Merge branches 'master' and 'master' of https://github.com/treangenla…

…b/treangenlab.github.io

CUSTOMIZE.md

@@ -44,9 +44,9 @@ All changes made to this file are only visible after you rebuild the website. Th
 
 ## Modifying the CV information
 
-There are currently 2 different ways of generating the CV page content. The first one is by using a json file located in [assets/json/resume.json](assets/json/resume.json). It is a [known standard](https://jsonresume.org/) for creating a CV programmatically. The second one, currently used as a fallback when the json file is not found, is by using a yml file located in [\_data/cv.yml](_data/cv.yml). This was the original way of creating the CV page content and since it is more human readable than a json file we decided to keep it as an option.
+There are currently 2 different ways of generating the CV page content. The first one is by using a json file located in [assets/json/resume_ae.json](assets/json/resume.json). It is a [known standard](https://jsonresume.org/) for creating a CV programmatically. The second one, currently used as a fallback when the json file is not found, is by using a yml file located in [\_data/cv.yml](_data/cv.yml). This was the original way of creating the CV page content and since it is more human readable than a json file we decided to keep it as an option.
 
-What this means is, if there is no resume data defined in [\_config.yml](_config.yml) and loaded via a json file, it will load the contents of [\_data/cv.yml](_data/cv.yml). If you want to use the [\_data/cv.yml](_data/cv.yml) file as the source of your CV, you must delete the [assets/json/resume.json](assets/json/resume.json) file.
+What this means is, if there is no resume data defined in [\_config.yml](_config.yml) and loaded via a json file, it will load the contents of [\_data/cv.yml](_data/cv.yml). If you want to use the [\_data/cv.yml](_data/cv.yml) file as the source of your CV, you must delete the [assets/json/resume.json](assets/json/resume_ae.json) file.
 
 ## Modifying the user and repository information
 

_bibliography/papers.bib

@@ -76,6 +76,7 @@ @article{balaji2022komb
 @article{balaji2022seqscreen,
         bibtex_show={true},
 	selected={true},
+	altmetric={130006025},
 	google_scholar_id={CHSYGLWDkRkC},
 	title        = {SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning},
 	author       = {Balaji, Advait and Kille, Bryce and Kappell, Anthony D and Godbold, Gene D and Diep, Madeline and Elworth, RA Leo and Qian, Zhiqin and Albin, Dreycey and Nasko, Daniel J and Shah, Nidhi and others},
@@ -169,6 +170,7 @@ @article{curry2022emu
 	bibtex_show={true},
 	google_scholar_id={1sJd4Hv_s6UC},
 	selected={true},
+	altmetric={130469175},
 	title        = {Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data},
 	author       = {Curry, Kristen D and Wang, Qi and Nute, Michael G and Tyshaieva, Alona and Reeves, Elizabeth and Soriano, Sirena and Wu, Qinglong and Graeber, Enid and Finzer, Patrick and Mendling, Werner and others},
 	year         = 2022,
@@ -833,6 +835,7 @@ @article{sapoval2022current
 	title        = {Current progress and open challenges for applying deep learning across the biosciences},
 	selected={true},
 	google_scholar_id={1qzjygNMrQYC},
+	altmetric={125736934},
 	author       = {Sapoval, Nicolae and Aghazadeh, Amirali and Nute, Michael G and Antunes, Dinler A and Balaji, Advait and Baraniuk, Richard and Barberan, CJ and Dannenfelser, Ruth and Dun, Chen and Edrisi, Mohammadamin and others},
 	year         = 2022,
 	journal      = {Nature Communications},

_pages/about.md

@@ -20,9 +20,9 @@ social: true # includes social icons at the bottom of the page
 
 Welcome to the Treangen lab website, a bioinformatics and computational biology research group at Rice University, led by Dr. Todd J. Treangen (Associate Professor in the Department of Computer Science and affiliated Associate Professor in the Department of Bioengineering). 
 
-Since launching in 2018, the Treangen lab has focused on developing scalable and accurate computational algorithms, methods, and open-source software tools to answer research questions specific to (i) identifying and tracking intentionally and unintentionally created biothreats, (ii) detecting and characterizing microbial pathogens, and (iii) tracking microbial genome and microbiome variation across time and space in the environment and human-host-associated microbiomes.
+Since launching in 2018, the Treangen lab has focused on developing scalable and accurate computational algorithms, methods, and open-source software tools to answer research questions specific to: (i) identifying and characterizing known and novel microbial pathogens, (ii) population scale microbial genome variation and evolution, and (iii) studying microbial communities across time and space in the environment and human-host-associated microbiomes.
 
-The Treangen lab is actively funded by CDC, NIH (NIAID), and NSF (EF, IIS, SHF). Prior support from: c3.ai DTI, DHS, IARPA, and NIH. 
+The Treangen lab is actively funded by CDC, NIH (NIA, NIAID), and NSF (EF, IIS, SHF). Prior support from: c3.ai DTI, DHS, IARPA, and NIH. 
 
 <div class="row">
     <div class="col-sm mt-3 mt-md-0">

_profiles/rdoughty.md

@@ -9,3 +9,5 @@ related_publications: true
 ---
 
 Ryan (1st year PhD student, Computer Science), obtained his BS in Computer Science from Case Western Reserve University. During his undergraduate studies, he worked with Dr. Treangen on large-scale wastewater analyses and targeted metagenomic sequencing methods. He also spent six months in Vigo, Spain, working in Dr. David Posada’s lab, focusing on gut-virome biomarkers in colorectal cancer. Additionally, he interned at Intellia Therapeutics for a summer, where he contributed to developing machine learning methods for CRISPR Cas-9 guide design. Ryan's current research interests center around comprehending the global virosphere through viral genomic analyses.
+
+A few of Ryan's recent publications: {% cite mccall2023targeted %}.