X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=dla-resume.org;h=9604e257ca88b4a8603a7ad2c370e0c49e0ad877;hb=ce83b2150998c0083af725daccb4b281484ad9ba;hp=6f2498543419f675664ba10cc7c718888fb8612e;hpb=62f24a7da8322071af24da6464c0648d54ad34b9;p=resume.git diff --git a/dla-resume.org b/dla-resume.org index 6f24985..9604e25 100644 --- a/dla-resume.org +++ b/dla-resume.org @@ -1,110 +1,81 @@ #+OPTIONS: ^:nil #+OPTIONS: toc:nil #+TITLE: Resume -#+AUTHOR: Don Armstrong +#+AUTHOR: Don L. Armstrong #+LATEX_CMD: xelatex #+LATEX_CLASS: dlaresume -#+LATEX_CLASS_OPTIONS: [10pt,breaklinks] +# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] -#+BEGIN_EXPORT latex - %% Name - \noindent{\color{headings}\fontsize{24pt}{24pt}\selectfont {\textsc{\textbf{\myauthor}}}} - \hfill - \begin{minipage}[t]{0.0in} - % dummy (needed here) - \end{minipage} -% \medskip - % Address and contact block - \hfill - \begin{minipage}[t]{1.7in} - \flushright {\footnotesize - \myphone \\ - \href{mailto:\myemail}{\myemail} \\ - \href{\myweb}{\myweb}} - \end{minipage} - % - \begin{minipage}[t]{0.75in} - \qrcode[tight,level=L,link,height=0.75in]{https://dla2.us/res} - \end{minipage} - -% \medskip - -#+END_EXPORT - -#+BEGIN_EXPORT latex -\begin{minipage}[t]{0.4\textwidth} -#+END_EXPORT +* Experience +** Research Scientist at UIUC \hfill 2015--2017 ++ Epigenetic modifications associated with PTSD, the genomic basis of + the development of parturition in mammals, and detecting adverse + pregnancy outcomes using urinary exosomes. +** Postdoctoral Researcher at USC \hfill 2013--2015 ++ Identifying genes and causal alleles associated with Systemic Lupus + Erythematosus using genome-wide association, next-generation + sequencing, computational and biochemical approaches. +** Postdoctoral Researcher at UCR \hfill 2010--2012 ++ Identifying genes which are associated with Systemic Lupus + Erythematosus using prior information and targeted trio-based + studies. +** Debian Developer \hfill 2004--Present ++ \emph{Debian Project}, Developer; Technical Committee Member + (2010--2016), Technical Committee Chair (2015--2016). * Education -** UC Riverside -+ *PhD* in Cell, Molecular and Developmental Biology -+ *BS* in Biology +** Doctor of Philosophy (PhD) \hfill UC Riverside + + Cell, Molecular and Developmental Biology. +** Batchelor of Science (BS) in Biology \hfill UC Riverside + * Skills ** Genomics and Epigenomics -+ Genomics and Epigenomics of complex human diseases including - PTSD, Systemic Lupus Erythematosus, and Alzheimer's Disease using - cross-sectional and longitudinal experimental designs ++ *NGS* and array-based Genomics and Epigenomics of complex human + diseases using *RNA-seq*, targeted DNA sequencing, *RRBS*, Illumina + bead arrays, and Affymetrix microarrays from sample collection to + publication. ++ Reproducible, scalable bioinformatics analysis using make, + *nextflow*, and *cwl* based workflows on cloud- and cluster-based + systems on terabyte-scale datasets ++ Alignment, annotation, and variant calling using existing and custom + software, including *GATK*, *bwa*, *STAR*, and *kallisto*. + Correcting for and experimental design to overcome multiple testing, confounders, and batch effects using Bayesian and frequentist methods approaches -+ Reproducible, scalable analysis using workflows on cloud- and - cluster-based systems on terabyte-scale datasets -+ Using evolutionary genomics to identify causal human variants +# + Using evolutionary genomics to identify causal human variants ** Statistics -+ Statistical modeling ++ Statistical modeling (regression, inference, prediction, and + learning in very large (> 1TB) datasets) + Addressing confounders and batch effects -+ Reproducible research +# + Reproducible research ** Big Data -+ Parallel and Cloud Computing -+ Inter-process communication: MPI, OpenMP, Hadoop ++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) ++ Inter-process communication: MPI, OpenMP + Filestorage: Gluster, CEFS, GPFS, Lustre -+ Cloud based-infrastructure: Azure, AWS, Docker, cloud-init -+ Debian GNU/Linux system administration ++ Linux system administration ** Mentoring and Leadership + Mentored graduate students and Outreachy and Google Summer of Code interns -+ Chairperson of the Debian Technical Committee ++ Former chair of Debian's Technical Committee + Head developer behind https://bugs.debian.org ** Software Development -+ Languages: perl, R, C, C++, python, groovy, assembly, sh, make ++ Languages: perl, R, C, C++, python, groovy, sh, make + Collaborative Development: git, travis, continuous integration, automated testing -+ Databases: Postgresql (PL/SQL), SQLite, Mysql ++ Web, Mobile: Shiny, jQuery, JavaScript ++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL ++ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel, + Powerpoint +** Communication ++ Strong written communication skills as evidenced by publication + record ++ Strong verbal and presentation skills as evidenced by presentation + and teaching record # ** Consortia Involvement # + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa # + *Psychiatric Genomics Consortium*: Identification of epigenetic # variants which are correlated with PTSD. # + *SLEGEN*: System lupus erythematosus genetics consortium. - -#+BEGIN_EXPORT latex -\end{minipage} - \hfill - \begin{minipage}[t]{0.0in} - % dummy (needed here) - \end{minipage} - \medskip -\hfill -\begin{minipage}[t]{0.55\textwidth} - -#+END_EXPORT -* Experience -** Research Scientist at UIUC -+ 2015--Present. University of Illinois at Urbana-Champaign. Epigenetic - modifications associated with PTSD, the genomic basis of the - development of parturition in mammals, and detecting adverse - pregnancy outcomes. -** Postdoctoral Researcher at USC -+ 2013--2015. Identifying genes and causal alleles associated with - Systemic Lupus Erythematosus using genome-wide association, - next-generation sequencing, computational and biochemical - approaches. -** Postdoctoral Researcher at UCR -+ 2010--2012. Identifying genes which are associated with Systemic - Lupus Erythematosus using prior information and targeted trio-based - studies. -** Debian Developer with the Debian Project -+ 2004--Present. \emph{Debian Project}, Developer; Technical Committee - Member (2010--Present), Technical Committee Chair (2015--2016). * Authored Software + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux distribution. [[https://bugs.debian.org]] @@ -113,13 +84,15 @@ enables Bayesian approaches to significance testing. + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel protein projections. [[http://rzlab.ucr.edu/scripts/wheel]] -* Publications -+ 20 peer-reviewed refereed publications cited over 1700 times -+ Publication record in GWAS, expression analysis - -#+BEGIN_EXPORT latex -\end{minipage} -#+END_EXPORT +* Publications and Presentations ++ 24 peer-reviewed publications cited over 1800 times: + https://dla2.us/pubs ++ Publication record in GWAS, expression analysis of microarrays, SLE, + GBM, epigenetics, comparative evolution of mammals, and lipid + membranes ++ H index of 11 ++ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open + Source: https://dla2.us/pres * Funding and Awards ** Grants @@ -128,39 +101,13 @@ + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian inference to identify disease-causing genetic variants* Role: Primary Investigator -+ BD2K Mentored Career Development Award: *Predicting individualized* - *chemotherapeutic treatment outcomes using large multi-omics and* - *clinical datasets* (K01 RFA-ES-16-002) (under review) Role: PI -+ *Mechanism of PR Resistance in Endometriosis* (R01 RFA-HD-16-036) - (under review) Role: Co-PI + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 - RFA-HD-16-037) (under review) Role: Key Personnel -+ *Molecular Transducers of Physical Activity Bioinformatics Center* - (U24 RFA-RM-15-012) (under review) Role: Key Personnel + RFA-HD-16-037) Role: Key Personnel + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. Role: Key Personnel -** Conference Awards -+ 2007 FOCIS Trainee Award -+ 2009 FOCIS Trainee Award ** Scholarships and Fellowships + 2001--2003: University of California, Riverside Doctoral Fellowship + 1997--2001: Regents of the University of California Scholarship. -* Service -** Consortiums -+ *H3A Bionet*: Generating workflows and cloud resources for - bioinformatics analysis as part of the H3 Africa consortium -+ *Psychiatric Genomics Consortium*: Identification of epigenetic - variants which are correlated with PTSD. -+ *SLEGEN*: System lupus erythematosus genetics consortium. -** Mentoring -+ *Laren Riesche*: Differential methylation of marmoset placentas - using RRBS. Statistical training and bioinformatics training - resulting in PhD in Nursing. 2016-2017. -+ *Christine Y. Chan*: Ancestral trees for disease predictions. 2016 -+ *[[https://developers.google.com/open-source/gsoc/2006/][Phillip Kern]]*: GUI for Debian's bug tracking system. -+ *[[https://gnome.org/opw/][Virginia King]]*: Improving documentation of Debian's Bug Tracking system. -** Reviewing -+ /Ad hoc/ reviewer for PLoS One.