From: Don Armstrong Date: Tue, 28 Nov 2017 21:30:33 +0000 (-0800) Subject: rework resume to hilight novozyme skills X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=refs%2Fheads%2Fnovozymes_bioinformatician;p=resume.git rework resume to hilight novozyme skills --- diff --git a/dla-resume.org b/dla-resume.org index 4c9717b..636fac0 100644 --- a/dla-resume.org +++ b/dla-resume.org @@ -37,67 +37,6 @@ ** UC Riverside + *PhD* in Cell, Molecular and Developmental Biology + *BS* in Biology -* 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-written 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. - -#+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 @@ -116,6 +55,15 @@ ** Debian Developer + 2004--Present. \emph{Debian Project}, Developer; Technical Committee Member (2010--2016), Technical Committee Chair (2015--2016). +* Publications/Presentations ++ 22 peer-reviewed refereed publications cited over 1700 times: + https://dla2.us/pubs ++ Publication record in GWAS, expression analysis of microarrays, + 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 + * Authored Software + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux distribution. [[https://bugs.debian.org]] @@ -124,16 +72,67 @@ 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 -+ 20 peer-reviewed refereed publications cited over 1700 times: - https://dla2.us/pubs -+ Publication record in GWAS, expression analysis of microarrays, - 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 +#+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 +* Skills +** Bioinformatics and Computational Biology ++ Illumina sequencing and array-based Genomics and Epigenomics of + complex eukaryotic phenotypes using *RNA-seq*, targeted DNA + sequencing, *RRBS*, Illumina bead arrays, and Affymetrix microarrays + from sample collection to publication. ++ Reproducible, scalable bioinformatics analysis using unix tools, + *R*, and *python* on cloud- and cluster-based systems on + terabyte-scale datasets ++ 16S rRNA analysis of microbiota and metagenomics ++ Alignment, annotation, and variant calling using existing and + custom-written software, including *GATK*, *bwa*, *STAR*, and + *kallisto*. +# + Using evolutionary genomics to identify causal human variants +# + Reproducible research +** Biology, Biochemistry, and Genetics ++ PCR, immunohistochemistry, protein quantification, biochemical + assays ++ Maintenance and characterization of primary and transformed cell + lines +** Big Data ++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure, + 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, sh ++ Collaborative Development: git, travis +# + 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 +** Interdisciplinary Teams ++ *H3A Bionet*: Workflows and cloud resources for H3 Africa ++ *Psychiatric Genomics Consortium*: Identification of genetic + correlates of PTSD. ++ *SLEGEN*: SLE genetics consortium. + +* Funding/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 @@ -152,5 +151,3 @@ \end{minipage} #+END_EXPORT - -