Flaherty P - Search Results

1

Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer.

Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, Xu H, Pai RK, Palm C, Regan JF, Chen H, Flaherty P, Ootani A, Zhang NR, Ford JM, Kuo CJ, Ji HP. Nadauld LD, et al. Among authors: flaherty p. Genome Biol. 2014 Aug 27;15(8):428. doi: 10.1186/s13059-014-0428-9. Genome Biol. 2014. PMID: 25315765 Free PMC article.

2

Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis.

Lee H, Flaherty P, Ji HP. Lee H, et al. Among authors: flaherty p. BMC Med Genomics. 2013 Dec 5;6:54. doi: 10.1186/1755-8794-6-54. BMC Med Genomics. 2013. PMID: 24308539 Free PMC article.

3

RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing.

Cushing A, Flaherty P, Hopmans E, Bell JM, Ji HP. Cushing A, et al. Among authors: flaherty p. BMC Res Notes. 2013 May 23;6:206. doi: 10.1186/1756-0500-6-206. BMC Res Notes. 2013. PMID: 23701658 Free PMC article.

4

Ultrasensitive detection of rare mutations using next-generation targeted resequencing.

Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Flaherty P, et al. Nucleic Acids Res. 2012 Jan;40(1):e2. doi: 10.1093/nar/gkr861. Epub 2011 Oct 19. Nucleic Acids Res. 2012. PMID: 22013163 Free PMC article.

5

Oncogenic BRAF mutation with CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas.

Schiffman JD, Hodgson JG, VandenBerg SR, Flaherty P, Polley MY, Yu M, Fisher PG, Rowitch DH, Ford JM, Berger MS, Ji H, Gutmann DH, James CD. Schiffman JD, et al. Among authors: flaherty p. Cancer Res. 2010 Jan 15;70(2):512-9. doi: 10.1158/0008-5472.CAN-09-1851. Epub 2010 Jan 12. Cancer Res. 2010. PMID: 20068183 Free PMC article.

6

Phase II Study of Gemcitabine, Carboplatin, and Iniparib As Neoadjuvant Therapy for Triple-Negative and BRCA1/2 Mutation-Associated Breast Cancer With Assessment of a Tumor-Based Measure of Genomic Instability: PrECOG 0105.

Telli ML, Jensen KC, Vinayak S, Kurian AW, Lipson JA, Flaherty PJ, Timms K, Abkevich V, Schackmann EA, Wapnir IL, Carlson RW, Chang PJ, Sparano JA, Head B, Goldstein LJ, Haley B, Dakhil SR, Reid JE, Hartman AR, Manola J, Ford JM. Telli ML, et al. J Clin Oncol. 2015 Jun 10;33(17):1895-901. doi: 10.1200/JCO.2014.57.0085. Epub 2015 Apr 6. J Clin Oncol. 2015. PMID: 25847929 Free PMC article. Clinical Trial.

7

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data.

Zhang F, Flaherty P. Zhang F, et al. Among authors: flaherty p. BMC Bioinformatics. 2017 Jan 19;18(1):45. doi: 10.1186/s12859-016-1451-5. BMC Bioinformatics. 2017. PMID: 28103803 Free PMC article.

8

RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.

He Y, Zhang F, Flaherty P. He Y, et al. Among authors: flaherty p. Bioinformatics. 2015 Sep 1;31(17):2785-93. doi: 10.1093/bioinformatics/btv275. Epub 2015 Apr 29. Bioinformatics. 2015. PMID: 25931517 Free PMC article.

9

SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.

Giguere C, Dubey HV, Sarsani VK, Saddiki H, He S, Flaherty P. Giguere C, et al. Among authors: flaherty p. BMC Bioinformatics. 2020 May 26;21(1):215. doi: 10.1186/s12859-020-03550-1. BMC Bioinformatics. 2020. PMID: 32456609 Free PMC article.

10

GEMINI: a computationally-efficient search engine for large gene expression datasets.

DeFreitas T, Saddiki H, Flaherty P. DeFreitas T, et al. Among authors: flaherty p. BMC Bioinformatics. 2016 Feb 24;17:102. doi: 10.1186/s12859-016-0934-8. BMC Bioinformatics. 2016. PMID: 26911289 Free PMC article.

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