From: Don Armstrong Date: Sat, 15 Feb 2014 05:40:42 +0000 (-0800) Subject: add resarch statement and teaching statement and links in resume X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=commitdiff_plain;h=5e1f47a06e05aea04f15a6145dd711af71d1d169 add resarch statement and teaching statement and links in resume --- diff --git a/resume.mdwn b/resume.mdwn index 3f239c5..a4a9b2c 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,55 +1,50 @@ -Resume -====== +[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]] -[Don Armstrong](http://www.donarmstrong.com/) +Introduction +------------ +A brief statement of my research interests and teaching mission +follows, and my [Curriculum Vitæ](resume/curriculum_vitae) +([pdf](resume/dla-cv.pdf)), +[Research Statement](resume/research_statement) +([pdf](resume/research_statement.pdf)), and +[Teaching Statement](resume/teaching_statement) +([pdf](resume/teaching_statement.pdf)) are also available. + +For my contact information or additional references, please e-mail - - -[Phone contact information available via e-mail.] - -I am a practitioner of the art of solving problems as elegantly and -practically as possible. I seek to enhance my abilities to solve -problems in the digital realm by learning (and inventing where -appropriate) new methods and techniques, and to help others achieve -their goals by removing or smoothing over ponderous obstacles in their -path. If you have difficult problems for which a digital approach -seems appropriate, I'm the person to talk to to find a solution. - -Education ----------- -* Doctor of Philosophy in Cell, Molecular and Developmental Biology from [UC Riverside](http://www.ucr.edu), 2008 -* Bachelor of Science in [Biology](http://bio.ucr.edu) from [UC Riverside](http://www.ucr.edu), 2001 -* Graduate, Scholar with Distinction from [Marina High School](http://www.hbuhsd.k12.ca.us/mhs/), 1997 - -Experience ----------- -* July 2002-July 2003: Researcher for Socratech, LLC - * Affymetrix Gene Microarray Analysis using R, and Perl. - * Custom designed cell, tissue and data tracking system in perl - * Analysis of MA results using Gene Ontology - * Literature minining using custom designed Perl scripts to search pubmed. -* Jun. 2000-Jun 2001: Computer Resource Coordinator for [UC Riverside](http://www.ucr.edu) - * Network administration/design of a 2000+ node network - * developed web based registration system using bash, dhcp, perl, php and mysql - * Developed network monitoring system - ([rnm](http://rnm.sourceforge.net)) using php, mysql, perl, and - snmp. - * Supervised a staff of 13 RCCs
  • Administration of 7+ Unix Servers (Apache,ISC DHCP, MySQL, mod_perl, slash) -
  • Computer Lab Administration (NT) -
  • Developed a printer recharge/tracking system using card readers, perl, mysql, and lpr-ng -
  • Developed a customer-tech Help Request System/Billing System using php, mysql, smtp, and perl - -Skills ------- - - -Projects --------- -[Current projects|projects] - -References ----------- -Available Upon Request. +Research Focus +-------------- + +My primary research focus is developing and using bioinformatics +techniques to identify causes and mechanisms underlying human +diseases, such as Systemic Lupus Erythematosus (SLE). I have +identified multiple novel genes associated with SLE using both +genome-wide association studies and trio-based studies in targeted +regions. In collaborative work, I have identified a causal variant in +NCF2 +([rs17849502](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs17849502)) +using both *in silico* and *in vitro* approaches. I am currently +working on identifying causal variants in additional associated genes +using targeted deep sequencing using high-throughput variant analysis +pipelines to prioritize variants for additional *in silico* and *in +vitro* experiments. In the future, utilizing my extensive +bioinformatic and software development experience, I will head a +development group working on techniques for the storage, alignment, +and analysis of terabytes (eventually petabytes) of next-generation +sequencing data from collaborations studying human-relevant diseases +and biological systems. + + +Teaching Mission +---------------- + +While teaching, my primary mission is to have my students experience +the excitement of scientific discovery for themselves. Secondarily, I +use that excitement to keep them engaged and interested in the +material. While a graduate student at UC Riverside, I was a teaching +assistant for [Introductory Biology, Genetics, Molecular Biology, and +Developmental Biology](http://www.biology.ucr.edu/courses/UGcourses.html) + diff --git a/resume/curriculum_vitae.mdwn b/resume/curriculum_vitae.mdwn new file mode 100644 index 0000000..e71f215 --- /dev/null +++ b/resume/curriculum_vitae.mdwn @@ -0,0 +1,160 @@ +[[!meta title="Curriculum Vitæ"]] +Curriculum Vitæ +=============== + +[Don Armstrong](http://www.donarmstrong.com/) + + + +Education +---------- +* Doctor of Philosophy + * 2001-2008 *Cell, Molecular and Developmental Biology*. + [University of California at Riverside](http://www.ucr.edu). + Dissertation: The Role of membrane Composition in the Activity of + Membrane-Associated Signal Transduction Proteins. +* Bachelor of Science + * 1997-2001 [Biology](http://bio.ucr.edu). + [University of California at Riverside](http://www.ucr.edu). + +Postdoctoral Experience +------------------------- + +### University of Southern California ### + +* 2013--Present. Postdoctoral researcher under Chaim O. Jacob. + Identifying genes and causal alleles associated with Systemic Lupus + Erythematosus using genome-wide association, next-generation + sequencing, computational and biochemical approaches. +* 2009--2010. Postdoctoral researcher under Florence M. Hofman. + Identifying signaling pathways which are responsible for the + functional alteration of endothelial cells in glioblastoma + multiforme and arteriovenous malformations. + +### University of California at Riverside ### +* 2010--2012. Postdoctoral researcher under Raphael Zidovetzki. + Identifying genes which are associated with Systemic Lupus + Erythematosus using prior information and targeted trio-based + studies. + +Teaching +-------- +### Teaching Assistant ### +* 2004--2007. University of California at Riverside. First and second + quarter introduction to biology for majors (BIO 5A and 5B). + Introduction to Genetics (BIO 102), Human Embryology (CBNS 169). + +Work in Industry +---------------- +### Non-Profit ### +* 2004--Present. [Debian Project](http://www.debian.org), Developer; + Technical Committee Member (2010--Present) + +### Employment Experience ### +* 2002-2003. *Socratech* in Rochester, NY. Bioinformatics researcher: + developed new microarray analysis methods for a start-up + biotechnology company working on developing treatments for + Alzheimer's disease + +Publications +------------ +### In Preparation ### +1. *Don L. Armstrong*, Raphael Zidovetzki, and Chaim O Jacob. Novel + lupus associated genes discovered in GWAS; two signals explain all + HLA SNPs in European Americans. /In preparation/. + +## Refereed Publications ## +1. Chaim O Jacob, Miriam Eisenstein, Mary C Dinauer, Wenyu Ming, + Qiang Liu, Sutha John, Francesco P Quismorio, Andreas Reiff, Barry + L Myones, Kenneth M Kaufman, Deborah McCurdy, John B Harley, Earl + Silverman, Robert P Kimberly, Timothy J Vyse, Patrick M Gaffney, + Kathy L Moser, Marisa Klein-Gitelman, Linda Wagner-Weiner, Carl D + Langefeld, *Don L Armstrong*, and Raphael Zidovetzki. + Lupus-associated causal mutation in neutrophil cytosolic factor 2 + (NCF2) brings unique insights to the structure and function of + NADPH oxidase. /Proc Natl Acad Sci USA/, 109(2):59--67, Jan 2012. +2. *Don L Armstrong*, Omer Markovitch, Raphael Zidovetzki, and Doron + Lancet. Replication of simulated prebiotic amphiphile vesicles + controlled by experimental lipid physicochemical properties. /Phys + Biol/, 8(6):066001, Dec 2011. + +3. Christopher J Stapleton, *Don L Armstrong*, Raphael Zidovetzki, + Charles Y Liu, Steven L Giannotta, and Florence M Hofman. + Thrombospondin-1 modulates the angiogenic phenotype of human + cerebral arteriovenous malformation endothelial cells. + /Neurosurgery/, 68(5):1342--53, May 2011. + +4. *D L Armstrong*, A Reiff, B L Myones, F P Quismorio, M + Klein-Gitelman, D McCurdy, L Wagner-Weiner, E Silverman, J O + Ojwang, K M Kaufman, J A Kelly, J T Merrill, J B Harley, S-C Bae, T + J Vyse, G S Gilkeson, P M Gaffney, K L Moser, C Putterman, J C + Edberg, E E Brown, J Ziegler, C D Langefeld, R Zidovetzki, and C O + Jacob. Identification of new SLE-associated genes with a two-step + Bayesian study design. /Genes Immun/, 10(5):446--56, Jul 2009. + +5. Chaim O Jacob, Jiankun Zhu, *Don L Armstrong*, /et al./ + Identification of IRAK1 as a risk gene with critical role in the + pathogenesis of systemic lupus erythematosus. /Proc Natl Acad Sci + USA/, 106(15):6256--61, Apr 2009. + +6. Bahram Namjou, Andrea L Sestak, *Don L Armstrong*, Raphael + Zidovetzki, /et al./ High-density genotyping of STAT4 reveals + multiple haplotypic associations with systemic lupus erythematosus + in different racial groups. /Arthritis Rheum/, 60(4):1085--95, Apr 2009. + +7. *Don Armstrong* and Raphael Zidovetzki. Amplification of + diacylglycerol activation of protein kinase c by cholesterol. + /Biophys J/, 94(12):4700--10, Jun 2008. + +8. *Don L Armstrong*, Chaim O Jacob, and Raphael Zidovetzki. + Function2gene: a gene selection tool to increase the power of + genetic association studies by utilizing public databases and + expert knowledge. *BMC Bioinformatics*, 9:311, 2008. + +9. Chaim O Jacob, Andreas Reiff, *Don L Armstrong*, Barry L Myones, + Earl Silverman, Marisa Klein-Gitelman, Deborah McCurdy, Linda + Wagner-Weiner, James J Nocton, Aaron Solomon, and Raphael + Zidovetzki. Identification of novel susceptibility genes in + childhood-onset systemic lupus erythematosus using a uniquely + designed candidate gene pathway platform. /Arthritis Rheum/, + 56(12):4164--73, Dec 2007. + +10. Raphael Zidovetzki, Burkhard Rost, /Don L Armstrong/, and Israel + Pecht. Transmembrane domains in the functions of fc receptors. + /Biophys Chem/, 100(1-3):555--75, 2003. + +11. *Don L Armstrong*, Dan B Borchardt, and Raphael Zidovetzki. + Synergistic perturbation of phosphatidylcholine/sphingomyelin + bilayers by diacylglycerol and cholesterol. /Biochem Biophys Res + Commun/, 296(4):806--12, Aug 2002. + +12. Zhenhua Wu, Huang Guo, Nienwen Chow, Jan Sallstrom, Robert D Bell, Rashid + Deane, Andrew I Brooks, Suhasini Kanagala, Anna Rubio, Abhay Sagare, Dong + Liu, Fang Li, *Don Armstrong*, Thomas Gasiewicz, Raphael Zidovetzki, Xiaomei + Song, Florence Hofman, and Berislav V Zlokovic. Role of the meox2 homeobox gene in neurovascular dysfunction in + alzheimer disease. /Nat Med/, 11(9):959--65, Sep 2005. + +13. Rashid Deane, Shi Du Yan, Ram Kumar Submamaryan, Barbara LaRue, + Suzana Jovanovic, Elizabeth Hogg, Deborah Welch, Lawrence Manness, + Chang Lin, Jin Yu, Hong Zhu, Jorge Ghiso, Blas Frangione, Alan + Stern, Ann Marie Schmidt, \textbf{Don L Armstrong}, Bernd Arnold, + Birgit Liliensiek, Peter Nawroth, Florence Hofman, Mark Kindy, + David Stern, and Berislav Zlokovic. Rage mediates amyloid-beta + peptide transport across the blood-brain barrier and accumulation + in brain. /Nat Med/, 9(7):907--13, Jul 2003. + +Selected Presentations +---------------------- +### Conference Presentations ### +* 2007-06-07. FOCIS 2007. Uniquely designed candidate gene + identification platform discovers novel genes in childhood-onset + SLE. + +Projects +-------- +[Current projects|projects] + +References +---------- +Please e-mail for references + diff --git a/resume/research_statement.mdwn b/resume/research_statement.mdwn new file mode 100644 index 0000000..397d4b6 --- /dev/null +++ b/resume/research_statement.mdwn @@ -0,0 +1,225 @@ + + +# Research Objectives + +## Uncovering genetic causes of diseases using a multidisciplinary bioinformatics-driven approach + + + +My research focuses on designing and using bioinformatics techniques +to identify causes and mechanisms underlying human diseases such as +Systemic Lupus Erythematosus, Glioblastoma Multiforme, and +Arteriovenous Malformations followed be designing appropriate +diagnostics and treatment methods. Once identified, I work with +collaborators to verify the bioinformatics-discovered mechanisms +utilizing *in silico*, *in vitro*, and *in vivo* techniques, and +develop therapeutic and diagnostic techniques to identify and treat +the underlying human disorder. Cell-culture-based methods are utilized +as the first step in designing multi-target treatments, followed by +appropriate animal models.. + +# Unique Qualifications + +## Straddling Biology, Computer Science, and Statistics + +In addition to being a cellular and molecular biologist, I have +extensive experience in algorithm design, computer programming, and +statistics. The combination of these areas enables me to handle +biological problems which involve large numbers of samples and data +and require statistical analysis which can address confounders which +are often present in non-laboratory settings. It also gives me a +unique perspective which enables me to design novel methods to analyze +and interpret large amounts of data. + +## Multidisciplinary approach + +I have published in multiple disciplines, including membrane +biophysics, bioinformatics, genetics, and cellular biology. My +experiences in these fields and my experiences while transitioning +fields has allowed me to apply unique insights garnered from my +previous work to new topics leading to novel approaches and +breakthrough discoveries. + +# Previous Research Projects + + + +## Genetic Basis of System Lupus Erythematosus (SLE) + +I developed novel bioinformatic methods which increase + + +likelihood of identifying reproducible genetic associations using +prior knowledge from publicly available databases and expert +information \cite{Armstrong2008:function2gene}. Using these methods, I +was able to identify genes previously unassociated with SLE in a +trio-based study \cite{Jacob2007:ar_lupus}. These genes were then +replicated in a larger case-control study which was funded by the NIH +on the basis of the original findings +\cite{Jacob2009:sle_irak1,Armstrong2009:sle_gi}. Among other findings, +this larger study identified a missense allele in NCF2 (H389Q, +rs17849502) which was associated with SLE. Collaborative work +indicated that H389Q altered the binding energy of NCF2 with VAV1 +using docking simulations, and in vitro experiments confirmed that +H389Q altered NADPH oxidase function \cite{Jacob2012:sle_ncf2}, thus +identifying it as a causative SLE mutation. + +## Cancer Stem Cells in Glioblastoma + +Glioblastoma is a almost invariably fatal form of brain cancerwhich is +diagnosed in \(\approx\) 9,000 people in the US annually. It is typified +by high levels of chemotherapeutic-resistant recurrences, some of +which is likely caused by cancer stem cells which are insensitive to +many chemotherapeutic agents. In collaboration with Florence Hoffman +at USC, I have classified glioblastoma-derived cancer stem cells and +cancer cell lines into distinct classes using gene microarrays and +various clustering approaches, which will enable the design of a +class-specific treatment of this devastating disease. + +## Regulatory pathways underlying cranial arteriovenous malformations + +The mechanisms underlying the formation of arteriovenous +malformations(AVMs) which +occur in the brain are unknown. Using gene microarrays, qtPCR, and *in +vitro* experiments on primary human endothelial cells cultured from +resected AVMs, I indentified multiple gene regulation pathways, many +of them novel, including the Id1/Thsb1 inhibitory pathway. Additional +experiments indicated that the *in vitro* pathology of endothelial +cells could be partially rescued using extracellular Thsb1 +\cite{Stapleton2011:thbs1}. + +# Future research directions + +## Identification of causal mutations in SLE + +While many regions and SNPs which are associated with SLE have been +identified, few of those regions have identified causal alleles with +known function. Furthermore, even for regions with identified causal +alleles, no systematic searches have been performed to identify +additional causal regions. Continuing my existing collaboration with +Chaim O. Jacob, I will rectify this by + +1. Deep sequencing the associated regions in 500 lupus cases and 1000 controls + +2. Identifying which newly found variants are associated with SLE + +3. Selecting variants with a high likelihood of producing functional variants + +4. Verifying biological relevance of variants by *in vitro* study + +5. Verifying functional relevance in human subjects + +## Developing analysis tools for massive amounts of sequencing data + +The ability to cheaply and rapidly sequence large numbers of samples +has massively increased the amount of data processing required by +researchers. Compounding this increase in data, most existing tools +have not been designed to take full advantage of the current advances +in computer architecture, which parallel solutions to problems which +can be run on architectures with vastly differing computational +abilities (such as GPUs). + +To resolve this, I am in the process of actively developing new open +source tools which are capable of running on massively parallel +architectures using both multiple computers (openMPI) and multiple +GPUs on the same computer (Nvidia's CUDA) to + +1. Develop an open source massively parallel imputation method which + can combine existing GWAS results with new deep sequencing + and genetic profiling results. + +2. Extend same tools to call SNPs both incrementally and in parallel. + +I am currently working on extending samtools (an Open Source SNP +calling suite) to support running on multiple computers. + +## Gut microbiota alteration in SLE + +Many autoimmune disorders are known to be affected by gut microbiota. +Preliminary evidence suggests that mice which develop SLE have +differences in gut microbiota from mice which do not develop SLE, +which suggests that SLE severity may also be affected by differences +in human gut microbiota. I am currently developing novel methods to + +1. Determine which gut microbiota differ between mice with and + without SLE and using 16S sequencing + +2. Determine which gut microbiota differ between humans with and + without SLE using 16S sequencing, given #1. + +## Continuous, incremental analysis + +Just as science requires continuous testing of hypotheses, +bioinformatics is slowly moving towards continuous incremental +analysis of data. Most current tools use iterative analysis, where +analyses must be completely re-run with each new piece of data that is +obtained. When the amount of data remains small relative to the +overall computing power available, this is a feasible approach. +However, as the amount of data increases, it stops being feasible to +completely reanalyze data as new data is obtained, and incremental +analysis approaches are necessary. I will be working to extend +existing analysis pipelines to handle the incremental analysis of +data. + +# Research Funding + +## Funding Opportunities + +I anticipate obtaining funding from the following sources to pursue +the research goals outlined previously: + +1. National Institute of Health + + 1. [Research Project Grant (RO1)](http://grants.nih.gov/grants/guide/pa-files/PA-13-302.html) (NHGRI, NIAID, BISTI) + + 2. [NLM Career Development Award in Biomedical Informatics (K01)](http://grants.nih.gov/grants/guide/pa-files/PAR-13-284.html) + + 3. [Continued Development and Maintenance of Software (R01)](http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html) (extending existing biofinformatics software) + +2. Alliance for Lupus Research + + 1. [Target Identification in Lupus](http://www.lupusresearch.org/news-and-events/press-releases/til.html) + +3. Institution specific funding + +## Track Record of Funding + +The projects that I am proposing have a strong track record of being +funded by both the NIH and the Alliance for Lupus Research. + +# Wider impact of research agenda + + +My research will identify genetic variants and pathways underlying SLE +and other important human diseases, leading to better methodologies +for both the diagnosis and treatment of those diseases, and resulting +in significant decreases is patient morbidity and mortality. +Secondarily, the tools that I develop to effect this work will enable +researchers in other fields to more rapidly and cheaply identify +relevant factors for economically and environmentally important +phenotypes, such as pathogen-resistance in crops or +disease-susceptibility in thylocenes. Furthermore, as all of my tools +will be released under Open Source licenses, external researchers will +be able to build upon and improve my tools without being forced to +reinvent them. + + +\newpage + +\printbibliography +
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    Direct artery to vein connection without an +intervening capilary bed; leads to high pressure arterial flow in +venous tissue and can lead to hemmorrhage and death.

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It is also quite rewarding to see the glimmer of +insight in my students eyes when they finally reach understanding for +themselves. + +# General Goals for Students + +## Desire and Excitement + +If my students are *only* interested in learning the material I am +teaching to earn credit, then I have failed as a teacher. I want to +covey at least some of my excitement in the subject to them. +Perhaps it's naïve, but I think that once students are excited about +the material, they are more likely to succeed. + +## Informed Skepticism + +While only a small percentage of my students will become scientists, I +want them all to know how science works, how to analyze claims, weigh +evidence, do background research, and come to an independent +understanding of nature. From politics to the latest false claim on +the Internet, an ability to become informed, think critically, and +analyze skeptically will help my students be conscientious members of +our democratic society. + +# How I Teach + +## Task Analysis + + +For each course, I identify course-specific overall goals that I want +all of my students to achieve. Then, I plan a path to these goals, +with a hierarchy of sub-goals along the way. This enables me to +measure the effectiveness of my teaching and the students' progress at +each step during the course. For example, in an introductory +bioinformatics course, an overall goal might be to have students be +able to use common bioinformatic databases to answer biological +questions. A corresponding sub goal would be for students to be able +to use dbSNP to select all genetic variants in a specific gene in a +specific organism. + +## Learn By Doing + +Even though lecturing, demonstrations, and similar passive learning +techniques are important, everyone learns best by doing. Mistakes, +failure, experimentation, and learning from them are important parts +of learning by doing, just as they are in science. To the greatest +extent possible, I want to provide opportunities for students to learn +by doing. I want students to learn by solving problems using the +knowledge and resources they have gained in the course. + +## Individual Engagement + +In large courses it is very difficult to keep individual students +engaged, as they feel they are just one face in a hundred and have +limited opportunities to ask questions. When lecturing, I like to +combat this by asking students questions directly, and getting +students (even those at the back) to participate in demonstrations. I +will also be accessible both in-person on campus, and via e-mail. +Finally, I will encourage my teaching assistants (TAs) to be engaged +with our students by asking TAs about students in their sections in TA +meetings. + +## Students Teaching Others + + +Having every student engaged with a teacher is a laudable goal, and +may be achievable in small in large ones, there will always +be some people who are not reached. Students teaching other students +is one method of extending a teacher's reach. In the past, I have had +online forums or mailing lists for all courses that I have taught. In +these forums, students are able to ask questions, and other students +are able to answer them. In addition, students are able to reinforce +their learning by answering other student's questions. You know a +concept when you can teach others. + +## Technology + +Classroom technology is very useful in increasing the ability of +students to learn, experiment, and measuring outcomes in the +classroom. I plan on using: + +1. Interactive websites to enable student's active learning by doing, + including exercises, experiments, and other activities. + +2. Real-time online feedback using automated grading on a website to + the extent possible on homework so students know whether they + understand the material. + +3. In-lecture questions through clickers or smart phones when the + course is too large to gauge student understanding of material by + asking questions of students or raising hands. + +4. Recording lectures so that students (and I) can refer to them + later. + +5. Forums, mailing lists, and other communication methods so that + students can learn cooperatively. When students explain material to + other students, it answers other student's questions and reinforces + their own knowledge. + +6. Demonstrations in class and online, both real and simulated, when + appropriate to the material being taught. + +# Measuring Outcomes + +## Success and Failure + +I'm continuing to study how to be a more effective teacher by learning +from other teachers and research into teaching techniques, and will +continue to do that as long as I teach. I will measure the outcomes of +my teaching in order to determine how effective I am. By correlating +the teaching methods I use for each sub-goal of my course with student +outcomes, over time I can identify the most effective teaching +strategies for me. + +# Teaching Experiences + +## Teaching Assistant + +While a graduate student at UC Riverside, I was a teaching assistant +for Introductory Biology, Introductory +Genetics, Molecular Biology, and Developmental Biology. +
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