Nandan Deshpande

Research Associate

PUBLICATIONS

Journal articles
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Li Y; Alhendi AMN; Yeh M-C; Elahy M; Santiago FS; Deshpande NP; Wu B; Chan E; Inam S; Prado-Lourenco L; Marchand J; Joyce RD; Wilkinson-White LE; Raftery MJ; Zhu M; Adamson SJ; Barnat F; Viaud-Quentric K; Sockler J; Mackay JP; Chang A; Mitchell P; Marcuccio SM; Khachigian LM, 2020, 'Thermostable small-molecule inhibitor of angiogenesis and vascular permeability that suppresses a pERK-FosB/Delta FosB-VCAM-1 axis', SCIENCE ADVANCES, vol. 6, http://dx.doi.org/10.1126/sciadv.aaz7815
2020
Bayat A; Deshpande NP; Wilkins MR; Parameswaran S, 2020, 'Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach', IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 17, pp. 334 - 338, http://dx.doi.org/10.1109/TCBB.2018.2875479
2020
Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 2020, 'RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia', Clinical cancer research : an official journal of the American Association for Cancer Research, vol. 26, pp. 3597 - 3607, http://dx.doi.org/10.1158/1078-0432.CCR-20-0184
2020
Uthicke S; Deshpande NP; Liddy M; Patel F; Lamare M; Wilkins MR, 2019, 'Little evidence of adaptation potential to ocean acidification in sea urchins living in “Future Ocean” conditions at a CO2 vent', Ecology and Evolution, vol. 9, pp. 10004 - 10016, http://dx.doi.org/10.1002/ece3.5563
2019
Paramsothy S; Nielsen S; Kamm MA; Deshpande NP; Faith JJ; Clemente JC; Paramsothy R; Walsh AJ; van den Bogaerde J; Samuel D; Leong RWL; Connor S; Ng W; Lin E; Borody TJ; Wilkins MR; Colombel JF; Mitchell HM; Kaakoush NO, 2019, 'Specific Bacteria and Metabolites Associated With Response to Fecal Microbiota Transplantation in Patients With Ulcerative Colitis', Gastroenterology, vol. 156, pp. 1440 - 1454.e2, http://dx.doi.org/10.1053/j.gastro.2018.12.001
2019
Holland SI; Edwards RJ; Ertan H; Wong YK; Russell TL; Deshpande NP; Manefield MJ; Lee M, 2019, 'Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture', PeerJ, vol. 2019, http://dx.doi.org/10.7717/peerj.7775
2019
Deshpande NP; Riordan SM; Castaño-Rodríguez N; Wilkins MR; Kaakoush NO, 2018, 'Signatures within the esophageal microbiome are associated with host genetics, age, and disease', Microbiome, vol. 6, pp. 227, http://dx.doi.org/10.1186/s40168-018-0611-4
2018
Hudson J; Gardiner M; Deshpande N; Egan S, 2018, 'Transcriptional response of Nautella italica R11 towards its macroalgal host uncovers new mechanisms of host–pathogen interaction', Molecular Ecology, vol. 27, pp. 1820 - 1832, http://dx.doi.org/10.1111/mec.14448
2018
Waters SA; McAteer SP; Kudla G; Pang I; Deshpande NP; Amos TG; Leong KW; Wilkins MR; Strugnell R; Gally DL; Tollervey D; Tree JJ, 2017, 'Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E', EMBO Journal, vol. 36, pp. 374 - 387, http://dx.doi.org/10.15252/embj.201694639
2017
Unnikrishnan A; Papaemmanuil E; Beck D; Deshpande NP; Verma A; Kumari A; Woll PS; Richards LA; Knezevic K; Chandrakanthan V; Thoms JAI; Tursky ML; Huang Y; Ali Z; Olivier J; Galbraith S; Kulasekararaj AG; Tobiasson M; Karimi M; Pellagatti A; Wilson SR; Lindeman R; Young B; Ramakrishna R; Arthur C; Stark R; Crispin P; Curnow J; Warburton P; Roncolato F; Boultwood J; Lynch K; Jacobsen SEW; Mufti GJ; Hellstrom-Lindberg E; Wilkins MR; MacKenzie KL; Wong JWH; Campbell PJ; Pimanda JE, 2017, 'Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes', Cell Reports, vol. 20, pp. 572 - 585, http://dx.doi.org/10.1016/j.celrep.2017.06.067
2017
Taha ; Siddiqui KS; Campanaro S; Najnin T; Deshpande N; Williams TJ; Aldrich-Wright J; Wilkins M; Curmi PMG; Cavicchioli R, 2016, 'Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii', Environmental microbiology, vol. 18, pp. 2810 - 2824, http://dx.doi.org/10.1111/1462-2920.13229
2016
Tan MK; Raman H; Chambers G; Sharma I; Chen Z; Deshpande N; Wilkins MR, 2016, 'Characterization of SNP and structural variations in the mitochondrial genomes of Tilletia indica and its closely related species formed basis for a simple diagnostic assay', PLoS ONE, vol. 11, http://dx.doi.org/10.1371/journal.pone.0166086
2016
Deshpande NP; Wilkins MR; Castaño-Rodríguez N; Bainbridge E; Sodhi N; Riordan SM; Mitchell HM; Kaakoush NO, 2016, 'Campylobacter concisus pathotypes induce distinct global responses in intestinal epithelial cells', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep34288
2016
Deshpande NP; Wilkins MR; Mitchell HM; Kaakoush NO, 2015, 'Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group', FEMS Microbiology Letters, vol. 362, http://dx.doi.org/10.1093/femsle/fnv193
2015
Kaakoush NO; Deshpande NP; Man SM; Burgos-Portugal JA; Khattak FA; Raftery MJ; Wilkins MR; Mitchell HM, 2015, 'Transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen Campylobacter concisus', Infection and Immunity, vol. 83, pp. 832 - 845, http://dx.doi.org/10.1128/IAI.03012-14
2015
Gilchrist AS; Shearman DCA; Frommer M; Raphael KA; Deshpande NP; Wilkins MR; Sherwin WB; Sved JA, 2014, 'The draft genome of the pest tephritid fruit fly Bactrocera tryoni: Resources for the genomic analysis of hybridising species', BMC Genomics, vol. 15, http://dx.doi.org/10.1186/1471-2164-15-1153
2014
Pang CNI; Tay AP; Aya C; Twine NA; Harkness L; Hart-Smith G; Chia SZ; Chen Z; Deshpande NP; Kaakoush NO; Mitchell HM; Kassem M; Wilkins MR, 2014, 'Tools to covisualize and coanalyze proteomic data with genomes and transcriptomes: Validation of genes and Alternative mRNA splicing', Journal of Proteome Research, vol. 13, pp. 84 - 98, http://dx.doi.org/10.1021/pr400820p
2014
Gilchrist AS; Shearman DCA; Frommer M; Raphael KA; Deshpande NP; Wilkins MR; Sherwin WB; Sved JA, 2014, 'The draft genome of the pest tephritid fruit fly Bactrocera tryoni: Resources for the genomic analysis of hybridising species', BMC Genomics, pp. 1 - 17, http://dx.doi.org/10.1186/1471-2164-15-1153
2014
Tay AP; Kaakoush NO; Deshpande NP; Chen Z; Mitchell H; Wilkins MR, 2013, 'Genome sequence of Campylobacter showae UNSWCD, isolated from a patient with Crohn's disease', Genome Announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.00193-12
2013
Deshpande NP; Wong YK; Manefield M; Wilkins MR; Lee M, 2013, 'Genome sequence of Dehalobacter UNSWDHB, a chloroform-dechlorinating bacterium', Genome Announcements, vol. 1, http://dx.doi.org/10.1128/genomeA.e00720-13
2013
Deshpande NP; Wong YK; Manefield M; Wilkins MR; Lee M, 2013, 'Genome Sequence of Dehalobacter UNSWDHB, a Chloroform-Dechlorinating Bacterium.', Genome Announc, vol. 1, http://dx.doi.org/10.1128/genomeA.00720-13
2013
Deshpande NP; Kaakoush NO; Wilkins MR; Mitchell HM, 2013, 'Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association', BMC Genomics, vol. 14, http://dx.doi.org/10.1186/1471-2164-14-585
2013
Kubicek CP; Herrera-Estrella A; Seidl-Seiboth V; Martinez DA; Druzhinina IS; Thon M; Zeilinger S; Casas-Flores S; Horwitz BA; Mukherjee PK; Mukherjee M; Kredics L; Alcaraz LD; Aerts A; Antal Z; Atanasova L; Cervantes-Badillo MG; Challacombe J; Chertkov O; McCluskey K; Coulpier F; Deshpande N; von Döhren H; Ebbole DJ; Esquivel-Naranjo EU; Fekete E; Flipphi M; Glaser F; Gómez-Rodríguez EY; Gruber S; Han C; Henrissat B; Hermosa R; Hernández-Oñate M; Karaffa L; Kosti I; Le Crom S; Lindquist E; Lucas S; Lübeck M; Lübeck PS; Margeot A; Metz B; Misra M; Nevalainen H; Omann M; Packer N; Perrone G; Uresti-Rivera EE; Salamov A; Schmoll M; Seiboth B; Shapiro H; Sukno S; Tamayo-Ramos JA; Tisch D; Wiest A; Wilkinson HH; Zhang M; Coutinho PM; Kenerley CM; Monte E; Baker SE; Grigoriev IV, 2011, 'Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma', Genome Biology, vol. 12, pp. R40 - R40, http://dx.doi.org/10.1186/gb-2011-12-4-r40
2011
Kaakoush NO; Deshpande NP; Wilkins MR; Tan C; Burgos-Portugal J; Raftery MJ; Day AS; Lemberg DA; Mitchell HM, 2011, 'The pathogenic potential of campylobacter concisus strains associated with chronic intestinal diseases', PLoS One, vol. 6, pp. e29045, http://dx.doi.org/10.1371/journal.pone.0029045
2011
Deshpande NP; Kaakoush NO; Mitchell HM; Janitz K; Raftery MJ; Li SS; Wilkins MR, 2011, 'Sequencing and validation of the genome of a Campylobacter concisus reveals intra-species diversity', PLoS ONE, vol. 6, pp. e22170, http://dx.doi.org/10.1371/journal.pone/0022170
2011
Kaakoush NO; Deshpande N; Wilkins MR; Raftery MJ; Janitz K; Mitchell HM, 2011, 'Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species.', Gut Pathogens, vol. 3, pp. 15, http://dx.doi.org/10.1186/1757-4749-3-15
2011
Deshpande N; Jensen PH; Packer NH; Kolarich D, 2010, 'GlycoSpectrumScan: Fishing Glycopeptides from MS Spectra of Protease Digests of Human Colostrum sIgA', Journal of Proteome Research, vol. 9, pp. 1063 - 1075, http://dx.doi.org/10.1021/pr900956x
2010
Deshpande N; Wilkins MR; Packer N; Nevalainen H, 2008, 'Protein glycosylation pathways in filamentous fungi', Glycobiology, vol. 18, pp. 626 - 637, http://dx.doi.org/10.1093/glycob/cwn044
2008
Nagaraj SH; Deshpande N; Gasser RB; Ranganathan S, 2007, 'ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform', Nucleic Acids Research, vol. 35, pp. W143 - W147, http://dx.doi.org/10.1093/nar/gkm378
2007
Mishra GR, 2006, 'Human protein reference database--2006 update', Nucleic Acids Research, vol. 34, pp. D411 - D414, http://dx.doi.org/10.1093/nar/gkj141
2006
Gandhi TKB; Zhong J; Mathivanan S; Karthick L; Chandrika KN; Mohan SS; Sharma S; Pinkert S; Nagaraju S; Periaswamy B; Mishra G; Nandakumar K; Shen B; Deshpande N; Nayak R; Sarker M; Boeke JD; Parmigiani G; Schultz J; Bader JS; Pandey A, 2006, 'Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets', Nature Genetics, vol. 38, pp. 285 - 293, http://dx.doi.org/10.1038/ng1747
2006
Muthusamy B; Hanumanthu G; Suresh S; Rekha B; Srinivas D; Karthick L; Vrushabendra BM; Sharma S; Mishra G; Chatterjee P; Mangala KS; Shivashankar HN; Chandrika KN; Deshpande N; Suresh M; Kannabiran N; Niranjan V; Nalli A; Prasad TSK; Arun KS; Reddy R; Chandran S; Jadhav T; Julie D; Mahesh M; John SL; Palvankar K; Sudhir D; Bala P; Rashmi NS; Vishnupriya G; Dhar K; Reshma S; Chaerkady R; Gandhi TKB; Harsha HC; Mohan SS; Deshpande KS; Sarker M; Pandey A, 2005, 'Plasma Proteome Database as a resource for proteomics research', PROTEOMICS, vol. 5, pp. 3531 - 3536, http://dx.doi.org/10.1002/pmic.200401335
2005
Harsha HC; Suresh S; Amanchy R; Deshpande N; Shanker K; Yatish AJ; Muthusamy B; Vrushabendra BM; Rashmi BP; Chandrika KN; Padma N; Sharma S; Badano JL; Ramya MA; Shivashankar HN; Peri S; Choudhury DR; Kavitha MP; Saravana R; Niranjan V; Gandhi TKB; Ghosh N; Chandran S; Menezes M; Joy M; Mohan SS; Katsanis N; Deshpande KS; Raghothama C; Prasad CK; Pandey A, 2005, 'A manually curated functional annotation of the human X chromosome', Nature Genetics, vol. 37, pp. 331 - 332, http://dx.doi.org/10.1038/ng0405-331
2005
Peri S, 2004, 'Human protein reference database as a discovery resource for proteomics', Nucleic Acids Research, vol. 32, pp. 497D - 501, http://dx.doi.org/10.1093/nar/gkh070
2004
Rhodes DR; Yu J; Shanker K; Deshpande N; Varambally R; Ghosh D; Barrette T; Pander A; Chinnaiyan AM, 2004, 'ONCOMINE: A Cancer Microarray Database and Integrated Data-Mining Platform', Neoplasia, vol. 6, pp. 1 - 6, http://dx.doi.org/10.1016/s1476-5586(04)80047-2
2004
Rhodes DR; Yu J; Shanker K; Deshpande N; Varambally R; Ghosh D; Barrette T; Pandey A; Chinnaiyan AM, 2004, 'Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression', Proceedings of the National Academy of Sciences, vol. 101, pp. 9309 - 9314, http://dx.doi.org/10.1073/pnas.0401994101
2004
Peri S, 2003, 'Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans', Genome Research, vol. 13, pp. 2363 - 2371, http://dx.doi.org/10.1101/gr.1680803
2003
Anande G; Deshpande NP; Mareschal S; Batcha AMN; Hampton HR; Herold T; Lehmann S; Wilkins MR; Wong JWH; Unnikrishnan A; Pimanda JE, 'RNA splicing alterations induce a cellular stress response associated with poor prognosis in AML', , http://dx.doi.org/10.1101/2020.01.10.895714
Conference Papers
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Paramsothy S; Kamm MA; Nielsen S; Deshpande N; Faith J; Clemente JC; Paramsothy R; Walsh A; van den Bogaerde J; Samuel D; Leong RW; Connor SJ; Ng WSW; Lin E; Wilkins M; Colombel JF; Borody TJ; Mitchell HM; Kaakoush NO, 2018, 'IN FECAL MICROBIOTA TRANSPLANTATION (FMT) FOR ULCERATIVE COLITIS, FUSOBACTERIUM IS ASSOCIATED WITH LACK OF REMISSION, WHILE METABOLIC SHIFTS TO STARCH DEGRADATION AND SHORT CHAIN FATTY ACID PRODUCTION ARE ASSOCIATED WITH REMISSION - RESULTS FROM THE RANDOMIZED CONTROLLED FOCUS STUDY', in GASTROENTEROLOGY, W B SAUNDERS CO-ELSEVIER INC, Washington, DC, pp. S35 - S35, presented at Annual Meeting of the American-Society-for-Gastrointestinal-Endoscopy / Digestive Disease Week, Washington, DC, 02 June 2018 - 05 June 2018, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000450011100099&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
2018
Conference Abstracts
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Egan S; Kumar V; Zozaya-Valdes ; Gardiner ME; Hudson J; Deshpande N; Campbell A; Thomas T, 2017, 'BREAKING BAD: OPPORTUNISTIC BACTERIAL PATHOGENS OF SEAWEEDS', in PHYCOLOGIA, INT PHYCOLOGICAL SOC, Vol. 56, pp. 48 - 48, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000412892000098&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a
2017
Conference Posters
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Deshpande N; Wilkins M; Mitchell H; Kaakoush NO, 2016, 'SBRS 2016', Charles Perkins Centre, University of Sydney, presented at SBRS 2016, Charles Perkins Centre, University of Sydney, 22 July 2016 - 22 July 2016, http://www.abacbs.org/sbrs_2016/
2016
Deshpande N; Wilkins M; Mitchell H; Kaakoush N, 2016, 'Deciphering the role of Campylobacter concisus in host pathogenesis using multi-omics techniques', Charles Perkins Centre, University of Sydney, presented at SBRS 2016, Charles Perkins Centre, University of Sydney, 22 July 2016 - 22 July 2016
2016
Deshpande N, 2015, 'Novel genetic markers define a subgroup of pathogenic Escherichia coli strains belonging to the B2 phylogenetic group', Garvin Institute of Medical Research, Sydney, presented at ABACBS 2015, Garvin Institute of Medical Research, Sydney, 10 October 2015 - 11 October 2015, http://amsi.org.au/events/event/abacbs-conference-2015/
2015
Deshpande N; Pang I, 2014, 'Sequencing, assembly and comparative analysis of five strains of the fungal pathogen Cryptococcus gatti', NOVOTEL SYDNEY BRIGHTON BEACH, Sydney, presented at INCOB 2014, NOVOTEL SYDNEY BRIGHTON BEACH, Sydney, 31 July 2014 - 02 August 2014
2014
Kaakoush NO; Mitchell H; Wilkins M; Deshpande N, 2013, 'Comparative genomics of eight Campylobacter concisus isolates provides insights into pathogenesis', presented at Lorne Genome Conference 2013, 17 February 2013 - 19 February 2013
2013