Difference between revisions of "User:Kdahlquist"

Latest revision as of 19:50, 2 May 2014

[edit] Kam D. Dahlquist, Ph.D.

[edit] Contact Information

Associate Professor
Department of Biology 
Loyola Marymount University 
1 LMU Drive, MS 8220 
Los Angeles, CA 90045-2659 
Tel: 310-338-7697 
Fax: 310-338-4479
E-mail: kdahlquist at lmu dot edu
Office: Seaver 218 
Lab: Seaver 222 

Office Hours (Fall 2013): Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment

For more information about me, please see my web pages:

• http://myweb.lmu.edu/kdahlqui
• My User Page at OpenWetware.org

[edit] Education

• Ph.D., University of California, Santa Cruz, Molecular, Cellular, and Developmental Biology Program, March 2000
• B.A., Pomona College, Claremont, California, Biology, cum laude, May 1993
• Study Abroad Program, University College, Oxford University, Oxford, England, Specialized tutorial in Philosophy of Science, Fall 1991

[edit] Work Experience

• Affiliate Faculty, Bioethics Institute, Loyola Marymount University, Los Angeles, California, 2013-present
• William F. McLaughlin Chair of Biology, 2010–2012
• Associate Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2009–present
• Assistant Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2005–2009,
• Assistant Professor, Department of Biology, Vassar College, Poughkeepsie, New York, 2003–2005
• Postdoctoral Fellow, Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, 2000–2003
• Adjunct Lecturer, Department of Biology, Santa Clara University, Santa Clara, California, Spring 2000
• Visiting Researcher, Department of Structural Biology, Stanford University, Stanford, California, 1997–2000
• Research Assistant, Department of Biology, University of California, Santa Cruz, California, 1994–1997

[edit] Personal Interests and Hobbies

• Reading science fiction
• Dance
• Needlework
• Cooking and baking

[edit] Gene Database Source Files

[edit] GO

• OBO XML .zip file
  • Creation date of unzipped file: 2013-10-21 12:54:57 pm

[edit] UniProt XML

From UniProt release 2013_10 - October 16, 2013

• Arabidopsis thaliana
  • Tax ID: 3702
  • Arabidopsis_thaliana_UniProt_20131031.xml.gz
    • Download page
• Escherichia coli
  • Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407)
  • Escherichia_coli_UniProt_20131031.xml.gz
    • Download page
• Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
  • Tax ID: 85962
  • Helicobacter_pylori_UniProt_20131029.xml.gz
    • Download page
• Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
  • Tax ID 246196
  • Mycobacterium_smegmatis_UniProt_20131029.xml.gz
    • Download page
• Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • Tax ID 83332; looks like ID has changed to 1773 which designate just Mycobacterium tuberculosis
  • Mycobacterium_tuberculosis_UniProt_20131031.xml.gz
    • Download page
• Plasmodium falciparum (isolate 3D7)
  • Tax ID 36329
  • Plasmodium_falciparum_UniProt_20131031.xml.gz
    • Download page
• Pseudomonas aerugenosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
  • Tax ID 208964
  • Pseudomonas_aerugenosa_UniProt_20131031.xml.gz
    • Download page
• Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
  • Tax ID 99287
  • Salmonella_typhimurium_UniProt_20131031.xml.gz
    • Download page
• Staphylococcus aureus (strain MRSA252)
  • Tax ID 282458
  • Staphylococcus_aureus_UniProt_20131031.xml.gz
    • Download page
• Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
  • Tax ID 243277
  • 46.V cholerae ATCC 39315-20131021.xml.zip
    • Download page

[edit] GOA

• Arabidopsis thaliana
  • 2009 version of Gene Database used file named "3.A_thaliana.goa"; however, did not find a file with this name on the GOA FTP site.
  • 217288.A_thaliana_20131031.goa version 10/15/2013 6:54:00 AM
    • Download link
• Escherichia coli
  • 2009 version of Gene Database used file named "18.E_coli_K12_.goa"; however, did dnot find a file with this name on the GOA FTP site.
  • 18.E_coli_MG1655_20131031.goa version 10/15/2013 10:53:00 AM
    • Download link for 18.E_coli_MG1655.goa
  • or 313660.E_coli_20131031.goa version 10/15/2013 10:50:00 AM
    • Download link for 313660.E_coli.goa
• Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
  • 23.H_pylori_26695_20131031.goa version 10/15/2013 11:52:00 AM
    • Download link for 23.H_pylori_26695.goa
• Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
  • 25827.M_smegmatis_20131105.goa version 10/15/2013 1:48:00 PM
    • Download link
• Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
  • 30.M_tuberculosis_ATCC_25618_20131031.goa version 10/15/2013 1:50:00 PM
    • Download link
• Plasmodium falciparum (isolate 3D7)
  • 493.P_falciparum_20131105.goa version 10/15/2013 3:05:00 PM
    • Download link
• Pseudomonas aerugenosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
  • 36.P_aeruginosa_LMG_12228_20131105.goa version 10/15/2013 3:21:00 PM
    • Download link
• Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
  • 69.S_typhimurium_ATCC_700720_20131105.goa version 10/15/2013 4:23:00 PM
    • Download link
• Staphylococcus aureus (strain MRSA252)
  • 19583.S_aureus_MRSA252_20131105.goa version 10/15/2013 4:55:00 PM
    • Download link
• Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
  • 46.V cholerae ATCC 39315-20131021.goa.zip version 10/15/2013 6:09:00 PM
    • Download link

In process species:

• Saccharomyces cerevisiae
  • 71242.S_cerevisiae_ATCC_204508.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/71242.S_cerevisiae_ATCC_204508.goa
• Sinorhizobium meliloti
  • 58.R_meliloti.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/58.R_meliloti.goa
• Streptococcus pneumoniae (strain TIGR4)
  • 57.S_pneumoniae_TIGR4.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/57.S_pneumoniae_TIGR4.goa
• Streptococcus pneumoniae (strain R6)
  • 64.S_pneumoniae_ATCC_BAA-255.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/64.S_pneumoniae_ATCC_BAA-255.goa
• Streptococcus pneumoniae (strain G54)
  • 31634.S_pneumoniae_19F.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/31634.S_pneumoniae_19F.goa
• Leishmania major
  • 21780.L_major.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/21780.L_major.goa
• Leishmania infantum
  • 83363.L_infantum.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/83363.L_infantum.goa
• Chlamydia trachomatis
  • 22183.C_trachomatis_A.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/22183.C_trachomatis_A.goa
• Pseudomonas putida KT2440
  • 109.P_putida_KT2440.goa
    • ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/109.P_putida_KT2440.goa

[edit] New gdb exports

• Vc-Std_External_20131122_attempt2.zip

• Hp-Std_External_20131122.zip

• Pf-Std_External_20131125.zip

• Media:Ms-Std_External_20131125.zip