contact

research

publications

presentations

teaching

professional

personal

bookmarks

pat flaherty

contact

pat flaherty
electrical engineering and computer science
uc berkeley
berkeley, ca 94720
flaherty at berkeley dot edu

research

I'm a Ph.D. student working with Professor Michael Jordan and Professor Adam Arkin.

publications

2005

Patrick Flaherty, Michael I. Jordan, Adam P. Arkin. Robust Design of Biological Experiments Proceedings of the Neural Information Processing Symposium 2005
abstract | pdf | supplementary information | NIPS*2005 home | citation

William Lee, Robert P. St.Onge Michael Proctor, Patrick Flaherty, Michael I. Jordan, Adam P. Arkin, Ronald W. Davis, Corey Nislow, Guri Giaever. Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents PLOS Genetics 2005 August; 1(2) 235-246
abstract | pdf | supplementary information | PLOS Genetics home | citation

Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin. A Latent Variable Model for Chemogenomic Profiling. Bioinformatics 2005 Aug 1;21(15):3286-93. Epub 2005 May 26.
abstract | pdf | supplementary information | Bioinformatics home | citation

2004

Guri Giaever, Patrick Flaherty, Jochen Kumm, Michael Proctor, Cory Nislow, Daniel F. Jaramillo, Angela M. Chu, Michael I. Jordan, Adam P. Arkin, Ronald W. Davis. “Chemogenomic profiling: identifying the functional interactions of small molecules in yeast.” Proc Natl Acad Sci U S A, 2004 Jan 20;101(3):793-8.
abstract | pdf | supplementary information | PNAS home | citation

2002

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, 2002 Jul 25;418(6896):387-91.
abstract | pdf | supplementary information | Nature home | citation

presentations

  • "Robust Design of Biological Experiments" Information Theory and Applications Inaugural Conference, (2006). [invited talk]

  • "Robust Design of Biological Experiments" ICSB, (2005) [poster presentation]

  • "A Kinetic Model for G protein-coupled Signal Transduction in Macrophage cells" ICSB, (2005) [poster presentation]

  • "A Latent Variable Model for Chemogenomic Profiling" Keystone Symposia: Biological Discovery Using Diverse High-Throughput Data, (2004). [poster presentation]

  • "Profiling S. cerevisiae for Functional Drug Targets using Chemogenomic Experiments" Gordon Research Conference: From predictive models to inference, (2003). [poster presentation]

  • "Functional Profiling of the Saccharomyces cerevisiae Genome: Microarray Analysis" Yeast Genetics and Molecular Biology Meeting, (2001). [oral presentation]

teaching

  • Summer 2005:
    		•  BioEngineering 190A - Modeling Biological Systems
  • Spring 2001:
    		•  Electrical Engineering 40 - Circuit Design
  • Fall 2000:
    		•  Electrical Engineering 126 - Probability and Random Processes

    professional

    I worked at Lucent Technologies in 1998 where I designed and analyzed experiments to develop the processing recipe for a high voltage semiconductor technology.

    In 1999 I worked at Lawrence Livermore National Labs on the National Ignition Facility project.

    Resume [pdf]

    personal

    bookmarks

    Pubmed | Google Scholar | Web of Science | JSTOR | ArXiv | MathSciNet | Curr. Index Stat. | Pathfinder | Melvyl | Eng. Lib. | Math/Stat. Lib. | Econ Lib. | Citeseer | MIT OCW | Cal Stat. | Cal EE | Cal MCB | NIST | Matrix Market | Netlib | Sundials | GSL | hyperstat | probability.net | Neymann Seminars | EE Seminars

    PNAS | Nature | Science | STKE | Nat. Genetics | Nat. Rev. Genetics | J. Biol. Chem. | Genome Res. | Bioinf. | PLoS Biol. | PLoS Comp. Biol. | PLoS Genetics | PLoS Pathogens | BMC Bioinf. | Genetics | J. Math. Biol.

    JASA | Stat Sci. | Biometrics | Biometrika | JRSSB | JRSSC | Amer. Stat. | NIPS | Annals of Stat. | Annals of Prob. | Technometrics | SIREV | SIOPT | Econometrica | J. Stat. Planning & Inference | JMLR