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index.xml
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<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>JRaviLab</title>
<link>/</link>
<atom:link href="/index.xml" rel="self" type="application/rss+xml" />
<description>JRaviLab</description>
<generator>Source Themes Academic (https://sourcethemes.com/academic/)</generator><language>en-us</language><copyright>© Janani Ravi, 2024</copyright><lastBuildDate>Fri, 07 Jul 2023 00:00:00 +0000</lastBuildDate>
<image>
<url>/img/jananiravi-grp-webpage-logo.png</url>
<title>JRaviLab</title>
<link>/</link>
</image>
<item>
<title>The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition</title>
<link>/publication/ggt_saureus/</link>
<pubDate>Fri, 07 Jul 2023 00:00:00 +0000</pubDate>
<guid>/publication/ggt_saureus/</guid>
<description></description>
</item>
<item>
<title>MolEvolvR BTS: When and how to build a web-app and software package?</title>
<link>/talk/2023-glbio/</link>
<pubDate>Mon, 15 May 2023 13:00:00 +0000</pubDate>
<guid>/talk/2023-glbio/</guid>
<description><p>Workshop material:
<a href="https://github.com/jraviLab/2023-glbio" target="_blank" rel="noopener">https://github.com/jraviLab/2023-glbio</a></p>
<p>Hosted w/
<a href="https://jravilab.github.io/authors/jacob-d-krol" target="_blank" rel="noopener">Jake Krol</a>, Faisal Alquaddoomi</p>
</description>
</item>
<item>
<title>Feedback in the β-catenin destruction complex imparts bistability and cellular memory</title>
<link>/publication/wnt_bistability/</link>
<pubDate>Tue, 10 Jan 2023 00:00:00 +0000</pubDate>
<guid>/publication/wnt_bistability/</guid>
<description></description>
</item>
<item>
<title>Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria</title>
<link>/publication/avcd_vcholerae/</link>
<pubDate>Mon, 25 Jul 2022 00:00:00 +0000</pubDate>
<guid>/publication/avcd_vcholerae/</guid>
<description><p>BYH and GBS are co-primary authors.</p>
</description>
</item>
<item>
<title>DciA Helicase Operators Exhibit Diversity across Bacterial Phyla</title>
<link>/publication/dcia_evolution/</link>
<pubDate>Sun, 24 Jul 2022 00:00:00 +0000</pubDate>
<guid>/publication/dcia_evolution/</guid>
<description><p>HCB and JTB are co-primary authors. JR and CLS are co-corresponding authors.</p>
</description>
</item>
<item>
<title>Ten simple rules to host an inclusive conference</title>
<link>/publication/10sr_inclusive_conference/</link>
<pubDate>Sun, 24 Jul 2022 00:00:00 +0000</pubDate>
<guid>/publication/10sr_inclusive_conference/</guid>
<description><p>RJ and AST are co-primary authors. RJ and JR are co-corresponding authors.</p>
</description>
</item>
<item>
<title>Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri</title>
<link>/publication/inlp_listeria/</link>
<pubDate>Wed, 20 Jul 2022 00:00:00 +0000</pubDate>
<guid>/publication/inlp_listeria/</guid>
<description><p>KNC and JTB are co-primary authors. JR and JWH are co-corresponding authors.</p>
</description>
</item>
<item>
<title>Cross-database integration using evolution and machine learning to identify multiscale molecular building blocks for antibiotic resistance</title>
<link>/talk/2022-ismb/</link>
<pubDate>Thu, 14 Jul 2022 13:45:00 +0000</pubDate>
<guid>/talk/2022-ismb/</guid>
<description></description>
</item>
<item>
<title>Using Tidyverse for Genomics</title>
<link>/talk/2022-iscb_academy/</link>
<pubDate>Sat, 28 May 2022 20:00:00 +0000</pubDate>
<guid>/talk/2022-iscb_academy/</guid>
<description></description>
</item>
<item>
<title>MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny</title>
<link>/publication/molevolvr_webapp/</link>
<pubDate>Tue, 22 Feb 2022 00:00:00 +0000</pubDate>
<guid>/publication/molevolvr_webapp/</guid>
<description><p>JTB, SZC, LMS are co-primary authors who contributed equally; they are listed alphabetically.</p>
</description>
</item>
<item>
<title>How I teach Life Scientists to Build Inclusive Communities</title>
<link>/talk/2022-lst/</link>
<pubDate>Thu, 17 Feb 2022 20:00:00 +0000</pubDate>
<guid>/talk/2022-lst/</guid>
<description></description>
</item>
<item>
<title>Computational approaches to study molecular pathogenesis and intervention of infectious diseases</title>
<link>/talk/2021-cu/</link>
<pubDate>Mon, 22 Nov 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-cu/</guid>
<description></description>
</item>
<item>
<title>Reconciling Multiple Connectivity Scores for Drug Repurposing</title>
<link>/publication/connectivity_scores/</link>
<pubDate>Fri, 05 Nov 2021 00:00:00 +0000</pubDate>
<guid>/publication/connectivity_scores/</guid>
<description><p>KS and PT are co-primary authors. AK and JR are co-corresponding authors.</p>
</description>
</item>
<item>
<title>Strategies to build a strong diverse AsiaR community</title>
<link>/talk/2021-bioc_asia/</link>
<pubDate>Wed, 03 Nov 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-bioc_asia/</guid>
<description></description>
</item>
<item>
<title>MolEvolvR: A webapp for characterizing proteins using molecular evolution and phylogeny</title>
<link>/talk/2021-ismb/</link>
<pubDate>Tue, 27 Jul 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-ismb/</guid>
<description></description>
</item>
<item>
<title>Incubator: Stop reinventing the wheel: R package(s) for conference and abstract management</title>
<link>/talk/2021-user_rconference/</link>
<pubDate>Fri, 09 Jul 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-user_rconference/</guid>
<description></description>
</item>
<item>
<title>MolEvolvR: Web-app and R-package for characterizing proteins using molecular evolution and phylogeny</title>
<link>/talk/2021-user/</link>
<pubDate>Fri, 09 Jul 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-user/</guid>
<description></description>
</item>
<item>
<title>Incubator: Strategies to build a strong AsiaR community</title>
<link>/talk/2021-user_asiar/</link>
<pubDate>Thu, 08 Jul 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-user_asiar/</guid>
<description></description>
</item>
<item>
<title>Using a computational molecular evolution and phylogeny to study pathogenic proteins</title>
<link>/talk/2021-glbio/</link>
<pubDate>Thu, 13 May 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-glbio/</guid>
<description><p>Related: Samuel Z Chen GLBio poster [video])(
<a href="https://www.youtube.com/watch?v=6rj3eTWxXkg" target="_blank" rel="noopener">https://www.youtube.com/watch?v=6rj3eTWxXkg</a>)</p>
</description>
</item>
<item>
<title>Making cool publication quality tables w/ R</title>
<link>/talk/2021-rlpune/</link>
<pubDate>Sun, 09 May 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-rlpune/</guid>
<description></description>
</item>
<item>
<title>RLadies+ featuring useR! meetup</title>
<link>/talk/2021-rladies_user/</link>
<pubDate>Wed, 28 Apr 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-rladies_user/</guid>
<description></description>
</item>
<item>
<title>Using Tidyverse for Genomics</title>
<link>/talk/2021-rltunis_rlbgl/</link>
<pubDate>Sat, 24 Apr 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-rltunis_rlbgl/</guid>
<description></description>
</item>
<item>
<title>S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens</title>
<link>/publication/slps_grampos/</link>
<pubDate>Thu, 15 Apr 2021 00:00:00 +0000</pubDate>
<guid>/publication/slps_grampos/</guid>
<description></description>
</item>
<item>
<title>MolEvolvR: a web-app for molecular evolution and phylogeny</title>
<link>/talk/2021-beacon/</link>
<pubDate>Fri, 26 Mar 2021 20:00:00 +0000</pubDate>
<guid>/talk/2021-beacon/</guid>
<description></description>
</item>
<item>
<title>Discovery of a predominant and distinct lineage of Mycobacterium tuberculosis in Brazilian indigenous population</title>
<link>/publication/brazil_genomes_mtb/</link>
<pubDate>Wed, 13 Jan 2021 00:00:00 +0000</pubDate>
<guid>/publication/brazil_genomes_mtb/</guid>
<description></description>
</item>
<item>
<title>Computational evolutionary approaches</title>
<link>/project/pathogenic-features/</link>
<pubDate>Sat, 10 Oct 2020 00:00:00 +0000</pubDate>
<guid>/project/pathogenic-features/</guid>
<description><h2 id="summary">Summary</h2>
<p>We are developing an integrated computational evolutionary framework that will bring together: 1) molecular evolution and phylogeny; and 2) comparative genomics/pangenomics to study any pathogen-group or protein family, and discover distinctive protein/genomic features relevant to biological comparisons of interest (such as identifying diagnostic or candidate vaccine targets in emerging, poorly characterized pathogens).</p>
<h2 id="team">Team</h2>
<h3 id="students">Students</h3>
<h4 id="current">Current</h4>
<ul>
<li>Joe Burke</li>
<li>Elliot Majlessi</li>
<li>Vignesh Sridhar</li>
<li>Ethan Wolfe</li>
</ul>
<h4 id="alumni">Alumni</h4>
<ul>
<li>Samuel Chen</li>
<li>Lo Sosinski</li>
<li>Karn Jongnarangsin</li>
<li>Lauryn Brooks</li>
</ul>
<h3 id="collaborators">Collaborators</h3>
<ul>
<li>Neal Hammer, MSU (Staphylococci)</li>
<li>Srinand Sreevatsan, Robert Abramovitch, and Andrew Olive (MSU), Christina Stallings, WUSTL (Mycobacteria)</li>
<li>Antonella Fioravanti, VUB Brussels (<em>B. anthracis</em>)</li>
<li>Chris Waters, MSU (Vibrio)</li>
<li>Jonathan Hardy, MSU (Listeria)</li>
<li>Stephanie Shames, KSU (Legionella)</li>
<li>Priya Shah, UCD (Flaviviruses)</li>
<li>Sean Crosson, MSU (Brucella, Caulobacter)</li>
</ul>
</description>
</item>
<item>
<title>sRNA discovery</title>
<link>/project/srna/</link>
<pubDate>Sat, 10 Oct 2020 00:00:00 +0000</pubDate>
<guid>/project/srna/</guid>
<description><h2 id="summary">Summary</h2>
<p>We are developing computational approaches to detect unique pathogenic (and host) small RNA in infected hosts (human and non-human).</p>
<h2 id="team">Team</h2>
<h3 id="students">Students</h3>
<ul>
<li>Philip Calhoun</li>
<li>Elliot Majlessi</li>
</ul>
<h3 id="collaborators">Collaborators</h3>
<ul>
<li>Srinand Sreevatsan (Mycobacteria)</li>
</ul>
</description>
</item>
<item>
<title>Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players</title>
<link>/publication/psp_evolution/</link>
<pubDate>Fri, 25 Sep 2020 00:00:00 +0000</pubDate>
<guid>/publication/psp_evolution/</guid>
<description></description>
</item>
<item>
<title>Phylogenetics & Comparative Genomics | MMG801</title>
<link>/talk/2020-mmg/</link>
<pubDate>Tue, 08 Sep 2020 09:00:00 +0000</pubDate>
<guid>/talk/2020-mmg/</guid>
<description></description>
</item>
<item>
<title>Computational evolutionary approaches for understanding pathogen proteins and genomes</title>
<link>/talk/2020-beacon/</link>
<pubDate>Thu, 13 Aug 2020 16:15:00 +0000</pubDate>
<guid>/talk/2020-beacon/</guid>
<description></description>
</item>
<item>
<title>Computational evolutionary approaches to characterize bacterial proteins</title>
<link>/talk/2020-ismb/</link>
<pubDate>Tue, 14 Jul 2020 03:00:00 +0000</pubDate>
<guid>/talk/2020-ismb/</guid>
<description></description>
</item>
<item>
<title>Molecular Evolution and Phylogeny</title>
<link>/talk/2020-cbp/</link>
<pubDate>Thu, 27 Feb 2020 09:00:00 +0000</pubDate>
<guid>/talk/2020-cbp/</guid>
<description></description>
</item>
<item>
<title>RLEL Workshop on RMarkdown & Reproducible Research</title>
<link>/talk/2020-rmarkdown/</link>
<pubDate>Mon, 24 Feb 2020 18:00:00 +0000</pubDate>
<guid>/talk/2020-rmarkdown/</guid>
<description><img src="https://raw.githubusercontent.com/rladies-eastlansing/meetup-presentations/master/event-flyers/202001to04-Spring-meetup-flyer.png" width="60%" />
</description>
</item>
<item>
<title>RLEL Workshop on DataViz 2.0</title>
<link>/talk/2020-rlel-dataviz2.0/</link>
<pubDate>Mon, 10 Feb 2020 18:00:00 +0000</pubDate>
<guid>/talk/2020-rlel-dataviz2.0/</guid>
<description><img src="https://raw.githubusercontent.com/rladies-eastlansing/meetup-presentations/master/event-flyers/202001to04-Spring-meetup-flyer.png" width="60%" />
</description>
</item>
<item>
<title>Tidyverse for Genomics</title>
<link>/talk/2020-plb/</link>
<pubDate>Wed, 05 Feb 2020 09:00:00 +0000</pubDate>
<guid>/talk/2020-plb/</guid>
<description></description>
</item>
<item>
<title>The Staphylococcus aureus cystine transporters, TcyABC and TcyP, facilitate nutrient sulfur acquisition during infection</title>
<link>/publication/tcy_saureus/</link>
<pubDate>Sun, 01 Dec 2019 00:00:00 +0000</pubDate>
<guid>/publication/tcy_saureus/</guid>
<description></description>
</item>
<item>
<title>Computational approaches for understanding host–pathogen biology</title>
<link>/talk/2019-cocoh/</link>
<pubDate>Tue, 27 Aug 2019 11:00:00 +0000</pubDate>
<guid>/talk/2019-cocoh/</guid>
<description></description>
</item>
<item>
<title>Conservation and modularity in the pan-bacterial psp stress response system</title>
<link>/talk/2019-grampos/</link>
<pubDate>Fri, 26 Jul 2019 03:00:00 +0000</pubDate>
<guid>/talk/2019-grampos/</guid>
<description></description>
</item>
<item>
<title>An integrative computational evolutionary approach to accelerate the discovery of molecular targets in prevalent under-studied pathogens</title>
<link>/talk/2019-cbps/</link>
<pubDate>Thu, 16 May 2019 09:00:00 +0000</pubDate>
<guid>/talk/2019-cbps/</guid>
<description></description>
</item>
<item>
<title>Using Tidyverse for Genomics workshop</title>
<link>/talk/2019-iitm/</link>
<pubDate>Tue, 05 Mar 2019 14:00:00 +0000</pubDate>
<guid>/talk/2019-iitm/</guid>
<description></description>
</item>
<item>
<title>Tidyverse workshop</title>
<link>/talk/2019-plb/</link>
<pubDate>Wed, 13 Feb 2019 09:00:00 +0000</pubDate>
<guid>/talk/2019-plb/</guid>
<description></description>
</item>
<item>
<title>Simple rules to make an effective scientific presentation</title>
<link>/talk/2019-cvm/</link>
<pubDate>Thu, 24 Jan 2019 12:00:00 +0000</pubDate>
<guid>/talk/2019-cvm/</guid>
<description></description>
</item>
<item>
<title>Join us!</title>
<link>/joinus/</link>
<pubDate>Tue, 15 Jan 2019 00:00:00 +0000</pubDate>
<guid>/joinus/</guid>
<description><h1 id="open-positions">Open positions</h1>
<p>
<a href="#postdoctoral-researcher">Postdoc</a> |
<a href="#scientific-programmer">Scientific programmer</a> |
<a href="#graduate-students">Grad students</a> |
<a href="#undergraduate-students">Undergrads</a> |
<a href="#visiting-scientist">Visiting scientist</a></p>
<h2 id="postdoctoral-researcher">Postdoctoral Researcher</h2>
<p>We are looking for a talented and motivated individual to join the JRaviLab (PI: Dr. Janani Ravi) at the
<a href="https://medschool.cuanschutz.edu/ai" target="_blank" rel="noopener">Center for Health AI</a>, University of Colorado, Anschutz Medical Campus as a postdoctoral researcher. In our group, we develop/apply computational approaches to analyze and visualize multiscale biological data to study microbial phenotypes and diseases, including genomes, protein sequence-structural features, transcriptomes, and pathway memberships.
Postdocs will contribute to this vision by 1) developing new computational approaches to analyze and integrate large collections of biological data, 2) applying these approaches to specific problems in microbiology and infectious diseases, and 3) communicating the methods and discoveries openly to the broader biomedical/clinical community.</p>
<p>In addition to participating in ongoing projects, we strongly encourage postdocs to come up with several research ideas, jointly develop them into creative projects, and lead the way in those new directions. We encourage postdocs to apply for federal/foundational fellowships.</p>
<p>We are committed to building a diverse team and sustaining an inclusive and supportive environment; we strongly encourage underrepresented minorities in STEM to apply, including but not limited to BIPOC and LGBTQIA+ folks. The position is open to international applicants, in addition to US citizens/permanent residents.</p>
<h3 id="qualifications">Qualifications</h3>
<ol>
<li>A PhD or equivalent, with a strong background in bioinformatics, computational biology, genetics/microbiology, statistics, computer science, machine learning, or other closely related fields.</li>
<li>Programming experience in R or Python w/ version control (Git). Experience with handling large datasets in a Unix/Linux environment, high-performance cluster computing is a plus. Familiarity with bioinformatics databases and tools would also be a bonus.</li>
<li>Good communication skills, willingness to collaborate openly, give/take constructive feedback, and sustain a friendly and fun lab culture.</li>
</ol>
<h3 id="what-will-you-get">What will you get</h3>
<ol>
<li>Freedom to work on your best ideas broadly aligned with the lab’s vision.</li>
<li>Several opportunities to collaborate with fantastic computational, experimental, and clinical researchers at the Center for Health AI and beyond.</li>
<li>Resources to develop your own research program and your technical skills as you plan to move to the next stage of your career.</li>
<li>Opportunities to mentor students, participate in peer-review and grant-writing, international conferences, and, based on your interests, participate in education and outreach activities.</li>
<li>A vibrant, supportive environment: A bunch of really smart and fun colleagues at CHAI and DBMI; Workspace in a contemporary open-office layout in the magnificent new Health Science building with a fabulous view of the Rocky Mountains, easy access to cafeterias; Beautiful campus; Supportive department environment and postdoctoral association (including slack) for professional development; Competitive salary commensurate with experience.</li>
<li>Mentoring &amp; support: In addition to being your scientific mentor, my primary responsibility is to help your personal and professional growth by facilitating all of the above. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests. You will also have the option to form a formal mentoring committee.</li>
<li>Inclusive, friendly, and supportive environment for underrepresented minorities in STEM and quantitative sciences, and safe space for members across all intersectionalities.</li>
</ol>
<h3 id="apply--find-out-more">Apply | Find out more</h3>
<p>If you have questions or want to chat about this position, please write to me (
<a href="mailto:janani.ravi@cuanschutz.edu">janani.ravi@cuanschutz.edu</a>). If you are interested in something like this, it’s never too early to reach out!
To apply, apply to this posting with 1) a detailed CV that includes a link to your Google Scholar page and a list of publications, 2) a cover letter that includes a description of your research accomplishments, how your interests connect with our group’s work, what might be some lines of future work that you are interested in, and what your future professional goals are, and 3) names &amp; contact information for three references.</p>
<p><strong>Benefits</strong>:
<a href="https://www.cu.edu/employee-services/benefits" target="_blank" rel="noopener">https://www.cu.edu/employee-services/benefits</a> |
<a href="https://www.cu.edu/employee-services/benefits-wellness/new-employee/PBO/post-doc" target="_blank" rel="noopener">postdoc benefits</a> <br>
<strong>Total Compensation Calculator</strong>:
<a href="https://www.cu.edu/employee-services/total-compensation" target="_blank" rel="noopener">https://www.cu.edu/employee-services/total-compensation</a> <br>
<strong>Diversity and Equity</strong>: Please contact
<a href="mailto:hr.adacoordinator@ucdenver.edu">hr.adacoordinator@ucdenver.edu</a> for information on disability accommodations.</p>
<hr>
<h2 id="scientific-programmer">Scientific Programmer</h2>
<p>We are looking for coding enthusiasts to join the JRaviLab as scientific programmers. In our group, we develop/apply computational approaches to analyze and visualize multiscale biological data to study microbial phenotypes and diseases, including genomes, protein sequence-structural features, transcriptomes, and pathway memberships.</p>
<p>The programmer is expected to contribute most of the code that goes into our analytical pipelines (that utilize high-performance clusters and cloud infrastructure) and production-ready webservers. They are expected to maintain high standards for code documentation, clarity, efficiency, and maintainability. In addition to maintaining these standards in their own code, they should set high expectations for other lab members and share their expertise to improve the code that all members of the lab are writing.
We are committed to building a diverse team and sustaining an inclusive and supportive environment; we strongly encourage underrepresented minorities in STEM to apply, including but not limited to BIPOC, LGBTQIA+ folks. The position is open to international applicants, in addition to US citizens/permanent residents.</p>
<h3 id="qualifications-1">Qualifications</h3>
<ol>
<li>Excellent programming skills in R and/or Python, Unix/Linux, shell scripting, and version controlling (with Git). Familiarity with bioinformatics databases/tools and setting up bioinformatics workflows would be a plus.</li>
<li>Experience in web development: R/Shiny, SQL, HTML5, CSS, and JavaScript.</li>
<li>It is a plus if you have experience with a) High-performance cluster computing, b) Distributed task queue, c) RESTful web services, d) Docker containers.</li>
<li>Have high coding standards for writing efficient, clear, well-documented, version-controlled code (Git).</li>
<li>Good communication skills, willingness to collaborate openly, give/take constructive feedback, and sustain a friendly and fun lab culture.</li>
</ol>
<h3 id="what-will-you-get-1">What will you get</h3>
<ol>
<li>Work on data science / machine learning applied to both pathogen and host research in infectious diseases, supported by ample computational resources.</li>
<li>Mentor me, trainees, and students to inculcate high standards of writing and maintaining code.</li>
<li>Publish papers on creative tools and pipelines, publish/maintain open-source software projects, and present in scientific meetings/conferences.</li>
<li>A vibrant, supportive environment: A bunch of really smart and fun colleagues; Office in a fancy central building with easy access to cafeterias; Beautiful campus; Low cost-of-living; Competitive salary commensurate with experience.</li>
<li>Guidance &amp; support: In addition to being your expert partner, my primary responsibility is to help your personal and professional growth. You will always find in me an audience to discuss opportunities/challenges and a strong advocate for your interests.</li>
<li>Safe space for underrepresented minorities in STEM and quantitative sciences.</li>
</ol>
<p>Additionally, you will also have the following if you are interested in pursuing a research career.</p>
<ol start="7">
<li>Freedom to work on your best ideas broadly aligned with the lab’s vision.</li>
<li>Several opportunities to collaborate with other smart computational and experimental researchers at MSU &amp; elsewhere.</li>
<li>Resources to develop your own research program and your technical skills as you plan to move to the next stage of your career.</li>
<li>Opportunities to mentor students, participate in peer-review and grant-writing, and, based on your interests, participate in teaching, education, and outreach activities.</li>
</ol>
<h3 id="apply--find-out-more-1">Apply | Find out more</h3>
<p>If you have questions or want to chat about this position, please write to me.
To apply, send me an
<a href="mailto:janani.ravi@cuanschutz.edu">email</a> with your detailed CV, highlighting your released software, reusable packages, and/or code repositories (GitHub), and names and contact information for three references. If you are interested in something like this, it’s never too early to reach out!</p>
<hr>
<h2 id="graduate-students">Graduate Students</h2>
<p>We are looking for highly motivated graduate students interested in developing computational approaches to study microbial function, phenotypes, and diseases. You will be a perfect fit if you have a background in bioinformatics, computational biology, statistics/biostatistics, computer science, microbiology/immunology, genetics/genomics, or related fields. Having programming experience in R, Python is a huge plus. In addition to these technical qualifications, we are looking for someone who can work well in a team, work hard, and give/take constructive feedback.</p>
<p>This research experience will give you the opportunity to i) use data analysis and visualization to address key biological questions as pertaining to molecular evolution, diagnosis, and treatment (using R), ii) present at group meetings, journals, technical workshops and conferences, iii) develop high coding standards for writing efficient, clear, well-documented, version-controlled code, iv) equip yourself professional for your next career step.</p>
<h3 id="start-a-conversation">Start a conversation</h3>
<p>Please send me your latest CV and a cover letter that includes i) a summary of your academic/work experience, ii) description of relevant coursework, research experience (incl. publications, conference talks/posters), iii) a brief note on familiarity in the field of phylogenetics, molecular evolution, and comparative pathogenomics, iv) coding experience, if any. If you are already at MSU, please
<a href="mailto:janani.ravi@cuanschutz.edu">email me</a> to set a time to meet and discuss your interest.</p>
<h3 id="want-to-rotate">Want to rotate?</h3>
<p>We welcome CU Denver | Anschutz students to rotate with us, esp. those from the
<a href="https://www.cuanschutz.edu/graduate-programs/biomedical-sciences-program/home" target="_blank" rel="noopener">Biomedical Sciences Program</a>,
<a href="https://www.cuanschutz.edu/graduate-programs/cell-biology-stem-cells-and-development/home" target="_blank" rel="noopener">Computational Biosciences</a>,
<a href="https://www.cuanschutz.edu/graduate-programs/microbiology/home" target="_blank" rel="noopener">Microbiology</a>,
<a href="https://www.cuanschutz.edu/graduate-programs/immunology/home" target="_blank" rel="noopener">Immunology</a>, and
<a href="https://www.cuanschutz.edu/graduate-programs/human-medical-genetics-and-genomics/home" target="_blank" rel="noopener">Human Medical Genetics and Genomics</a>.</p>
<hr>
<h2 id="undergraduate-students">Undergraduate Students</h2>
<p>We are looking for highly motivated and quantitatively-minded undergraduate students to work on a research project developing computational approaches to study infectious diseases. Currently, we prefer students coming in with fellowships/scholarships (<em>e.g.,</em> SROP, ENSURE, REU-ACRES, BRUSH, Professorial Assistantship, or other department/college-level awards).</p>
<p>We are happy to train them in many aspects of data-intensive biology. A keen interest in bioinformatics, computational biology, statistics/biostatistics, computer science, genetics, or related fields, and prior programming experience in R, Python would be a huge plus. As part of this project, they will have the opportunity to work closely with a senior members of the group (and me) and learn to: a) work with large datasets, b) write structured, well-documented code to analyze, integrate, and visualize these datasets, c) interpret the results in the context of pathogenesis, and d) communicate the results in the form of a paper and presentation.</p>
<p>We have high expectations for their level of commitment to research, and we are keen on incorporating their contributions into co-authored papers in conferences/journals. As an undergraduate student, if you are interested in discussing research opportunities, please send me an
<a href="mailto:janani.ravi@cuanschutz.edu">email</a> to set up a time to talk.</p>
<hr>
<h2 id="visiting-scientist">Visiting Scientist</h2>
<p>We welcome visiting scientists (postbac, postgrad, postdoc, etc) to come and collaborate with us for a short period (6mo–1Y). If you have a burning question or an interesting idea that is directly related to or complements our research project(s), we would be glad to share our space, experience, and resources with you to develop your project and execute it. Having your own funding would be the easiest way to make this happen. There are some funding sources that you can apply to (e.g.,
<a href="http://www.biologists.com/travelling-fellowships/" target="_blank" rel="noopener">CoB</a>). Please send me an
<a href="mailto:janani.ravi@cuanschutz.edu">email</a> to discuss this opportunity.</p>
<hr>
<h2 id="collaboration">Collaboration</h2>
<p>If you are interested in any of our specific areas of research or have other great ideas that we could work on together,
<a href="mailto:janani.ravi@cuanschutz.edu">email me</a> right away!</p>
<p>
<a href="https://jravilab.github.io/#contact" target="_blank" rel="noopener">Contact details</a></p>
</description>
</item>
<item>
<title>2018: Year in Books | Goodreads</title>
<link>/post/goodreads-2018/</link>
<pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate>
<guid>/post/goodreads-2018/</guid>
<description>
<p>Find my latest reads &amp; recommendations on <a href="//goodreads.com/jananiravi">Goodreads</a>!</p>
<div id="myyearinbooks-summary-stats" class="section level4">
<h4><a href="https://www.goodreads.com/user/year_in_books/2018/1671098">2018: #MyYearInBooks Summary Stats</a></h4>
</div>
<div id="book-read" class="section level4">
<h4><a href="https://www.goodreads.com/review/list/1671098-janani-ravi?shelf=2018-reads">Book Read</a></h4>
</div>
</description>
</item>
<item>
<title>2019: RLEL Upcoming Events</title>
<link>/post/rlel-2019-upcoming/</link>
<pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate>
<guid>/post/rlel-2019-upcoming/</guid>
<description><h2 id="a-little-background">A little background</h2>
<p>
<a href="https://rladies-eastlansing.github.io" target="_blank" rel="noopener">R-Ladies East Lansing</a> welcomes R-enthusiasts of all proficiency levels, including aspiring and experienced R programmers, who are interested in mentoring, networking &amp; expertise upskilling. This non-profit, civil society community is designed to develop members’ R skills &amp; knowledge through social, collaborative learning &amp; sharing. Supporting minority identity access to STEM skills &amp; careers, the Free Software Movement, and contributing to the global R community!</p>
<p>Anyone and everyone interested in R/Data Science should join the group. We encourage members to actively participate, contributing as learners, teachers, developers or innovators! We encourage women and minority genders to present/lead most sessions, conversations but we have no restrictions whatsoever about who can participate in membership, discussions and other activities. Please join us and bring your R-family &amp; R-friends!</p>
<h1 id="2019-whats-next">2019: What’s next?</h1>
<h2 id="upcoming-workshops">Upcoming Workshops</h2>
<ul>
<li>Intro to Statistics w/ R (Spring; workshop series)</li>
<li>Intro to RMarkdown (Summer)</li>
<li>Intro to Shiny (Summer)</li>
<li>Intro to Version Control (Git) w/ R (Summer)</li>
</ul>
<p><strong>Register &amp; RSVP on Meetup</strong>:
<a href="https://meetup.com/rladies-eastlansing" target="_blank" rel="noopener">https://meetup.com/rladies-eastlansing</a></p>
<p>Would you like to <em>team-lead a workshop</em>? Contact us if you’d to present for 5–10 min slots within the workshop or longer if desired.</p>
<p><strong>Join</strong> the channels on <strong>Slack</strong>: #workshop-rstats #workshop-shiny #workshop-rmarkdown OR Email us:
<a href="mailto:eastlansing@rladies.org">eastlansing@rladies.org</a></p>
<h2 id="introduce-a-girl-to-engineering-2019-02-16">Introduce a Girl to Engineering (2019-02-16)</h2>
<p>Register for R-Ladies East Lansing’s activity booth:
<a href="http://meetu.ps/e/Gfntz/yBMBS/f" target="_blank" rel="noopener">http://meetu.ps/e/Gfntz/yBMBS/f</a></p>
<p>MSU Women in Engg. outreach:
<a href="http://bit.ly/msu-wie-k12-outreach" target="_blank" rel="noopener">http://bit.ly/msu-wie-k12-outreach</a></p>
<h2 id="women-in-data-science-conference-2019-04">Women in Data Science Conference (2019-04)</h2>
<p>
<a href="https://widsconference.org" target="_blank" rel="noopener">https://widsconference.org</a></p>
<p><strong>Register</strong>: TBA</p>
<p>Would like to give a talk/present a poster? Stay tuned on
<a href="https://meetup.com/rladies-eastlansing" target="_blank" rel="noopener">Meetup</a>.
Contact us:
<a href="mailto:eastlansing@rladies.org">eastlansing@rladies.org</a></p>
<h2 id="r-ladies-east-lansing-bookclub">R-Ladies East Lansing Bookclub</h2>
<h3 id="academic-incl">Academic incl.</h3>
<ul>
<li>R for Data Science</li>
<li>Learning Statistics with R</li>
<li>R programming for Data Science</li>
<li>Hands-On Programming with R</li>
</ul>
<h3 id="nonfiction-incl">Nonfiction incl.</h3>
<ul>
<li>Algorithms to Live by</li>
<li>Weapons of Math Destruction</li>
</ul>
<h3 id="blog-posts--articles-incl">Blog posts &amp; Articles incl.</h3>
<ul>
<li>Excuse me, do you have a moment to talk about version control?</li>
<li>Good enough practices in Scientific Computing</li>
<li>Happy Git w/ R</li>
</ul>
<h2 id="meetup-presentationsmaterial">Meetup Presentations/Material</h2>
<p>
<a href="https://github.com/rladies-eastlansing/meetup-presentations-eastlansing/tree/master/presentations" target="_blank" rel="noopener">GitHub</a> |
<a href="http://bit.ly/rlel-meetup-presentations-gd" target="_blank" rel="noopener">Google Drive</a> |
<a href="http://bit.ly/rlel-pics-2018" target="_blank" rel="noopener">Photos</a></p>
<h1 id="you--r-ladies-east-lansing">You &amp; R-Ladies East Lansing</h1>
<ul>
<li>
<p>Join the R-Ladies Community on Slack (
<a href="https://bit.ly/rlel-slack-signup" target="_blank" rel="noopener">https://bit.ly/rlel-slack-signup</a>)</p>
</li>
<li>
<p>Lead (or team-lead) presentations/discussions in a meetup</p>
</li>
<li>
<p>Help run the meetup(s) (help R-newbies, help pick up pizza)</p>
</li>
<li>
<p>Contribute to Blog Entries, Webpage (
<a href="https://rladies-eastlansing.github.io" target="_blank" rel="noopener">https://rladies-eastlansing.github.io</a>)</p>
</li>
<li>
<p>Be a Social Butterfly (
<a href="https://twitter.com/RLadiesELansing" target="_blank" rel="noopener">Twitter</a> |
<a href="https://facebook.com/rladieseastlansing" target="_blank" rel="noopener">Facebook</a> | Courier pigeon?)</p>
</li>
<li>
<p>Sponsor a meeting (OR help find us monthly meeting sponsors; &lt;$75)</p>
</li>
<li>
<p>Bring in a speaker and/or Bring in fellow R-users!</p>
</li>
<li>
<p>Suggest a topic &amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!</p>
</li>
<li>
<p>Getting Involved @ R-Ladies:
<a href="https://rladies.org/about-us/help/" target="_blank" rel="noopener">https://rladies.org/about-us/help/</a></p>
</li>
</ul>
<h2 id="how-to-be-in-touch">How to be in touch?</h2>
<p>Access our presentations, R scripts and more on
<a href="//github.com/rladies-eastlansing">Github</a> and follow us on twitter to stay up to date about R-Ladies news! <em>Join the
<a href="https://meetup.com/rladies-east-lansing/" target="_blank" rel="noopener">Meetup group</a> to be notified of our upcoming meetings!</em></p>
<ul>
<li>
<a href="https://www.rladies.org" target="_blank" rel="noopener">R-Ladies Global</a>
<ul>
<li>Meetup:
<a href="https://meetup.com/rladies-east-lansing/" target="_blank" rel="noopener">https://meetup.com/rladies-east-lansing/</a>
<ul>
<li>Twitter:
<a href="http://twitter.com/RLadiesELansing" target="_blank" rel="noopener">@RLadiesELansing</a> &amp;
<a href="http://twitter.com/RLadiesGlobal" target="_blank" rel="noopener">@RLadiesGlobal</a></li>
</ul>
</li>
<li>Slack:
<a href="https://rladies-eastlansing.slack.com" target="_blank" rel="noopener">https://rladies-eastlansing.slack.com</a></li>
<li>Github:
<a href="https://github.com/rladies-eastlansing" target="_blank" rel="noopener">@rladies-eastlansing</a> &amp;
<a href="https://github.com/rladies" target="_blank" rel="noopener">@rladies</a></li>
<li>E-mail:
<ul>
<li>eastlansing [at] rladies [dot] org</li>
<li>janani [at] rladies [dot] org</li>
<li>info [at] rladies [dot] org</li>
</ul>
</li>
</ul>
</li>
</ul>
<h2 id="the-team">The Team</h2>
<p><strong>Organizers</strong>:
<a href="janani@rladies.org">Janani Ravi</a>,
<a href="camille@rladies.org">Camille Archer</a></p>
<p><strong>Co-organizers</strong>: Kayla Johnson, Arjun Krishnan (~
<a href="https://thekrishnanlab.org" target="_blank" rel="noopener">Krishnan Lab</a>)</p>
<p><em>PS</em> Community Policies &amp; Code of Conduct:</p>
<p>Full community guidelines are found here:
<a href="https://github.com/rladies/starter-kit/wiki" target="_blank" rel="noopener">https://github.com/rladies/starter-kit/wiki</a></p>
</description>
</item>
<item>
<title>Bio</title>
<link>/bio/</link>
<pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate>
<guid>/bio/</guid>
<description></description>
</item>
<item>
<title>R-Ladies East Lansing: 2018, Year in Review</title>
<link>/post/rlel-2018/</link>
<pubDate>Tue, 01 Jan 2019 00:00:00 +0000</pubDate>
<guid>/post/rlel-2018/</guid>
<description>
<div id="TOC">
<ul>
<li><a href="#whats-next">2019: What’s Next?</a><ul>
<li><a href="#upcoming-workshops">Upcoming Workshops</a></li>
<li><a href="#introduce-a-girl-to-engineering-2019-02-16">Introduce a Girl to Engineering (2019-02-16)</a></li>
<li><a href="#women-in-data-science-conference-2019-04">Women in Data Science Conference (2019-04)</a></li>
<li><a href="#r-ladies-east-lansing-bookclub">R-Ladies East Lansing Bookclub</a><ul>
<li><a href="#academic-incl.">Academic incl.</a></li>
</ul></li>
</ul></li>
<li><a href="#year-in-review">2018: Year in Review</a><ul>
<li><a href="#the-team">The Team</a></li>
<li><a href="#meetup-presentationsmaterial">Meetup Presentations/Material</a></li>
<li><a href="#sponsors">2018 Sponsors</a></li>
<li><a href="#meetups">2018 Meetups</a><ul>
<li><a href="#kickoff-meeting">Kickoff meeting</a></li>
<li><a href="#lightning-talks">Lightning talks</a></li>
<li><a href="#workshops">Workshops</a></li>
</ul></li>
</ul></li>
<li><a href="#you-r-ladies-east-lansing">You &amp; R-Ladies East Lansing</a><ul>
<li><a href="#how-to-be-in-touch">How to be in touch?</a></li>
<li><a href="#organizers">Organizers</a></li>
<li><a href="#ps-community-policies-code-of-conduct"><em>PS</em> Community Policies &amp; Code of Conduct:</a></li>
</ul></li>
</ul>
</div>
<p>Thanks to everyone who attended, participated or sponsored R-Ladies East Lansing in 2018! We had a fantastic start &amp; a very successful first 6mo on campus! We hosted 7 meetups since July 2018 including two very well-attended workshops (70+ attendees) and a DataViz challenge! Help us continue spreading the R &amp; Data Science spirit across MSU in 2019! Contact us <a href="mailto:eastlansing@rladies.org" class="email">eastlansing@rladies.org</a> about co-hosting or sponsoring a meetup/workshop in Spring 2019. As always, R-Ladies events are open to all R-users across all levels of expertise including students, faculty and staff, and non-MSU folks.</p>
<div id="whats-next" class="section level1">
<h1>2019: What’s Next?</h1>
<div id="upcoming-workshops" class="section level2">
<h2>Upcoming Workshops</h2>
<p>Intro to Statistics w/ R (Spring; workshop series)
Intro to RMarkdown (Summer)
Intro to Shiny (Summer)
Intro to Version Control (Git) w/ R (Summer)</p>
<p>Register &amp; RSVP on Meetup: <a href="https://meetup.com/rladies-eastlansing" class="uri">https://meetup.com/rladies-eastlansing</a>
Would you like to team-lead a workshop? Contact us if you’d to present for 5–10 min slots within the workshop or longer if desired.
Join the channels on Slack: #workshop-rstats #workshop-shiny #workshop-rmarkdown OR Email us: <a href="mailto:eastlansing@rladies.org" class="email">eastlansing@rladies.org</a></p>
</div>
<div id="introduce-a-girl-to-engineering-2019-02-16" class="section level2">
<h2>Introduce a Girl to Engineering (2019-02-16)</h2>
<p>Register for R-Ladies East Lansing’s activity booth: <a href="http://meetu.ps/e/Gfntz/yBMBS/f" class="uri">http://meetu.ps/e/Gfntz/yBMBS/f</a>
MSU Women in Engg. outreach: <a href="http://bit.ly/msu-wie-k12-outreach" class="uri">http://bit.ly/msu-wie-k12-outreach</a></p>
</div>
<div id="women-in-data-science-conference-2019-04" class="section level2">
<h2>Women in Data Science Conference (2019-04)</h2>
<p><a href="https://widsconference.org" class="uri">https://widsconference.org</a></p>
<p>Register:
Would like to give a talk/present a poster? Stay tuned on Meetup.
Contact us: <a href="mailto:eastlansing@rladies.org" class="email">eastlansing@rladies.org</a></p>
</div>
<div id="r-ladies-east-lansing-bookclub" class="section level2">
<h2>R-Ladies East Lansing Bookclub</h2>
<div id="academic-incl." class="section level3">
<h3>Academic incl.</h3>
<ul>
<li>R for Data Science</li>
<li>Learning Statistics with R</li>
<li>R programming for Data Science</li>
<li>Hands-On Programming with R
### Nonfiction incl.</li>
<li>Algorithms to Live by</li>
<li>Weapons of Math Destruction
### Blog posts &amp; Articles incl.</li>
<li>Excuse me, do you have a moment to talk about version control?</li>
<li>Good enough practices in Scientific Computing</li>
<li>Happy Git w/ R</li>
</ul>
</div>
</div>
</div>
<div id="year-in-review" class="section level1">
<h1>2018: Year in Review</h1>
<div id="the-team" class="section level2">
<h2>The Team</h2>
<p>Organizers: Janani Ravi, Camille Archer
Other co-organizers: Kayla Johnson, Arjun Krishnan, Nate Davis</p>
</div>
<div id="meetup-presentationsmaterial" class="section level2">
<h2>Meetup Presentations/Material</h2>
<p>GitHub | Google Drive | Photos</p>
</div>
<div id="sponsors" class="section level2">
<h2>2018 Sponsors</h2>
<p><em>INSERT</em>
Grand Traverse Pie (2018-12) | Business Analytics (2018-11) | SSDA (2018-10) |
Krishnan Lab (2018-09) | College of Veterinary Medicine (2018-09) |
BEACON (2018-08) | iCER (2018-07)</p>
</div>
<div id="meetups" class="section level2">
<h2>2018 Meetups</h2>
<div id="kickoff-meeting" class="section level3">
<h3>Kickoff meeting</h3>
<p>Welcome to RLEL | Who We Are | What We Do | Upcoming Meetups</p>
<p><em>PICTURE</em></p>
</div>
<div id="lightning-talks" class="section level3">
<h3>Lightning talks</h3>
<p><strong>Aug 13, 2018</strong>
Git &amp; R by Melissa Dale
Experimental languages w/ R by Le Ni La
Having fun w/ Rcade by Kayla Johnson
Websites w/ R by Camille Archer
UpSet plots w/ R by Janani Ravi
<span class="citation">@bigdataignite</span> for their conference promo.</p>
<p><strong>Sep 10, 2018</strong>
Morphospaces w/ #Geomorph by Acacia Ackles
Integrating Python &amp; R w/ #Reticulate by Anna Yannakopoulos
Literature Survey w/ #Bibliometrix by Veronica Frans
GLM w/ #glmulti by Lauren Wisnieski
Cool #dataviz resources Data-to-Viz RGraph Gallery by Janani Ravi</p>
<p><strong>Sep 24, 2018</strong>
Spatial Humanities w/ R Rachael White
R/qtl Miranda Haus
Hyenas, Microbes &amp; R Connie Rojas
Publication quality figures w/ #ggpubr by Taylor Dunivin
R+LaTeX=knitr Cara Feldscher</p>
<p><em>COLLAGES</em></p>
</div>
<div id="workshops" class="section level3">
<h3>Workshops</h3>
<p>Intro to Tidy Data Workshop: GitHub • Google Drive
Data Visualization Workshop: GitHub • Google Drive</p>
</div>
</div>
</div>
<div id="you-r-ladies-east-lansing" class="section level1">
<h1>You &amp; R-Ladies East Lansing</h1>
<ul>
<li>Join the R-Ladies Community on Slack (bit.ly/rlel-slack-signup)</li>
<li>Lead (or team-lead) presentations/discussions in a meetup</li>
<li>Help run the meetup(s) (help R-newbies, help pick up pizza)</li>
<li>Contribute to Blog Entries, Webpage (rladies-eastlansing.github.io)</li>
<li>Be a Social Butterfly (Twitter | Facebook | Courier pigeon?)</li>
<li>Sponsor a meeting (OR help find us monthly meeting sponsors; &lt;$75)</li>
<li>Bring in a speaker and/or Bring in fellow R-users!</li>
<li><p>Suggest a topic &amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!</p></li>
<li><p>Getting Involved @ R-Ladies: <a href="https://rladies.org/about-us/help/" class="uri">https://rladies.org/about-us/help/</a></p></li>
</ul>
<div id="how-to-be-in-touch" class="section level2">
<h2>How to be in touch?</h2>
<p>Access our presentations, R scripts and more on <a href="//github.com/rladies-eastlansing">Github</a> and follow us on twitter to stay up to date about R-Ladies news! <em>Join the <a href="https://meetup.com/rladies-east-lansing/">Meetup group</a> to be notified of the first meeting in July!</em></p>
<ul>
<li><a href="https://www.rladies.org">R-Ladies Global</a>
<ul>
<li>Meetup: <a href="https://meetup.com/rladies-east-lansing/" class="uri">https://meetup.com/rladies-east-lansing/</a>
<ul>
<li>Twitter: <a href="http://twitter.com/RLadiesELansing">@RLadiesELansing</a> &amp; <a href="http://twitter.com/RLadiesGlobal">@RLadiesGlobal</a></li>
</ul></li>
<li>Slack: <a href="https://rladies-eastlansing.slack.com" class="uri">https://rladies-eastlansing.slack.com</a></li>
<li>Github: <a href="https://github.com/rladies-eastlansing">@rladies-eastlansing</a> &amp; <a href="https://github.com/rladies">@rladies</a></li>
<li>E-mail:
<ul>
<li>eastlansing [at] rladies [dot] org</li>
<li>janani [at] rladies [dot] org</li>
<li>info [at] rladies [dot] org</li>
</ul></li>
</ul></li>
</ul>
</div>
<div id="organizers" class="section level2">
<h2>Organizers</h2>
<p><a href="janani@msu.edu">Janani Ravi</a> &amp; <a href="archerc5@msu.edu">Camille Archer</a></p>
</div>
<div id="ps-community-policies-code-of-conduct" class="section level2">
<h2><em>PS</em> Community Policies &amp; Code of Conduct:</h2>
<p>Full community guidelines are found here: <a href="https://github.com/rladies/starter-kit/wiki" class="uri">https://github.com/rladies/starter-kit/wiki</a></p>
</div>
</div>
</description>
</item>
<item>
<title>Useful Resources</title>
<link>/post/useful-resources/</link>
<pubDate>Mon, 12 Nov 2018 00:00:00 +0000</pubDate>
<guid>/post/useful-resources/</guid>
<description>
<p><em>My posts with some <a href="/categories/resources">#useful-resources</a>.</em></p>
<div id="great-posts-academic" class="section level2">
<h2>Great posts | academic</h2>
<ul>
<li><a href="https://blogs.scientificamerican.com/guest-blog/the-awesomest-7-year-postdoc-or-how-i-learned-to-stop-worrying-and-love-the-tenure-track-faculty-life/">The Awesomest 7-year Postdoc <em>by</em> Radhika Nagpal | Scientific American</a></li>
<li><a href="/post/2016/matt-might-blog/">Matt Might’s Blog</a></li>
<li><a href="/post/2018/modelers-hippocratic-oath">Modeler’s Hippocratic oath</a></li>
</ul>
</div>
<div id="bioinformatics" class="section level2">
<h2>Bioinformatics</h2>
<ul>
<li><a href="https://c2-d2.github.io/hanage-lab/Microbial-Bioinformatics-starter-kit/">Microbial Bioinformatics Starter Kit <em>by</em> Lauren Cowley</a></li>
<li>Microbial genome annotation <em>by</em> Michael Eisen
<ul>
<li><a href="https://twitter.com/phylogenomics/status/999406494859718662">Twitter thread</a> &amp; <a href="https://twitter.com/i/moments/999641962025074696">moment</a></li>
</ul></li>
<li><a href="https://holtlab.net/2015/02/25/tools-for-bacterial-comparative-genomics/">Tools for bacterial comparative genomes <em>by</em> Holt lab</a></li>
</ul>
</div>
<div id="r" class="section level2">
<h2>R</h2>
<ul>
<li><a href="/post/2018/git-github-links">Git, GitHub and R</a></li>
<li><a href="https://paulvanderlaken.com/2017/08/10/r-resources-cheatsheets-tutorials-books/">R resources</a> <em>by</em> <a href="paulvanderlaken.com">Paul Vanderlaken</a></li>
<li>Related post: <a href="https://paulvanderlaken.com/2018/05/21/r-tips-and-tricks/">R Tips and Tricks</a></li>
</ul>
</div>
<div id="data-visualization" class="section level2">
<h2>Data Visualization</h2>
<ul>
<li><a href="https://holtlab.net/2015/10/03/plotting-trees-data/">Plotting trees + data <em>by</em> Holt Lab</a></li>
</ul>
</div>
<div id="blogdown-hugo-academic-r-markdown" class="section level2">
<h2>Blogdown, Hugo, Academic &amp; R Markdown</h2>
<ul>
<li><a href="https://bookdown.org/yihui/blogdown/">Blogdown: Creating websites with R Markdown <em>by</em> Yihui Xie</a></li>
<li><a href="https://github.com/gohugoio">Hugo</a>
<ul>
<li><a href="https://discourse.gohugo.io/">Hugo discussion forum</a></li>
</ul></li>
<li><a href="https://github.com/gcushen/hugo-academic">Hugo Academic <em>by</em> George Cushen</a>
<ul>
<li><a href="https://sourcethemes.com/academic/">Academic</a></li>
</ul></li>
<li><a href="https://rmarkdown.rstudio.com/index.html">R Markdown</a></li>
<li><a href="http://mcdussault.rbind.io/post/building-your-blog-using-blogdown/">Building your blog using blogdown <em>by</em> Marie Dussault</a></li>
</ul>
</div>
<div id="blogging-tips" class="section level2">
<h2>Blogging tips</h2>
<ul>
<li><a href="http://hackerspace.lifehacker.com/top-tips-for-writing-a-blog-post-in-30-minutes-1688838523">Lifehacker</a></li>
<li><a href="http://matt.might.net/articles/how-to-blog-as-an-academic/">6 tips for low-cost academic blogging <em>by</em> Matt Might</a></li>
<li><a href="http://www.masalmon.eu/rladiesct/slides#1">Ready to start your data science blog? <em>by</em> Maëlle Salmon</a></li>
</ul>
</div>
</description>
</item>
<item>
<title>Bacterial Stress Response</title>
<link>/project/stress-response/</link>
<pubDate>Wed, 07 Nov 2018 00:00:00 +0000</pubDate>
<guid>/project/stress-response/</guid>
<description><h2 id="summary">Summary</h2>
<p>I started working on bacterial stress responses during my postdoctoral research at Rutgers University, I continue to focus on using computational evolutionary approaches to study various facets of pathogen biology including:</p>
<ul>
<li>delineating the molecular mechanism underlying a newly identified stress response operon in the tubercle bacterium involving the phage-shock-proteins (psp);</li>
<li>unraveling the evolution of bacterial stress response systems (psp) across the tree of life using protein sequence-structure-function relationships;</li>
<li>reconstructing and analyzing the mycobacterial sigma factor regulatory network.</li>
</ul>
<h2 id="students">Students</h2>
<ul>
<li>Samuel Chen (Alumni)</li>
</ul>
<h2 id="collaborators">Collaborators</h2>
<ul>
<li>Marila Gennaro (Rutgers)</li>
<li>L Aravind (NCBI, NIH)</li>
<li>Vivek Anantharaman (NCBI, NIH)</li>
</ul>
</description>
</item>
<item>
<title>R-Ladies East Lansing | Workshop on Intro to Tidy Data w/ R</title>
<link>/talk/2018-rlel-tidydata/</link>
<pubDate>Mon, 05 Nov 2018 18:00:00 +0000</pubDate>
<guid>/talk/2018-rlel-tidydata/</guid>
<description><img src="https://github.com/rladies-eastlansing/meetup-presentations-eastlansing/blob/master/event-planning-promos/201811-Meetup-flyer.png?raw=true" width="60%" />
<p>Workshop material:
<a href="https://github.com/rladies-eastlansing/meetup-presentations-eastlansing/tree/master/presentations/20181105-workshop-tidydata" target="_blank" rel="noopener">GitHub</a> •
<a href="https://bit.ly/rlel-20181105" target="_blank" rel="noopener">Google Drive</a></p>
</description>
</item>
<item>
<title>R-Ladies East Lansing | Workshop on Intro to Data Visualization w/ R</title>
<link>/talk/2018-rlel-dataviz/</link>
<pubDate>Mon, 08 Oct 2018 18:00:00 +0000</pubDate>
<guid>/talk/2018-rlel-dataviz/</guid>
<description><img src="https://github.com/rladies-eastlansing/meetup-presentations-eastlansing/blob/master/event-planning-promos/201810-Meetup-flyer.png?raw=true" width="60%" />
<p>Workshop material:
<a href="https://github.com/rladies-eastlansing/meetup-presentations-eastlansing/tree/master/presentations/20181008-workshop-dataviz" target="_blank" rel="noopener">GitHub</a> •
<a href="https://drive.google.com/drive/folders/1tSrhZ_TymJfxeZbe8hAdtPjcmhoeAJls?usp=sharing" target="_blank" rel="noopener">Google Drive</a></p>
</description>
</item>
<item>
<title>Using computational appraches to understand host-pathogen biology</title>
<link>/talk/2018-ismb/</link>
<pubDate>Mon, 09 Jul 2018 15:50:00 +0000</pubDate>
<guid>/talk/2018-ismb/</guid>
<description></description>
</item>
<item>
<title>Launching R-Ladies East Lansing!</title>
<link>/post/rlel-launch/</link>
<pubDate>Sun, 01 Jul 2018 00:00:00 +0000</pubDate>
<guid>/post/rlel-launch/</guid>
<description>
<div id="welcome-to-our-new-chapter" class="section level2">
<h2><em>Welcome to our new chapter!</em></h2>
</div>
<div id="what-were-about" class="section level2">
<h2>What we’re about</h2>