Difference between revisions of "User:Kdahlquist"
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** Tax ID: 3702 | ** Tax ID: 3702 | ||
** [[Media:Arabidopsis_thaliana_UniProt_20131031.xml.gz | Arabidopsis_thaliana_UniProt_20131031.xml.gz]] | ** [[Media:Arabidopsis_thaliana_UniProt_20131031.xml.gz | Arabidopsis_thaliana_UniProt_20131031.xml.gz]] | ||
| − | *** [http://www.uniprot.org/uniprot/?query=organism%3a3702+keyword%3a1185&format=*&compress=yes Download page | + | *** [http://www.uniprot.org/uniprot/?query=organism%3a3702+keyword%3a1185&format=*&compress=yes Download page] |
* ''Escherichia coli'' | * ''Escherichia coli'' | ||
** Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407) | ** Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407) | ||
** [[Media:Escherichia_coli_UniProt_20131031.xml.gz | Escherichia_coli_UniProt_20131031.xml.gz]] | ** [[Media:Escherichia_coli_UniProt_20131031.xml.gz | Escherichia_coli_UniProt_20131031.xml.gz]] | ||
| + | *** [http://www.uniprot.org/uniprot/?query=organism%3a562+keyword%3a181&format=*&compress=yes Download page] | ||
* ''Helicobacter pylori'' (strain ATCC 700392 / 26695) (Campylobacter pylori) | * ''Helicobacter pylori'' (strain ATCC 700392 / 26695) (Campylobacter pylori) | ||
** Tax ID: 85962 | ** Tax ID: 85962 | ||
** [[Media:Helicobacter_pylori_UniProt_20131029.xml.gz | Helicobacter_pylori_UniProt_20131029.xml.gz]] | ** [[Media:Helicobacter_pylori_UniProt_20131029.xml.gz | Helicobacter_pylori_UniProt_20131029.xml.gz]] | ||
| − | * ''Mycobacterium smegmatis'' | + | *** [http://www.uniprot.org/uniprot/?query=organism%3a85962+keyword%3a1185&format=*&compress=yes Download page] |
| + | * ''Mycobacterium smegmatis'' (strain ATCC 700084 / mc(2)155) | ||
** Tax ID 246196 | ** Tax ID 246196 | ||
** [[Media:Mycobacterium_smegmatis_UniProt_20131029.xml.gz | Mycobacterium_smegmatis_UniProt_20131029.xml.gz]] | ** [[Media:Mycobacterium_smegmatis_UniProt_20131029.xml.gz | Mycobacterium_smegmatis_UniProt_20131029.xml.gz]] | ||
| − | * ''Mycobacterium tuberculosis'' | + | *** [http://www.uniprot.org/uniprot/?query=organism%3a246196+keyword%3a1185&format=*&compress=yes Download page] |
| − | ** Tax ID 83332; looks like ID has changed to 1773 | + | * ''Mycobacterium tuberculosis'' (strain ATCC 25618 / H37Rv) |
| + | ** Tax ID 83332; looks like ID has changed to 1773 which designate just ''Mycobacterium tuberculosis'' | ||
** [[Media:Mycobacterium_tuberculosis_UniProt_20131031.xml.gz | Mycobacterium_tuberculosis_UniProt_20131031.xml.gz]] | ** [[Media:Mycobacterium_tuberculosis_UniProt_20131031.xml.gz | Mycobacterium_tuberculosis_UniProt_20131031.xml.gz]] | ||
*** [http://www.uniprot.org/uniprot/?query=organism%3a1773+keyword%3a1185&format=*&compress=yes Download page] | *** [http://www.uniprot.org/uniprot/?query=organism%3a1773+keyword%3a1185&format=*&compress=yes Download page] | ||
| − | * ''Plasmodium falciparum'' | + | * ''Plasmodium falciparum'' (isolate 3D7) |
** Tax ID 36329 | ** Tax ID 36329 | ||
** [[Media:Plasmodium_falciparum_UniProt_20131031.xml.gz | Plasmodium_falciparum_UniProt_20131031.xml.gz]] | ** [[Media:Plasmodium_falciparum_UniProt_20131031.xml.gz | Plasmodium_falciparum_UniProt_20131031.xml.gz]] | ||
| − | * ''Pseudomonas aerugenosa'' | + | *** [http://www.uniprot.org/uniprot/?query=organism%3a36329+keyword%3a1185&format=* Download page] |
| + | * ''Pseudomonas aerugenosa'' (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) | ||
** Tax ID 208964 | ** Tax ID 208964 | ||
**[[Media:Pseudomonas_aerugenosa_UniProt_20131031.xml.gz | Pseudomonas_aerugenosa_UniProt_20131031.xml.gz]] | **[[Media:Pseudomonas_aerugenosa_UniProt_20131031.xml.gz | Pseudomonas_aerugenosa_UniProt_20131031.xml.gz]] | ||
*** [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=*&compress=yes Download page] | *** [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=*&compress=yes Download page] | ||
| − | * ''Salmonella typhimurium'' | + | * ''Salmonella typhimurium'' (strain LT2 / SGSC1412 / ATCC 700720) |
** Tax ID 99287 | ** Tax ID 99287 | ||
** [[Media:Salmonella_typhimurium_UniProt_20131031.xml.gz | Salmonella_typhimurium_UniProt_20131031.xml.gz]] | ** [[Media:Salmonella_typhimurium_UniProt_20131031.xml.gz | Salmonella_typhimurium_UniProt_20131031.xml.gz]] | ||
*** [http://www.uniprot.org/uniprot/?query=organism%3a99287+keyword%3a1185&format=*&compress=yes Download page] | *** [http://www.uniprot.org/uniprot/?query=organism%3a99287+keyword%3a1185&format=*&compress=yes Download page] | ||
| − | * ''Staphylococcus aureus'' | + | * ''Staphylococcus aureus'' (strain MRSA252) |
** Tax ID 282458 | ** Tax ID 282458 | ||
** [[Media:Staphylococcus_aureus_UniProt_20131031.xml.gz | Staphylococcus_aureus_UniProt_20131031.xml.gz]] | ** [[Media:Staphylococcus_aureus_UniProt_20131031.xml.gz | Staphylococcus_aureus_UniProt_20131031.xml.gz]] | ||
*** [http://www.uniprot.org/uniprot/?query=organism%3a282458+keyword%3a181&format=*&compress=yes Download page] | *** [http://www.uniprot.org/uniprot/?query=organism%3a282458+keyword%3a181&format=*&compress=yes Download page] | ||
| − | * ''Vibrio cholerae'' | + | * ''Vibrio cholerae'' serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) |
** Tax ID 243277 | ** Tax ID 243277 | ||
** [[Media:46.V cholerae ATCC 39315-20131021.xml.zip | 46.V cholerae ATCC 39315-20131021.xml.zip]] | ** [[Media:46.V cholerae ATCC 39315-20131021.xml.zip | 46.V cholerae ATCC 39315-20131021.xml.zip]] | ||
| − | *** [http://www.uniprot.org/uniprot/?query=organism | + | *** [http://www.uniprot.org/uniprot/?query=organism%3a243277+keyword%3a1185&format=*&compress=yes Download page] |
==== GOA ==== | ==== GOA ==== | ||
| − | * ''Vibrio cholerae'' | + | * ''Arabidopsis thaliana'' |
| − | ** [[Media:46.V cholerae ATCC 39315-20131021.goa.zip | 46.V cholerae ATCC 39315-20131021.goa.zip]] | + | ** 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. |
| + | ** [[Media:217288.A_thaliana_20131031.goa | 217288.A_thaliana_20131031.goa]] version 10/15/2013 6:54:00 AM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/217288.A_thaliana.goa 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. | ||
| + | ** [[Media:18.E_coli_MG1655_20131031.goa | 18.E_coli_MG1655_20131031.goa]] version 10/15/2013 10:53:00 AM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa Download link for 18.E_coli_MG1655.goa] | ||
| + | ** or [[Media:313660.E_coli_20131031.goa | 313660.E_coli_20131031.goa]] version 10/15/2013 10:50:00 AM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/313660.E_coli.goa Download link for 313660.E_coli.goa] | ||
| + | * ''Helicobacter pylori'' (strain ATCC 700392 / 26695) (Campylobacter pylori) | ||
| + | ** [[Media:23.H_pylori_26695_20131031.goa | 23.H_pylori_26695_20131031.goa]] version 10/15/2013 11:52:00 AM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/23.H_pylori_26695.goa Download link for 23.H_pylori_26695.goa] | ||
| + | * ''Mycobacterium smegmatis'' (strain ATCC 700084 / mc(2)155) | ||
| + | ** [[Media:25827.M_smegmatis_20131105.goa | 25827.M_smegmatis_20131105.goa]] version 10/15/2013 1:48:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/25827.M_smegmatis.goa Download link] | ||
| + | * ''Mycobacterium tuberculosis'' (strain ATCC 25618 / H37Rv) | ||
| + | ** [[Media:30.M_tuberculosis_ATCC_25618_20131031.goa | 30.M_tuberculosis_ATCC_25618_20131031.goa]] version 10/15/2013 1:50:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/30.M_tuberculosis_ATCC_25618.goa Download link] | ||
| + | * ''Plasmodium falciparum'' (isolate 3D7) | ||
| + | ** [[Media:493.P_falciparum_20131105.goa | 493.P_falciparum_20131105.goa]] version 10/15/2013 3:05:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/493.P_falciparum.goa Download link] | ||
| + | * ''Pseudomonas aerugenosa'' (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) | ||
| + | ** [[Media:36.P_aeruginosa_LMG_12228_20131105.goa | 36.P_aeruginosa_LMG_12228_20131105.goa]] version 10/15/2013 3:21:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/36.P_aeruginosa_LMG_12228.goa Download link] | ||
| + | * ''Salmonella typhimurium'' (strain LT2 / SGSC1412 / ATCC 700720) | ||
| + | ** [[Media:69.S_typhimurium_ATCC_700720_20131105.goa | 69.S_typhimurium_ATCC_700720_20131105.goa]] version 10/15/2013 4:23:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/69.S_typhimurium_ATCC_700720.goa Download link] | ||
| + | * ''Staphylococcus aureus'' (strain MRSA252) | ||
| + | ** [[Media:19583.S_aureus_MRSA252_20131105.goa | 19583.S_aureus_MRSA252_20131105.goa]] version 10/15/2013 4:55:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/19583.S_aureus_MRSA252.goa Download link] | ||
| + | * ''Vibrio cholerae'' serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) | ||
| + | ** [[Media:46.V cholerae ATCC 39315-20131021.goa.zip | 46.V cholerae ATCC 39315-20131021.goa.zip]] version 10/15/2013 6:09:00 PM | ||
| + | *** [ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/46.V_cholerae_ATCC_39315.goa 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 | ||
| + | |||
| + | === New gdb exports === | ||
| + | |||
| + | * [[Media:Vc-Std_External_20131122_attempt2.zip | Vc-Std_External_20131122_attempt2.zip]] | ||
| + | |||
| + | [[Image:TallyEngine_Vc_20131122.jpg]] | ||
| + | |||
| + | * [[Media:Hp-Std_External_20131122.zip | Hp-Std_External_20131122.zip]] | ||
| + | |||
| + | [[Image:Hp_TallyEngine_20131122.jpg]] | ||
| + | |||
| + | * [[Media:Pf-Std_External_20131125.zip | Pf-Std_External_20131125.zip]] | ||
| + | |||
| + | [[Image:Pf_TallyEngine_20131125.jpg]] | ||
| + | |||
| + | * [[Media:Ms-Std_External_20131125.zip]] | ||
| + | |||
| + | [[Image:Ms_TallyEngine_20131125.jpg]] | ||
Latest revision as of 19:50, 2 May 2014
Contents |
[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:
[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
- Escherichia coli
- Tax ID: 83333 (includes MG1655 Tax ID 511145 and W3110 Tax ID 316407)
- Escherichia_coli_UniProt_20131031.xml.gz
- Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
- Tax ID: 85962
- Helicobacter_pylori_UniProt_20131029.xml.gz
- Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
- Tax ID 246196
- Mycobacterium_smegmatis_UniProt_20131029.xml.gz
- 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
- Plasmodium falciparum (isolate 3D7)
- Pseudomonas aerugenosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
- Tax ID 208964
- Pseudomonas_aerugenosa_UniProt_20131031.xml.gz
- Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
- Staphylococcus aureus (strain MRSA252)
- Tax ID 282458
- Staphylococcus_aureus_UniProt_20131031.xml.gz
- Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
- Tax ID 243277
- 46.V cholerae ATCC 39315-20131021.xml.zip
[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
- 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
- or 313660.E_coli_20131031.goa version 10/15/2013 10:50:00 AM
- Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
- 23.H_pylori_26695_20131031.goa version 10/15/2013 11:52:00 AM
- Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
- 25827.M_smegmatis_20131105.goa version 10/15/2013 1:48:00 PM
- Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
- 30.M_tuberculosis_ATCC_25618_20131031.goa version 10/15/2013 1:50:00 PM
- Plasmodium falciparum (isolate 3D7)
- 493.P_falciparum_20131105.goa version 10/15/2013 3:05:00 PM
- 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
- Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
- 69.S_typhimurium_ATCC_700720_20131105.goa version 10/15/2013 4:23:00 PM
- Staphylococcus aureus (strain MRSA252)
- 19583.S_aureus_MRSA252_20131105.goa version 10/15/2013 4:55:00 PM
- 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
In process species:
- Saccharomyces cerevisiae
- 71242.S_cerevisiae_ATCC_204508.goa
- Sinorhizobium meliloti
- 58.R_meliloti.goa
- Streptococcus pneumoniae (strain TIGR4)
- 57.S_pneumoniae_TIGR4.goa
- Streptococcus pneumoniae (strain R6)
- 64.S_pneumoniae_ATCC_BAA-255.goa
- Streptococcus pneumoniae (strain G54)
- 31634.S_pneumoniae_19F.goa
- Leishmania major
- 21780.L_major.goa
- Leishmania infantum
- 83363.L_infantum.goa
- Chlamydia trachomatis
- 22183.C_trachomatis_A.goa
- Pseudomonas putida KT2440
- 109.P_putida_KT2440.goa
[edit] New gdb exports
