Initiation literature for master and PhD students.

 

A sense of history:

First Nature article ever by Goethe (1869)

The 3 nature papers on DNA structure published in 1953: The Watson-Crick paper is one of the best written manuscripts I have ever read. Please read the delicate three lines on p. 558 by Watson & Crick starting with ("It has not escaped our notice.....", rarely has ONE sentence hidden so much depth and comprehension).

 

Guides: 

How to become a scientist by Pr. Yewdell: First, Second

Microbiota terminology by Pr. Ravel.

Microbiota in numbers by Dr. Sender: Sender et al. PLoS Biology 2016

Immunity - self versus non-self to the danger model: Matzinger et al. Scand J Immunology 2003

B cell immunology at the extremes of age: Blanco et al. JACI 2018

 

Shortest articles and thesis ever

 

Specific litterature for Immunity & Microbiota Ecology:

IgA regulatory mechanisms: Bunker et al. Immunity 2018 Review

    Immune exclusion: Moor et al. Nature 2017

    Immune inclusion: Donaldson et al. Science 2018

IgA immunity to microbes:

    IgA binds colitogenic bacteria: Palm et al. Cell 2014

    IgA bindings associated with infant malnutrition: Kau et al. STM 2015

    IgA binds preferentially Small Intestine microbes: Bunker et al. Immunity 2015

    IgA regulates microbiota ecology: Fadlallah et al. STM 2018

    Microbial superantigens target immunoglobulin Fab region (C. comes, R. gnavus): Bunker et al. STM 2019

 

IgG immunity to microbes:

    Seric IgG binds microbiota (flow cytometry): Slack et al. Science 2009

    Seric IgG microbial specificity converge with gut IgA: Fadlallah et al. JACI 2019

    Seric IgG responses to fungi: Moreno-Sabater et al. Microbiome 2020

Bacterial degradation of secretory component: Moon et al. Nature 2015

Immune memory and persistance (long-term effect of early-life exposure): Vergani et al. Immunity 2022 and Ramanan et al. Immunity 2020

Technical/experimental limitations in microbiota research:

    Minimum 107 microbes for robust WGS (solid): Plaza-Onate et al. BMC Genomics 2015

    Minimum 106 microbes for robust 16S rRNA gene analysis: VILLETTE et al. Sci Rep 2021

Video tutorials



ChatGPT and OpenAI - Martin LARSEN (Slides)

Of note, since my video presentation I have added a few slides (you can download above). In particular I realised that a ChatGPT detection tool exist (GPT-2 Output Detector). I tried the tool and it works well for texts completely generated by ChatGPT, but if you ask it to improve a text not written by ChatGPT, it doesn't seem to be able to detect the improvements. Generally, it seems to work best with long texts. In conclusion, the tool works but does suffer from a significant number of false positives and false negatives. I'm not convinced that we have the time to verify all texts and hand written text (copied from ChatGPT) would be difficult to test.

 

DADA2 Tutorial - Remy VILLETTE

 

 

Lab Guru Tutorial - Manon CHAUVIN

 

 

 

 

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