BIOL 4850F - Problem in Botany
Fall 2026 Syllabus, Section 01, CRN 43997,
Credit hours: 3
Course Meeting Times
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Instructor
Santosh Rana Magar
Email: skranamagar@ysu.edu
Course Description
Course Readings
| Group | Title | Author | ISBN |
|---|---|---|---|
| Required | Selected Research Articles in Plant Invasion Genomics, Polyploidy, and Copy-Number | Various authors | |
| Optional | Bioinformatics and Functional Genomics | Jonathan Pevsner (2009) | 9780470451496 |
Required readings will consist of selected peer-reviewed research articles and instructor-provided materials related to biological invasion, plant genomics, polyploidy, copy-number variation, and genomic data analysis. Specific readings will be assigned throughout the semester to correspond with the student's research progress. The recommended text may be used as a reference for working with genomic data, command-line tools, and reproducible bioinformatics workflows.
The course readings are subject to change in the event of extenuating circumstances, research developments, current events, and/or to ensure better learning.
Assignments/Assessments
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Problems in Botany
| Week of | Reading(s) | Proposed Topic | Due/To Prepare for Class |
|---|---|---|---|
| 8/24 | Project overview | Introduction to Research Project – Wild sugarcane, biological invasion, and project goals | Review syllabus and project overview |
| 8/31 | Selected invasion-genomics paper | Invasion Genomics & Polyploidy – Genomic variation and polyploid invasive plants | Read and summarize assigned paper |
| 9/7 | No Class | ||
| 9/14 | Bioinformatics materials Selected CNV paper |
Working with Genomic Data – WGS, reference genomes, BAM, BED, GFF/GTF, and genomic coordinates Structural Variation & CNV – Structural variants, copy-number variation, and gene dosage |
Prepare research questions Genomic-data exercise |
| 9/21 | Selected R tutorial | Introduction to R/RStudio – Data import, organization, filtering, and basic visualization | R practice |
| 9/28 | R/bioinformatics tutorial | Genomic Data Analysis in R – Data manipulation, summaries, and visualization | R exercise |
| 10/5 | Selected CNV methods paper | Sequencing Depth & CNV – Coverage, read depth, normalization, and relative copy-number signals | CNV methods exercise |
| 10/12 | Project materials | Building the CNV Dataset – Gene-level read depth and data quality assessment | Preliminary dataset |
| 10/19 | Selected methods reading | CNV Normalization & Quality Assessment – Normalizing and evaluating gene-level CNV signals | Normalized dataset |
| 10/26 | Selected CNV paper | Gene-Level CNV Analysis – Dosage-conserved and dosage-variable genes | Preliminary analysis |
| 11/2 | Project materials | CNV Variation Among Individuals – Comparing CNV profiles using R | Preliminary figures |
| 11/9 | Selected genomics paper | Genome-Wide CNV Landscape – Chromosomal distribution and CNV-rich regions | Genome-wide CNV analysis |
| 11/16 | Selected functional-genomics paper | Functional Interpretation of CNV – Annotation and biological functions of variable genes | Candidate gene/function summary |
| 11/23 | Selected invasion-genomics paper | CNV, Polyploidy & Biological Invasion – Integrating genomic patterns with invasion biology | Draft results and interpretation |
| 11/30 | Scientific-writing materials | Research Synthesis & Scientific Writing – Figures, methods, results, limitations, and conclusions | Draft report and final figures |
| 12/7 | Project materials | Final Research Presentation & Project Synthesis | Final report and presentation |
The course schedule, policies, procedures, and assignments in this course are subject to change in the event of extenuating circumstances, by mutual agreement, and/or to ensure better learning.