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Results: 1 to 20 of 24

1.

Returning individual research results for genome sequences of pancreatic cancer.

Johns AL, Miller DK, Simpson SH, Gill AJ, Kassahn KS, Humphris JL, Samra JS, Tucker K, Andrews L, Chang DK, Waddell N, Pajic M, Pearson JV, Grimmond SM, Biankin AV, Zeps N.

Genome Med. 2014 May 29;6(5):42. doi: 10.1186/gm558. eCollection 2014.

PMID:
24963353
[PubMed]
Free PMC Article
2.

Integrating massively parallel sequencing into diagnostic workflows and managing the annotation and clinical interpretation challenge.

Kassahn KS, Scott HS, Caramins MC.

Hum Mutat. 2014 Apr;35(4):413-23. doi: 10.1002/humu.22525. Epub 2014 Mar 6. Review.

PMID:
24510514
[PubMed - indexed for MEDLINE]
3.

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.

Int J Cancer. 2014 Sep 1;135(5):1110-8. doi: 10.1002/ijc.28765. Epub 2014 May 9.

PMID:
24500968
[PubMed - indexed for MEDLINE]
4.

Somatic point mutation calling in low cellularity tumors.

Kassahn KS, Holmes O, Nones K, Patch AM, Miller DK, Christ AN, Harliwong I, Bruxner TJ, Xu Q, Anderson M, Wood S, Leonard C, Taylor D, Newell F, Song S, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Steptoe A, Pajic M, Cowley MJ, Pinese M, Chang DK, Gill AJ, Johns AL, Wu J, Wilson PJ, Fink L, Biankin AV, Waddell N, Grimmond SM, Pearson JV.

PLoS One. 2013 Nov 8;8(11):e74380. doi: 10.1371/journal.pone.0074380. eCollection 2013.

PMID:
24250782
[PubMed - in process]
Free PMC Article
5.

Clinical and molecular characterization of HER2 amplified-pancreatic cancer.

Chou A, Waddell N, Cowley MJ, Gill AJ, Chang DK, Patch AM, Nones K, Wu J, Pinese M, Johns AL, Miller DK, Kassahn KS, Nagrial AM, Wasan H, Goldstein D, Toon CW, Chin V, Chantrill L, Humphris J, Mead RS, Rooman I, Samra JS, Pajic M, Musgrove EA, Pearson JV, Morey AL, Grimmond SM, Biankin AV.

Genome Med. 2013 Aug 31;5(8):78. doi: 10.1186/gm482. eCollection 2013.

PMID:
24004612
[PubMed]
Free PMC Article
6.

Computational approaches to identify functional genetic variants in cancer genomes.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

PMID:
23900255
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Cerebellar output in zebrafish: an analysis of spatial patterns and topography in eurydendroid cell projections.

Heap LA, Goh CC, Kassahn KS, Scott EK.

Front Neural Circuits. 2013 Apr 1;7:53. doi: 10.3389/fncir.2013.00053. eCollection 2013.

PMID:
23554587
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Complex evolutionary relationships among four classes of modular RNA-binding splicing regulators in eukaryotes: the hnRNP, SR, ELAV-like and CELF proteins.

Tang YH, Han SP, Kassahn KS, Skarshewski A, Rothnagel JA, Smith R.

J Mol Evol. 2012 Dec;75(5-6):214-28. doi: 10.1007/s00239-012-9533-0. Epub 2012 Nov 24.

PMID:
23179353
[PubMed - indexed for MEDLINE]
9.

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-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA, Grimmond SM.

Nature. 2012 Nov 15;491(7424):399-405. doi: 10.1038/nature11547. Epub 2012 Oct 24.

PMID:
23103869
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PLoS One. 2012;7(9):e45835. doi: 10.1371/journal.pone.0045835. Epub 2012 Sep 25.

PMID:
23049875
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The mammalian PYHIN gene family: phylogeny, evolution and expression.

Cridland JA, Curley EZ, Wykes MN, Schroder K, Sweet MJ, Roberts TL, Ragan MA, Kassahn KS, Stacey KJ.

BMC Evol Biol. 2012 Aug 7;12:140.

PMID:
22871040
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma.

Mann KM, Ward JM, Yew CC, Kovochich A, Dawson DW, Black MA, Brett BT, Sheetz TE, Dupuy AJ; Australian Pancreatic Cancer Genome Initiative, Chang DK, Biankin AV, Waddell N, Kassahn KS, Grimmond SM, Rust AG, Adams DJ, Jenkins NA, Copeland NG.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):5934-41. doi: 10.1073/pnas.1202490109. Epub 2012 Mar 15.

PMID:
22421440
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

MicroRNAs and their isomiRs function cooperatively to target common biological pathways.

Cloonan N, Wani S, Xu Q, Gu J, Lea K, Heater S, Barbacioru C, Steptoe AL, Martin HC, Nourbakhsh E, Krishnan K, Gardiner B, Wang X, Nones K, Steen JA, Matigian NA, Wood DL, Kassahn KS, Waddell N, Shepherd J, Lee C, Ichikawa J, McKernan K, Bramlett K, Kuersten S, Grimmond SM.

Genome Biol. 2011 Dec 30;12(12):R126. doi: 10.1186/gb-2011-12-12-r126.

PMID:
22208850
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

PINA v2.0: mining interactome modules.

Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, Biankin AV, Hautaniemi S, Wu J.

Nucleic Acids Res. 2012 Jan;40(Database issue):D862-5. doi: 10.1093/nar/gkr967. Epub 2011 Nov 8.

PMID:
22067443
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.

Kolle G, Shepherd JL, Gardiner B, Kassahn KS, Cloonan N, Wood DL, Nourbakhsh E, Taylor DF, Wani S, Chy HS, Zhou Q, McKernan K, Kuersten S, Laslett AL, Grimmond SM.

Genome Res. 2011 Dec;21(12):2014-25. doi: 10.1101/gr.119321.110. Epub 2011 Oct 31.

PMID:
22042643
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Mineralocorticoid receptors: evolutionary and pathophysiological considerations.

Kassahn KS, Ragan MA, Funder JW.

Endocrinology. 2011 May;152(5):1883-90. doi: 10.1210/en.2010-1444. Epub 2011 Feb 22.

PMID:
21343255
[PubMed - indexed for MEDLINE]
17.

Sequencing transcriptomes in toto.

Kassahn KS, Waddell N, Grimmond SM.

Integr Biol (Camb). 2011 May;3(5):522-8. doi: 10.1039/c0ib00062k. Epub 2011 Feb 4. Review.

PMID:
21298135
[PubMed - indexed for MEDLINE]
18.

Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts.

Han SP, Kassahn KS, Skarshewski A, Ragan MA, Rothnagel JA, Smith R.

RNA. 2010 Sep;16(9):1760-8. doi: 10.1261/rna.2142810. Epub 2010 Jul 22.

PMID:
20651029
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

A visual framework for sequence analysis using n-grams and spectral rearrangement.

Maetschke SR, Kassahn KS, Dunn JA, Han SP, Curley EZ, Stacey KJ, Ragan MA.

Bioinformatics. 2010 Mar 15;26(6):737-44. doi: 10.1093/bioinformatics/btq042. Epub 2010 Feb 3.

PMID:
20130028
[PubMed - indexed for MEDLINE]
Free Article
20.

Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.

Kassahn KS, Dang VT, Wilkins SJ, Perkins AC, Ragan MA.

Genome Res. 2009 Aug;19(8):1404-18. doi: 10.1101/gr.086827.108. Epub 2009 May 13.

PMID:
19439512
[PubMed - indexed for MEDLINE]
Free PMC Article

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