User:Andrew Herman: Difference between revisions

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=== Lecture notes 10/12/10 ===
Biological pathways
*metabolic- breakdown of molecules
*signaling- transmission of info. from outside to inside the cell
*Gene regulatory- controls gene activity
* these pathways create functional modules, that make up the large scale organization of the cell (universality). These universal traits, found through the organisms genome, can lead to mathematical modeling for the cell's reaction to the environment.
Microarray technology
*red/green ratio = (signal-background red)/(signal-background green)
*determines what genes are turned on/off. This can help in determining genetic pathways.
* Up regulation (>1) vs. down regulation (<1)
* log2 ratios taken of these numbers is necessary to determine magnitude difference, and reduces the outliers.
*Normalization- evens out florescence intensity for an within chips/entire chip/whole experiments.
*Statistical analysis- determines the confidence level of the results (expressed in a P value < 0.05, this is the difference in the data due to chance)
*multiple testing problem- with enough statistical test are performed, there will be significant variations in the data due to chance. Bonferroni correction - multiples the P value by the number of tests, if it is < 0.05 it passes.
GenMAPP
*program that maps biological data from a microarray database into pathway diagrams.
* Gene ontology- allows for a categorization of the data into terms that are ranked based upon the groups functions (MAPPFinder)
XMLpipeDB
*Takes in data from uniprot and gene databases, and creates a GenMAPP gene database. DNA microarray data, analyzed through MAPPFinder. Combining this knowledge, we can discover new results that the original research did not display.


==Useful links==
==Useful links==

Revision as of 20:59, 13 October 2010

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Contact Info

Andrew Herman (an artistic interpretation)
  • Andrew Herman
  • Loyola Marymount University
  • 1 lmu Dr., Hannon Apartment 309, Los Angeles, CA

I work in the Dahlquist Laboratory at Loyola Marymount University.

Education

  • Expected graduate- 2012, BS in Biology, Loyola Marymount University

Posters

Graphs

File:Andrew Herman’s Matlab Network Practice 2282010.ppt

Research Interests

  • Changes to the genetic expression of yeast through temperature variations.
  • Cellular and genetic responses to environmental stress variation and temperature shifts.
  • Mathematical modeling of genetic regulatory networks.

Pictures

Awards and Honors

  • American Chemical Society's Outstanding Organic Chemist for 2010 at LMU
  • Academic Chairmen for the Tribeta Biological Honors Society at LMU for the 2010-2011 school year.

Publications

  1. Goldbeter A and Koshland DE Jr. An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A. 1981 Nov;78(11):6840-4. DOI:10.1073/pnas.78.11.6840 | PubMed ID:6947258 | HubMed [Paper1]
  2. JACOB F and MONOD J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol. 1961 Jun;3:318-56. DOI:10.1016/s0022-2836(61)80072-7 | PubMed ID:13718526 | HubMed [Paper2]
  3. Levin DE. Cell wall integrity signaling in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 2005 Jun;69(2):262-91. DOI:10.1128/MMBR.69.2.262-291.2005 | PubMed ID:15944456 | HubMed [Paper3]

    This is a paper about the cellular signaling pathways used by yeast in the cell wall

  4. ISBN:0879697164 [Book1]

All Medline abstracts: PubMed | HubMed


Useful links

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