Difference between revisions of "User:Kdahlquist"

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| 18-Jan
 
| 18-Jan
 
| <!--Reading-->
 
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| DNA structure
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* DNA structure
 
 
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| rowspan="2" | 3
 
| rowspan="2" | 3
 
| 23-Jan
 
| 23-Jan
 
| <!--Reading-->
 
| <!--Reading-->
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|  
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| Aipotu work session
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* Aipotu work session
 
 
| rowspan="2" | [[Week 3]]<br /><br />(due 12:01am 2/1)<br /><br />[[Class Journal Week 3]]<br />
 
| rowspan="2" | [[Week 3]]<br /><br />(due 12:01am 2/1)<br /><br />[[Class Journal Week 3]]<br />
 
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| 6-Feb
 
| 6-Feb
 
| <!--Reading-->
 
| <!--Reading-->
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| Week 4 work session<br />
−
* Week 4 work session<br />
 
 
| rowspan="2" | [[Week 5]]<br /><br />(due 12:01am 2/15)<br /><br />[[Class Journal Week 5]]<br />
 
| rowspan="2" | [[Week 5]]<br /><br />(due 12:01am 2/15)<br /><br />[[Class Journal Week 5]]<br />
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
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| 13-Feb
 
| 13-Feb
 
| <!--Reading-->
 
| <!--Reading-->
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|  
+
| Database presentations part 1
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* Database presentations part 1
 
 
| rowspan="2" | [[Week 6]]<br /><br />(due 12:01am 2/22)<br /><br />[[Class Journal Week 6]]<br />
 
| rowspan="2" | [[Week 6]]<br /><br />(due 12:01am 2/22)<br /><br />[[Class Journal Week 6]]<br />
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| 15-Feb
 
| 15-Feb
 
| <!--Reading-->
 
| <!--Reading-->
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|  
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| Database presentations part 2
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* Database presentations part 2
 
 
|- style="background-color:#dae8fc;"
 
|- style="background-color:#dae8fc;"
 
| colspan="5" | '''Part 2: Going Deeper (Gene Expression Data and Relational Databases)'''
 
| colspan="5" | '''Part 2: Going Deeper (Gene Expression Data and Relational Databases)'''
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| 20-Feb
 
| 20-Feb
 
| <!--Reading-->
 
| <!--Reading-->
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| Human Genome Project to 'omics era<br />
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* Human Genome Project to 'omics era<br />
 
 
| rowspan="2" | No Week 7 Assignment
 
| rowspan="2" | No Week 7 Assignment
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| 22-Feb
 
| 22-Feb
 
| <!--Reading-->
 
| <!--Reading-->
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| Review Week 6 assignment
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* Review Week 6 assignment
 
 
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|- style="vertical-align:bottom; background-color:#e5fee8;"
 
| rowspan="2" | Spring Break
 
| rowspan="2" | Spring Break
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| 5-Mar
 
| 5-Mar
 
| <!--Reading-->
 
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| More about 'omics analysis<br />
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* More about 'omics analysis<br />
 
 
| rowspan="2" | [[Week 8]]<br /><br />(due 12:01am 3/14)<br /><br />[[Class Journal Week 8]]<br />
 
| rowspan="2" | [[Week 8]]<br /><br />(due 12:01am 3/14)<br /><br />[[Class Journal Week 8]]<br />
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| 7-Mar
 
| 7-Mar
 
| <!--Reading-->
 
| <!--Reading-->
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| Begin transcriptomic analysis (part 1)<br />
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* Begin transcriptomic analysis (part 1)<br />
 
 
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| rowspan="2" | 9
 
| rowspan="2" | 9
 
| 12-Mar
 
| 12-Mar
 
| <!--Reading-->
 
| <!--Reading-->
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|  
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| Transcriptomic analysis (part 2)<br />
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* Transcriptomic analysis (part 2)<br />
 
 
| rowspan="2" | [[Week 9]]<br /><br />(due 12:01am 3/21)<br /><br />[[Class Journal Week 9]]<br />
 
| rowspan="2" | [[Week 9]]<br /><br />(due 12:01am 3/21)<br /><br />[[Class Journal Week 9]]<br />
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| 14-Mar
 
| 14-Mar
 
| <!--Reading-->
 
| <!--Reading-->
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| Transcriptomic analysis (part 3)
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* Transcriptomic analysis (part 3)
 
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| rowspan="2" | 10
 
| rowspan="2" | 10
 
| 19-Mar
 
| 19-Mar
 
| <!--Reading-->
 
| <!--Reading-->
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|  
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| Transcriptomic analysis (part 4)<br />
−
* Transcriptomic analysis (part 4)<br />
 
 
| rowspan="2" | [[Week 10]]<br /><br />(due 12:01am 3/26, note Tuesday due date)<br /><br />[[Class Journal Week 10]]<br />
 
| rowspan="2" | [[Week 10]]<br /><br />(due 12:01am 3/26, note Tuesday due date)<br /><br />[[Class Journal Week 10]]<br />
 
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| 2-Apr
 
| 2-Apr
 
| <!--Reading-->
 
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| Literature searching and annotated bibliographies<br />
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* Literature searching and annotated bibliographies<br />
 
 
| rowspan="2" | [[Week 12]]<br /><br />(due 12:01am 4/11)<br />
 
| rowspan="2" | [[Week 12]]<br /><br />(due 12:01am 4/11)<br />
 
|- style="vertical-align:bottom;"
 
|- style="vertical-align:bottom;"
 
| 4-Apr
 
| 4-Apr
 
| <!--Reading-->
 
| <!--Reading-->
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| * Journal club presentations<br />
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| Journal club presentations<br />
 
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| rowspan="2" | 13
 
| rowspan="2" | 13

Revision as of 22:15, 8 January 2024

Kam D. Dahlquist, Ph.D.

Contact Information

Professor
Department of Biology 
Loyola Marymount University 
1 LMU Drive, MS 8888 
Los Angeles, CA 90045-2659 
Tel: 310-338-7697 
Fax: 310-338-5317
E-mail: kdahlquist at lmu dot edu
Office: FEA 289 
Lab: FEA 263

Office Hours (Spring 2024)

Mondays 2:00-3:30 PM, Tuesdays 3:15-4:45 PM and by appointment. See the course Brightspace page for a link to my Calendly to make an in-person or Zoom appointment.

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

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

Work Experience

  • Professor, Department of Biology, Loyola Marymount University, Los Angeles, California, 2017-present
  • Chair, Department of Biology, Loyola Marymount University, Los Angeles, California, 2020-2023
  • 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, 2009–2017
  • 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

Publications

See the Dahlquist Lab Publications page or my Google Scholar profile.

Software and Datasets

  • GRNmap (Gene Regulatory Network Modeling and Parameter Estimation)
  • GRNsight (Web Application and Service for Visualizing Models of Gene Regulatory Networks)
  • NCBI Gene Expression Omnibus Series GSE83656 Global transcriptional response of wild type and transcription factor deletion strains of Saccharomyces cerevisiae to the environmental stress of cold shock and subsequent recovery

Personal Interests and Hobbies

  • Cooking and baking
  • Reading science fiction
  • Dance
  • Needlework
    • cross stitch
    • needlepoint

BioDB Home page

LMU home page

Sandbox

Template:Course Schedule Divider

  1. Item 1
  2. Item 2
    • sub-item 2


Week
 Date
 Before Class Reading
 During Class Topic After Class Assignment
Part 1: Building Blocks (Genetic Code and Manipulating Text)
1 9-Jan
  • Syllabus walkthrough
  • Pairwise interviews and introductions
  • Academic Honesty case studies
  • Wiki account setup
 Week 1

(due 12:01am 1/18)


Class Journal Week 1
11-Jan
  • What is a model?
  • Model of a cell/model of a computer
2 16-Jan
  • Discuss the Week 1 assignment
    • Wiki syntax overview
    • Lab session to setup User wiki page
 Week 2

(due 12:01am 1/25)

Class Journal Week 2
18-Jan DNA structure
3 23-Jan Aipotu work session Week 3

(due 12:01am 2/1)

Class Journal Week 3
25-Jan
  • Genes as models
  • Central model of molecular biology
  • Paper and pencil exercise
4 30-Jan

Introduction to biological databases (part 1)

  • What is bioinformatics?
  • Open Science Ecosystem
  • DataONE: Data management and the life cycle of data
 Week 4

(due 12:01am 2/8)

Class Journal Week 4
1-Feb

Introduction to biological databases (part 2)

  • Where's my stuff?
  • An overview of computers, networks, files, web applications, web services, and databases
  • Names, URLs, identifiers
    • As applied to biology: genes, species
  • "Stuff" on the worldwide web
    • Accessing the web on a browser
5 6-Feb Week 4 work session
 Week 5

(due 12:01am 2/15)

Class Journal Week 5
8-Feb

Introduction to biological databases (part 3)

  • Terminology, types, evaluation, four "Gold Standard" databases
  • A closer look at evaluating biological databases
  • DataONE: Data sharing
  • Presentation Guidelines
6 13-Feb Database presentations part 1 Week 6

(due 12:01am 2/22)

Class Journal Week 6
15-Feb Database presentations part 2
Part 2: Going Deeper (Gene Expression Data and Relational Databases)
7 20-Feb Human Genome Project to 'omics era
 No Week 7 Assignment
22-Feb Review Week 6 assignment
Spring Break 27-Feb No class
29-Feb
8 5-Mar More about 'omics analysis
 Week 8

(due 12:01am 3/14)

Class Journal Week 8
7-Mar Begin transcriptomic analysis (part 1)
9 12-Mar Transcriptomic analysis (part 2)
 Week 9

(due 12:01am 3/21)

Class Journal Week 9
14-Mar Transcriptomic analysis (part 3)
10 19-Mar Transcriptomic analysis (part 4)
 Week 10

(due 12:01am 3/26, note Tuesday due date)

Class Journal Week 10
21-Mar
  • Transcriptomic analysis (part 5)
  • Group requests due in class
Part 3: Integrating for Research (GRNsight Gene Expression Database Project)
11 26-Mar

Begin Database Project

  • Team assignments
  • Overview of project
  • Work session to create Team wiki pages
 Week 11

(due 12:01am 4/4)
Easter 28-Mar No class
12 2-Apr Literature searching and annotated bibliographies
 Week 12

(due 12:01am 4/11)
4-Apr Journal club presentations
13 9-Apr
  • Status report
  • Work session
 Week 13

(due 12:01am 4/18)
11-Apr
  • Status report
  • Work session
14 16-Jan
  • Status report
  • Work session
 Week 14

(due 12:01am 4/25)
18-Apr
  • Status report
  • Work session
15 23-Apr
  • Status report
  • Work session
 Week 15

(due 12:00 noon 5/3)
25-Apr
  • Status report
  • Work session
Finals 2-May Final Presentations 11:00am
3-May Project Deliverables Due 12:00 noon
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