Reference cleanup and Markdown corrections

[agitter]

Please provide a description of your changes: After the latest Manubot issue, I skimmed the paper and fixed obvious problems with references and Markdown formatting. There was one broken DOI I think was supposed to be https://doi.org/10.1021/ac4001223, but I'm not positive.

Please check the following about your suggested changed:

• [x] The new text has one sentence per line
• [x] preprints that are cited are listed as an issue for discussion and peer review

[jessegmeyerlab]

Thank you!