Publications

1. Devasahayam Arokia Balaya R, Sen P, Grant CW, Zenka R, Sappani M, Lakshmanan J, Athreya AP, Kandasamy RK, Pandey A, Byeon SK. An integrative multi-omics analysis reveals a multi-analyte signature of pancreatic ductal adenocarcinoma in serum. J Gastroenterol. 2025 Apr; 60 (4):496-511 Epub 2024 Dec 12
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2. Ham H, Isham CR, Ristagno EH, Correia C, Ennis SM, Kandasamy RK, Garapati K, Zhang C, Kohlhagen MC, Sadighi Akha E, Rodriguez-Quevedo MF, Schultz DF, Chen B, Boyce TG, Gregory SW, Kohorst MA, Dasari S, Murray DL, Halling KC, Kipp BR, Kumanovics A, Li H, Pandey A, Billadeau DD, Sadighi Akha AA. A novel dominant-negative variant of IRF8 in a mother and son: Clinical, phenotypic and biological characteristics. J Allergy Clin Immunol. 2025 Mar 8 Epub 2025 Mar 08
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3. Nisar M, Soman SP, Sreelan S, John L, Pinto SM, Kandasamy RK, Subbannayya Y, Prasad TSK, Kanekar S, Raju R, Devasahayam Arokia Balaya R. ProteoArk: A One-Pot Proteomics Data Analysis and Visualization Tool for Biologists. J Proteome Res. 2025 Mar 7; 24 (3):1008-1016 Epub 2025 Feb 10
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4. Zhang B, Orning P, Lehman JW, Dinis A, Torres-Ulloa L, Elling R, Kelliher MA, Bertin J, Proulx MK, Goguen JD, Ryan L, Kandasamy RK, Espevik T, Pai AA, Fitzgerald KA, Lien E. Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance. Proc Natl Acad Sci U S A. 2025 Feb 18; 122 (7):e2420802122 Epub 2025 Feb 13
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5. Fonseca R, Zhu YX, Bruins LA, Ahmann J, de Bonolo Campos C, Braggio E, Chen X, Arribas M, Darvish S, Welsh S, Meermeier E, Mangalaparthi KK, Kandasamy RK, Ahmann G, Wiedmeier-Nutor JE, Pandey A, Chesi M, Bergsagel PL, Fonseca R. Exploring BCL2 regulation and upstream signaling transduction in venetoclax resistance in multiple myeloma: potential avenues for therapeutic intervention. Blood Cancer J. 2025 Feb 5; 15 (1):10 Epub 2025 Feb 05
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6. Tang H, Yan H, Shivaram S, Lehman S, Sharma N, Smadbeck J, Zepeda-Mendoza C, Tian S, Asmann Y, Vachon C, Gaspar Maia A, Keats J, Bergsagel PL, Fonseca R, Stewart AK, Hsu JS, Kandasamy RK, Pandey A, Kaddoura MA, Maura F, Mitra A, Rajkumar SV, Kumar SK, Elhaik E, Braggio E, Baughn LB. Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14). Leukemia. 2025 Jan; 39 (1):42-50 Epub 2024 Oct 14
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7. Ramarajan MG, Parthasarathy KTS, Gaikwad KB, Joshi N, Garapati K, Kandasamy RK, Sharma J, Pandey A. Alterations in Hurler-Scheie Syndrome Revealed by Mass Spectrometry-Based Proteomics and Phosphoproteomics Analysis. OMICS. 2024 Nov; 28(11):548-562. Epub 2024 Oct 29.
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8. Najm R, Yavuz L, Jain R, El Naofal M, Ramaswamy S, Abuhammour W, Loney T, Nowotny N, Alsheikh-Ali A, Abou Tayoun A, Kandasamy RK. IFIH1 loss of function predisposes to inflammatory and SARS-CoV-2-related infectious diseases. Scand J Immunol. 2024 Aug; 100 (2):e13373 Epub 2024 May 16
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9. Mun DG, Bhat FA, Joshi N, Sandoval L, Ding H, Jain A, Peterson JA, Kang T, Pujari GP, Tomlinson JL, Budhraja R, Zenka RM, Kannan N, Kipp BR, Dasari S, Gaspar-Maia A, Smoot RL, Kandasamy RK, Pandey A. Diversity of post-translational modifications and cell signaling revealed by single cell and single organelle mass spectrometry. Commun Biol. 2024 Jul 19; 7(1):884.
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10. Bhat FA, Mangalaparthi KK, Ding H, Jain A, Hsu JS, Peterson JA, Zenka RM, Mun DG, Kandasamy RK, Pandey A. Exploration of Nitrotyrosine-Containing Proteins and Peptides by Antibody-Based Enrichment Strategies. Mol Cell Proteomics. 2024 Mar; 23 (3):100733 Epub 2024 Feb 10
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11. Joshi N, Garapati K, Ghose V, Kandasamy RK, Pandey A. Recent progress in mass spectrometry-based urinary proteomics. Clin Proteomics. 2024 Feb 22; 21 (1):14
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12. Garapati K, Ding H, Charlesworth MC, Kim Y, Zenka R, Saraswat M, Mun DG, Chavan S, Shingade A, Lucien F, Zhong J, Kandasamy RK, Pandey A. sBioSITe enables sensitive identification of the cell surface proteome through direct enrichment of biotinylated peptides. Clin Proteomics. 2023 Dec 5; 20 (1):56 Epub 2023 Dec 05
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13. Pinto SM, Subbannayya Y, Kim H, Hagen L, Gorna MW, Nieminen AI, Bjoras M, Espevik T, Kainov D, Kandasamy RK. Multi-OMICs landscape of SARS-CoV-2-induced host responses in human lung epithelial cells. iScience. 2023 Jan 20; 26 (1):105895 Epub 2022 Dec 28
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14. Kumar S, Balaya RDA, Kanekar S, Raju R, Prasad TSK, Kandasamy RK. Computational tools for exploring peptide-membrane interactions in gram-positive bacteria. Comput Struct Biotechnol J. 2023; 21:1995-2008. Epub 2023 Mar 02.
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15. Najm R, Hachim MY, Kandasamy RK. Divulging a Pleiotropic Role of Succinate Receptor SUCNR1 in Renal Cell Carcinoma Microenvironment. Cancers (Basel). 2022 Dec 9; 14 (24) Epub 2022 Dec 09
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16. Soorajkumar A, Alakraf E, Uddin M, Du Plessis SS, Alsheikh-Ali A, Kandasamy RK. Computational Analysis of Short Linear Motifs in the Spike Protein of SARS-CoV-2 Variants Provides Possible Clues into the Immune Hijack and Evasion Mechanisms of Omicron Variant. Int J Mol Sci. 2022 Aug 8; 23 (15) Epub 2022 Aug 08
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17. Rex DAB, Keshava Prasad TS, Kandasamy RK. Revisiting Regulated Cell Death Responses in Viral Infections. Int J Mol Sci. 2022 Jun 24; 23(13).
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18. Rex DAB, Deepak K, Vaid N, Dagamajalu S, Kandasamy RK, Flo TH, Keshava Prasad TS. A modular map of Bradykinin-mediated inflammatory signaling network. J Cell Commun Signal. 2022 Jun; 16(2):301-310. Epub 2021 Oct 29.
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19. Subbannayya Y, Bhatta A, Pinto SM, Fitzgerald KA, Kandasamy RK. Proteogenomics Analysis Reveals Novel Micropeptides in Primary Human Immune Cells Immuno. 2022; 2:283-292.
    
20. Omolaoye TS, Omolaoye VA, Kandasamy RK, Hachim MY, Du Plessis SS. Omics and Male Infertility: Highlighting the Application of Transcriptomic Data. Life (Basel). 2022 Feb 14; 12 (2)
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21. Jalaleddine N, Hachim M, Al-Hroub H, Saheb Sharif-Askari N, Senok A, Elmoselhi A, Mahboub B, Samuel Kurien NM, Kandasamy RK, Semreen MH, Halwani R, Soares NC, Al Heialy S. N6-Acetyl-L-Lysine and p-Cresol as Key Metabolites in the Pathogenesis of COVID-19 in Obese Patients. Front Immunol. 2022; 13:827603 Epub 2022 May 19
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22. Rex DAB, Dagamajalu S, Kandasamy RK, Raju R, Prasad TSK. SARS-CoV-2 signaling pathway map: A functional landscape of molecular mechanisms in COVID-19. J Cell Commun Signal. 2021 Dec; 15(4):601-608. Epub 2021 Jun 28.
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23. Nassir N, Tambi R, Bankapur A, Al Heialy S, Karuvantevida N, Khansaheb HH, Zehra B, Begum G, Hameid RA, Ahmed A, Deesi Z, Alkhajeh A, Uddin KMF, Akter H, Safizadeh Shabestari SA, Almidani O, Islam A, Gaudet M, Kandasamy RK, Loney T, Tayoun AA, Nowotny N, Woodbury-Smith M, Rahman P, Kuebler WM, Yaseen Hachim M, Casanova JL, Berdiev BK, Alsheikh-Ali A, Uddin M. Single-cell transcriptome identifies FCGR3B upregulated subtype of alveolar macrophages in patients with critical COVID-19. iScience. 2021 Sep 24; 24 (9):103030 Epub 2021 Aug 25
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24. Pinto SM, Kim H, Subbannayya Y, Giambelluca MS, Bosl K, Ryan L, Sharma A, Kandasamy RK. Comparative Proteomic Analysis Reveals Varying Impact on Immune Responses in Phorbol 12-Myristate-13-Acetate-Mediated THP-1 Monocyte-to-Macrophage Differentiation. Front Immunol. 2021; 12:679458 Epub 2021 June 21
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25. Kim H, Subbannayya Y, Humphries F, Skejsol A, Pinto SM, Giambelluca M, Espevik T, Fitzgerald KA, Kandasamy RK. UMP-CMP kinase 2 gene expression in macrophages is dependent on the IRF3-IFNAR signaling axis. PLoS One. 2021; 16 (10):e0258989 Epub 2021 Oct 27
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26. Subbannayya Y, Haug M, Pinto SM, Mohanty V, Meas HZ, Flo TH, Prasad TSK, Kandasamy RK. The Proteomic Landscape of Resting and Activated CD4+ T Cells Reveal Insights into Cell Differentiation and Function. Int J Mol Sci. 2020 Dec 29; 22 (1)
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27. Agarwal S, Vierbuchen T, Ghosh S, Chan J, Jiang Z, Kandasamy RK, Ricci E, Fitzgerald KA. The long non-coding RNA LUCAT1 is a negative feedback regulator of interferon responses in humans. Nat Commun. 2020 Dec 11; 11 (1):6348
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28. Rex DAB, Agarwal N, Prasad TSK, Kandasamy RK, Subbannayya Y, Pinto SM. A comprehensive pathway map of IL-18-mediated signalling. J Cell Commun Signal. 2020 Jun; 14(2):257-266. Epub 2019 Dec 20.
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29. Girardi E, Cesar-Razquin A, Lindinger S, Papakostas K, Konecka J, Hemmerich J, Kickinger S, Kartnig F, Gurtl B, Klavins K, Sedlyarov V, Ingles-Prieto A, Fiume G, Koren A, Lardeau CH, Kumaran Kandasamy R, Kubicek S, Ecker GF, Superti-Furga G. A widespread role for SLC transmembrane transporters in resistance to cytotoxic drugs. Nat Chem Biol. 2020 Apr; 16 (4):469-478 Epub 2020 Mar 09
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30. Subbannayya Y, Pinto SM, Bosl K, Prasad TSK, Kandasamy RK. Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling. Int J Mol Sci. 2019 Apr 27; 20 (9)
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31. Skjesol A, Yurchenko M, Bosl K, Gravastrand C, Nilsen KE, Grovdal LM, Agliano F, Patane F, Lentini G, Kim H, Teti G, Kumar Sharma A, Kandasamy RK, Sporsheim B, Starheim KK, Golenbock DT, Stenmark H, McCaffrey M, Espevik T, Husebye H. The TLR4 adaptor TRAM controls the phagocytosis of Gram-negative bacteria by interacting with the Rab11-family interacting protein 2. PLoS Pathog. 2019 Mar; 15 (3):e1007684 Epub 2019 Mar 18
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32. Bosl K, Ianevski A, Than TT, Andersen PI, Kuivanen S, Teppor M, Zusinaite E, Dumpis U, Vitkauskiene A, Cox RJ, Kallio-Kokko H, Bergqvist A, Tenson T, Merits A, Oksenych V, Bjoras M, Anthonsen MW, Shum D, Kaarbo M, Vapalahti O, Windisch MP, Superti-Furga G, Snijder B, Kainov D, Kandasamy RK. Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis. Front Immunol. 2019; 10:2186 Epub 2019 Oct 04
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33. Karonitsch T, Kandasamy RK, Kartnig F, Herdy B, Dalwigk K, Niederreiter B, Holinka J, Sevelda F, Windhager R, Bilban M, Weichhart T, Saemann M, Pap T, Steiner G, Smolen JS, Kiener HP, Superti-Furga G. mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation. Cell Rep. 2018 May 15; 23 (7):2157-2167
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34. Yurchenko M, Skjesol A, Ryan L, Richard GM, Kandasamy RK, Wang N, Terhorst C, Husebye H, Espevik T. SLAMF1 is required for TLR4-mediated TRAM-TRIF-dependent signaling in human macrophages. J Cell Biol. 2018 Apr 2; 217 (4):1411-1429 Epub 2018 Feb 12
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35. Lee SE, Song J, Bosl K, Muller AC, Vitko D, Bennett KL, Superti-Furga G, Pandey A, Kandasamy RK, Kim MS. Proteogenomic Analysis to Identify Missing Proteins from Haploid Cell Lines. Proteomics. 2018 Apr; 18 (8):e1700386
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36. Bosl K, Giambelluca M, Haug M, Bugge M, Espevik T, Kandasamy RK, Bergstrom B. Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response. Front Physiol. 2018; 9:618 Epub 2018 May 29
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37. Hansen MD, Johnsen IB, Stiberg KA, Sherstova T, Wakita T, Richard GM, Kandasamy RK, Meurs EF, Anthonsen MW. Hepatitis C virus triggers Golgi fragmentation and autophagy through the immunity-related GTPase M. Proc Natl Acad Sci U S A. 2017 Apr 25; 114 (17):E3462-E3471 Epub 2017 Apr 07
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38. Bigenzahn JW, Fauster A, Rebsamen M, Kandasamy RK, Scorzoni S, Vladimer GI, Muller AC, Gstaiger M, Zuber J, Bennett KL, Superti-Furga G. An Inducible Retroviral Expression System for Tandem Affinity Purification Mass-Spectrometry-Based Proteomics Identifies Mixed Lineage Kinase Domain-like Protein (MLKL) as an Heat Shock Protein 90 (HSP90) Client. Mol Cell Proteomics. 2016 Mar; 15 (3):1139-50
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39. Kandasamy RK, Vladimer GI, Snijder B, Muller AC, Rebsamen M, Bigenzahn JW, Moskovskich A, Sabler M, Stefanovic A, Scorzoni S, Bruckner M, Penz T, Cleary C, Kralovics R, Colinge J, Bennett KL, Superti-Furga G. A time-resolved molecular map of the macrophage response to VSV infection. NPJ Syst Biol Appl. 2016; 2:16027 Epub 2016 Oct 27
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40. Bhattacharya A, Hegazy AN, Deigendesch N, Kosack L, Cupovic J, Kandasamy RK, Hildebrandt A, Merkler D, Kuhl AA, Vilagos B, Schliehe C, Panse I, Khamina K, Baazim H, Arnold I, Flatz L, Xu HC, Lang PA, Aderem A, Takaoka A, Superti-Furga G, Colinge J, Ludewig B, Lohning M, Bergthaler A. Superoxide Dismutase 1 Protects Hepatocytes from Type I Interferon-Driven Oxidative Damage. Immunity. 2015 Nov 17; 43 (5):974-86
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41. Heinz LX, Baumann CL, Koberlin MS, Snijder B, Gawish R, Shui G, Sharif O, Aspalter IM, Muller AC, Kandasamy RK, Breitwieser FP, Pichlmair A, Bruckner M, Rebsamen M, Bluml S, Karonitsch T, Fauster A, Colinge J, Bennett KL, Knapp S, Wenk MR, Superti-Furga G. The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity. Cell Rep. 2015 Jun 30; 11 (12):1919-28 Epub 2015 June 18
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42. Rebsamen M, Pochini L, Stasyk T, de Araujo ME, Galluccio M, Kandasamy RK, Snijder B, Fauster A, Rudashevskaya EL, Bruckner M, Scorzoni S, Filipek PA, Huber KV, Bigenzahn JW, Heinz LX, Kraft C, Bennett KL, Indiveri C, Huber LA, Superti-Furga G. SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature. 2015 Mar 26; 519 (7544):477-81 Epub 2015 Jan 07
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43. Schliehe C, Flynn EK, Vilagos B, Richson U, Swaminanthan S, Bosnjak B, Bauer L, Kandasamy RK, Griesshammer IM, Kosack L, Schmitz F, Litvak V, Sissons J, Lercher A, Bhattacharya A, Khamina K, Trivett AL, Tessarollo L, Mesteri I, Hladik A, Merkler D, Kubicek S, Knapp S, Epstein MM, Symer DE, Aderem A, Bergthaler A. The methyltransferase Setdb2 mediates virus-induced susceptibility to bacterial superinfection. Nat Immunol. 2015 Jan; 16 (1):67-74 Epub 2014 Nov 24
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44. Winter GE, Radic B, Mayor-Ruiz C, Blomen VA, Trefzer C, Kandasamy RK, Huber KVM, Gridling M, Chen D, Klampfl T, Kralovics R, Kubicek S, Fernandez-Capetillo O, Brummelkamp TR, Superti-Furga G. The solute carrier SLC35F2 enables YM155-mediated DNA damage toxicity. Nat Chem Biol. 2014 Sep; 10 (9):768-773 Epub 2014 July 27
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45. Snijder B, Kandasamy RK, Superti-Furga G. Toward effective sharing of high-dimensional immunology data. Nat Biotechnol. 2014 Aug; 32 (8):755-9
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46. Rebsamen M, Kandasamy RK, Superti-Furga G. Protein interaction networks in innate immunity. Trends Immunol. 2013 Dec; 34 (12):610-9 Epub 2013 July 02
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47. Pichlmair A, Kandasamy K, Alvisi G, Mulhern O, Sacco R, Habjan M, Binder M, Stefanovic A, Eberle CA, Goncalves A, Burckstummer T, Muller AC, Fauster A, Holze C, Lindsten K, Goodbourn S, Kochs G, Weber F, Bartenschlager R, Bowie AG, Bennett KL, Colinge J, Superti-Furga G. Viral immune modulators perturb the human molecular network by common and unique strategies. Nature. 2012 Jul 26; 487 (7408):486-90
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48. Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GS, Venugopal A, Sekhar NR, Kelkar DS, Nemade H, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A. A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani. Proteomics. 2012 Mar; 12(6):832-44.
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49. Chaerkady R, Kelkar DS, Muthusamy B, Kandasamy K, Dwivedi SB, Sahasrabuddhe NA, Kim MS, Renuse S, Pinto SM, Sharma R, Pawar H, Sekhar NR, Mohanty AK, Getnet D, Yang Y, Zhong J, Dash AP, MacCallum RM, Delanghe B, Mlambo G, Kumar A, Keshava Prasad TS, Okulate M, Kumar N, Pandey A. A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Res. 2011 Nov; 21(11):1872-81. Epub 2011 Jul 27.
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50. Goel R, Raju R, Maharudraiah J, Sameer Kumar GS, Ghosh K, Kumar A, Lakshmi TP, Sharma J, Sharma R, Balakrishnan L, Pan A, Kandasamy K, Christopher R, Krishna V, Mohan SS, Harsha HC, Mathur PP, Pandey A, Keshava Prasad TS. A Signaling Network of Thyroid-Stimulating Hormone. J Proteomics Bioinform. 2011 Oct 29; 4
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51. Pawar H, Kashyap MK, Sahasrabuddhe NA, Renuse S, Harsha HC, Kumar P, Sharma J, Kandasamy K, Marimuthu A, Nair B, Rajagopalan S, Maharudraiah J, Premalatha CS, Kumar KV, Vijayakumar M, Chaerkady R, Prasad TS, Kumar RV, Kumar RV, Pandey A. Quantitative tissue proteomics of esophageal squamous cell carcinoma for novel biomarker discovery. Cancer Biol Ther. 2011 Sep 15; 12(6):510-22.
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52. Kim MS, Zhong J, Kandasamy K, Delanghe B, Pandey A. Systematic evaluation of alternating CID and ETD fragmentation for phosphorylated peptides. Proteomics. 2011 Jun; 11(12):2568-72. Epub 2011 May 20.
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53. Zhong J, Chaerkady R, Kandasamy K, Gucek M, Cole RN, Pandey A. The interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. J Proteomics. 2011 Mar 01; 74(3):294-303. Epub 2010 Nov 13.
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54. Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform. 2011; 4 (2):22-35
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55. Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome. Cancer Biol Ther. 2010 Oct 15; 10(8):796-810.
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56. Yang Y, Chaerkady R, Kandasamy K, Huang TC, Selvan LD, Dwivedi SB, Kent OA, Mendell JT, Pandey A. Identifying targets of miR-143 using a SILAC-based proteomic approach. Mol Biosyst. 2010 Oct; 6(10):1873-82. Epub 2010 Jun 14.
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57. Kim MS, Kandasamy K, Chaerkady R, Pandey A. Assessment of resolution parameters for CID-based shotgun proteomic experiments on the LTQ-Orbitrap mass spectrometer. J Am Soc Mass Spectrom. 2010 Sep; 21(9):1606-11. Epub 2010 Apr 24.
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58. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. The BioPAX community standard for pathway data sharing. Nat Biotechnol. 2010 Sep; 28(9):935-42. Epub 2010 Sep 09.
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59. Chaerkady R, Kerr CL, Kandasamy K, Marimuthu A, Gearhart JD, Pandey A. Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells. Proteomics. 2010 Apr; 10(7):1359-73.
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60. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010 Jan 12; 11(1):R3.
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61. Keerthikumar S, Bhadra S, Kandasamy K, Raju R, Ramachandra YL, Bhattacharyya C, Imai K, Ohara O, Mohan S, Pandey A. Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. DNA Res. 2009 Dec; 16(6):345-51. Epub 2009 Oct 03.
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62. Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S, Pandey A. PathBuilder--open source software for annotating and developing pathway resources. Bioinformatics. 2009 Nov 01; 25(21):2860-2. Epub 2009 Jul 23.
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63. Kandasamy K, Pandey A, Molina H. Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem. 2009 Sep 01; 81(17):7170-80.
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64. Harsha HC, Kandasamy K, Ranganathan P, Rani S, Ramabadran S, Gollapudi S, Balakrishnan L, Dwivedi SB, Telikicherla D, Selvan LD, Goel R, Mathivanan S, Marimuthu A, Kashyap M, Vizza RF, Mayer RJ, Decaprio JA, Srivastava S, Hanash SM, Hruban RH, Pandey A. A compendium of potential biomarkers of pancreatic cancer. PLoS Med. 2009 Apr 07; 6(4):e1000046.
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65. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database--2009 update. Nucleic Acids Res. 2009 Jan; 37(Database issue):D767-72. Epub 2008 Nov 06.
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66. Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A, Ohara O, Mohan S. RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic Acids Res. 2009 Jan; 37 (Database issue):D863-7 Epub 2008 Oct 08
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67. Prasad TS, Kandasamy K, Pandey A. Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology. Methods Mol Biol. 2009; 577:67-79.
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68. Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S, Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS, Pandey A. Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic Acids Res. 2009 Jan; 37(Database issue):D773-81. Epub 2008 Oct 23.
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69. Molina H, Matthiesen R, Kandasamy K, Pandey A. Comprehensive comparison of collision induced dissociation and electron transfer dissociation. Anal Chem. 2008 Jul 01; 80(13):4825-35. Epub 2008 Jun 10.
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