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RUGGLES LAB

BMIN-GA2001
Summer 2016 - 2 credits


Instructor:                
Kelly Ruggles

kelly.ruggles@nyumc.org

Course Time:
Mondays 3:00-6:00
July 10- August 164 2017

Alexandria west conference room 508

 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 each session will be completely lecture-based, focusing on basic biology 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. A main 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
Purchase: 

  • The Processes of Life by Lawrence E. Hunter 


Books from which select chapters will electronically supplied to you: 

  • Campbell Biology (9th Edition)

  • Biochemistry (7th Edition) Berg JM, Tymoczko JL and L Stryer


IV. Grade Distribution
Class Participation 50%
Paper Presentations 50%

V. Class Schedule

Week 1: Introduction to Cellular Biology

  • Topics covered: Macromolecules, cell organization, membrane structure, Cell cycle, DNA to protein synthesis

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

  • Reading List:

    • Radiolab Cellmates (Audio)

    • The Processes of Life, Chapters 5-6

    • Campbell Biology, Chapters 15-17



Week 2: Genomics

  • Topics covered: DNA structure, replication and genetic inheritance, single gene disorders, next generation sequencing, genetic variation, personalized medicine.

  • Methodology: Quantitative PCR, microarrays, next generation sequencing and assembly, methylation studies, genome-wide association studies (GWAS).  

  • Reading List:

    • Radiolab Inheritance (Audio)

    • Campbell Biology, Chapter 17-18, 21

  • Discussion Readings:

    • Bush WS and JH Moore.  Chapter 11: Genome-Wide Association Studies. PLoS Comput Biol (2012) 8(12)

    • 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 Regulation

  • Topics covered: Eukaryotic transcription, transcriptional regulation, RNA splicing, miRNA, epigenetics, transposable elements

  • Methodology: RNA-sequencing and alignment, RNA interference, transcriptome annotation, methylation studies, ChIP-sequencing, HiC (Chromosome Confirmation Capture)

  • Reading List:

    • Radiolab Antibodies Part 1: CRISPR (Audio)

    • Brookes E and Y Shi. Diverse epigenetic mechanisms of human disease. Annu Rev Genet (2014)

    • Hawkins D, Hon GC and B Ren. Next-generation genomics: an integrative approach. Nat Rev Genet (2010)

    • ​Wang Z, Gerstein M and Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009)

  • Discussion Readings:

    • Belton JM, McCord RP, Gibcus J, Naumova N, Zhan Y and J Dekker. Hi-C: A comprehensive technique to capture the confirmation of genomes. Methods (2012)

    • Curtis et al., The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012)


Week 4: Proteins and post-translational modifications

  • 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:

    • Radiolab (So Called) Life (Audio)

    • Biochemistry: Chapter 3 (83-102), Chapter 4 (136-154)

  • Discussion Readings:

    • Ptacek J. et al. Global analysis of protein phosphorylation in Yeast. Nature (2005) 438:679-684

    • Aebersold R and M Mann. Mass spectrometry-based proteomics. Nature (2003)


Week 5: Cell signaling and Systems Biology

  • Topics covered: Network biology, cell-signaling, biomarker discovery, metabolism.

  • Methodology: Network analysis and available tools, metabolomics.

  • Reading List:

    • Radiolab Famous Tumors (Audio)

    • The Processes of Life, Chapters 7-9

    • Biochemistry: Chapter 15 (395-403, 416-424)

  • Discussion Readings:

    • Downward J. The ins and outs of signaling.  Nature (2001) 411:759-762

    • Chuang H, Hofree M and T Ideker. A Decade of Systems Biology (2010)


Week 6: Lipidomics and the Microbiome

  • Topics covered: Lipid synthesis, function and storage, and the human microbiome.  

  • Methodology: Lipid imaging, lipid extraction and mass spectrometry, 16S rRNA sequencing, metagenomics and metatranscriptomics.  

  • Reading List:

    • Radiolab Diagnosis (Audio)

    • Biochemistry: Chapter 12

    • Cho I and MJ Blaser.  The human microbiome: at the interface of health and disease. Nat Rev Genet (2012)

  • Discussion Readings:

    • Loizides-Mangold U. On the future of mass spectrometry based-lipidomics.  FEBS (2013) 280(12):2817-2829

    • The Human Microbiome Project Consortium.  Structure, function and diversity of the healthy human microbiome. Nature (2012)