Center for Integrated Bioinformatics

     1.1.   System Biology - Lecture 1.pdf
     1.2.   System Biology - Lecture 2.pdf
     1.3.   System Biology - Lecture 3.ppt
     1.4.   System Biology - Lecture 3.pdf
     1.5.   System Biology - Lecture 4.ppt
     1.6.   System Biology - Lecture 4.pdf

     1.7.   Lecture Videos 1
     1.8.   Lecture Videos 2
     1.9.   Lecture Videos 3
     1.10. Lecture Videos 4

  MICROARRAYS & DIFFERENTIAL GENE EXPRESSION: Baldwin, Ochs

    Lecture Notes

     2.1.   Microarray Lab lecture.pdf
     2.2.   Lab protocol week two 2004.doc
     2.3.   Cell Culture.doc
     2.4.   Luciferase Assays.doc
     2.5.   Protein Assay.doc
     2.6.   RNA Spectrophotometry.doc
     2.7.   Fluorescent Microscopy.doc
     2.8.   Pipetting.doc
     2.9.   RNA gels.doc
     2.10.  Transfection.doc

     2.11.  Lecture Videos 1
     2.12.  Lecture Videos 2
     2.13.  Lecture Videos 3
     2.14.  Lecture Videos 4

  PATTERN RECOGNITION & GENE EXPRESSION PROFILES: Baldwin, Ochs

    Lecture Notes

     3.1.   Week 3 Day 1.pdf
     3.2.   Week 3 Day 2.pdf
     3.3.   Week 3 Day 3.pdf
     3.4.   Week 3 Day 4.pdf
     3.5.   FGDP.pdf
     3.6.   FGDPOutput.zip
     3.7.   Article - Cho1998.pdf
     3.8.   Article - Pritchard2001.pdf
     3.9.   Article - Cherepinsky2003.pdf
     3.10. Article - Dudoit2003.pdf
     3.11. Wilcoxon Rank Sum Test Revised.pdf

  GENE & PROTEIN NETWORKS: Baldwin, Ochs, Gonye

    Lecture Notes

     4.1.   GPBA Week 4 Day 1.pdf
     4.2.   GPBA Week 4 Day 2.pdf

     4.3.   GPBA Week 4 Day (ppt - 12.9Mb)
       Part 1 (pdf)
       Part 2 (pdf)
       Part 3 (pdf)
       Part 4 (pdf)

     4.4.   ipa_guide.pdf
     4.5.   ipa_tutorial.pdf
     4.6.   ipa_faq.pdf
              

  PROTEOMICS: Rogers, Speicher

    Background Reading - Papers in Proteomic Patterns

     5.1.   Rogers/Asilomar2003_final.pdf
     5.2.   Rogers/Baggerly_BioinformatSELDI.pdf
     5.3.   Rogers/Conrads_ERMD_2003.pdf
     5.4.   Rogers/conrads_et_al_figs_1-4_7-8.pdf
     5.5.   Rogers/conrads_et_al_figs_5_6.pdf
     5.6.   Rogers/Liotta_Lancet.pdf
     5.7.   Rogers/Petricoin_CurrentOpinionBiotech_2004.pdf
     5.8.   Rogers/Proteomics_wavelets.pdf
     5.9.   Rogers/Sorace_2003.pdf

     5.10.   Rogers/Mass Spectrometry Data Analysis Demonstration.doc
     5.11.   Rogers/mass_spec_demo.m

     5.12.   Speicher/Day 1 hour 1.pdf
     5.13.   Speicher/Aminio Acid Table lecture 1.pdf
     5.14.   Speicher/Day1 hour 2.pdf
     5.15.   Speicher/Day 1 hour 3.pdf
     5.16.   Rogers/Day 1 hour 4.pdf
     5.17.   Rogers/Day 2 hour 1.pdf
     5.18.   Speicher/Day 2 hour 2 and 3.pdf
     5.19.   Speicher/Day 2 hour 4.pdf
     5.20.   Speicher/Day 4 hour 1 and 2 .pdf
     5.21.   Rogers/Pattern Discovery for Proteomics.pdf

     5.22.   Rogers/MatLab exercises 1.pdf
     5.23.   Rogers/exercise_1.m
     5.24.   Rogers/MatLab Exercises 2.pdf
     5.25.   Rogers/exercise_2.m
     5.26.   Rogers/MatLab Exercises 3.pdf
     5.27.   Rogers/exercise_3.m
     5.28.   Sampled Spectra - Normal (Rogers/ndata.mat)
     5.29.   Sampled Spectra - Cancer (Rogers/cdata.mat)
     5.30.   Single sampled normal (Rogers/daf0181_32.txt)
     5.31.   Single sampled normal - Downloadable version
     5.32.   Single sampled cancer (Rogers/daf0601_32.txt)
     5.33.   Single sampled cancer - Downloadable version