1. Home
  2. BIOL
  3. BIOL 625: Bioinformatics and Genomics

BIOL 625: Bioinformatics and Genomics Report a Broken Link

Course Orientation

Hendrix, D. A. (2019). Applied bioinformatics of nucleic acid sequences (1st ed.). Oregon State University. https://open.oregonstate.education/appliedbioinformatics/
Kellis, M. (Ed.). (2016). Computational biology: Genomes, networks, evolution. MIT OpenCourseWare. https://ocw.mit.edu/ans7870/6/6.047/f15/MIT6_047F15_Compiled.pdf

Unit 1: Biological Information: Storage and Flow

Required Readings
Fowler, S., Roush, R., & Wise, J. (2013). Concepts of biology. Rice University.
Parker, N., Schneegurt, M., Tu, A.-H. T., Lister, P., & Forster, B. M. (2016). Microbiology. Rice University.
Additional Resources
European Molecular Biology Laboratory. (n.d.). EMBOSS transeq. EMBL-EBI. https://www.ebi.ac.uk/jdispatcher/st/emboss_transeq
Nucleic Acid Converter. (2016). DNA to mRNA to protein converter. https://skaminsky115.github.io/nac/DNA-mRNA-Protein_Converter.html
Herráez, A. (n.d.). Transcription and translation tool. https://biomodel.uah.es/en/lab/cybertory/analysis/trans.htm
Rice, P., Bleasby, A., Ison, J., Uludag, M., Carver, T., Mullan, L., & Schuster, M. (2011). EMBOSS. https://emboss.sourceforge.net/

Unit 2: DNA and RNA Sequencing Technology

Required Readings
Abdurakhmonov, I. Y., & Ikehara, K. (2025). DNA sequencing - History, present and future. InTechOpen. https://www.intechopen.com/books/1003888
Oxford Nanopore Technologies. (n.d.). How nanopore sequencing works. https://nanoporetech.com/platform/technology
PacBio. (2020, February 4). PacBio sequencing – How it works [Video]. YouTube. https://www.youtube.com/watch?v=_lD8JyAbwEo
Additional Resources
Illumina. (n.d.). For every lab, everywhere. https://www.illumina.com/
Oxford Nanopore Technologies. (n.d.). To enable the analysis of anytthing, by anyone, anywhere. https://nanoporetech.com/
PacBiol. (n.d.). https://www.pacb.com/
Thermo Fisher Scientific. (n.d.). https://www.thermofisher.com/ca/en/home.html

Unit 3: Comparing Biological Sequences

Required Resources
Bozeman Science. (2012, May 9). Mutations [Video]. YouTube. https://www.youtube.com/watch?v=eDbK0cxKKsk
Arends, D. (2022, January 15). Sequence alignment, scoring, and analysis (bioinformatics S11E1) [Video]. YouTube. https://www.youtube.com/watch?v=C4LLXxLnHVs
National Library of Medicine. (2025, July 21). Basic local alignment search tool. https://blast.ncbi.nlm.nih.gov/Blast.cgi
National Library of Medicine. (n.d.). Nucleotide. https://www.ncbi.nlm.nih.gov/nuccore/
Moeckel, C., Mareboina, M., Konnaris, M. A., Chan, C. S. Y., Mouratidis, I., Montgomery, A., Chantzi, N., Pavlopoulos, G. A., & Georgakopoulous-Soares, I. (2024). A survey of k-mer methods and applications in bioinformatics. Computational and Structural Biotechnology Journal, 23, 2289–2303. https://doi.org/10.1016/j.csbj.2024.05.025
Additional Resources
European Molecular Biology Laboratory. (n.d.). Clustal omega. https://www.ebi.ac.uk/jdispatcher/msa/clustalo?stype=protein

Unit 4: Phylogeny and Evolution

Additional Resources
Price, M. N. (n.d.). FastTree 2.2: Approximately-maximum-likelihood trees for large alignments. GitHub. https://morgannprice.github.io/fasttree/
MEGA. (n.d.). MEGA software. https://www.megasoftware.net/
Zhang, C., Huelsenbeck, J., van der Mark, P., Ronquist, F., & Teslenko, M. (n.d.). MrBayes: Bayesian interface of phylogeny. GitHub. https://nbisweden.github.io/MrBayes/
The Elelixis Lab. (2013). The exelixis lab: Enabling research in evolutionary biology. https://cme.h-its.org/exelixis/web/software/raxml/
National Library of Medicine. (n.d.). Database of clusters of orthologous genes (COGs). https://www.ncbi.nlm.nih.gov/research/cog/
Kanehisa Laboratories. (2025). KO (KEGG orthology) database. https://www.genome.jp/kegg/ko.html
European Molecular Biology Laboratory. (n.d.). Interpro. https://www.ebi.ac.uk/interpro/
O'Halloran, D. (2014). A practical guide to phylogenetics for nonexperts. Journal of Visualized Experiments. https://dx.doi.org/10.3791/50975
Zou, Y., Zhang, Z., Zeng, Y., Hu, H., Hao, Y., Huang, Z., & Li, B. (2024). Common methods for phylogenetic tree construction and their implementation in R. Bioengineering, 11(5), 480. https://doi.org/10.3390/bioengineering11050480
Quang Minh, B., Lanfear, R., Wong, T., Ly-Trong, H., Demotte, P., Chernomor, O., Schmidt., H. A., Schrempf, D., Woodhams, M., Hoang, D. T., von Haeseler, A., Nguyen, L. T., Trifinopoulos, J., & Barbetti, J. (n.d.). Documentation. IQ-TREE. https://iqtree.github.io/doc/
Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009). Calculation of trees from alignments. Jalview. https://www.jalview.org/help/html/calculations/tree.html

Unit 5: Genomics and Genome Assembly

Required Readings
Lewin, H. A., Larkin, D. M., Pontius, J., & O'Brien, S. J. (2009). Every genome sequence needs a good map. Genome Research, 19, 1925–1928. https://doi.org/10.1101/gr.094557.109
Pareek, C. S., Smoczynski, R., & Tretyn, A. (2011). Sequencing technologies and genome sequencing. Journal of Applied Genetics, 52, 413–435. https://doi.org/10.1007/s13353-011-0057-x
Jung, H., Ventura, T., Chung, J. S., Kim, W.-J., Nam, B.-H., Kong, H. J., Kim, Y.-O., Jeon, M.-S., & Eyun, S. (2020). Twelve quick steps for genome assembly and annotation in the classroom. PLoS Computational Biology, 16(11), e1008325. https://doi.org/10.1371/journal.pcbi.1008325
Parfrey, L. W., Lahr, D. J. G., & Katz, L. A. (2008). The dynamic nature of eukaryotic genomes. Molecular Biology and Evolution, 25(4), 787–794. https://doi.org/10.1093/molbev/msn032
Ekblom, R., & Wolf, J. B. W. (2014). A field guide to whole-genome sequencing, assembly and annotation. Evolutionary Applications, 7(9), 1026–1042. https://doi.org/10.1111/eva.12178
The Galaxy Community. (2024). The Galaxy platform for accessible, reproducible, and collaborative data analyses (2024 update). Nucleic Acids Research. https://doi.org/10.1093/nar/gkae410
Goff, K. L., Suresh, S., Stadfeld, J. M., & Bhatnagar, S. (2025). Complete genome sequences of nine isolates from microplastics in the Bow River, Calgary, Canada. Microbial Resource Announcements, 14(5). https://doi.org/10.1128/mra.01085-24
Additional Resources
Li, Z., Chen, Y., Mu, D., Yuan, J., Shi, Y., Zhang, H., Gan, J., Li, N., Hu, X., Liu, B., Yang, B., & Fan, W. (2012). Comparison of the two major classes of assembly algorithms: Overlap–layout–consensus and de–bruijn–graph. Briefings in Functional Genomics, 11(1), 25–37. https://doi.org/10.1093/bfgp/elr035
Forouzan, E., Shariati, P., Maleki, M. S. M., Karkhane, A. A., & Yakhchali, B. (2018). Practical evaluation of 11 de novo assemblers in metagenome assembly. Jounral of Microbiological Methods, 151, 99–105. https://doi.org/10.1016/j.mimet.2018.06.007

Unit 6: Genes: Prediction and Annotation

Required Resources
Center for Comparative Genomics and Bioinformatics. (n.d.). Galaxy. https://galaxy-main.usegalaxy.org/
Schwengers, O. (2025, July 3). Bakta: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids. GitHub. https://github.com/oschwengers/bakta
Seemann, T. (2019, November 11). Prokka: Rapid prokaryotic genome annotation. GitHub. https://github.com/tseemann/prokka

Unit 7: Metagenomics

Additional Resources
Nishimura, Y., & Yoshizawa, S. (2022). The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Scientific Data, 9, 305. https://doi.org/10.1038/s41597-022-01392-5
Zeng, S., Patangia, D., Almeida, A., Zhou, Z., Mu, D., Ross, R. P., Stanton, C., & Wang, S. (2022). A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human microbiome. Nature Communications, 13, 5139. https://doi.org/10.1038/s41467-022-32805-z
Salgado, J. F. M., Hervé, V., Vera, M. A. G., Tokuda, G., & Brune, A. (2024). Unveiling lignocellulolytic potential: A genomic exploration of bacterial lineages within the termite gut. Microbiome, 12, 201. https://doi.org/10.1186/s40168-024-01917-7
Liu, J., Taft, D. H., Maldonado-Gomez, M. X., Johnson, D., Treiber, M. L., Lemay, D. G., DePeters, E. J., & Mills, D. A. (2019). The fecal resistome of dairy cattle is associated with diet during nursing. Nature Communications, 10, 4406. https://doi.org/10.1038/s41467-019-12111-x
Borton, M. A., McGivern, B. B., Willi, K. R., Woodcroft, B. J., Moiser, A. C., Singleton, D. M., Bambakidis, T., Pelly, A., Daly, R. A., Liu, F., Freiburger, A., Edirisinghe, J. N., Faria, J. P., Danczak, R., Leleiwi, I., Goldman, A. E., Wilkins, M. J., Hall, E. K., Pennacchio, C., ... Wrighton, K. C. (2025). A functional microbiome catalogue crowdsourced from North American rivers. Nasture, 637, 103–112. https://doi.org/10.1038/s41586-024-08240-z
Li, D., Liu, C.-M., Luo, R., Sadakane, K., Lam, T.-W. (2015). Megahit (Version 1.2.9) [Genome assembler]. GitHub. https://github.com/voutcn/megahit?tab=readme-ov-file#readme
National Research Council Committee on Metagenomics: Challenges and Funcational Applications. (2007). The new science of metagenomics: Revealing the secrets of microbial planet. National Academies Press. https://www.ncbi.nlm.nih.gov/books/NBK54006/
Meyer, F., Fritz, A., Deng, Z.-L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P. T. L. C., Cristian, A., ... McHardy, A. C. (2022). Critical assessment of metagenome interpretation: The second round of challenges. Nature Methods, 19, 429–440. https://doi.org/10.1038/s41592-022-01431-4

Unit 8: Transcriptomics

Required Readings
Tzec-Interián, J. A., González-Padilla, D., & Góngora-Castillo, E. B. (2025). Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses. Quantitative Biology, 13(2), e78. https://doi.org/10.1002/qub2.78
Williams, C. G., Lee, H. J., Asatsuma, T., Vento-Tormo, R., & Haque, A. (2022). An introduction to spatial transcriptomics for biomedical research. Genome Medicine, 14, 68. https://doi.org/10.1186/s13073-022-01075-1
Shakya, M., Lo, C.-C., & Chain, P. S. G. (2019). Advances and Challenges in Metatranscriptomic Analysis. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.00904
Ojala, T., Häkkinen, A.-E., Kankuri, E., & Kankainen, M. (2023). Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics. Trends in Genetics, 39(9), 686–702. https://doi.org/10.1016/j.tig.2023.05.004
Additional Resources
Trent University. (n.d.). How to write a research proposal. https://www.trentu.ca/academicskills/how-guides/how-write-university/how-approach-any-assignment/how-write-research-proposal
Rachel R. N. (2024, June 22). How to write the methods section of a research proposal. StudyingHQ. https://studyinghq.com/how-to/how-to-write-the-methods-section-of-a-research-proposal/
Lowe, R., Shirley, N., Bleackley, M., Dolan, S., & Shafee, T. (2017). Transcriptomics technologies. PLOS Computational Biology, 13(5), e1005457. https://doi.org/10.1371/journal.pcbi.1005457

Assignments

Assignment 1
Google. (n.d.). Google scholar. https://scholar.google.ca/
National Library of Medicine. (n.d.). Welcome to NCBI. https://www.ncbi.nlm.nih.gov/
European Molecular Biology Laboratory. (n.d.). EMBL's European bioinformatics institute. https://www.ebi.ac.uk/
DDBJ. (n.d.). https://www.ddbj.nig.ac.jp/index-e.html
Scite. (n.d.). Scite_. https://scite.ai/
Assignment 2
PLOS. (n.d.). Submission guidelines. https://journals.plos.org/plosone/s/submission-guidelines#loc-references
Springer Nature. (n.d.). Submission guidelines. https://www.nature.com/srep/author-instructions/submission-guidelines#references
PeerJ. (n.d.). Download template. https://peerj.com/about/author-instructions/#reference-format
Springer Nature. (n.d.). Research article. BMC Genomics. https://bmcgenomics.biomedcentral.com/submission-guidelines/preparing-your-manuscript/research-article
Elsevier. (n.d.). Mendeley. https://www.mendeley.com/
Digital Scholar. (n.d.). Zotero. https://www.zotero.org/