Timothy Stephens
Curriculum vitae

```{r setup, include=FALSE} knitr::opts_chunk$set(echo = FALSE) library(tidyverse) library(knitr) library(lubridate) source("utility-functions.R") #### publications ##### publications <- read_csv("../publications.csv") %>% mutate(date=paste(publication_date_year, publication_date_month, publication_date_day, sep='-')) %>% mutate(year = publication_date_year) %>% filter(include_in_full_cv == 'y') %>% arrange(-publication_date_year, -publication_date_month, -publication_date_day) #### cv entries ##### cv_entries <- read_csv("../cv_entries.csv") %>% filter(include_in_full_cv == 'y') %>% mutate(date_start=paste(date_start_year, date_start_month, date_start_day, sep='-')) %>% mutate(date_end=paste(date_end_year, date_end_month, date_end_day, sep='-')) %>% mutate(year_begin = date_start_year) %>% mutate(year_end = date_end_year) %>% mutate(year = ifelse((is.na(year_end) | year_begin == year_end), year_begin, str_c(year_begin, " --- ", year_end))) %>% mutate(across(2:4, as.numeric)) %>% arrange(-date_start_year, -date_start_month, -date_start_day) ```

```{block type="grid-item", echo=TRUE} ## Personal summary {.summary} I am a computational biologist working on understanding the forces that govern the interactions between organisms in ecologically critical environments, such as coral reefs, and the forces that drive major evolutionary transitions, such as the one that gave rise to the first photosynthetic Eukaryotas. I am also CEO of OceanOmics, a company dedicated to developing salable tools for environmental health monitoring. ``` ```{block type='grid-item', echo=TRUE} ## Contact information {.box}

| left | Left | |:-|:--------------------------------------------| | |Department of Biochemistry and Microbiology, Rutgers University, USA| | | ts942\@sebs.rutgers.edu | | | [timothystephens.github.io](https://timothystephens.github.io) | | | [TimothyStephens](https://github.com/TimothyStephens) | | | [\@timstep1383](https://mobile.twitter.com/timstep1383) |

```

## Education and Research Experience {.nohead .set-width-range} ```{r} cv_entries %>% filter(type == 'education') %>% mutate(what = str_c(what, ", ", where)) %>% select(year, what) %>% kable() ``` ## Awards and honours {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'awards') %>% mutate(what = str_c(what, ", ", where)) %>% select(year_begin, what) %>% kable() ``` ## Publications {.nohead .set-width-year} ```{r} publications %>% mutate(ref2print = str_c(authors_full, " ", title, ". *", journal, "*")) %>% mutate(ref2print = ifelse(!is.na(ref_info), str_c(ref2print, ", ", ref_info, ", ", year(date), "."), str_c(ref2print, ", ", year(date), ".")) ) %>% mutate(ref2print = ifelse(!is.na(preprint), str_c(ref2print, " [[Preprint](", preprint, ")]"), ref2print) ) %>% mutate(ref2print = ifelse(!is.na(url), str_c(ref2print, " [[URL](", url, ")]"), ref2print) ) %>% mutate(ref2print = ifelse(!is.na(pdf), str_c(ref2print, " [[PDF](", pdf, ")]"), ref2print) ) %>% mutate(ref2print = ifelse(!is.na(additional_info), str_c(ref2print, " ", additional_info), ref2print) ) %>% select(year, ref2print) %>% #manual_page_break_after_row("ref2print", "Inferring phylogenomic relationship of microbes using scalable alignment-free methods") %>% #manual_page_break_after_row("ref2print", "encode tandemly repeated single-exon genes with adaptive functions") %>% knitr::kable() ``` ## Grants {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'minor_grants' | type == 'major_grants') %>% mutate(what = if_else(!is.na(additional_info), str_c(what, ", ", additional_info, ", ", where), str_c(what, ", ", where))) %>% select(year_begin, what) %>% #manual_page_break_after_row("what", "Funds to continue development of our coral health monitoring toolkit.") %>% kable() ``` ## Teaching experience {.nohead .set-width-range} ```{r} cv_entries %>% filter(type == 'teaching') %>% mutate(what = ifelse(!is.na(additional_info), str_c("", what, "
", where, "
", additional_info), str_c("", what, "
", where))) %>% select(year, what) %>% manual_page_break_after_row("what", "Duties included guiding undergraduate chemistry students through") %>% kable() ``` ## Professional development {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'prof-dev') %>% mutate(what = str_c(what, ", ", where)) %>% select(year_begin, what) %>% #manual_page_break_after_row("what", "UQ Idea Hub") %>% kable() ``` ## Talks {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'talk') %>% select(year_begin, what) %>% manual_page_break_after_row("what", "22-26th March 2021") %>% kable() ``` ## Poster presentations {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'poster') %>% select(year_begin, what) %>% kable() ``` ## Media coverage {.nohead .set-width-year} ```{r} cv_entries %>% filter(type == 'media') %>% select(year_begin, what) %>% #manual_page_break_after_row("what", "Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis") %>% kable() ``` ## Service {.nohead .set-width} ```{r} cv_entries %>% filter(type == 'service') %>% mutate(year_end = ifelse(year_end == "present", "", year_end)) %>% mutate(where = ifelse(!is.na(url), str_c("[", where, "](", url, ")"), where)) %>% mutate(what = str_c(what, ", ", where)) %>% select(year, what) %>% #manual_page_break_after_row("what", "Associate Editor: Symbiotic and Parasitic Protists section") %>% kable() ``` ## Patents {.nohead .set-width} ```{r} cv_entries %>% filter(type == 'patent') %>% mutate(what = ifelse(!is.na(additional_info), str_c(what, "
", additional_info), what)) %>% select(year, what) %>% kable() ``` ```{r eval=FALSE} ## Reference letter writers {.nohead .set-width} Prof. Debashish Bhattacharya (dbhattac@rutgers.edu) Dr. Cheong Xin Chan (c.chan1@uq.edu.au) Dr. Arthur Grossman (arthurg@stanford.edu) ``` ```{r eval=FALSE} ## Personal skills & volunteering {.nohead .set-width} cv_entries %>% filter(type == 'volunteering') %>% mutate(what = str_c("", what, "
", where)) %>% mutate(what = ifelse(!is.na(additional_info), str_c(what, "
", additional_info), what)) %>% select(year, what) %>% kable() ```

Timothy G. Stephens