Introduction to Biology for BMI

Instructor: Dr. Kelly

Course Website:

I. Course Description:

This course serves as an introduction to biology and biochemistry for biomedical informatics (BMI) students. We will cover basic concepts in genetics, cellular biology, and human health with an emphasis on understanding the literature and lab methodology. The goal of this course is to familiarize students with basic biological systems to allow for better understanding integration into bioinformatics based projects.

II. General Course Format and Procedure

A combination of text book chapters, reviews and scientific papers will be assigned for each weekly topic. The first half of eachsession will be completely lecture-based, focusing on basicbiology within that field. The second half will be discussion. During the first half we will review frequently used methods in each field. The discussion session will be spent discussing the readings assigned for that week. Amain goal of the discussion sessions is to understand the biology from an informatics perspective and to brainstorm ways to efficiently use computation techniques to analyze these data.

III. Course Readings/Materials

Books from which select chapters will electronically supplied to you

  • Campbell Biology (9th Edition)
  • The Processes of Life by Lawrence E. Hunter
  • Biochemistry (5th Edition) Berg JM, Tymoczko JL and L Stryer

IV. Grade Distribution

The grades will be calculated according to the table below. Although attendance is not included, in class participation is a portion of your grade. If distribution of grades necessitates it, the final grades will be curved. However if all students do well, there will not be a forced distribution (or lowering of grades based on a bell curve).

Course Component / Percentage
Assignments / 40%
Presentation / 30%
Participation / 30%

Week 1: Introduction to Cellular Biology

Topics covered: Macromolecules, cell organization, membrane structure, Cell cycle, DNA to protein synthesis, cell differentiation.

Methodology: Microscopy (light, confocal, EM), Model organisms, PCR, gel electrophoresis, Northern blots, Western blots.

Reading List:

  • Campbell Biology, Chapter II (6-8), Chapter 12-13
  • The Processes of Life, Chapter 5-7

Week 2: Genetics and Genomics

Topics covered: DNA structure, replication andgenetic inheritance, single gene disorders, Genomic sequencing, epigenetics and genetic variation.

Methodology: Quantitative PCR, microarrays, ChIP, Whole genome sequencing and assembly, methylation studies, genome annotation.

Reading List:

  • Watson JD, FHC Crick. Molecular Structure of Nucleic Acids. Nature (1953) 171:737-738
  • Campbell Biology, Chapter 15-16
  • Radiolab Antibodies Part 1: CRISPR
  • Discussion Readings:
  • Heidi C. Rare genetic disorders: Learning about genetic disease though gene mapping, SNPs and microarray data. Nature Education (2008). 1:1
  • The 1000 Genomes Project Consortium. A map of human genome variation from population scale sequencing. Nature (2010) 461:1061-1073

Week 3: Transcriptomics and Gene Biomarkers

Topics covered: Eukaryotic transcription, transcriptional regulation, RNA splicing, miRNA, cancer genetics, personalized medicine,genome-wide association studies.

Methodology: RNA-sequencing and alignment, RNA interference, transcriptome annotation

Reading List:

  • Campbell Biology, Chapter 17-18
  • Bush WS and JH Moore. Chapter 11: Genome-Wide Association Studies. PLoSComputBiol (2012) 8(12)
  • Discussion Readings:
  • Costa V, Angelini C, De Feis I and A Ciccodicola. Uncovering the complexity of transcriptomes with RNA-Seq. J Biomed Biotechnol. (2010)
  • Garraway LA and ES Lander. Lessons from the Cancer Genome. Cell. (2013) 153(1): 17-37

Week 4: Proteins and proteomics

Topics covered: Protein synthesis and structure, protein complexes, global and phospho proteomics.

Methodology: Antibody-based quantitation, immunoprecipitation, fluorescence and super-resolution microscopy, mass Spectrometry and downstream analysis.

Reading List:

  • Biochemistry: Chapter 3 (41-55), Chapter 4 (77-89)
  • Discussion Readings:
  • Gillette MA, and SA Carr. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nature Methods (2013) 10(1):28-34
  • Dwane S and PA Kiely. Tools used to study how protein complexes are assembled in signaling cascades. Bioeng Bugs. (2011) 2:247-259
  • Baker M. Microscopy: Bright light, better labels. Nature (2011) 478:137-142

Week 5: Post-translational modifications and cell signaling

Topics covered: Protein folding, post-translational modifications, network biology, cell signaling pathways.

Methodology: Basic structural proteomics, enzyme activity assays, network analysis and available tools

Reading List:

  • Biochemistry: Chapter 15 (395-403, 416-424)
  • Discussion Readings:
  • Ptacek J. et al. Global analysis of protein phosphorylation in Yeast. Nature (2005) 438:679-684
  • Downward J. The ins and outs of signaling. Nature (2001) 411:759-762

Week 6: Lipidomics and biomarker discovery

Topics covered: Lipid synthesis, function and storage. Role of lipids in disease. Methods for biomarker discovery.

Methodology: Lipid imaging, lipid extraction and mass spectrometry.

Reading List:

  • Biochemistry: Chapter 12 (319-334)
  • Radiolab Famous Tumors
  • Discussion Readings:
  • Loizides-Mangold U. On the future of mass spectrometry based-lipidomics. FEBS (2013) 280(12):2817-2829
  • Hanash SM, JP Sharon and VM Faca. Mining the plasma proteome for biomarkers. Nature (2008) 452:571-579.