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| ==Eun-Hae "EK" Kim, Ph.D.==
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| [[Image:ek.jpg|thumb|left|Eun-Hae "EK" Kim]]
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| '''''Mailing Address:'''''<br>
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| Dr. Eun-Hae Kim<br>
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| 1177 E Fourth St<br>
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| Tucson, AZ 85721-0038
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| or
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| P.O. Box 210038<br>
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| Tucson, AZ 85721-0038
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| '''''Physical Address:'''''<br>
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| Saguaro Hall Rm 315<br>
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| 1110 E. South Campus <br>
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| Tucson, AZ 85721
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| '''''Laboratory:'''''<br>
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| Saguaro Hall Rm 301
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| '''Email: ''eunhae.kim at arizona dot edu'''''
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| ==Education==
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| '''Ph.D., Environmental Science, Biochemistry'''
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| :University of Arizona<br>
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| :Dept of Biochemistry and Molecular Biophysics and Soil, Water, and Environmental Science<br>
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| :''Integrating an interdisciplinary approach of comparative genomics, molecular microbiology,'' <br>
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| :''and biochemistry to better understand mechanisms of metal transport systems in bacteria.''
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| '''M.S., Microbiology'''
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| :University of Nevada, Las Vegas<br>
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| :School of Life Sciences<br>
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| :''Elucidation of the roles and regulation of virulence factors in bacterial intracellular pathogens by''<br>
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| :''employing biochemical and genetic methods.''
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| '''B.S., Biological Sciences'''
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| :University of Southern California<br>
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| :Wrigley Institute of Environmental Studies<br>
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| :''Characterization of microbial communities in aquatic and terrestrial environments on Santa Catalina'' <br>
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| :''Island utilizing 16S rRNA genes as a phylogenetic marker.''
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| ==Research interests==
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| <!-- Feel free to add brief descriptions to your research interests as well -->
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| I graduated from the University of Southern California with a B.S. degree in Biological Sciences.
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| I was afforded the opportunity to do some really awesome field research at the USC Wrigley Institute for Environmental Studies where I studied phylogenetics and phylogeography of microbial populations around Catalina Island.
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| I then moved to the city that never sleeps, Las Vegas, NV where I obtained my Masters of Science degree in Microbiology. It was at UNLV where my work was extended from molecular biology to honing the skills necessary for employing biochemical methodologies. The focus of my research was analyzing virulence factors of the bacterial pathogen, Shigella.
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| I had a passion for creative and critical thinking and decided to continue my graduate career by obtaining a Ph.D. On an interview at the University of Arizona in the great Sonoran desert, I had arrived at an opportune time during monsoon season, which instantly made me fall in love with Tucson. I obtained my Doctorate degree at the University of Arizona in Environmental Science with a focus in Biochemistry. As a Ph.D. student, my research integrated a multidisciplinary approach of comparative genomics, molecular biology, and biochemistry to better understand mechanisms of metal homeostasis in microorganisms.
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| These acquired biochemical tools now have led me to the incredible field of proteomics, specifically community proteomics. My research focuses on how microbial communities impact biogeochemistry and global change.
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| I use the techniques of molecular microbial ecology and biochemistry via metagenomics and metaproteomics to examine microbial community interactions within populations and their environment, specifically in critical terrestial environments.
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| A driving question of my research is: What is the role microbes play in carbon gas emissions from thawing permafrost?
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| ==Publications==
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| <!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed -->
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| <biblio>
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| #Paper1 pmid=22267509
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| #Paper2 pmid=22176720
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| #Paper3 pmid=21398536
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| // Selected as high impact publication by ASM Press and included in Journal Highlights section in Microbe Magazine, June 2011
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| #Paper5 pmid=20497225
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| #Paper6 pmid=20442961
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| #Paper7 pmid=19895645
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| </biblio>
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| ==Useful links==
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| *[http://rc.arizona.edu/hpc-htc/using-systems Using the HPC]
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| *[[Help|OpenWetWare help pages]]
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| ==Proteomics Links==
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| *[http://en.wikipedia.org/wiki/Mass_spectrum_analysis Mass Spectrometry Analysis]
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| *[http://en.wikipedia.org/wiki/Mass_spectrometry_software Mass Spectrometry Software]
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| *[http://en.wikipedia.org/wiki/Mass_spectrometry_data_format Mass Spectrometry Data Format]
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| *[http://web.ornl.gov/sci/csd/Research_areas/obms_rd_ASMS.html ORNL OBMS ASMS Posters]
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| *[http://stackoverflow.com/questions/11402887/what-exactly-is-a-virtual-core-on-amazon-ec2 What exactly is a 'virtual core' on Amazon EC2?]
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| *[http://aws.amazon.com/ec2/instance-types/ Amazon Instance Types]
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| *[http://tools.proteomecenter.org/wiki/index.php?title=AMZTPP:FAQ TPP on Amazon Cloud FAQ]
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| ==Proteomic Tools==
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| *[https://github.com/wwood/divvy_proteomics Ben's spectra divvying Script]
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| *[http://www.sequenceserver.com SequenceServer]
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| *[http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP Trans-Proteomic Pipeline (TPP)]
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| *[http://www.proteomesoftware.com/products/free-viewer Scaffold Download]
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| *[http://www.proteomesoftware.com/products/free-viewer Proteome Software: Scaffold Download]
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| *[http://omics.pnl.gov/software/software.php#MsAnalysisTools PNNL MS Tools]
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| *[http://fenchurch.mc.vanderbilt.edu/software.php Software from the Tabb Lab]
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| *[http://www.thegpm.org/GPMDB/tutorials.html The Global Proteome Machine: Tutorial]
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| *[https://chorusproject.org/ The Chorus Project]
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| *[http://proteowizard.sourceforge.net ProteoWizard]
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| *[http://omics.pnl.gov/software/VennDiagramPlotter.php Venn Diagram Plotter]
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| *[http://www.cbs.dtu.dk/services/SignalP/ SignalP]
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| *[http://www.protbase.org/bioinfo/proteomics/enter.mhtml ProtBase]
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| *[http://www.molbiol-tools.ca/Convert.htm Fasta Converters]
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| *[http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/subcellular/ Prediction Tools]
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| *[http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine msconvert wine]
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| *[http://string-db.org/newstring_cgi/show_input_page.pl STRING known protein-protein interactions]
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| ==Search Engines==
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| *[http://thegpm.org/tandem/ X!Tandem]
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| *[http://thegpm.org/tandem/api/ XTandem Parameters]
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| ==Proteomic References==
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| General Label-Free Statistics<br>
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| (1) '''Detecting Differential and Correlated Protein Expression in Label-Free Shotgun Proteomics'''
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| <biblio>#Paper1 pmid=17081042</biblio>
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| (2) '''Significance analysis of spectral count data in label-free shotgun proteomic'''s
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| <biblio>#Paper2 pmid=18644780 </biblio>
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| (3) '''Mass spectrometry-based label-free quantitative proteomics'''
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| <biblio>#Paper3 pmid=19911078 </biblio>
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| (4) '''Less label, more free: Approaches in label‐free quantitative mass spectrometry'''
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| <biblio>#Paper5 pmid=21243637</biblio>
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| (5) '''Statistical similarities between transcriptomics and quantitative shotgun proteomics data'''
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| <biblio>#Paper6 pmid=18029349 </biblio>
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| (6) '''PatternLab for proteomics: a tool for differential shotgun proteomics'''
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| <biblio>#Paper7 pmid=18644148</biblio>
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| (7) '''Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments'''
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| <biblio>#Paper8 pmid=17905794</biblio>
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| BIG ONE
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| (8) The effects of shared peptides on protein quantitation in label-free proteomics by LC/MS/MS
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| (9) Peek a peak: a glance at statistics for quantitative label-free proteomics
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| (10) Relative, label-free protein quantitation: spectral counting error statistics from nine replicate MudPIT samples
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| (11) An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters
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| (12) PepC: proteomics software for identifying differentially expressed proteins based on spectral counting
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| (13) Quantitative mass spectrometry in proteomics: a critical review
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| (14) The Spectra Count Label-free Quantitation in Cancer Proteomics
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| PROBABLY VERY GOOD
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| (15) Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins
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| (16) Significance analysis of spectral count data in label-free shotgun proteomics
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| (17) Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis
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| HERE IS FIRST PAPER ON SPECTRAL COUNTS!!! Must reference this
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| (18) A model for random sampling and estimation of relative protein abundance in shotgun proteomics
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| other papers on Spectral Counting including NSAF
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| (19) Role of spectral counting in quantitative proteomics
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| NSAF PAPER MUST REFERENCE:
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| (20) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors
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| the first very good paper comparing methods for label free quant
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| (21) Comparison of label-free methods for quantifying human proteins by shotgun proteomics
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| APPLICATIONS:
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| (22) Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae
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| (23) A label free quantitative proteomic analysis of the< i> Saccharomyces cerevisiae</i> nucleus
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| (24) Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry
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| (25) Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing “Leptospirillum rubarum”(group II) and “Leptospirillum ferrodiazotrophum”(group III)
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| (26) Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
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| (27) Shotgun metaproteomics of the human distal gut microbiota
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| (28) Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use
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| Instrument concerns:
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| (29) Effect of dynamic exclusion duration on spectral count based quantitative proteomics
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| ==Proteomic Papers Search Algorithms==
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| (1)[[Media:Kapp2005_SearchAlgorithms.pdf | Kapp et al 2005, Search Algorithm Summary]]
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| ==Scripts==
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| [[Media:Extract_from_fasta2.txt | Extract_from_fasta]]
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