Genome mining (Pro/Seminar)

Genome mining (Pro/Seminar)

About

Genome mining is a computational technique to identify previously uncharacterized natural product biosynthetic gene clusters (BGCs) within the genomes of sequenced organisms. These BGCs are responsible for the synthesis of natural products, many of which carry essential bioactivities, such as antibiotics or anticancer compounds. This block pro-/seminar covers various genome mining tools and methods. Master students who attend the seminar will be required to run the respective genome mining tool on the provided genome sequence, in addition to fulfilling the regular pro-/seminar requirements of presentation and text summary (required for both bachelors and masters).

General information

Tutor: Jun.-Prof. Dr. Alexey Gurevich

Language: English

Registration: email to gurevich@cs.uni-saarland.de before 23:59 on 28.04.2024 (also register in LSF to get CPs). Please provide brief information about

1. Your background/experience,
2. Previously passed seminars (if any),
3. A short statement of motivation to attend this seminar (250 words maximum)

Grading

The final grade will rely on the following course components:

• Presentation:
  • Talk of approx. 30 minutes (BSc) / 40 minutes (MSc)
  • Answering the questions from the audience after the presentation
• Text summary:
  • Short description of your presented topic
  • Ca. 2 pages of text (with or without subsections), excluding title page, references, figures, tables, etc.
  • It is recommended to write the report using LaTeX to train scientific writing (11 pt, 1.5 line spacing)
• Trying the tool (MSc only!)
• Participation in the Q&A sessions.

The component weights are 55%/50% (presentation, BSc/MSc) + 30% (summary) + 15% (participation) + 0%/5% (trying the tool, BSc/MSc).

Useful materials

• Presentation preparation
  • Guidelines & checklist (borrowed from the CCB group)
  • UdS templates (MS PowerPoint & LaTeX); Simple Overleaf template (LaTex)
• Text summary preparation
  • "How to Summarize a Research Article" (borrowed from UConn)
  • Simple Overleaf template (LaTeX)

Papers

1. [antiSMASH] antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters (Nucleic Acids Research, 2011) (+ consider follow-up papers)
2. [deepBGC] A deep learning genome-mining strategy for biosynthetic gene cluster prediction (Nucleic Acids Research, 2019)
3. [GECCO] Accurate de novo identification of biosynthetic gene clusters with GECCO (bioRxiv, 2021)
4. [RODEO] A new genome-mining tool redefines the lasso peptide biosynthetic landscape (Nature Chemical Biology, 2017)
5. [RRE-Finder] RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery (mSystems, 2019)
6. [SemPI] SeMPI 2.0—A Web Server for PKS and NRPS Predictions Combined with Metabolite Screening in Natural Product Databases (Metabolites, 2021) (+ consider the first paper)
7. [PRISM] Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences (Nature Communications, 2020) (+ consider the previous papers)
8. [BAGEL] BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins (Nucleic Acids Research, 2018) (+ consider the previous papers)
9. [decRiPPter] Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides (PLOS Biology, 2020)
10. [NeuRiPP] NeuRiPP: Neural network identification of RiPP precursor peptides (Scientific Reports, 2019)
11. (TBA more..)

Important dates

Kick-off meeting (introduction to the field by A.G., general questions, paper assignment): week 6-8.5.2024. The exact date/time will be doodled among the registered participants. The event will probably be online via MS Teams.

Deadline for paper selection: 23:59 on the kick-off date + 1 week

Summary submission deadline: 23:59 on 30.06.2024

Deadline for feedback on your slides (optional): 2 weeks before the presentations

Presentations (i.e., the seminar day/s): TBA (August/September). The event will be in person in E2.1 (CBI), R1.06 (the seminar room). In exceptional circumstances, it will be possible to join the seminar online -- contact the tutor in advance.