Cell Proteomics. 10, 2038-47.

9. Mathivanan, S., Ahmed, M. et al. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-7.


2007

 


8. Molina, H., Horn, D. M., Tang, N., Mathivanan, S. and Pandey, A. (2007). Global Proteomic Profiling of Phosphopeptides using Electron Transfer Dissociation Tandem Mass Spectrometry. Proceedings of the National Academy of Sciences, USA. 104, 2199-2204.

7. Amanchy, R., Periaswamy, B., Mathivanan, S., Reddy, R., Tattikota, S. G. and Pandey, A. (2007). A compendium of curated phosphorylation-based substrate and binding motifs. Nature Biotechnology. 25, 285-286.


2006

 


6. Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood, R., Ramachandra, Y. L. and Pandey, A. (2006). An Evaluation of Human Protein-Protein Interaction Data in the Public Domain. BMC Bioinformatics. 7, S19.

5. Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S., Sharma, S., Pinkert, S., Nagaraju, S., Periaswamy, B., Mishra, G., Nandakumar, K., Shen, B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J. S. and Pandey, A. (2006). Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nature Genetics. 3, 285-293.

4. Mishra, G., Mathivanan, S., Kumaran, K. et al. (2006). Human Protein Reference Database 2006 Update. Nucleic Acids Research. 34, D411-D414.


2005

 


3. Muthusamy, B., Hanumanthu, G., Reshmi, R., Sriranjini, S., Suresh, S., Rekha, B., Srinivas, D., Karthick, L., Vrushabendra, B. M., Sharma, S., Mishra, G., Rashmi, B. P., Kadekar, S., Chatterjee, P., Mangala, K. S., Shivashankar, H. N., Chandrika, K. N., Deshpande, N., Mathivanan, S., Kannabiran, N., et al. (2005). Plasma Proteome Database as a resource for proteomics research. Proteomics. 5, 3531-3536.

2. Bala, P., Georgantas, R. W., Sudhir, D., Mathivanan, S., Shanker, K., Vrushbendra, B. M., Civin, C. I., and Pandey, A. TAGmapper: A web-based tool for mapping SAGE tags. (2005). Gene. 364, 123-129.

1. Suresh, S., Mohan, S., Mishra, G., Hanumanthu, G., Mathivanan, S., Reddy, R. and Pandey, A. (2005). Proteomic resources: Integrating biomedical information in humans. Gene. 364, 13-18.