Karen R. Thickman, Ph.D.

Education

2006    Johns Hopkins University, Baltimore, MD                                                                  

            PhD in Molecular Biophysics

            Thesis: Structural and thermodynamic analysis of an essential pre-messenger RNA splicing factor

            Advisor: Clara L. Kielkopf

1999    Dartmouth College, Hanover, NH                                                    

            BA in Biophysical Chemistry, minor in Moral Philosophy

Professional Appointments and Positions

Carnegie Mellon University, Pittsburgh, Pennsylvania

2010-present    Assistant Teaching Professor,

                            Computational Biology Department, School of Computer Science

                            Courtesy Appointment,

                            Department of Biological Sciences, Mellon College of Science

2011-present    Assistant Director,

                            MS in Biotechnology Innovation and Computation

2012-present    Assistant Director,

                            MS in Computational Biology

University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania

2006-2010        Postdoctoral Fellow,

                            Department of Molecular Genetics & Biochemistry

                            Project: Intramolecular domain movements of PcrA during its helicase function

                            Mentors: Saleem A. Khan and Sanford H. Leuba

Honors and Awards

2012             Carnegie Mellon University Eberly Center Wimmer Faculty Grant  

2007-2010     NIH Ruth L. Kirschstein National Research Service Award Fellow

2005             Biophysical Society Student Travel Award

2004             Johns Hopkins University Institute for Biophysical Research Retreat, Student Co-Chair

2001-2003     Johns Hopkins University, The Francis D. Carlson Fellowship

2002             NSF East Asia and Pacific Summer Institutes for U.S. Graduate Students 

Professional Organizations

1999-present    American Chemical Society                        

2003-present    Biophysical Society                                                              

2009-present    American Association for the Advancement of Science

2011-present    International Society for Computational Biology          

Teaching Experience

Carnegie Mellon University, Pittsburgh, Pennsylvania

Computational Biology Department

Spring 2010-2015   Laboratory Methods for Computational Biologists, 02-760

•    6 credit hours

•    Enrollment: 6-12 graduate students

•    Co-instructor

Fall 2012-2014       Quantitative Cell and Molecular Biology Laboratory, 02-261

•    9 credit hours

•    Developed course to introduce undergraduate students to quantitative and computational biology questions and skills

•    Enrollment: 10-20 undergraduate students, 1 graduate student

1. •   Primary instructor
   

Fall 2014                 Fundamentals of Biotechnology, 02-652

•    12 credit hours

•    Enrollment: 36 graduate students

1. •  Primary instructor
   

Fall 2014

Spring 2015            Professional Issues in Computational Biology, 02-602

1. •   1 credit hours
   

2. •   Developed course to provide professional development training for masters students
   

•    Enrollment: 16 graduate students

1. •  Co-instructor
   

Department of Biological Sciences

Falls 2010-2012    Cellular Response to the Environment, 03-126

•    Half-semester course, 6 credit hours, taught twice per semester

•    Developed course to provide first-year students a research-based laboratory experience

•    Enrollment: 10-20 undergraduate students

•    Primary instructor

Fall 2011     Molecular Biology of Eukaryotes, 03-442 and 03-742

•    9 credit hours for undergraduate section, 12 credit hours for graduate section

•    Enrollment: 16 undergraduate students, 18 graduate students

•    Primary instructor

Howard Hughes Summer Research Institute

Summer 2014    Biological Science Undergraduate Research Experience

1.                •   Taught laboratory skills in 2 week boot camp, then mentored 2 research projects for 8 weeks
   

•    Enrollment: 15 undergraduate rising sophomore students

1. •   Co-instructor
   

Summer Academy for Mathematics + Science

Summer 2012-2013 Influenza Monitoring, Science and Engineering Project

•   Developed program to expose high school students to the power of computational biology to understanding illness and medicine

•   Enrollment: 8-10 high school students from under-represented minority groups

•   Primary instructor

University of Pittsburgh, Pittsburgh, Pennsylvania

2009 Survival Skills and Ethics Workshop, Ethics Discussion Leader

Dartmouth College, Hanover, New Hampshire

1999                General Chemistry, Teaching Laboratory Developer

1998-1999        General Chemistry, Laboratory Teaching Assistant

1997-1998        Organic Chemistry, Laboratory Teaching Assistant

Invited Talks, Workshops, and Conferences

Invited talks

Thickman, K. R.. (2013) ‘Putting Computation in Biology and Biology in Computer Science’, Undergraduate Bioinformatics Conference, St. Vincent College, Latrobe, PA.

Workshops attended

May 2013    Undergraduate Bioinformatics Conference

                    St. Vincent College, Latrobe, Pennsylvania

Jan. 2013    NIMBioS/SCALE-IT Tutorial

                    Using Bioinformatics Data and Tools to Engage Students in Problem Solving:

                    A Curriculum Development Workshop

May 2012    Undergraduate Bioinformatics Conference

                    St. Vincent College, Latrobe, Pennsylvania

Conferences presentations

Thickman, K.R., Ayoob, J.C. (2014) ‘Training Computer Mice to be Lab Rats: Teaching Experimental Design and Laboratory Techniques to Computational Biology Graduate Students’,

2014 RECOMB-BE, Pittsburgh, PA.

Thickman, K. R., Leuba, S. H., Khan, S. A. (2010) ‘DNA Structure Specificity of Bacillus stearothermophilus PcrA’,

2010 Biophysical Society Annual Meeting, San Francisco, CA.

Thickman, K. R., Leuba, S. H., Khan, S. A. (2008) ‘Correlating Intramolecular Motions of PcrA with Translocation along and Unwinding of DNA One Molecule at a Time’,

2008 Single Molecule Approaches To Biology, Gordon Research Conference, New London, NH.

Thickman, K. R., Swenson, M. Gryczynski, Z. & Kielkopf, C. L. (2005) ‘Sequential Protein Interactions at the 3’ Splice Site: Implications for Constitutive and Alternative Splicing’,

2005 Eukaryotic mRNA Processing, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (selected speaker)

Thickman, K. R., Gryczynski, Z. & Kielkopf, C. L. (2005) ‘Characterization of Binding of SAP155 with U2AF65 by Intrinsic Tryptophan Fluorescence’,

2005 Biophysical Society Annual Meeting, Long Beach, CA. (platform presentation)

Service

Department and University Service

Carnegie Mellon University, Lane Center for Computational Biology

Undergraduate Programs in Computational Biology   

    2010-present    Undergraduate Advisor, BS and minor in Computational Biology

    2011-present    Undergraduate Curriculum Committee                                   

Carnegie Mellon-University of Pittsburgh PhD Program in Computational Biology

    2011-present    Advising Committee

    2010-2011       Admissions Committee

    2013-present    Professional Development Series Co-coordinator

MS in Biotechnology Innovation and Computation

    2011-present    Assistant Director

    2011-present    Academic Advisor

    2011-present    Admissions Committee               

MS in Computational Biology program

    2012-present    Assistant Director (Internships and Job Placement)

    2012-present    Advising Committee                  

    2012-present    Admissions Committee

    2012-present    Curriculum Committee     

Other Service and Outreach

Johns Hopkins Center for Talented Youth Science and Technology Series hosted by the Lane Center for Computational Biology, Pittsburgh, PA

    2013                Volunteer Coordinator and Presenter

Pittsburgh Regional Science and Engineering Fair, Pittsburgh, Pennsylvania                          

    2009-present    Category judge

Intel International Science and Engineering Fair, Pittsburgh, Pennsylvania

    2012                Grand Awards Judge, Biochemistry

    2015                Grand Awards Judge

Biophysical Society, Bethesda, Maryland

    2006-2012        Public Affairs Committee Member

University of Pittsburgh, Pittsburgh, Pennsylvania

    2008-2010        Vice-President, University of Pittsburgh Postdoctoral Association

Peer-Reviewed Publications

1.Wang, W., Maucuer, A., Gupta, A., Manceau, V, Thickman, K.R., Bauer, W.J., Kennedy, S.D., Wedekind, J.E., Green, M.R., Kielkopf, C.L. (2013). Structure of Phosphorylated SF1 Bound to U2AF65 in an Essential Splicing Factor Complex. Structure. 21(2), 197–208.

2.Fagerburg, M. V., Thickman, K. R., Bianco, P. R., Khan, S. A., Sanford H. Leuba, S. H., Anand, S. P. (2012) PcrA-mediated disruption of RecA nucleoprotein filaments – essential role of the ATPase activity of RecA. Nucleic Acids Research. 40 (17), 8416-8424.

3.Lan, L., Nakajima, S., Kapetanaki, M. G., Hsieh, C. L., Fagerburg, M., Thickman, K., Rodriguez-Collazo, P., Leuba, S. H., Levine, A. S., Rapic-Otrin, V. (2012). Monoubiquitinated H2A destabilizes photolesion-containing nucleosomes with the concomitant release of the UV-damaged DNA-binding protein E3 ligase. Journal of Biological Chemistry 287 (15), 12036-12049.

4.Thickman, K. R., Sickmier, E. A. & Kielkopf, C. L. (2007). Alternative conformations at the RNA binding surface of the N-terminal U2AF65 RNA recognition motif. Journal of Molecular Biology 366, 703-710.

5.Thickman, K. R., Swenson, M. C., Kabogo, J. M., Gryczynski, Z. & Kielkopf, C. L. (2006). Multiple U2AF65 Binding Sites within SF3b155: Thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors. Journal of Molecular Biology 356, 664-683.

6.Thickman, K. R., Davis, A. & Berg, J. M. (2004). Site selection in tandem arrays of metal-binding domains. Inorganic Chemistry 43, 7897-7901.

7.Malkin, B. D., Thickman, K. R., Markworth,.C. J., Wilcox, D. E. & Kull, F. J. (2001). Inhibition of potato polyphenol oxidase by anions and activity in various carboxylate buffers (pH 4.8) at constant ionic strength. Journal of Enzyme Inhibition 16, 135-145.

8.Clevenger, C. V., Thickman, K., Ngo, W., Chang, W.-P., Takayama, S. & Reed, J. C. (1997). Role of Bag-1 in the survival and proliferation of the cytokine-dependent lymphocyte lines, Ba/F3 and Nb2. Molecular Endocrinology 11, 608-618.

Presentations

1.Thickman, K.R., Ayoob, J.C. (2014) Training Computer Mice to be Lab Rats: Teaching Experimental Design and Laboratory Techniques to Computational Biology Graduate Students, 2014 RECOMB-BE, Pittsburgh, PA, in review.

2.Thickman, K. R.. (2013) Putting Computation in Biology and Biology in Computer Science, Undergraduate Bioinformatics Conference, St. Vincent College, Latrobe, PA.

3.Thickman, K. R., Leuba, S. H., Khan, S. A. (2010) DNA Structure Specificity of Bacillus stearothermophilus PcrA’, 2010 Biophysical Society Annual Meeting, San Francisco, CA.

4.Thickman, K. R., Leuba, S. H., Khan, S. A. (2008) Correlating Intramolecular Motions of PcrA with Translocation along and Unwinding of DNA One Molecule at a Time, Single Molecule Approaches To Biology, Gordon Research Conference, New London, NH.

5.Thickman, K. R., Kielkopf, C. L. (2006) Calorimetric Analysis of the U2AF65-binding Domains of SF1 and SF3b155, 2006 Biophysical Society Annual Meeting, Salt Lake City, UT.

6.Thickman, K. R., Swenson, M. Gryczynski, Z. & Kielkopf, C. L. (2005) Sequential Protein Interactions at the 3’ Splice Site: Implications for Constitutive and Alternative Splicing, Eukaryotic mRNA Processing, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. (selected speaker)

7.Thickman, K. R., Gryczynski, Z. & Kielkopf, C. L. (2005) Characterization of Binding of SAP155 with U2AF65 by Intrinsic Tryptophan Fluorescence, 2005 Biophysical Society Annual Meeting, Long Beach, CA. (platform presentation)

8.Thickman, K. R., Sickmier, E. A. & Kielkopf, C. L. (2005) High Resolution X-ray Structure of the First RNA Recognition Motif of U2AF65, American Crystallographic Association Annual Meeting, Orlando, FL.

9.Thickman, K. R., Sickmier, E. A. & Kielkopf, C. L. (2004) High Resolution X-ray Structure of the First RNA Recognition Motif of U2AF65, RNA Society Annual Meeting, Madison, WI.

Revised:2/26/15