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qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.
Song S, Nones K, Miller D, Harliwong I, Kassahn KS, Pinese M, Pajic M, Gill AJ, Johns AL, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Newell F, Cowley MJ, Wu J, Wilson P, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV. Song S, et al. Among authors: miller d. PLoS One. 2012;7(9):e45835. doi: 10.1371/journal.pone.0045835. Epub 2012 Sep 25. PLoS One. 2012. PMID: 23049875 Free PMC article.
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.
Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N; Australian Pancreatic Cancer Genome Initiative; Kakkar N, Zhao F, Wu YQ, Wang M, Muzny DM, Fisher WE, Brunicardi FC, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Manc… See abstract for full author list ➔ Biankin AV, et al. Among authors: miller dk. Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24. Nature. 2012. PMID: 23103869 Free PMC article.
A de novo mutation in the β-tubulin gene TUBB4A results in the leukoencephalopathy hypomyelination with atrophy of the basal ganglia and cerebellum.
Simons C, Wolf NI, McNeil N, Caldovic L, Devaney JM, Takanohashi A, Crawford J, Ru K, Grimmond SM, Miller D, Tonduti D, Schmidt JL, Chudnow RS, van Coster R, Lagae L, Kisler J, Sperner J, van der Knaap MS, Schiffmann R, Taft RJ, Vanderver A. Simons C, et al. Among authors: miller d. Am J Hum Genet. 2013 May 2;92(5):767-73. doi: 10.1016/j.ajhg.2013.03.018. Epub 2013 Apr 11. Am J Hum Genet. 2013. PMID: 23582646 Free PMC article.
MicroRNAs-140-5p/140-3p modulate Leydig cell numbers in the developing mouse testis.
Rakoczy J, Fernandez-Valverde SL, Glazov EA, Wainwright EN, Sato T, Takada S, Combes AN, Korbie DJ, Miller D, Grimmond SM, Little MH, Asahara H, Mattick JS, Taft RJ, Wilhelm D. Rakoczy J, et al. Among authors: miller d. Biol Reprod. 2013 Jun 6;88(6):143. doi: 10.1095/biolreprod.113.107607. Print 2013 Jun. Biol Reprod. 2013. PMID: 23616593
Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.
Taft RJ, Vanderver A, Leventer RJ, Damiani SA, Simons C, Grimmond SM, Miller D, Schmidt J, Lockhart PJ, Pope K, Ru K, Crawford J, Rosser T, de Coo IF, Juneja M, Verma IC, Prabhakar P, Blaser S, Raiman J, Pouwels PJ, Bevova MR, Abbink TE, van der Knaap MS, Wolf NI. Taft RJ, et al. Among authors: miller d. Am J Hum Genet. 2013 May 2;92(5):774-80. doi: 10.1016/j.ajhg.2013.04.006. Am J Hum Genet. 2013. PMID: 23643384 Free PMC article.
Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling.
Nones K, Waddell N, Song S, Patch AM, Miller D, Johns A, Wu J, Kassahn KS, Wood D, Bailey P, Fink L, Manning S, Christ AN, Nourse C, Kazakoff S, Taylor D, Leonard C, Chang DK, Jones MD, Thomas M, Watson C, Pinese M, Cowley M, Rooman I, Pajic M; APGI; Butturini G, Malpaga A, Corbo V, Crippa S, Falconi M, Zamboni G, Castelli P, Lawlor RT, Gill AJ, Scarpa A, Pearson JV, Biankin AV, Grimmond SM. Nones K, et al. Among authors: miller d. Int J Cancer. 2014 Sep 1;135(5):1110-8. doi: 10.1002/ijc.28765. Epub 2014 May 9. Int J Cancer. 2014. PMID: 24500968 Free article.
A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing.
Quek K, Nones K, Patch AM, Fink JL, Newell F, Cloonan N, Miller D, Fadlullah MZ, Kassahn K, Christ AN, Bruxner TJ, Manning S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Wani S, Steptoe A, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q; Australian Pancreatic Cancer Genome Initiative; Wilson P, Biankin AV, Pearson JV, Waddell N, Grimmond SM. Quek K, et al. Among authors: miller d. Biotechniques. 2014 Jul 1;57(1):31-8. doi: 10.2144/000114189. eCollection 2014 Jul. Biotechniques. 2014. PMID: 25005691 Free article.
Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis.
Nones K, Waddell N, Wayte N, Patch AM, Bailey P, Newell F, Holmes O, Fink JL, Quinn MCJ, Tang YH, Lampe G, Quek K, Loffler KA, Manning S, Idrisoglu S, Miller D, Xu Q, Waddell N, Wilson PJ, Bruxner TJC, Christ AN, Harliwong I, Nourse C, Nourbakhsh E, Anderson M, Kazakoff S, Leonard C, Wood S, Simpson PT, Reid LE, Krause L, Hussey DJ, Watson DI, Lord RV, Nancarrow D, Phillips WA, Gotley D, Smithers BM, Whiteman DC, Hayward NK, Campbell PJ, Pearson JV, Grimmond SM, Barbour AP. Nones K, et al. Among authors: miller d. Nat Commun. 2014 Oct 29;5:5224. doi: 10.1038/ncomms6224. Nat Commun. 2014. PMID: 25351503 Free PMC article.
Mutations in the voltage-gated potassium channel gene KCNH1 cause Temple-Baraitser syndrome and epilepsy.
Simons C, Rash LD, Crawford J, Ma L, Cristofori-Armstrong B, Miller D, Ru K, Baillie GJ, Alanay Y, Jacquinet A, Debray FG, Verloes A, Shen J, Yesil G, Guler S, Yuksel A, Cleary JG, Grimmond SM, McGaughran J, King GF, Gabbett MT, Taft RJ. Simons C, et al. Among authors: miller d. Nat Genet. 2015 Jan;47(1):73-7. doi: 10.1038/ng.3153. Epub 2014 Nov 24. Nat Genet. 2015. PMID: 25420144
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