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Many people use R2 summary statistics for ordinary linear regression analyses. However, you can’t use the regular types of R2 methods for non-linear regressions, like those that you would use for logistic regression. There are several different R2-analogues out there, but they all do different things and can be useful in different ways. In this paper, we used spore trap data from my PhD thesis to understand how two different metrics work, and what they can tell us about the data. This paper is the culmination of a workshop that Neil and I held at ICPP in 2018; you can find the material for that workshop at https://robchoudhury.github.io/InformationTheory/index.html .
Phytopathology 109: In Press, 2018

Climate change is affecting how plants interact with pests and pathogens. Karen and I gave a talk on how changing weather patterns might affect laurel wilt disease, and we were invited to contribute to a summary paper that focused on how CO2 and climate change might impact different things, with a focus on coffee as a case study.
Agronomy 8:152, 2018

Network analysis can help to address a lot of different problems within plant pathology. In this review, we highlight some uses of networks, and discuss their future.
Annual Review of Phytopathology 56:25.1-25.22, 2018

The phylogenetic relationship between downy mildews and Phytophthoras has always been kind of cryptic. Are they all in the same genus? Closely related genera? Tyler and I deeply wanted these questions answered. He loves Phytophthora, and was entangled in a project to figure out how different forest pathogens were related, and I wanted to know how downy mildews tied in to this important group. We were able to wrangle up some samples and DNA from various downy mildews from all over California, and figured out that 1) the downy mildews are polyphyletic (they arose multiple times, 2) all nested within the ‘genus’ Phytophthora, and 3) that there seems to be differences between the mitochondrial phylogeny and nuclear phylogeny, suggesting there might be some horizontal mitochondrial movement between clades.
PLOS One, 2018

Its often challenging to set a complete, no-holds-barred phytosanitary thresholds. Theyre costly and they can sometimes backfire, resulting in insufficient seeds necessary for a planting season. Setting a non-zero threshold can allow for a reduction in the amount of inoculum imported while still only reducing the number of useable seedlots by a fraction. Here we outline a framework for setting non-zero phytosanitary thresholds.
Phytopathology 107: 1219-1228, 2017

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Full analysis is here Published in Plant Disease Management Reports 2014, 2015, and 2016. Throughout my PhD work, it became obvious that the challenges of spinach downy mildew were most heavily impacting organic growers. They were unable to rely on conventional synthetic pesticides that were able to suitably control disease in the conventional crop, and had to rely on resistance to control the disease. I wanted to see if any biofungicide had effect on the disease.

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Full analysis is here

Published in Plant Disease Management Reports 2011, and 2012.

UNDER CONSTRUCTION!

The Results

Conclusions

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Full analysis here Haiti is one of our nation’s nearest neighbors, and has been a key player in world history over the past 200 years. The Haitian revolution took nearly 15 years and cost countless lives, but resulted in one of the first nations that was slave-free and ruled by non-whites and former captives. The loss of Haiti (then called Saint-Domingue) forced the cash-starved Napoleon to sell the Louisiana territory to the United States, one of the single largest land purchases in our countries history.

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Full analysis here Global avocado production mostly focuses in Mexico, with the most prominent variety being ‘Hass’. I work on a project researching a disease of avocados (and other plants in the same family, Lauraceae) that causes rapid death, laurel wilt. Avocados in Florida are threatened by laurel wilt. Most production occurs in Miami-Dade county, mostly around the Homestead production region. The avocados grown in Florida tend to be of the West Indian races, whereas Hass are Mexican-Guatamalan hybrid races.

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Full data and analysis here Publication here Powdery Mildew on Whitestem Filaree I was walking around my neighborhood in Davis, CA one day when I noticed a strange looking weed on the ground that had powdery mildew on it’s surface. Powdery mildews are a group of biotrophic fungi that I had studied for my master’s degree. They are often times host specific, and do not regularly kill their host, but rather sap nutrients and water from the epidermal cells.

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Science Art

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Ying-Yu Liao gave a nice seminar about her ongoing PhD work looking at Magnesium Oxide nanoparticles and their use for control of bacterial tomato spot disease.

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I have three awesome sisters, so this was the painting I made for my sister Mimi’s birthday card. I’m lucky that my work is close by to some really cool gardens on campus, including the Ficke Garden just north of the Microbiology Building.
I put this art up on my redbubble account (https://www.redbubble.com/people/robchoudhury) so that I could buy it in sticker format

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My former advisor Neil McRoberts gave a seminar at the UF Plant Pathology department about his work on managing the citrus HLB outbreak in California. They have currently found about 1000 trees in the LA basin with HLB, and the program spends about $40m each year, which he has to fight tooth and nail to get. The disease could devestate California’s citrus market, so managing it early is critical.

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I have three awesome sisters, so this was the painting I made for my sister Abby’s birthday card. Florida lights up with tons of azaleas every spring, and my house is surrounded by them, so I wanted her to get a glimpse of some while they were in season. I put this art up on my redbubble account (https://www.redbubble.com/people/robchoudhury) so that I could buy it in sticker format

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I was part of an upcoming book chapter on the threat of climate change for pathogens, and all I could think of was the idea of pathogens on the horizon. I painted a watercolor illustration for the book chapter, maybe it’ll be used as the book cover! The painting draws inspiration from Outrun/vaporwave sort of art that became popular in the late 2010’s, although the color palette is wayyyy off, it should be neon blue and pink!

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Teaching

In the past, I have assisted in teaching several courses, including:

  • PLP148: Introduction to Mycology with Dr. David Rizzo
  • SAS030: Mushrooms, Molds, and Society with Dr. Thomas Gordon
  • SAS013: Disease and Society with Dr. Johan Leveau
  • GDB101: Introduction to Epidemiology with Dr. Neil McRoberts
  • PLSC100: Introduction to Horticulture with Dr. Chris Walsh

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