index.json

[{"authors":["admin"],"categories":null,"content":" Bio I am a computational biologist (Dept. of Pathobiology and Diagnostic Investigation, Michigan State University) working on host-pathogen biology, protein sequence-structure-function relationships, and drug repurposing (@cpathogeno). I am interested in quantitative biology, like to code \u0026amp; develop methods, and enjoy being in a collaborative environment addressing interesting biological questions.\nI also like teaching statistical data analysis and visualization, and R/Python programming. I recently founded the  programming chapter, R-Ladies East Lansing (year in review), and co-host our meetups \u0026amp; workshops! Check out our ß-webpage here.\nI love to read most non-fiction genres, sing classical carnatic music \u0026amp; dabble in keyboard, guitar!\n","date":-62135596800,"expirydate":-62135596800,"kind":"taxonomy","lang":"en","lastmod":-62135596800,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"https://jananiravi.github.io/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Bio I am a computational biologist (Dept. of Pathobiology and Diagnostic Investigation, Michigan State University) working on host-pathogen biology, protein sequence-structure-function relationships, and drug repurposing (@cpathogeno). I am interested in quantitative biology, like to code \u0026amp; develop methods, and enjoy being in a collaborative environment addressing interesting biological questions.\nI also like teaching statistical data analysis and visualization, and R/Python programming. I recently founded the  programming chapter, R-Ladies East Lansing (year in review), and co-host our meetups \u0026amp; workshops!","tags":null,"title":"Janani Ravi","type":"authors"},{"authors":null,"categories":null,"content":"","date":1554436800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554436800,"objectID":"d6966f10f5847a8b0f875c7b401690ce","permalink":"https://jananiravi.github.io/group/","publishdate":"2019-04-05T00:00:00-04:00","relpermalink":"/group/","section":"","summary":"","tags":null,"title":"Research","type":"widget_page"},{"authors":["Janani Ravi","Praveena Mathews"],"categories":["R","Resources"],"content":"","date":1551812400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1551812400,"objectID":"b9c8852ece634e754a3ddda1aa0987e5","permalink":"https://jananiravi.github.io/talk/2019-iitm/","publishdate":"2019-02-15T00:00:00-05:00","relpermalink":"/talk/2019-iitm/","section":"talk","summary":" ","tags":["R","data-science","compbio-bioinfo","software-tools"],"title":"Using Tidyverse for Genomics workshop","type":"talk"},{"authors":["Janani Ravi"],"categories":["R","Resources"],"content":"","date":1550066400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1550066400,"objectID":"c44d15c476a7a30f3dbcc15148bdfdc7","permalink":"https://jananiravi.github.io/talk/2019-plb/","publishdate":"2019-01-15T00:00:00-05:00","relpermalink":"/talk/2019-plb/","section":"talk","summary":" ","tags":["academic","R","compbio-bioinfo","data-science","software-tools"],"title":"Tidyverse workshop","type":"talk"},{"authors":["Janani Ravi"],"categories":["Resources","Research"],"content":"","date":1548349200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1548349200,"objectID":"d517e9ac1a63ba39aeede31c1178198a","permalink":"https://jananiravi.github.io/talk/2019-cvm/","publishdate":"2019-01-15T00:00:00-05:00","relpermalink":"/talk/2019-cvm/","section":"talk","summary":" ","tags":["academic","refs","software-tools"],"title":"Simple rules to make an effective scientific presentation","type":"talk"},{"authors":["Janani Ravi"],"categories":["R-Ladies"],"content":" Open positions Undergraduate Student Research We are looking for highly motivated and quantitatively-minded undergraduate students to work on a research project developing computational approaches to accelerate drug-/vaccine-target discovery against infectious diseases. Currently, we prefer students coming in with fellowships/scholarships (e.g., SROP, ENSURE, other department/college-level awards).\nWe 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, Perl, and/or C/C++ would be a huge plus. As part of this project, they will have the opportunity to work closely with a senior scientist 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.\nWe 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 email to set up a time to talk.\nGraduate Student Research We are looking for a highly motivated Masters student who is looking to do an internship or a long-term project (6mo–1yr) in developing computational approaches to accelerate drug-/vaccine-target discovery against infectious diseases. You will be a perfect fit if you have a background in bioinformatics, computational biology, statistics/biostatistics, computer science, genetics, or related fields. Having programming experience in R, Python, Perl, and/or C/C++ 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.\nThis 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.\nStart a conversation 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 email me to set a time to meet and discuss your interest.\nVisiting Scientist We welcome visiting scientists to come and collaborate with us for a short period (summer/6mo). 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., CoB). Please send me an email to discuss this opportunity.\nCollaboration If you are interested in any of our specific areas of research or have other great ideas that we could work on together, email me right away!\nContact details\n","date":1547528400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1553486400,"objectID":"fba6c149775da15c6a5b2adae893dd1c","permalink":"https://jananiravi.github.io/joinus/","publishdate":"2019-01-15T00:00:00-05:00","relpermalink":"/joinus/","section":"","summary":"Looking for undergrads, graduate students \u0026 visiting scientists!","tags":["jobs","phylogeny-evolution","data-science","compbio-bioinfo","R"],"title":"Join us!","type":"page"},{"authors":["Janani Ravi"],"categories":["R"],"content":" Thanks to everyone who attended, participated or sponsored R-Ladies East Lansing in 2018! We had a fantastic start \u0026amp; 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 \u0026amp; Data Science spirit across MSU in 2019! Contact us eastlansing@rladies.org 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.\n2018: Year in Review The Team Organizers: Janani Ravi, Camille Archer\nCo-organizers: Kayla Johnson, Arjun Krishnan, Nate Davis (~ Krishnan Lab)\nMeetup Presentations/Material GitHub | Google Drive | Photos\n2018 Sponsors 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)\n2018 Meetups Kickoff meeting Welcome to RLEL | Who We Are | What We Do | Upcoming Meetups\nLightning talks Aug 13, 2018  Git \u0026amp; 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 BigDataIgnite conference promo  Sep 10, 2018  Morphospaces w/ #Geomorph by Acacia Ackles Integrating Python \u0026amp; 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  Sep 24, 2018  Spatial Humanities w/ R Rachael White R/qtl Miranda Haus Hyenas, Microbes \u0026amp; R Connie Rojas Publication quality figures w/ #ggpubr by Taylor Dunivin R+LaTeX=knitr Cara Feldscher  Workshops  Intro to Tidy Data Workshop: GitHub • Google Drive Data Visualization Workshop: GitHub • Google Drive  Year in pictures             You \u0026amp; R-Ladies East Lansing  Join the R-Ladies Community on Slack (https://bit.ly/rlel-slack-signup) Lead (or team-lead) presentations/discussions in a meetup Help run the meetup(s) (help R-newbies, help pick up pizza) Contribute to Blog Entries, Webpage (https://rladies-eastlansing.github.io) Be a Social Butterfly (Twitter | Facebook | Courier pigeon?) Sponsor a meeting (OR help find us monthly meeting sponsors; \u0026lt;$75) Bring in a speaker and/or Bring in fellow R-users! Suggest a topic \u0026amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!\n Getting Involved @ R-Ladies: https://rladies.org/about-us/help/\n  How to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of our upcoming meetings!\n R-Ladies Global  Meetup: https://meetup.com/rladies-east-lansing/  Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal  Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail:  eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org    Organizers Janani Ravi \u0026amp; Camille Archer\nPS Community Policies \u0026amp; Code of Conduct:\nFull community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n","date":1546318800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1547528400,"objectID":"ea94d577465ad174bf2cce54bae2ebbc","permalink":"https://jananiravi.github.io/post/rlel-2018/rlel-2018/","publishdate":"2019-01-01T00:00:00-05:00","relpermalink":"/post/rlel-2018/rlel-2018/","section":"post","summary":"Some accomplishments from 2018 \u0026 announcements for 2019!","tags":["rladies","software-tools","blogs"],"title":"2018: Year in Review | RLEL","type":"post"},{"authors":["Janani Ravi"],"categories":null,"content":" A little background R-Ladies East Lansing welcomes R-enthusiasts of all proficiency levels, including aspiring and experienced R programmers, who are interested in mentoring, networking \u0026amp; expertise upskilling. This non-profit, civil society community is designed to develop members’ R skills \u0026amp; knowledge through social, collaborative learning \u0026amp; sharing. Supporting minority identity access to STEM skills \u0026amp; careers, the Free Software Movement, and contributing to the global R community!\nAnyone 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 \u0026amp; R-friends!\n2019: What’s next? Upcoming Workshops  Intro to Statistics w/ R (Spring; workshop series) Intro to RMarkdown (Summer) Intro to Shiny (Summer) Intro to Version Control (Git) w/ R (Summer)  Register \u0026amp; RSVP on Meetup: https://meetup.com/rladies-eastlansing\nWould 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.\nJoin the channels on Slack: #workshop-rstats #workshop-shiny #workshop-rmarkdown OR Email us: eastlansing@rladies.org\nIntroduce a Girl to Engineering (2019-02-16) Register for R-Ladies East Lansing’s activity booth: http://meetu.ps/e/Gfntz/yBMBS/f\nMSU Women in Engg. outreach: http://bit.ly/msu-wie-k12-outreach\nWomen in Data Science Conference (2019-04) https://widsconference.org\nRegister: TBA\nWould like to give a talk/present a poster? Stay tuned on Meetup. Contact us: eastlansing@rladies.org\nR-Ladies East Lansing Bookclub Academic incl.  R for Data Science Learning Statistics with R R programming for Data Science Hands-On Programming with R  Nonfiction incl.  Algorithms to Live by Weapons of Math Destruction  Blog posts \u0026amp; Articles incl.  Excuse me, do you have a moment to talk about version control? Good enough practices in Scientific Computing Happy Git w/ R  Meetup Presentations/Material GitHub | Google Drive | Photos\nYou \u0026amp; R-Ladies East Lansing  Join the R-Ladies Community on Slack (https://bit.ly/rlel-slack-signup) Lead (or team-lead) presentations/discussions in a meetup Help run the meetup(s) (help R-newbies, help pick up pizza) Contribute to Blog Entries, Webpage (https://rladies-eastlansing.github.io) Be a Social Butterfly (Twitter | Facebook | Courier pigeon?) Sponsor a meeting (OR help find us monthly meeting sponsors; \u0026lt;$75) Bring in a speaker and/or Bring in fellow R-users! Suggest a topic \u0026amp; bring in volunteers from the 200+ Meetup/Slack R-Ladies!\n Getting Involved @ R-Ladies: https://rladies.org/about-us/help/\n  How to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of our upcoming meetings!\n R-Ladies Global  Meetup: https://meetup.com/rladies-east-lansing/  Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal  Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail:  eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org    The Team Organizers: Janani Ravi, Camille Archer\nCo-organizers: Kayla Johnson, Arjun Krishnan (~ Krishnan Lab)\nPS Community Policies \u0026amp; Code of Conduct:\nFull community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n","date":1546318800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1547528400,"objectID":"6e8e427dca699fb8797141b21446567c","permalink":"https://jananiravi.github.io/post/rlel-upcoming-2019/rlel-2019-upcoming/","publishdate":"2019-01-01T00:00:00-05:00","relpermalink":"/post/rlel-upcoming-2019/rlel-2019-upcoming/","section":"post","summary":"What's in store for 2019: workshops, conference, bookclubs \u0026 more!","tags":["rladies","software-tools","blogs"],"title":"2019: RLEL Upcoming Events","type":"post"},{"authors":null,"categories":null,"content":"","date":1546318800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546318800,"objectID":"299a077dcf7d88d57edc9080508f2dd4","permalink":"https://jananiravi.github.io/bio/","publishdate":"2019-01-01T00:00:00-05:00","relpermalink":"/bio/","section":"","summary":"Interests \u0026 Experience","tags":null,"title":"Bio","type":"widget_page"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2018: #MyYearInBooks Summary Stats  Book Read  ","date":1546300800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1546300800,"objectID":"ae0e06da576d2483e1b0f498c600da0d","permalink":"https://jananiravi.github.io/post/goodreads-2018/goodreads-2018/","publishdate":"2019-01-01T00:00:00Z","relpermalink":"/post/goodreads-2018/goodreads-2018/","section":"post","summary":"My Year in Books: 2018!","tags":["books"],"title":"2018: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Resources","R"],"content":" My posts with some #useful-resources.\nGreat posts | academic  The Awesomest 7-year Postdoc by Radhika Nagpal | Scientific American Matt Might’s Blog Modeler’s Hippocratic oath   Bioinformatics  Microbial Bioinformatics Starter Kit by Lauren Cowley Microbial genome annotation by Michael Eisen  Twitter thread \u0026amp; moment  Tools for bacterial comparative genomes by Holt lab   R  Git, GitHub and R R resources by Paul Vanderlaken Related post: R Tips and Tricks   Data Visualization  Plotting trees + data by Holt Lab   Blogdown, Hugo, Academic \u0026amp; R Markdown  Blogdown: Creating websites with R Markdown by Yihui Xie Hugo  Hugo discussion forum  Hugo Academic by George Cushen  Academic  R Markdown Building your blog using blogdown by Marie Dussault   Blogging tips  Lifehacker 6 tips for low-cost academic blogging by Matt Might Ready to start your data science blog? by Maëlle Salmon   ","date":1541980800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541980800,"objectID":"b28671ace434a68e24d75eccaeea9fbc","permalink":"https://jananiravi.github.io/post/useful-links/useful-resources/","publishdate":"2018-11-12T00:00:00Z","relpermalink":"/post/useful-links/useful-resources/","section":"post","summary":"A lazy mixed post: #academic #bioinformatics #r #blog","tags":["academic","blogs","compbio-bioinfo","git","R","refs","software-tools"],"title":"Useful Resources","type":"post"},{"authors":null,"categories":["Research"],"content":" Summary During my postdoctoral research at Rutgers University, I focused on using computational approaches to study various facets of host and pathogen biology including:\n delineating the molecular mechanism underlying a newly identified stress response operon in the tubercle bacterium involving the phage-shock-proteins (psp); unraveling the evolution of bacterial stress response systems (psp) across the tree of life using protein sequence-structure-function relationships; reconstructing and analyzing the mycobacterial sigma factor regulatory network.  Related publications  The evolution, conservation, and covariation of the Psp envelope-stress-response system across the tree of life, in preparation. Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis  Collaborators Rutgers University  Marila Gennaro Pratik Datta Matt Neiditch Arnold Barton Rasel Khan Rinki Chauhan  NCBI, NIH  L Aravind Vivek Anantharaman  SUNY Buffalo  Gabor Balazsi  Rice University  Oleg Igoshin  ","date":1541566800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541566800,"objectID":"ec8097df46c1e8aa83d5f05ee5cf7623","permalink":"https://jananiravi.github.io/projects/stress-response/","publishdate":"2018-11-07T00:00:00-05:00","relpermalink":"/projects/stress-response/","section":"projects","summary":"Summary During my postdoctoral research at Rutgers University, I focused on using computational approaches to study various facets of host and pathogen biology including:\n delineating the molecular mechanism underlying a newly identified stress response operon in the tubercle bacterium involving the phage-shock-proteins (psp); unraveling the evolution of bacterial stress response systems (psp) across the tree of life using protein sequence-structure-function relationships; reconstructing and analyzing the mycobacterial sigma factor regulatory network.","tags":["stress-response","phylogeny-evolution","host/pathogen","compbio-bioinfo"],"title":"Bacterial Stress Response","type":"projects"},{"authors":["Janani Ravi","Nafiseh Haghtalab"],"categories":["R","Resources"],"content":"Workshop material: GitHub • Google Drive\n","date":1541458800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1541458800,"objectID":"f1a624e7a9a4f26355ee7567e7e30c71","permalink":"https://jananiravi.github.io/talk/2018-rlel-tidydata/","publishdate":"2018-11-05T00:00:00-05:00","relpermalink":"/talk/2018-rlel-tidydata/","section":"talk","summary":" ","tags":["R","data-science","software-tools"],"title":"R-Ladies East Lansing | Workshop on Intro to Tidy Data w/ R","type":"talk"},{"authors":["Janani Ravi","Veronica Frans","Kayla Johnson","Cara Feldscher"],"categories":["R","Resources"],"content":"Workshop material: GitHub • Google Drive\n","date":1539036000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1539036000,"objectID":"a18603f0d3b95ce49833d6a7d0dd2ce1","permalink":"https://jananiravi.github.io/talk/2018-rlel-dataviz/","publishdate":"2018-10-08T00:00:00-04:00","relpermalink":"/talk/2018-rlel-dataviz/","section":"talk","summary":" ","tags":["R","data-science","software-tools"],"title":"R-Ladies East Lansing | Workshop on Intro to Data Visualization w/ R","type":"talk"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":["Research"],"content":"","date":1531165800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1531165800,"objectID":"b11af00340e22728fd14edd229e814c9","permalink":"https://jananiravi.github.io/talk/2018-ismb/","publishdate":"2017-01-01T00:00:00-05:00","relpermalink":"/talk/2018-ismb/","section":"talk","summary":"","tags":["phylogeny-evolution","compbio-bioinfo","stress-response"],"title":"Using computational appraches to understand host-pathogen biology","type":"talk"},{"authors":null,"categories":["R"],"content":" Welcome to our new chapter!  What we’re about R-Ladies East Lansing is a local chapter of R-Ladies Global. We meet to discuss, learn, teach, present, work on all things R! Our priority is to provide a safe community space for anyone identifying as a minority gender who is interested in and/or working with R. The group exists to promote gender diversity in the R community worldwide. We are pro-actively inclusive of queer, trans, and all minority identities, with additional sensitivity to intersectional identities.\n Who should join? R-Ladies East Lansing welcomes members of all R proficiency levels, whether you are a new or aspiring R user, or an experienced R programmer interested in mentoring, networking \u0026amp; expert upskilling. Our non-profit, civil society community is designed to develop our members’ R skills \u0026amp; knowledge through social, collaborative learning \u0026amp; sharing. Supporting minority identity access to STEM skills \u0026amp; careers, the Free Software Movement, and contributing to the global R community!\nAnyone and everyone interested in R/Data Science should join our group and participate/contribute in any way you can, be they learners, teachers, developers or innovators! We encourage women and minority genders to present/lead most sessions, conversations but we have no restrictions whatsoever when it comes to membership, participation, and discussions. So, please join us and bring your R-family \u0026amp; R-friends!\n How to be in touch? Access our presentations, R scripts and more on Github and follow us on twitter to stay up to date about R-Ladies news! Join the Meetup group to be notified of the first meeting in July!\n R-Ladies Global  Meetup: https://meetup.com/rladies-east-lansing/  Twitter: @RLadiesELansing \u0026amp; @RLadiesGlobal  Slack: https://rladies-eastlansing.slack.com Github: @rladies-eastlansing \u0026amp; @rladies E-mail:  eastlansing [at] rladies [dot] org janani [at] rladies [dot] org info [at] rladies [dot] org     Organizers Janani Ravi \u0026amp; Camille Archer\n PS Community Policies \u0026amp; Code of Conduct: Full community guidelines are found here: https://github.com/rladies/starter-kit/wiki\n ","date":1530403200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1530403200,"objectID":"bca3f4082b3d31472773b2031c008d97","permalink":"https://jananiravi.github.io/post/rlel-launch/rlel-launch/","publishdate":"2018-07-01T00:00:00Z","relpermalink":"/post/rlel-launch/rlel-launch/","section":"post","summary":"Welcome to our new chapter: *Who we are \u0026 What we do.*","tags":["rladies","software-tools"],"title":"Launching R-Ladies East Lansing!","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" I recently came across the Modeler\u0026rsquo;s Hippocratic Oath while reading Cathy O\u0026rsquo;Neil\u0026rsquo;s \u0026lsquo;Weapons of Math Destruction\u0026rsquo;.\nThis was originally written by Emanuel Derman and Paul Wilmott in the wake of the 2008 financial crisis.\nThe Oath  I will remember that I didn’t make the world, and it doesn’t satisfy my equations. Though I will use models boldly to estimate value, I will not be overly impressed by mathematics. I will never sacrifice reality for elegance without explaining why I have done so. Nor will I give the people who use my model false comfort about its accuracy. Instead, I will make explicit its assumptions and oversights. I understand that my work may have enormous effects on society and the economy, many of them beyond my comprehension.   ","date":1527120000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1527120000,"objectID":"ad2cf3ca6b5a8d0e231ae7a58a0ae0dd","permalink":"https://jananiravi.github.io/post/modelers-oath/modelers-hippocratic-oath/","publishdate":"2018-05-24T00:00:00Z","relpermalink":"/post/modelers-oath/modelers-hippocratic-oath/","section":"post","summary":"Simple and sensible pointers laid out by Emanuel Derman \u0026 Paul Wilmott.","tags":["math-modeling","blogs","academic","data-science"],"title":"Modeler's Hippocratic Oath","type":"post"},{"authors":null,"categories":["R"],"content":"R-Ladies East Lansing Posts \u0026amp; Workshops\n","date":1525665600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525665600,"objectID":"1a2102621c9d896978ad35426ab37ebe","permalink":"https://jananiravi.github.io/projects/rladies-eastlansing/","publishdate":"2018-05-07T00:00:00-04:00","relpermalink":"/projects/rladies-eastlansing/","section":"projects","summary":"R-Ladies East Lansing Posts \u0026amp; Workshops","tags":["rladies","software-tools","blogs","compbio-bioinfo","R"],"title":"R-Ladies East Lansing","type":"projects"},{"authors":null,"categories":["Books-Blogs"],"content":"Check out my Goodreads profile for my latest reads and recommendations! :)\n","date":1525665600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525665600,"objectID":"6da302e29c14c780e10955c05f7c11ad","permalink":"https://jananiravi.github.io/reading/","publishdate":"2018-05-07T00:00:00-04:00","relpermalink":"/reading/","section":"","summary":"Posts and updates on [books \u0026 blogs](/categories/Books-Blogs) that caught my eye!","tags":["books","blogs"],"title":"Reading","type":"page"},{"authors":null,"categories":["Resources"],"content":" My posts with some useful resources\n Git, GitHub and R Modeler\u0026rsquo;s Hippocratic oath  Great posts | academic  The Awesomest 7-year Postdoc by Radhika Nagpal | Scientific American  Bioinformatics  Microbial Bioinformatics Starter Kit by Lauren Cowley Microbial genome annotation by Michael Eisen  Twitter thread \u0026amp; moment  Tools for bacterial comparative genomes by Holt lab  R  R resources by Paul Vanderlaken  Related post: R Tips and Tricks   Blogdown, Hugo, Academic \u0026amp; R Markdown  Blogdown: Creating websites with R Markdown by Yihui Xie Hugo  Hugo discussion forum  Hugo Academic by George Cushen  Academic  R Markdown Building your blog using blogdown by Marie Dussault  Data Visualization  Plotting trees + data by Holt Lab  Blogging tips  Lifehacker 6 tips for low-cost academic blogging by Matt Might Ready to start your data science blog? by Maëlle Salmon  ","date":1525665600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525665600,"objectID":"c6625328e7b2e36b114847f299065f54","permalink":"https://jananiravi.github.io/resources/","publishdate":"2018-05-07T00:00:00-04:00","relpermalink":"/resources/","section":"","summary":"Posts and updates on useful academic blogs \u0026 resources!","tags":["academic","blogs","compbio-bioinfo","git","R","refs"],"title":"Resources","type":"page"},{"authors":null,"categories":["Resources","R"],"content":" See also:  My tweet dated: 2017-03-11 Resources for more links related to Blogdown, Rmarkdown \u0026amp; GitHub   Git  Version control with Git on Software Carpentry Git workflow for beginners Mozilla Git Getting started with Git Git, the simple guide Git exercises GitHowTo Introduction to Git and command line Friendly introduction to Git, Jane Git for humans, slides by Bartlett Learn Git branching Git cheat sheet and best practices Getting yourself out of a Git mess Try Git   Git and GitHub  GitHub tutorial, Broman New GitHub repo Git \u0026amp; Github | Seankross GitHub on Mac   R and Git  R with Git and GitHub   GitHub Pages, Gists | Jekyll  Github pages #1 #2 Creating gists on Github Jekyll GCC Ruby Ruby Gems   ","date":1525305600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525305600,"objectID":"7f313d16696af6326064e0c827364be1","permalink":"https://jananiravi.github.io/post/git-links/git-github-links/","publishdate":"2018-05-03T00:00:00Z","relpermalink":"/post/git-links/git-github-links/","section":"post","summary":"... on how to get started, incl. integration with R/RStudio.","tags":["software-tools","refs","git","R"],"title":"Useful Git/GitHub links","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":["Research"],"content":"","date":1519707600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1519707600,"objectID":"3b556e0dcf39d6b6ecb31c987f264098","permalink":"https://jananiravi.github.io/publication/psp-actino/anto/","publishdate":"2018-02-27T00:00:00-05:00","relpermalink":"/publication/psp-actino/anto/","section":"publication","summary":" ","tags":["stress-response","phylogeny-evolution","host/pathogen","compbio-bioinfo","R"],"title":"Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria","type":"publication"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2017: #MyYearInBooks Summary Stats  Books Read  ","date":1514678400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1514678400,"objectID":"afa976f654666b9490d7ce683ff2570d","permalink":"https://jananiravi.github.io/post/goodreads-2017/goodreads-2017/","publishdate":"2017-12-31T00:00:00Z","relpermalink":"/post/goodreads-2017/goodreads-2017/","section":"post","summary":"My Year in Books: 2017!","tags":["books"],"title":"2017: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Book Review I find myself increasingly drawn to the field of Behavioral Economics (so much so that I was considering a second PhD to channelize my love!), and how beautifully evasive these concepts are in real life. Starting with Daniel Kahneman’s Thinking Fast and Slow, followed by the writings and blogs of Steven Levitt, Dan Ariely, Nate Silver and Barry Schwartz (and still others like Malcolm Gladwell), has set me thinking a lot about how insane and illogical we are. We do see ourselves as logical and reasonably intelligent people who do not fall for the usual traps (OK, maybe you didn’t see me that way, but we’ll let that slide for now…), but how fool-proof are we? What about the narrative fallacy - ‘aah, that makes sense now’ or ‘I thought so’ or confirmation biases?\n‘The Black Swan’ by Nassim Nicholas Taleb (http://fooledbyrandomness.com/) has been on my list ever since I first got infatuated with this topic. I finally finished it last month. Man, is it it well-written! The guy is brilliant, and his wit and humor are unmatchable! Among other things, he leads (and concludes) with our love for everything normal, statistically speaking and otherwise, and how we can’t but help make the obvious blunders of predicting, quite erroneously, based on the past, even though we know fully well that life doesn’t present itself as a series of bell curves stringed together just so that we can get away with some easy math! You’ll hear a lot about epistemology (defined in PS3; truth be told, I hadn’t heard of this word until last month), mediocristan (the Gaussian life) vs extremistan (scale-free distributions encountered more often than not in real-life)\nHere’s a snippet: https://drive.google.com/file/d/0B7_wAV4HsNrkQmdFMndHSHhldFE/view Never mind if you don’t get it. I enjoyed every last bit of the book, and hope that you do too! Give it a try - whether you love it or hate it, it would be time well-spent! :)\nHappy reading!\nPS1. I’ve heard that people either love it or hate it. Clearly, I fall in the bin #1. Do I agree with everything? Well, yeah, almost everything. PS2. Luckily, none of you are directly tied to economics or financial sectors. :D Well, scientists and statisticians have been insulted too, but the elegance of it makes it OK! Lots to think about.:) PS3. Epistemology studies the nature of knowledge, justification, and the rationality of belief. Much of the debate in epistemology centers on four areas: (1) the philosophical analysis of the nature of knowledge and how it relates to such concepts as truth, belief, and justification, (2) various problems of skepticism, (3) the sources and scope of knowledge and justified belief, and (4) the criteria for knowledge and justification.\nTags #behavioraleconomics #books #suggestions #mustread #randomness #economics #business #philosophy\nblurb, review, snapshot below\n  Blurb A black swan is a highly improbable event with three principal characteristics: It is unpredictable; it carries a massive impact; and, after the fact, we concoct an explanation that makes it appear less random, and more predictable, than it was.\nThe astonishing success of Google was a black swan; so was 9/11. For Nassim Nicholas Taleb, black swans underlie almost everything about our world, from the rise of religions to events in our own personal lives.\nWhy do we not acknowledge the phenomenon of black swans until after they occur? Part of the answer, according to Taleb, is that humans are hardwired to learn specifics when they should be focused on generalities.\nWe concentrate on things we already know and time and time again fail to take into consideration what we don’t know. We are, therefore, unable to truly estimate opportunities, too vulnerable to the impulse to simplify, narrate, and categorize, and not open enough to rewarding those who can imagine the “impossible.”\nFor years, Taleb has studied how we fool ourselves into thinking we know more than we actually do. We restrict our thinking to the irrelevant and inconsequential, while large events continue to surprise us and shape our world. Now, in this revelatory book, Taleb explains everything we know about what we don’t know. He offers surprisingly simple tricks for dealing with black swans and benefiting from them.\nElegant, startling, and universal in its applications ‘The Black Swan’ will change the way you look at the world. Taleb is a vastly entertaining writer, with wit, irreverence, and unusual stories to tell. He has a polymathic command of subjects ranging from cognitive science to business to probability theory.\n‘The Black Swan’ is a landmark book – itself a black swan.\n ","date":1493164800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1493164800,"objectID":"8b40a96d92f81a37e1ff06d49df422fa","permalink":"https://jananiravi.github.io/post/black-swan/black-swan-nassim-taleb/","publishdate":"2017-04-26T00:00:00Z","relpermalink":"/post/black-swan/black-swan-nassim-taleb/","section":"post","summary":"Brief book review/book recommendation.","tags":["books"],"title":"Black Swan by Nassim Taleb","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":["Research"],"content":"","date":1491253200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1491253200,"objectID":"a7e54386f219201ea221cf704105e281","permalink":"https://jananiravi.github.io/talk/2017-asm-tb/","publishdate":"2017-04-01T00:00:00-04:00","relpermalink":"/talk/2017-asm-tb/","section":"talk","summary":"","tags":["phylogeny-evolution","compbio-bioinfo"],"title":"Evolution and Conservation of the Psp Envelope Stress-Response System","type":"talk"},{"authors":null,"categories":["Resources"],"content":"  Why I’m writing this The initial process, where you read and imbibe! Helpful links:  Approximate order of key events \u0026amp; things-to-do Initial set of documents needed for the Indian Consulate attestation Documents to be sent to Indian Home Department Documents to be sent to the other two departments: List of documents  Addresses for mailing your packages TN State Department Regional Passport Office (RPO)  Additional documents required for police verification Main letters/documents Supporting documents  Final set of documents to be sent to the USCIS, Department of State Address for the package to be sent Tracking progress    Why I’m writing this I went through this rather painful \u0026amp; ghastly process from Rutgers University, Newark, NJ. My closest consulate was the one in New York (CGNY). I am originally from Chennai, Tamil Nadu (India). So, most of the state department and RPO/police verification guidelines I’ve enlisted below worked for my specific case. Folks from other countries can skip ahead from their consulate to the last step reading some country-specific blogs in-between.\n The initial process, where you read and imbibe! Helpful links:  US govt. websites  http://travel.state.gov/content/visas/english/study-exchange/student/residency-waiver.html  http://travel.state.gov/content/visas/english/study-exchange/student/residency-waiver/ds-3035-instructions.html  https://j1visawaiverrecommendation.state.gov  https://j1visawaiverrecommendation.state.gov/accessController.asp?page=26 https://j1visawaiverrecommendation.state.gov/cancelHandler.asp   Blogs  http://www.sameetmehta.com/2015/01/the-j1-waiver-process-for-indian.html https://sciash.wordpress.com/2016/03/20/j1-waiver-step-by-step-guide/ http://www.immihelp.com/forum/showthread.php/113424-J1-visa-home-residency-requirement-waiver-from-India http://j1.aruppukottai.net/ (old 2009) http://prashanth-jaikumar.blogspot.com/2010/05/how-i-learned-to-stop-worrying-and-love.html (2010 May) Tip: Find specific blogs for your state since the rules and guidelines might be somewhat different. Mine was Tamil Nadu. Other useful PDFs that may include some of the above: The_process     Approximate order of key events \u0026amp; things-to-do  Read \u0026amp; decipher the resources. It’s a one-time thing. So, do it! Start at least 1–1.5yrs before your current employment ends/your extended J1 expires. The process takes time \u0026amp; patience. Give time for ‘worst case scenarios’! Tip: Talk to your department admin and your university’s international/J1 office. Note: First extend your J1 \u0026amp; then apply for the waiver. You can’t extend once you apply for your waiver. Notarization of your biodata and affidavit (your local bank or other notary publics) Attestation of your biodata and affidavit: Local Indian consulate with the necessary documents  Some require passport-sized photo taken within the last 6 mo (CGNY did ‘require’ but they didn’t ’need’ it!!) Call to get their full list and check their website before going  Send your packages to the 3 departments back home (web portal/postal mail w/ tracking) Back to the local Indian consulate  Take your 3 NORIs and forms to get a NORI that they will forward to the Department of State, US)  Send your package to USCIS (w/ tracking)  Include all the necessary background documents NORIs from all of the above DS-3035 form Preferably, don’t include what’s not in the govt. list  Note: You can migrate your J1 to a different university during your J1’s duration of validity.  Talk to both the universities’ J1 departments. This would take 24-48h but can only happen before you terminate your current appointment. Once you are out, you need to process a new J1 and, possibly, go this whole process once again! This could happen even while your J1 is being petitioned.    Initial set of documents needed for the Indian Consulate attestation  Original Passport + Visa (+ copy) All DS-2019s (+ copy) Latest I-94 (+ copy)  https://i94.cbp.dhs.gov/I94  Proof of residence in the US (preferably 2) Cash, money order or cashier’s cheque Biodata \u0026amp; Affidavit  unfilled sample: J1-waiver-biodata-affidavit-NY_unfilled.pdf The first page is for New York Consulate General but others could use it as a guide too.    Documents to be sent to Indian Home Department Govt. of India Ministry of Human Resource Development (HRD) No Obligation to Return to India http://www.nori.ac.in/ (quite straightforward; trackable (!); they are really fast \u0026amp; responsive)\n Biodata and Affidavit (Notarized \u0026amp; Attested by the Consulate General of India, New York, USA) e-Copy of Passport (New and Old) and J1-Visa e-Copy of all DS-2019s e-Copies of PhD \u0026amp; BTech (other, as applicable) Degree Certificate I don’t remember if I included:  Employment letter from the department chair (I needed this somewhere) Proof of current residence in the US    Documents to be sent to the other two departments: your state government your Regional Passport Office (likely, where you got your first passport)  List of documents Biodata and Affidavit (Notarized \u0026amp; Attested by the Consulate General of India, New York, USA) Copy of Passport (New and Old) and J1-Visa Copy of all DS-2019s Proof of current residence in the US Copies of Ph.D. \u0026amp; B.Tech (other, as applicable) Degree Certificate   Cover letter with your request to grant NORI  Your correct address \u0026amp; theirs (of course!) including your email ID (you never know!) Where you are studying/working Passport number (new and old) Why you need the waiver (change of job, extending the same one, …) List of attested/enclosed copies of documents  Letter of consent from your parent saying that you have no legal obligation to return. Include these details, if possible/applicable  Who they are, where they are working/retired from Brief family history Your residential address (India) Your brief educational history When and why you came to the US Your marital \u0026amp; dependent info (briefly) when applicable Your current residential address in the US Why you are requesting the waiver (in their words) And something along these lines (sample below)    With regard to the NORI certification, I confirm that all the details stated above are true to the best of my knowledge and all supporting documents have been attached for your perusal (the shipping document list is on the next page). There is no civil or criminal case against my daughter, XYZ. Also, she did not take any educational loan from the Indian or US governments. Therefore, she does not have any commitments here in India for legal, financial or personal reasons.\n  I, therefore, request you to kindly provide the necessary NORI certificate that will help her continue working towards her professional and personal goals in the US. The experience and expertise that she gains during her stay there will help her serve India better in the long run.\n   Addresses for mailing your packages TN State Department The Secretary Home (Citz II) Department Government of Tamil Nadu Secretariat, Fort St. George Chennai 600 009 Tamil Nadu, India  Regional Passport Office (RPO) The Passport Officer Regional Passport Office Royala Towers No. 2 and 3, IV Floor, Old No. 785, New No. 158, Anna Salai, Chennai 600002 Tamil Nadu, India   Additional documents required for police verification [At least, I needed it (Chennai, Tamil Nadu)]\nMain letters/documents  Consent letter and Pro Forma from the applicant’s parent Letter from the applicant’s spouse Biodata of the applicant   Supporting documents Applicant’s: Mark sheets and certificates 10th 12th mark sheets B. Tech. degree certificate Ph.D. degree certificate  Applicant’s: Passport and Visa Passport (front/back) J-1 Visa \u0026amp; Certificate of eligibility for exchange visitor (J-1) status (DS-2019) Old passport and old J1 and F1 visas  Applicant’s: Graduate assistantship letter for PhD Applicant’s: Employment letter (current place of work) Spouse’s: Mark sheets and certificates 10th, 12th mark sheets B. Tech. degree certificate Ph.D. degree certificate  Applicant’s Spouse’s: Passport and Visa Passport (front/back) H1B visa approval notice (I-797)  Applicant’s Spouse’s: Employment letter (MSU) Both: Marriage certificate Both: Present address proof (Wells Fargo bank statement) Applicant’s Parents’: Chennai address proof (Ration card, gas bill) Applicant’s Parents’: Aadhar card    Final set of documents to be sent to the USCIS, Department of State  Read the How to apply for a waiver page on the travel.state.gov website again. DS-3035 \u0026amp; SOR J1 waiver application packet for USCIS and Department of State  Application fee  Non-refundable — do it at the end cashier’s cheque written out to ’The US Department of State’ Include your name and case number (from the DS-3035 barcode)  Waiver review division barcode Statement of reason (below)   Sample statement: I am XYZ working at ABC as a PQR. I am currently on J1 visa sponsored by QWERTY. My J1 visa started on 7/19/2013 and ends on 7/19/2018 with a two-year home residency requirement. The main purpose of my J1 visa is to allow me to do research. My research work is progressing well, and it needs more time (longer than 7/19/2018) to complete my research projects. Since I am the lead person in the research projects, my employer and I feel that the opportunity for me to stay here in the US and complete the projects by obtaining the J1 visa waiver will be great. I am requesting a waiver of the two-year home residence requirement to complete my work here on the basis of No Objection certificate. My home country “ABC” has no objection in allowing me to continue working here in the US, and has issued a No Objection certificate to that effect. The ABCian Embassy in the USA will be issuing the No Objection statement to you. I kindly request you to grant me the J1 visa waiver at the earliest.\n  The actual completed DS-3035  https://j1visawaiverrecommendation.state.gov/ If you make a mistake, fill it out from the beginning  Passport data page All DS2019s, IAP-66 Degree Certificates (Bachelors, Masters, PhD, …) Statement of Reason Two self-addressed stamped envelopes (legal-size) Your NORI letters from  India: i) home department, ii) state department and iii) regional passport office (for police verification) and US (local Indian Consulate, although they would be sending a copy)    Address for the package to be sent Postal Service Department of State J-1 Waiver P.O. Box 979037 St. Louis, MO 63197-9000 Courier Service Department of State J-1 Waiver P.O. Box 979037 1005 Convention Plaza St. Louis, MO 63101-1200  Tracking progress https://j1visawaiverrecommendation.state.gov/\n  ","date":1489449600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1489449600,"objectID":"223d118418c403d60ada80e1aab6621e","permalink":"https://jananiravi.github.io/post/j1-waiver/j1-visa-waiver-nori/","publishdate":"2017-03-14T00:00:00Z","relpermalink":"/post/j1-waiver/j1-visa-waiver-nori/","section":"post","summary":"Applying for the J1 visa waiver and No Obligation to Return to India (NORI) certificate from the Indian/US governments.","tags":["refs","India"],"title":"J1 visa waiver | How to obtain your NORI?","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2015: #MyYearInBooks Summary Stats   Books Read   ","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1483228800,"objectID":"a18c3c61dab73f83c2d1ce79fe4439d8","permalink":"https://jananiravi.github.io/post/goodreads-2015/goodreads-2015/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/post/goodreads-2015/goodreads-2015/","section":"post","summary":"My Year in Books: 2015!","tags":["books"],"title":"2015: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Find my latest reads \u0026amp; recommendations on Goodreads!\n2016: #MyYearInBooks Summary Stats  Books Read  ","date":1483228800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1483228800,"objectID":"8eed61fb23a3de1d5d1e07955c7e5524","permalink":"https://jananiravi.github.io/post/goodreads-2016/goodreads-2016/","publishdate":"2017-01-01T00:00:00Z","relpermalink":"/post/goodreads-2016/goodreads-2016/","section":"post","summary":"My Year in Books: 2016!","tags":["books"],"title":"2016: Year in Books | Goodreads","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Becoming Steve Jobs by Brent Schlender is a well-written biography of Steve Jobs \u0026amp; is definitely much better than Walter Isaacson’s ‘official’ one! And yeah, it is much more than a boring compendium of wiki and news articles. :)\nSo, happy reading!\n","date":1475539200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1475539200,"objectID":"57c45de2ebb3dbdc2a22d3a40de0e99d","permalink":"https://jananiravi.github.io/post/becoming-steve-jobs/becoming-steve-jobs/","publishdate":"2016-10-04T00:00:00Z","relpermalink":"/post/becoming-steve-jobs/becoming-steve-jobs/","section":"post","summary":"Book recommendation","tags":["books"],"title":"Becoming Steve Jobs by Brent Schlender","type":"post"},{"authors":["Janani Ravi","Vivek Anantharaman","L Aravind Iyer","Maria L Gennaro"],"categories":null,"content":"","date":1466275500,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1466275500,"objectID":"7d1b66cfaa6602959075f195b872ded1","permalink":"https://jananiravi.github.io/talk/2016-asm/","publishdate":"2016-06-18T00:00:00-04:00","relpermalink":"/talk/2016-asm/","section":"talk","summary":"","tags":["phylogeny-evolution","compbio-bioinfo"],"title":"Microbial Mechanosensing: Phage Shock Protein Response System in Gram-positive Bacteria","type":"talk"},{"authors":null,"categories":["Books-Blogs"],"content":" Background Matt Might has an awesome easy-to-read blog that has inspired us in many ways! Matt is a tenured CS professor at Utah and a visiting professor at HMS (Harvard Medical School). He’s the dad of 3 kids, one of whom has a very rare genetic disorder. He \u0026amp; his wife have spent a good part of their lives educating themselves and others about the disease.\n Some of his useful blog posts Health | Strength-training | JustDoIt  HOWTO: Gain strength and muscle Least resistance weight loss Path of least resistance Handling repetitive strain injury (e.g. carpal tunnel syndrome)   Efficiency | Productivity | work-life-balance  Productivity tips for academics How to send and reply to email Tips for work-life balance Travel hacks 12 resolutions for programmers   Academic | Professorship  Academic job hunt advice HOWTO: Get tenure  … = lots more where this came from!\n  ","date":1464220800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1464220800,"objectID":"9d17b8f4d6440fffe59a2512c8ff5155","permalink":"https://jananiravi.github.io/post/mattmight/matt-might-blog/","publishdate":"2016-05-26T00:00:00Z","relpermalink":"/post/mattmight/matt-might-blog/","section":"post","summary":"Compilation of some useful posts *by* Matt Might.","tags":["blogs","academic"],"title":"Matt Might's Blog","type":"post"},{"authors":null,"categories":["Books-Blogs"],"content":" Authors: Janani Ravi, Arjun Krishnan\nSrinivasa Ramanujan has been noted as one of the classic ‘genius-mathematicians’ of all time! Hailing from the same state/country as him, Arjun Krishnan and I have always looked up to him \u0026amp; his elegant math as a source of inspiration right through our formative years!\nThe Movie Recent movie that has drastically increased Ramanujan’s international visibility The Man Who Knew Infinity by Matthew Brown.\n The Play We watched this beautiful play in the University of Virginia campus during our grad school. Such unmistakable passion for math, that’s almost art-like or was it art!\n A Disappearing Number by Simon McBurney   The Book Here is a great companion book to better understand the Man and little bit of the Math!\n The Man Who Knew Infinity: A Life of the Genius Ramanujan by Robert Kanigel   The People Without the help of the following people (and many more we haven’t mentioned here), Ramanujan would have remained an unknown \u0026amp; obsolete genius!\nGH Hardy: Collaborator, Mentor Hardy was an English mathematician who brought Ramanujan to Cambridge, encouraged his professional growth and helped publish his many theorems and elegant solutions.\n Matthew Brown: The Director The director of the new Ramanujan movie, The Man Who Knew Infinity\n Manjul Bhargava: Math advisor \u0026amp; associate producer Princeton number theorist, winner of the Field’s medal, and Associate Producer of the movie.\nVideo made for Manjul Bhargava Princeton\n Ken Ono: Math advisor \u0026amp; associate producer Ken Ono is this very accomplished mathematician who’s central research questions revolve around the work of Ramanujan. He is also a fantastic and sincere communicator, teacher and author so much so that you can read/listen to almost anything that he has to say.\nHere’s a great video of a conversation he had with another mathematician where he talks about Ramanujan and his connection with him.\n Steven Strogatz: Applied mathematician Famous applied mathematician and author of superb books \u0026amp; articles on mathematics.\n Steven Strogatz, Manjul Bhargava \u0026amp; Matt Brown Video\n  Some more interesting articles Ramanujan surprises again| plus.maths.org  Remembering Ramanujan: India Celebrates Its Famous Mathematical Son December 22, 2012, marks the 125th anniversary of the birth of legendary Indian mathematician Srinivasa Ramanujan. An intuitive mathematical genius, Ramanujan’s discoveries have influenced several areas of mathematics, but he is probably most famous for his contributions to number theory and infinite series, among them fascinating formulas that can be used to calculate digits of pi in unusual ways.\nMore\n  ","date":1460678400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1460678400,"objectID":"414d8a30b594a49873b3cd0b12a48018","permalink":"https://jananiravi.github.io/post/ramanujan/ramanujan/","publishdate":"2016-04-15T00:00:00Z","relpermalink":"/post/ramanujan/ramanujan/","section":"post","summary":"... one of the greatest mathematicians of all time!","tags":["math-modeling","India","books"],"title":"A dedication to Ramanujan","type":"post"},{"authors":["Rinki Chauhan","Janani Ravi","Pratik Datta","Tian Chen","Dirk Schnappinger","Kevin E Bassler","Gabor Balázsi","Maria L Gennaro"],"categories":["Research"],"content":"","date":1456808400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1456808400,"objectID":"b3404ddcd2ebfe6bd8a66518202548ef","permalink":"https://jananiravi.github.io/publication/sigfac-mtb/natcomm/","publishdate":"2016-03-01T00:00:00-05:00","relpermalink":"/publication/sigfac-mtb/natcomm/","section":"publication","summary":"Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics.","tags":["stress-response","compbio-bioinfo","host/pathogen","R"],"title":"Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis","type":"publication"},{"authors":null,"categories":["Research"],"content":" Summary In addition to stress-response systems on the pathogenic side, I studied some host responses to M. tuberculosis infection using computational approaches as well:\n characterizing the transcriptional response in infected macrophages under various small molecule perturbations using RNA-Seq analysis; understanding the dysregulation of lipid metabolism in M. tuberculosis-infected macrophages using dynamic Bayesian model and statistical analyses of heterogeneous single-cell populations.  Related publications  Lipid Metabolism and TB, in preparation. Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection  Collaborators Rutgers University  Marila Gennaro Sanjay Tyagi Gili Kaufmann (now in \u0026hellip;) Richard Pine Eduardo Sontag (now in NorthEastern) Evgeni \u0026lsquo;Zhenya\u0026rsquo; Nikolaev Valentina Guerrini Natalie Bruiners  Tulane University  Deepak Kaushal Smriti Mehta  Knowledge Synthesis  Hugh Salamon Ken Yamaguchi  ","date":1451538000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1451538000,"objectID":"d1c37c3547429febe8b9a5f8f0b73169","permalink":"https://jananiravi.github.io/projects/lipid-metabolism/","publishdate":"2015-12-31T00:00:00-05:00","relpermalink":"/projects/lipid-metabolism/","section":"projects","summary":"Summary In addition to stress-response systems on the pathogenic side, I studied some host responses to M. tuberculosis infection using computational approaches as well:\n characterizing the transcriptional response in infected macrophages under various small molecule perturbations using RNA-Seq analysis; understanding the dysregulation of lipid metabolism in M. tuberculosis-infected macrophages using dynamic Bayesian model and statistical analyses of heterogeneous single-cell populations.  Related publications  Lipid Metabolism and TB, in preparation.","tags":["lipid-metabolism","host/pathogen","compbio-bioinfo"],"title":"TB \u0026 Lipid metabolism","type":"projects"},{"authors":null,"categories":["Research"],"content":"","date":1446741900,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1446741900,"objectID":"1836d0fca7e4c0db37c9167dd78ffd38","permalink":"https://jananiravi.github.io/talk/2015-rutgers-symp/","publishdate":"2015-11-05T00:00:00-05:00","relpermalink":"/talk/2015-rutgers-symp/","section":"talk","summary":"","tags":["host/pathogen","compbio-bioinfo","lipid-metabolism"],"title":"Stochastic nature of adipogenic and inflammatory responses in tuberculous macrophages","type":"talk"},{"authors":["Pratik Datta","Janani Ravi","Valentina Guerrini","Rinki Chauhan","Matt B Neiditch","Scarlet S Shell","Sarah M Fortune","Baris Hancioglu","Oleg A Igoshin","Maria L Gennaro"],"categories":["Research"],"content":"","date":1438574400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1438574400,"objectID":"383669789a11e46e90f65202d4ebff3d","permalink":"https://jananiravi.github.io/publication/psp-mtb/molmicro/","publishdate":"2015-08-03T00:00:00-04:00","relpermalink":"/publication/psp-mtb/molmicro/","section":"publication","summary":"The bacterial envelope integrates essential stress-sensing and adaptive functions; thus, envelope-preserving functions are important for survival. In Gram-negative bacteria, envelope integrity during stress is maintained by the multi-gene Psp response. Mycobacterium tuberculosis was thought to lack the Psp system since it encodes only pspA and no other psp ortholog. Intriguingly, pspA maps downstream from clgR, which encodes a transcription factor regulated by the MprAB-σ(E) envelope-stress-signaling system. clgR inactivation lowered ATP concentration during stress and protonophore treatment-induced clgR-pspA expression, suggesting that these genes express Psp-like functions. We identified a four-gene set - clgR, pspA (rv2744c), rv2743c, rv2742c - that is regulated by clgR and in turn regulates ClgR activity. Regulatory and protein-protein interactions within the set and a requirement of the four genes for functions associated with envelope integrity and surface-stress tolerance indicate that a Psp-like system has evolved in mycobacteria. Among Actinobacteria, the four-gene module occurred only in tuberculous mycobacteria and was required for intramacrophage growth, suggesting links between its function and mycobacterial virulence. Additionally, the four-gene module was required for MprAB-σ(E) stress-signaling activity. The positive feedback between envelope-stress-sensing and envelope-preserving functions allows sustained responses to multiple, envelope-perturbing signals during chronic infection, making the system uniquely suited to tuberculosis pathogenesis.","tags":["stress-response","host/pathogen","phylogeny-evolution","compbio-bioinfo","R"],"title":"The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions","type":"publication"},{"authors":null,"categories":["Research"],"content":"","date":1414774800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1414774800,"objectID":"f6b4f57dd933a921edaddda1e9ecd788","permalink":"https://jananiravi.github.io/talk/2014-imsc/","publishdate":"2014-10-31T00:00:00-04:00","relpermalink":"/talk/2014-imsc/","section":"talk","summary":"","tags":["math-modeling"],"title":"Mathematical modeling of pathways involved in cell cycle regulation and Differentiation","type":"talk"},{"authors":["Hugh Salamon","Natalie Bruiners","Karim Lakehal","Lanbo Shi","Janani Ravi","Ken D Yamaguchi","Richard Pine","Maria L Gennaro"],"categories":["Research"],"content":"","date":1404187200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1404187200,"objectID":"605cb9dc5a1258eccc8208939236204d","permalink":"https://jananiravi.github.io/publication/vitd/jimm/","publishdate":"2014-07-01T00:00:00-04:00","relpermalink":"/publication/vitd/jimm/","section":"publication","summary":" ","tags":["compbio-bioinfo","host/pathogen"],"title":"Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection","type":"publication"},{"authors":null,"categories":["Research"],"content":" Research During my graduate research with Dr John Tyson, I built mathematical models to understand dynamical aspects:\n Modeling the START transition in the budding yeast cell cycle:\n Built a detailed mathematical model (~100 ODEs, ~150 parameters) for the START transition in yeast and integrated it with our published model of the whole cell cycle. Model addresses outstanding issues related to the precise mechanism and timing of transcriptional, post- translational and localization events, as well as size control under varying growth conditions. Model consistent with ~200 experimental mutant phenotypes pertaining to the START transition and rest of the cell cycle. Built a basic model for the nutritional effect of size control in budding yeast cells. This mechanism has been incorporated into the existing model of the yeast cell cycle to explain an initial set of START mutants.  Modeling bistability in the canonical Wnt pathway:\n Built a simplified model based upon the core module of the Wnt canonical pathway, and incorporated additional key regulatory interactions. Model shows that the Wnt signaling pathway can display bistability, in agreement with preliminary experimental results.   Related publications  Ravi J, Tyson JJ. Modeling the START transition in the budding yeast cell cycle. Submitted. Thorne C, Ravi J, Tyson JJ, Lee E. Modeling bistability in the canonical Wnt signaling pathway. Submitted.  Collaborators Virginia Tech  Kathy Chen (now retd.)  Vanderbilt University  Ethan Lee Curtis A. Thorne (now at University of Arizona)  ","date":1322715600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1322715600,"objectID":"e4a148dd5b29e320a508da355d836821","permalink":"https://jananiravi.github.io/dynamical-systems/","publishdate":"2011-12-01T00:00:00-05:00","relpermalink":"/dynamical-systems/","section":"","summary":"Research During my graduate research with Dr John Tyson, I built mathematical models to understand dynamical aspects:\n Modeling the START transition in the budding yeast cell cycle:\n Built a detailed mathematical model (~100 ODEs, ~150 parameters) for the START transition in yeast and integrated it with our published model of the whole cell cycle. Model addresses outstanding issues related to the precise mechanism and timing of transcriptional, post- translational and localization events, as well as size control under varying growth conditions.","tags":["dynamical-systems","math-modeling"],"title":"Dynamical Systems \u0026 Math Biology","type":"page"},{"authors":null,"categories":["Research"],"content":"","date":1301436000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1301436000,"objectID":"e80cb395f19766ec4eced6b8f142853d","permalink":"https://jananiravi.github.io/talk/2011-cshl/","publishdate":"2011-03-29T00:00:00-04:00","relpermalink":"/talk/2011-cshl/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition in the budding yeast cell cycle","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1246813200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1246813200,"objectID":"abe5043793937d3a5368aa191c94e394","permalink":"https://jananiravi.github.io/talk/2009-grc/","publishdate":"2009-05-05T00:00:00-04:00","relpermalink":"/talk/2009-grc/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition in the budding yeast cell cycle","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1237914000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1237914000,"objectID":"32f0f3d3c853bafe6bd9e3367ec8fa3e","permalink":"https://jananiravi.github.io/talk/2009-cshl/","publishdate":"2009-01-01T00:00:00-05:00","relpermalink":"/talk/2009-cshl/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition and size control in budding yeast","type":"talk"},{"authors":null,"categories":["Research"],"content":"","date":1235930400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1235930400,"objectID":"b16942501164b097278f3ac42414d4c9","permalink":"https://jananiravi.github.io/talk/2009-vt-symp/","publishdate":"2009-03-01T00:00:00-05:00","relpermalink":"/talk/2009-vt-symp/","section":"talk","summary":"","tags":["math-modeling"],"title":"Modeling the START transition and size control in budding yeast","type":"talk"},{"authors":null,"categories":null,"content":" Welcome to Slides Academic\nFeatures  Efficiently write slides in Markdown 3-in-1: Create, Present, and Publish your slides Supports speaker notes Mobile friendly slides  Controls  Next: Right Arrow or Space Previous: Left Arrow Start: Home Finish: End Overview: Esc Speaker notes: S Fullscreen: F Zoom: Alt + Click PDF Export: E  Code Highlighting Inline code: variable\nCode block:\nporridge = \u0026quot;blueberry\u0026quot; if porridge == \u0026quot;blueberry\u0026quot;: print(\u0026quot;Eating...\u0026quot;)  Math In-line math: $x + y = z$\nBlock math:\n$$ f\\left( x \\right) = \\;\\frac{{2\\left( {x + 4} \\right)\\left( {x - 4} \\right)}}{{\\left( {x + 4} \\right)\\left( {x + 1} \\right)}} $$\nFragments Make content appear incrementally\n{{% fragment %}} One {{% /fragment %}} {{% fragment %}} **Two** {{% /fragment %}} {{% fragment %}} Three {{% /fragment %}}  Press Space to play!\nOne  Two  Three \nA fragment can accept two optional parameters:\n class: use a custom style (requires definition in custom CSS) weight: sets the order in which a fragment appears  Speaker Notes Add speaker notes to your presentation\n{{% speaker_note %}} - Only the speaker can read these notes - Press `S` key to view {{% /speaker_note %}}  Press the S key to view the speaker notes!\n Only the speaker can read these notes Press S key to view   Themes  black: Black background, white text, blue links (default) white: White background, black text, blue links league: Gray background, white text, blue links beige: Beige background, dark text, brown links sky: Blue background, thin dark text, blue links   night: Black background, thick white text, orange links serif: Cappuccino background, gray text, brown links simple: White background, black text, blue links solarized: Cream-colored background, dark green text, blue links  Custom Slide Customize the slide style and background\n{{\u0026lt; slide background-image=\u0026quot;/img/boards.jpg\u0026quot; \u0026gt;}} {{\u0026lt; slide background-color=\u0026quot;#0000FF\u0026quot; \u0026gt;}} {{\u0026lt; slide class=\u0026quot;my-style\u0026quot; \u0026gt;}}  Custom CSS Example Let\u0026rsquo;s make headers navy colored.\nCreate assets/css/reveal_custom.css with:\n.reveal section h1, .reveal section h2, .reveal section h3 { color: navy; }  Questions? Ask\nDocumentation\n","date":-62135596800,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":-62135596800,"objectID":"c2915ec5da95791851caafdcba9664af","permalink":"https://jananiravi.github.io/slides/example-slides/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/slides/example-slides/","section":"slides","summary":"Welcome to Slides Academic\nFeatures  Efficiently write slides in Markdown 3-in-1: Create, Present, and Publish your slides Supports speaker notes Mobile friendly slides  Controls  Next: Right Arrow or Space Previous: Left Arrow Start: Home Finish: End Overview: Esc Speaker notes: S Fullscreen: F Zoom: Alt + Click PDF Export: E  Code Highlighting Inline code: variable\nCode block:\nporridge = \u0026quot;blueberry\u0026quot; if porridge == \u0026quot;blueberry\u0026quot;: print(\u0026quot;Eating...\u0026quot;)  Math In-line math: $x + y = z$","tags":null,"title":"Slides","type":"slides"}]