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Items: 32

1.

A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping.

Sathyanarayanan A, Gupta R, Thompson EW, Nyholt DR, Bauer DC, Nagaraj SH.

Brief Bioinform. 2019 Nov 27. pii: bbz121. doi: 10.1093/bib/bbz121. [Epub ahead of print]

PMID:
31774481
2.

Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease.

Monkman JH, Thompson EW, Nagaraj SH.

Cancers (Basel). 2019 Nov 7;11(11). pii: E1745. doi: 10.3390/cancers11111745. Review.

3.

Multi-Omics Characterization of the Spontaneous Mesenchymal-Epithelial Transition in the PMC42 Breast Cancer Cell Lines.

Bhatia S, Monkman J, Blick T, Duijf PH, Nagaraj SH, Thompson EW.

J Clin Med. 2019 Aug 19;8(8). pii: E1253. doi: 10.3390/jcm8081253.

4.

Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer.

Bhatia S, Monkman J, Blick T, Pinto C, Waltham M, Nagaraj SH, Thompson EW.

J Clin Med. 2019 Jun 21;8(6). pii: E893. doi: 10.3390/jcm8060893.

5.

Transition states that allow cancer to spread.

Thompson EW, Nagaraj SH.

Nature. 2018 Apr;556(7702):442-444. doi: 10.1038/d41586-018-04403-x. No abstract available.

PMID:
29686367
6.

Targeting epithelial-mesenchymal plasticity in cancer: clinical and preclinical advances in therapy and monitoring.

Bhatia S, Monkman J, Toh AKL, Nagaraj SH, Thompson EW.

Biochem J. 2017 Sep 20;474(19):3269-3306. doi: 10.1042/BCJ20160782. Review.

PMID:
28931648
7.

Whole-genome landscape of pancreatic neuroendocrine tumours.

Scarpa A, Chang DK, Nones K, Corbo V, Patch AM, Bailey P, Lawlor RT, Johns AL, Miller DK, Mafficini A, Rusev B, Scardoni M, Antonello D, Barbi S, Sikora KO, Cingarlini S, Vicentini C, McKay S, Quinn MC, Bruxner TJ, Christ AN, Harliwong I, Idrisoglu S, McLean S, Nourse C, Nourbakhsh E, Wilson PJ, Anderson MJ, Fink JL, Newell F, Waddell N, Holmes O, Kazakoff SH, Leonard C, Wood S, Xu Q, Nagaraj SH, Amato E, Dalai I, Bersani S, Cataldo I, Dei Tos AP, Capelli P, Davì MV, Landoni L, Malpaga A, Miotto M, Whitehall VL, Leggett BA, Harris JL, Harris J, Jones MD, Humphris J, Chantrill LA, Chin V, Nagrial AM, Pajic M, Scarlett CJ, Pinho A, Rooman I, Toon C, Wu J, Pinese M, Cowley M, Barbour A, Mawson A, Humphrey ES, Colvin EK, Chou A, Lovell JA, Jamieson NB, Duthie F, Gingras MC, Fisher WE, Dagg RA, Lau LM, Lee M, Pickett HA, Reddel RR, Samra JS, Kench JG, Merrett ND, Epari K, Nguyen NQ, Zeps N, Falconi M, Simbolo M, Butturini G, Van Buren G, Partelli S, Fassan M; Australian Pancreatic Cancer Genome Initiative, Khanna KK, Gill AJ, Wheeler DA, Gibbs RA, Musgrove EA, Bassi C, Tortora G, Pederzoli P, Pearson JV, Waddell N, Biankin AV, Grimmond SM.

Nature. 2017 Mar 2;543(7643):65-71. doi: 10.1038/nature21063. Epub 2017 Feb 15. Erratum in: Nature. 2017 Sep 27;:.

PMID:
28199314
8.

Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer.

Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MC, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, Leong HS; Australian Ovarian Cancer Study Group, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Arnau GM, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJ, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DD.

Nature. 2015 Nov 19;527(7578):398. doi: 10.1038/nature15716. Epub 2015 Oct 21. No abstract available.

PMID:
26503049
9.

Whole-genome characterization of chemoresistant ovarian cancer.

Patch AM, Christie EL, Etemadmoghadam D, Garsed DW, George J, Fereday S, Nones K, Cowin P, Alsop K, Bailey PJ, Kassahn KS, Newell F, Quinn MC, Kazakoff S, Quek K, Wilhelm-Benartzi C, Curry E, Leong HS; Australian Ovarian Cancer Study Group, Hamilton A, Mileshkin L, Au-Yeung G, Kennedy C, Hung J, Chiew YE, Harnett P, Friedlander M, Quinn M, Pyman J, Cordner S, O'Brien P, Leditschke J, Young G, Strachan K, Waring P, Azar W, Mitchell C, Traficante N, Hendley J, Thorne H, Shackleton M, Miller DK, Arnau GM, Tothill RW, Holloway TP, Semple T, Harliwong I, Nourse C, Nourbakhsh E, Manning S, Idrisoglu S, Bruxner TJ, Christ AN, Poudel B, Holmes O, Anderson M, Leonard C, Lonie A, Hall N, Wood S, Taylor DF, Xu Q, Fink JL, Waddell N, Drapkin R, Stronach E, Gabra H, Brown R, Jewell A, Nagaraj SH, Markham E, Wilson PJ, Ellul J, McNally O, Doyle MA, Vedururu R, Stewart C, Lengyel E, Pearson JV, Waddell N, deFazio A, Grimmond SM, Bowtell DD.

Nature. 2015 May 28;521(7553):489-94. doi: 10.1038/nature14410. Erratum in: Nature. 2015 Nov 19;527(7578):398.

PMID:
26017449
10.

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.

Nagaraj SH, Waddell N, Madugundu AK, Wood S, Jones A, Mandyam RA, Nones K, Pearson JV, Grimmond SM.

J Proteome Res. 2015 May 1;14(5):2255-66. doi: 10.1021/acs.jproteome.5b00029. Epub 2015 Apr 17.

PMID:
25760677
11.

Cloning and tissue distribution of novel splice variants of the ovine ghrelin gene.

Menzies M, Seim I, Josh P, Nagaraj SH, Lees M, Walpole C, Chopin LK, Colgrave M, Ingham A.

BMC Vet Res. 2014 Sep 6;10:211. doi: 10.1186/s12917-014-0211-x.

12.

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D.

Mol Cell Proteomics. 2013 Nov;12(11):3388-97. doi: 10.1074/mcp.M112.027169. Epub 2013 Jul 23.

13.

Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors.

Fortes MR, Snelling WM, Reverter A, Nagaraj SH, Lehnert SA, Hawken RJ, DeAtley KL, Peters SO, Silver GA, Rincon G, Medrano JF, Islas-Trejo A, Thomas MG.

J Anim Sci. 2012 Sep;90(9):2894-906. doi: 10.2527/jas.2011-4601. Epub 2012 Jun 27.

PMID:
22739780
14.

Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep.

Nagaraj SH, Harsha HC, Reverter A, Colgrave ML, Sharma R, Andronicos N, Hunt P, Menzies M, Lees MS, Sekhar NR, Pandey A, Ingham A.

J Proteomics. 2012 Apr 3;75(7):2141-52. doi: 10.1016/j.jprot.2012.01.016. Epub 2012 Jan 25.

PMID:
22285630
15.

Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.

Hudson NJ, Gu Q, Nagaraj SH, Ding YS, Dalrymple BP, Reverter A.

PLoS One. 2011;6(9):e25457. doi: 10.1371/journal.pone.0025457. Epub 2011 Sep 23.

16.

A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle.

Fortes MR, Reverter A, Nagaraj SH, Zhang Y, Jonsson NN, Barris W, Lehnert S, Boe-Hansen GB, Hawken RJ.

J Anim Sci. 2011 Jun;89(6):1669-83. doi: 10.2527/jas.2010-3681. Epub 2011 Feb 25.

PMID:
21357453
17.
18.

Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle.

De Jager N, Hudson NJ, Reverter A, Wang YH, Nagaraj SH, Cafe LM, Greenwood PL, Barnard RT, Kongsuwan KP, Dalrymple BP.

Physiol Genomics. 2011 May 13;43(9):467-78. doi: 10.1152/physiolgenomics.00226.2010. Epub 2011 Feb 15.

PMID:
21325062
19.

Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle.

Gu Q, Nagaraj SH, Hudson NJ, Dalrymple BP, Reverter A.

BMC Genomics. 2011 Jan 12;12:23. doi: 10.1186/1471-2164-12-23.

20.

The interplay between evolution, regulation and tissue specificity in the Human Hereditary Diseasome.

Nagaraj SH, Ingham A, Reverter A.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S23. doi: 10.1186/1471-2164-11-S4-S23.

21.

Association weight matrix for the genetic dissection of puberty in beef cattle.

Fortes MR, Reverter A, Zhang Y, Collis E, Nagaraj SH, Jonsson NN, Prayaga KC, Barris W, Hawken RJ.

Proc Natl Acad Sci U S A. 2010 Aug 3;107(31):13642-7. doi: 10.1073/pnas.1002044107. Epub 2010 Jul 19.

22.

The evolution of tropical adaptation: comparing taurine and zebu cattle.

Chan EK, Nagaraj SH, Reverter A.

Anim Genet. 2010 Oct;41(5):467-77. doi: 10.1111/j.1365-2052.2010.02053.x.

PMID:
20477791
23.

Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data.

Reverter A, Hudson NJ, Nagaraj SH, Pérez-Enciso M, Dalrymple BP.

Bioinformatics. 2010 Apr 1;26(7):896-904. doi: 10.1093/bioinformatics/btq051. Epub 2010 Feb 9.

PMID:
20144946
24.
25.

Proteomics analysis of the excretory/secretory component of the blood-feeding stage of the hookworm, Ancylostoma caninum.

Mulvenna J, Hamilton B, Nagaraj SH, Smyth D, Loukas A, Gorman JJ.

Mol Cell Proteomics. 2009 Jan;8(1):109-21. doi: 10.1074/mcp.M800206-MCP200. Epub 2008 Aug 26.

26.

High-throughput functional annotation and data mining with the Blast2GO suite.

Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A.

Nucleic Acids Res. 2008 Jun;36(10):3420-35. doi: 10.1093/nar/gkn176. Epub 2008 Apr 29.

27.
28.

Transcriptional changes in the hookworm, Ancylostoma caninum, during the transition from a free-living to a parasitic larva.

Datu BJ, Gasser RB, Nagaraj SH, Ong EK, O'Donoghue P, McInnes R, Ranganathan S, Loukas A.

PLoS Negl Trop Dis. 2008 Jan 9;2(1):e130. doi: 10.1371/journal.pntd.0000130.

29.

A transcriptomic analysis of the adult stage of the bovine lungworm, Dictyocaulus viviparus.

Ranganathan S, Nagaraj SH, Hu M, Strube C, Schnieder T, Gasser RB.

BMC Genomics. 2007 Sep 5;8:311.

30.

Gender-enriched transcripts in Haemonchus contortus--predicted functions and genetic interactions based on comparative analyses with Caenorhabditis elegans.

Campbell BE, Nagaraj SH, Hu M, Zhong W, Sternberg PW, Ong EK, Loukas A, Ranganathan S, Beveridge I, McInnes RL, Hutchinson GW, Gasser RB.

Int J Parasitol. 2008 Jan;38(1):65-83. Epub 2007 Jul 26.

PMID:
17707841
31.

ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform.

Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W143-7. Epub 2007 Jun 1.

32.

A hitchhiker's guide to expressed sequence tag (EST) analysis.

Nagaraj SH, Gasser RB, Ranganathan S.

Brief Bioinform. 2007 Jan;8(1):6-21. Epub 2006 May 23. Review.

PMID:
16772268

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