Digital Reading Room 2.0 -- BIOL 520: Microbial Genomics

BIOL 520: Microbial Genomics Report a Broken Link

Course Orientation

Unit 1

Land, M., Hauser, L., Jun, S.-R., Nookaew, I., Leuze, M. R., Ahn, T.-H., Karpinets, T., Lund, O., Kora, G., Wassenaar, T., Poudel, S., & Ussery, D. W. (2015). Insights from 20 years of bacterial genome sequencing. Functional and Integrative Genomics, 15, 141–161. https://doi.org/10.1007/s10142-015-0433-4

Wetterstrand, K. A. (n.d.). DNA sequencing costs: Data from the NHGRI genome sequencing program. National Human Genome Research Institute. Retrieved October 7, 2025, from https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data

Pray, L. A. (2008). Discovery of DNA structure and function: Watson and Crick. Nature Education, 1(1), 100. https://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397/

Rosalind Franklin. (n.d.). In Wikipedia. https://en.wikipedia.org/wiki/Rosalind_Franklin

CD Genomics. (2021, September 12). The introduction of microbial genomics [Video]. YouTube. https://www.youtube.com/watch?v=fPNFk_BHi3Q

Unit 2

IslandViewer. (n.d.). Genomic island prediction and genome visualization tool. Simon Fraser University. https://www.pathogenomics.sfu.ca/islandviewer/

See also Bertelli, C., Laird, M. R., Williams, K. P., Lau, B. Y., Hoad, G., Winsor, G. L., & Brinkman, F. S. L. (2017). IslandViewer 4: Expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research, 45(W1), W30–W35. https://doi.org/10.1093/nar/gkx343

SnapGene. (2022, January 18). Introduction to restriction enzyme cloning [Video]. YouTube. https://www.youtube.com/watch?v=kbLGr7O24ng

SnapGene. (2022, January 18). A detailed look at restriction cloning [Video]. YouTube. https://www.youtube.com/watch?v=MXMR1i4qwkM

SnapGene. (2022, August 7). A detailed look at Gibson assembly [Video]. YouTube. https://www.youtube.com/watch?v=etPiygqEv5E

SnapGene. (2022, August 7). Gibson assembly pros and cons [Video]. YouTube. https://www.youtube.com/watch?v=Pkuy2iaqy1E

SnapGene. (2022, January 17). A brief look at gateway cloning [Video]. YouTube. https://www.youtube.com/watch?v=8VwoUZwZpXQ

SnapGene. (n.d.). SnapGene Viewer. https://www.snapgene.com/snapgene-viewer/

Benchling. (n.d.). https://www.benchling.com/

Restriction enzyme cloning. (2025). SnapGene. https://www.snapgene.com/guides/restriction-enzyme-cloning

Assignment 1

AddGene. (n.d.). How to design a primer. https://www.addgene.org/protocols/primer-design/

AddGene. (n.d.). Polymerase chain reaction (PCR). https://www.addgene.org/protocols/pcr/

Pseudomonas Genome Database. (n.d.). Pseudomonas genome annotations and tools. https://www.pseudomonas.com

SnapGene. (n.d.). pMCSG59. https://www.snapgene.com/plasmids/structural_genomics_vectors/pMCSG59

Unit 3

Dideoxynucleotide. (n.d.) In Wikipedia. https://en.wikipedia.org/wiki/Dideoxynucleotide

Illumina. (2016, October 5). Overview of Illumina sequencing by synthesis workflow | Standard SBS chemistry [Video]. YouTube. https://www.youtube.com/watch?v=fCd6B5HRaZ8

Henrik's Lab. (2020, April 23). Next generation sequencing (Illumina) - An introduction [Video]. YouTube. https://www.youtube.com/watch?v=CZeN-IgjYCo

National DNA Database. (2016, May 23). Nanopore DNA sequencing [Video]. YouTube. https://www.youtube.com/watch?v=E9-Rm5AoZGw

Thermo Fisher Scientific. (2020, May 21). Ion torrent next-generation sequencing [Video]. YouTube. https://www.youtube.com/watch?v=zBPKj0mMcDg

PacBio. (2020, February 4). PacBio sequencing – How it works [Video]. YouTube. https://www.youtube.com/watch?v=_lD8JyAbwEo

Shideler, S., Headley, J., Gauthier, J., Kukavica-Ibrulj, I., Levesque, R. C., Lewenza, S. (2021).Complete genome sequence of a pseudomonas species isolated from tailings pond water in Alberta, Canada. Microbiology Resource Announcements, 10(9). https://doi.org/10.1128/mra.01174-20

Novogene. (2023, February 22). 2. Microbial whole genome sequencing [Video]. YouTube. https://www.youtube.com/watch?v=ckPuqAS3rdc

Unit 4

National Center for Biotechnology Information (NCBI). (n.d.). Genome datasets. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/datasets/genome/

National Center for Biotechnology Information (NCBI). (n.d.). Pathogen detection. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/pathogens/

National Center for Biotechnology Information (NCBI). (n.d.). NCBI datasets. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/datasets

Kanehisa Laboratories. (2024). Glycolysis / gluconeogenesis - Reference pathway. KEGG. (https://www.kegg.jp/pathway/map00010

Assignment 2

National Library of Medicine. (n.d.). SARS-COV-2 data hub. NCBI Virus. Retrieved October 7, 2025, from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049

Aksamentov, I., Roemer, C., Hudcroft, E. B., & Neher, R. A. (2021). Nextclade: Clade assignment, mutation calling, and sequence quality checks. Nextclade. https://clades.nextstrain.org/

Bedford, T., Neher, R., Askamentov, I., Anderson, J. S. J., Andrews, K., Chang, J., Hadfield, J., Hodcroft, E., Huddleston, J., Lee, J., Lin, V., Roemer, C., & Sibley, T. (n.d.). Nextstrain: Real-time tracking of pathogen evolution. Nextstrain. https://nextstrain.org/

Unit 5

Novogene. (2021, June 25). A beginner's guide to RNA-Seq [Video]. YouTube. https://www.youtube.com/watch?v=oDB_DG3vP48

The Ahmed Lab: Northwestern Neurosurgery. (2020, May 13). Intro to proteomics / Mass spectrometry (MS) [Video]. YouTube. https://www.youtube.com/watch?v=JPpKL1uzE0I

Graham, R. L. J., Graham, C., & McMullan, G. (2007). Microbial proteomics: A mass spectrometry primer for biologists. Microbial Cell Factories, 6, 26. https://doi.org/10.1186/1475-2859-6-26

Unit 6

There are no additional readings for this unit.

Assignment 3

DSMZ Digital Diversity. (n.d.). SILVA: Alignment, classification and tree service [Version 1.2.12]. Retrieved October 7, 2025, from https://www.arb-silva.de/aligner/

Unit 7

Hug et al. (2016). A new view of the tree of life. Nature Microbiology, 1. https://doi.org/10.1038/nmicrobiol.2016.48

Syntrophy. (2025, October 3). In Wikipedia. https://en.wikipedia.org/w/index.php?title=Syntrophy&oldid=1314903178

Letunic, I., & Bork, P. (2024). Interactive tree of life. https://itol.embl.de/itol.cgi

Unit 8

Signma factor. (2025, October 3). In Wikipedia. https://en.wikipedia.org/w/index.php?title=Sigma_factor&oldid=1314840197

iGEM Parts Registry. (n.d.). Registry of standard biological parts. Retrieved October 7, 2025. from https://parts.igem.org/Main_Page

iGEM Parts Registry. (n.d.). Promotors. Registry of Standard Biological Parts. Retrieved October 7, 2025, from https://parts.igem.org/Promoters

iGEM Parts Registry. (n.d.). Ribosome binding sites/design. Registry of Standard Biological Parts. Retrieved October 7, 2025, from https://parts.igem.org/Ribosome_Binding_Sites/Design

iGEM Parts Registry. (n.d.). Protein coding sequences. Registry of Standard Biological Parts. Retrieved October 7, 2025, from https://parts.igem.org/Protein_coding_sequences

Softberry. (2016, October 24). Operon and gene finding in bacteria. http://www.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb

Ramons, J. L., Martínez-Bueno, M., Molina-Henares, A. J., Terán, W., Watanabe, K., Zhang, X., Gallegos, M. T., Brennan, R., & Tobes, R. (2005). The TetR family of trasncriptional repressors. Microbiology and Moelcular Biology Reviews, 69. https://doi.org/10.1128/mmbr.69.2.326-356.2005

Unit 9

Pizza, M., Scarlato, V., Masignani, V., Giuliani, M. M., Aricò, B., Comanducci, M., Jennings, G. T., Baldi, L., Bartonlini, E., Capecchi, B., Galeotti, C. L., Luzzi, E., Manetti, R., Marchetti, E., Mora, M., Nuti, S., Ratti, G., Santini, L., Savino, S., ... Rappuoli, R. (2000). Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science, 287(5459), 1816–1820. https://doi.org/10.1126/science.287.5459.1816

Assignment 4

Kanehisa Laboratories. (n.d.). KEGG: Kyoto encyclopedia of genes and genomes. Retrieved October 7, 2025, from https://www.kegg.jp/

Unit 10

Rodriguez, J., Cordaillat-Simmons, M., Badalato, N., Berger, B., Breton, H., de Lahondès, R., Deschasaux-Tanguy, M., Desvignes, C., D’Humières, C. Kampshoff, S., Lavelle, A., Metwaly, A., Quijada, N. M., Seegers, J. F. M. L., Udocor, A., Zwart, H., Human Microbiome Action Consortium, Manguin, E., Doré, J., & Druart, C. (2024). Microbiome testing in Europe: Navigating analytical, ethical and regulatory challenges. Microbiome, 12, 258. https://doi.org/10.1186/s40168-024-01991-x

Ma, Y., Chen, H., Lan, C., & Ren, J. (2018). Help, hope, and hype: Ethical considerations of human microbiome research and applications. Protein & Cell, 9(5), 404–415. https://doi.org/10.1007/s13238-018-0537-4

Solbach, T., & Kalinka, K. (2023, October 9). The accelerating rise of microbiome-based therapeutics. Strategy&. https://www.strategyand.pwc.com/de/en/industries/pharma-life-sciences/impact-microbiome-therapeutics.html

WIRED Events. (2025, March 25). Ara Katz on the microbiome and its impact on science society and self | WIRED health [Video]. YouTube. https://www.youtube.com/watch?v=O245bU53XaY

Hoffman, S. A., Diggans, J., Desnmore, D., Dai, J., Knight, T., Leproust, E., Boeke, J. D., Wheeler, N., & Cai, Y. (2023). Safety by design: Biosafety and biosecurity in the age of synthetic genomics. iScience, 26(3), 106165. https://doi.org/10.1016/j.isci.2023.106165

Final Project

KEGG. (2024, September 20). KEGG mapper [Version 5.2]. https://www.genome.jp/kegg/mapper/