Projects

GLAD

GLAD

A mixed membership model for heterogeneous tumor subtype classification.

RVD

RVD

A hierarchical Bayesian model to detect rare single nucleotide variants in next-generation sequencing data.

GEMINI

GEMINI

A scalable genomic data search engine.

Publications

He Y, Zhang F, Flaherty P.. RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data. Bioinformatics 31(17) Sept. 1, 2015 doi: 10.1093/bioinformatics/btv275
Carvalho P, Kesari A, Weaver S, Flaherty P, Fischer GS. Robotic Assistive Device for Phlebotomy Proceedings of ASME ICETC/CIE 1(None) Aug. 2, 2015
Flaherty P and Davis RW. Robust Optimization of Biological Protocols Technometrics 57(2) July 13, 2015 doi: 10.1080/00401706.2014.915890
Saddiki H, Flaherty P. Subtype Prediction Intervals for Samples with Intratumor Heterogeneity Proceedings of Great Lakes Bioinformatics Conference (GLBIO) 0(None) March 11, 2015
Saddiki H, McAuliffe J, Flaherty P. GLAD: A mixed-membership model for heterogeneous tumor subtype classification Bioinformatics 31(2) Jan. 15, 2015 doi: 10.1093/bioinformatics/btu618
Yan S, Tsurumi A, Que YA, Ryan CM, Bandyopadhaya A, Morgan AA, Flaherty PJ, Tompkins RG, Rahme LG. Prediction of Multiple Infections After Severe Burn Trauma: A Prospective Cohort Study Annals of Surgery 261(4) June 29, 2014 doi: 10.1097/SLA.0000000000000759
Lee H, Flaherty P, Ji HP. Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis BMC Medical Genomics 6(54) Dec. 5, 2013 doi: 10.1186/1755-8794-6-54
Cushing A, Flaherty P, Hopmans E, Bell J, Ji HP. RVD: a command-line program for ultrasensitive rare single nucleotide variant detection using targeted next-generation DNA resequencing BMC Research Notes 6(206) May 23, 2013 doi: 10.1186/1756-0500-6-206
Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Ultrasensitive detection of rare mutations using next-generation targeted resequencing Nucleic Acids Research 40(1) Jan. 1, 2012 doi: 10.1093/nar/gkr861
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. Oncogenic BRAF mutation with CDKN2A inactivation is characteristic of a subset of pediatric malignant astrocytomas Cancer Research 70(2) Jan. 15, 2010 doi: 10.1158/0008-5472.CAN-09-1851
Flaherty P, Radhakrishnan M, Dinh, T, Jordan MI, Arkin AP. A Dual Receptor Cross-talk Model of G protein-coupled Signal Transduction in RAW Macrophage Cells PLOS Computational Biology 4(9) Sept. 26, 2008 doi: 10.1371/journal.pcbi.1000185
Lee W, St Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G. Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents PLOS Genetics 1(2) Aug. 19, 2005 doi: 10.1371/journal.pgen.0010024
Flaherty P, Giaever G, Kumm J, Jordan MI, Arkin AP. A Latent Variable Model for Chemogenomic Profiling Bioinformatics 21(15) Aug. 1, 2005
Flaherty P, Jordan MI, Arkin AP. Robust Design of Biological Experiments Proceedings of Neural Information Processing Systems (NIPS) 1(0) Jan. 1, 2005
Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW. Chemogenomic profiling: Identifying the functional interactions of small molecules in yeast Proc. Natl. Acad. Sci. USA 101(3) Jan. 20, 2004
Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Guldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kotter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. Functional Profiling of the Saccharomyces cerevisiae Genome Nature 418(6896) July 25, 2002