BIOL 6964 - Advanced Molecular Genetics
Fall 2026 Syllabus, Section 01, CRN 44076,
Credit hours: 3
Course Meeting Times
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Instructor
Santosh Rana Magar
Email: skranamagar@ysu.edu
Course Description
6964. Advanced Molecular Genetics. An examination of the mechanisms of transcription, translation, DNA replication, and RNA processing and transposition in both prokaryotes and eukaryotes. Prereq.: BIOL 4890 Molecular Genetics or permission of instructor. 3 s.h.
Course Readings
| Group | Title | Author | ISBN |
|---|---|---|---|
| Required | Genetics: From genes to genomes | Hartwell et al | 0-07-246248-5 |
| Optional | Molecular Biology | Weaver RF | 978-0-07-352532-7 |
| Optional | Selected contemporary CRISPR-Cas research articles (2020–2026) | Various |
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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Advanced Molecular Genetics
| Day | Date | Reading(s) | Proposed Topic | Due/To Prepare for Class |
|---|---|---|---|---|
| Mon | 8/24 | Course materials | Introduction to Advanced Molecular Genetics – Course overview; molecular mechanisms, genomics, and research-based learning | Review syllabus and course expectations |
| Wed | 8/26 | R introductory materials | Practical: Introduction to R/RStudio – Data import, objects, tables, and basic data handling | Bring laptop; install R/RStudio |
| Fri | 8/28 | Research project overview | Graduate Research Project Introduction – Stellera chamaejasme, genomic resources, RNA-seq data, and TE research questions | Review project overview |
| Mon | 8/31 | Selected reading | Genome Organization – Prokaryotic and eukaryotic genomes, genes, regulatory regions, and repetitive DNA | Reading |
| Wed | 9/2 | R/data tutorial | Practical: Biological Data in R – Metadata, expression matrices, data organization, and visualization | R exercise |
| Fri | 9/4 | Selected CRISPR paper | CRISPR Paper Discussion I – Contemporary CRISPR-Cas application | Read and summarize paper |
| Mon | 9/7 | Selected reading | DNA Replication – Mechanisms, enzymes, replication fidelity; prokaryotes vs. eukaryotes | Reading |
| Wed | 9/9 | Practical materials | Practical: Genome Data – Reference genomes, FASTA files, genome annotations, and sequence information | R/data exercise |
| Fri | 9/11 | Project materials | Research Analysis – Genome and annotation exploration | Research activity |
| Mon | 9/14 | Selected reading | DNA Damage, Repair & Genome Stability – Mutation, DNA repair pathways, and genome integrity | Reading |
| Wed | 9/16 | Practical materials | Practical: Genome Variation – Exploring sequence variation and molecular consequences | R exercise |
| Fri | 9/18 | Selected CRISPR paper | CRISPR Paper Discussion II – Genome editing and DNA repair | Read and summarize paper |
| Mon | 9/21 | Selected reading | Transcription – RNA polymerases, promoters, initiation, elongation, and termination | Reading |
| Wed | 9/23 | RNA-seq tutorial | Practical: Introduction to RNA-seq – Counts, sample metadata, and expression matrices | R exercise |
| Fri | 9/25 | Project dataset | Research Analysis – Exploring the Stellera RNA-seq dataset | Research activity |
| Mon | 9/28 | Selected reading | Regulation of Transcription – Promoters, enhancers, transcription factors, and gene regulation | Reading |
| Wed | 9/30 | R/RNA-seq materials | Practical: Gene Expression in R – Normalization concepts and expression visualization | R exercise |
| Fri | 10/2 | Selected CRISPR paper | CRISPR Paper Discussion III – CRISPR-mediated gene regulation | Read and summarize paper |
| Mon | 10/5 | Selected reading | RNA Processing – RNA maturation, capping, polyadenylation, introns, and splicing | Reading |
| Wed | 10/7 | Practical materials | Practical: Gene & Transcript Structure – Genes, transcripts, exons, and introns | R exercise |
| Fri | 10/9 | Project materials | Research Analysis – RNA-seq exploration and visualization | Research activity |
| Mon | 10/12 | Selected reading | Alternative Splicing & RNA Regulation – Alternative transcripts and post-transcriptional regulation | Reading |
| Wed | 10/14 | R tutorial | Practical: Expression Visualization – PCA, heatmaps, and expression plots | R exercise |
| Fri | 10/16 | Mid-term exam | Paper Discussion (randomly selected manuscript): evaluation/grading based on presentation style/contents/interpretation/critiques/recommendations (each 8-10 min) | |
| Mon | 10/19 | Selected reading | Translation – Genetic code, ribosomes, initiation, elongation, and termination | Reading |
| Wed | 10/21 | Practical materials | Practical: From Transcript to Protein – Coding sequences, annotation, and predicted proteins | Data exercise |
| Fri | 10/23 | Project materials | Research Analysis – Molecular interpretation and preparation for TE analysis | Research activity |
| Mon | 10/26 | Selected reading | Regulation of Gene Expression – Transcriptional, post-transcriptional, and translational regulation | Reading |
| Wed | 10/28 | RNA-seq/R materials | Practical: Differential Expression – Fold change, statistical significance, and visualization | R exercise |
| Fri | 10/30 | Selected CRISPR paper | CRISPR Paper Discussion V – Functional validation of genes/phenotypes | Read and summarize paper |
| Mon | 11/2 | Selected TE reading | Transposable Elements I – TE classes and mechanisms of transposition | Reading |
| Wed | 11/4 | TE analysis materials | Practical: TE Annotation & Classification – TE classes, superfamilies, and families | TE/R exercise |
| Fri | 11/6 | Project dataset | TE Research Project: Genome Landscape – Characterizing TEs in the Stellera genome | Research analysis |
| Mon | 11/9 | Selected TE reading | Transposable Elements II – Retrotransposons, DNA transposons, and genome consequences | Reading |
| Wed | 11/11 | No Class | Legal holiday-university closed | |
| Fri | 11/13 | Project materials | Research Analysis: TE Landscape – Interpretation and research-question refinement Practical: TE Landscape in R – TE abundance, composition, and visualization |
TE/R exercise |
| Mon | 11/16 | Selected TE reading | Transposable Elements III: TE Regulation – Silencing, chromatin, methylation, and genome defense | Reading |
| Wed | 11/18 | Project dataset | Practical: TE Expression from RNA-seq – Identifying transcriptionally active TE families | TE/R exercise |
| Fri | 11/20 | Selected CRISPR paper | CRISPR Paper Discussion VI – CRISPR and genome/gene regulation | Read and summarize paper |
| Mon | 11/23 | Selected reading | TE Activity & Genome Dynamics – TE activation, suppression, genome regulation, and phenotypic variation | Reading |
| Wed | 11/25 | NO CLASS | No Class-university closed | |
| Fri | 11/27 | NO CLASS | No Class – Thanksgiving Break | |
| Mon | 11/30 | Selected reading | Integrating Molecular Genetics – Transcription, genome regulation, and TE activity | Reading |
| Wed | 12/2 | Project dataset | Practical: Comparative TE Activity – Comparing PP, RW, and RWh using R Practical: Final TE Analysis & Visualization – Research-quality figures and major patterns |
Draft figures/results |
| Fri | 12/4 | Project materials | Research Project Workshop – Interpretation, limitations, and research synthesis | Project progress |
| Mon | 12/7 | Selected reading | Emerging Directions in Molecular Genetics – Contemporary approaches to genome regulation | Reading |
| Wed | 12/9 | Project materials | Research Project Synthesis/presentation – Final figures, conclusions, and presentation preparation | Finalize project |
| Fri | 12/11 | Final Exam | Graduate Course Synthesis/Exam |
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.