From: Don Armstrong Date: Wed, 21 Feb 2018 00:29:41 +0000 (-0800) Subject: rename dla-resume.org to don_armstrong_resume.org X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=0336d02a78b905e2d1f1e4be4b48705021a83417;p=resume.git rename dla-resume.org to don_armstrong_resume.org --- diff --git a/.gitignore b/.gitignore index ed83e5e..d49ea0f 100644 --- a/.gitignore +++ b/.gitignore @@ -7,8 +7,8 @@ auto *.bcf *.blg *.run.xml -dla-resume.pdf -dla-resume.tex -dla-resume.fls -dla-resume.txt +don_armstrong_resume.pdf +don_armstrong_resume.tex +don_armstrong_resume.fls +don_armstrong_resume.txt references.bib diff --git a/Makefile b/Makefile index bfd885a..ff9a3c8 100644 --- a/Makefile +++ b/Makefile @@ -4,13 +4,13 @@ EMACSARGS=--batch -l ~/.emacs EMACS=emacs -all: dla-resume.pdf +all: don_armstrong_resume.pdf -# dla-resume.pdf: dla-resume.tex $(wildcard *.bib) +# don_armstrong_resume.pdf: don_armstrong_resume.tex $(wildcard *.bib) # latexmk -pdf -pdflatex="xelatex -interaction=nonstopmode" -bibtex -use-make $< -dla-resume.pdf: dla-resume.org dlaresume.cls +don_armstrong_resume.pdf: don_armstrong_resume.org dlaresume.cls $(EMACS) $(EMACSARGS) --visit $< \ --eval "(setq org-latex-remove-logfiles nil)" \ --funcall org-latex-export-to-pdf diff --git a/dla-resume.org b/dla-resume.org deleted file mode 100644 index 9604e25..0000000 --- a/dla-resume.org +++ /dev/null @@ -1,113 +0,0 @@ -#+OPTIONS: ^:nil -#+OPTIONS: toc:nil -#+TITLE: Resume -#+AUTHOR: Don L. Armstrong -#+LATEX_CMD: xelatex -#+LATEX_CLASS: dlaresume -# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] - -* 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 -** 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 -+ *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 -# + Using evolutionary genomics to identify causal human variants -** Statistics -+ Statistical modeling (regression, inference, prediction, and - learning in very large (> 1TB) datasets) -+ Addressing confounders and batch effects -# + Reproducible research -** Big Data -+ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) -+ Inter-process communication: MPI, OpenMP -+ Filestorage: Gluster, CEFS, GPFS, Lustre -+ Linux system administration -** Mentoring and Leadership -+ Mentored graduate students and Outreachy and Google Summer of Code - interns -+ Former chair of Debian's Technical Committee -+ Head developer behind https://bugs.debian.org -** Software Development -+ Languages: perl, R, C, C++, python, groovy, sh, make -+ Collaborative Development: git, travis, continuous integration, - automated testing -+ 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. -* Authored Software -+ *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux - distribution. [[https://bugs.debian.org]] -+ *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R. -+ *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which - 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 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 -+ 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role: - Co-PI -+ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian - inference to identify disease-causing genetic variants* Role: - Primary Investigator -+ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 - RFA-HD-16-037) Role: Key Personnel -+ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. - Role: Key Personnel -** Scholarships and Fellowships -+ 2001--2003: University of California, Riverside Doctoral Fellowship -+ 1997--2001: Regents of the University of California Scholarship. - - - diff --git a/don_armstrong_resume.org b/don_armstrong_resume.org new file mode 100644 index 0000000..9604e25 --- /dev/null +++ b/don_armstrong_resume.org @@ -0,0 +1,113 @@ +#+OPTIONS: ^:nil +#+OPTIONS: toc:nil +#+TITLE: Resume +#+AUTHOR: Don L. Armstrong +#+LATEX_CMD: xelatex +#+LATEX_CLASS: dlaresume +# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks] + +* 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 +** 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 ++ *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 +# + Using evolutionary genomics to identify causal human variants +** Statistics ++ Statistical modeling (regression, inference, prediction, and + learning in very large (> 1TB) datasets) ++ Addressing confounders and batch effects +# + Reproducible research +** Big Data ++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) ++ Inter-process communication: MPI, OpenMP ++ Filestorage: Gluster, CEFS, GPFS, Lustre ++ Linux system administration +** Mentoring and Leadership ++ Mentored graduate students and Outreachy and Google Summer of Code + interns ++ Former chair of Debian's Technical Committee ++ Head developer behind https://bugs.debian.org +** Software Development ++ Languages: perl, R, C, C++, python, groovy, sh, make ++ Collaborative Development: git, travis, continuous integration, + automated testing ++ 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. +* Authored Software ++ *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux + distribution. [[https://bugs.debian.org]] ++ *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R. ++ *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which + 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 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 ++ 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role: + Co-PI ++ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian + inference to identify disease-causing genetic variants* Role: + Primary Investigator ++ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 + RFA-HD-16-037) Role: Key Personnel ++ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. + Role: Key Personnel +** Scholarships and Fellowships ++ 2001--2003: University of California, Riverside Doctoral Fellowship ++ 1997--2001: Regents of the University of California Scholarship. + + +