Questions on the Final

Post questions about the Final Exam hear, as well as emailing them to John Wikswo. This will ensure that everyone can benefit from any clarifications.

Class -

What questions might you like your classmates to answer on the final?

Explain the microbiome to your grandfather, or another close senior friend.



John

SysBio15 Asgn_27A_Class_27_Article_22_2015_04_14

Effective Models: Read Article 22  Automated adaptive inference of phenomenological dynamical models, Bryan C. Daniels and Ilya Nemenman. Look carefully at all the figures, including those in the Supplemental Material. Be sure to note the section on the models that don't work. Post a PCRC.

SysBio15 Asgn_25A_Class_25_Article_21_2015_04_07

Networks: Read Article 21  J. A. Papin, T. Hunter, B. O. Palsson, and S. Subramaniam. Reconstruction of cellular signalling networks and analysis of their properties. Nature Rev.Mol.Cell Biol. 6 (2):99-111, 2005. Post a PCRC.

SysBio15 Asgn_24B_Class_24_Article_20_2015_04_02

EGFR signaling: Scan Article 20  K. Oda, Y. Matsuoka, A. Funahashi, and H. Kitano. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol.Sys.Biol. 1:Article 2005.0010, 2005. Do NOT get lost in the details!! Post a PCRC.

SysBio15 Asgn_24A_Class_24_Article_19_2015_04_02

EGFR signaling: Read carefully Article 19  Boris N. Kholodenko. Cell-signalling dynamics in time and space. Nature Rev.Mol.Cell Biol. 7 (3):165-176, 2006. Figure out how EGFR works. Post a PCRC.

SysBio15 Asgn_23A_Class_23_Article_18_2015_03_31

EGFR signaling: Read carefully Article 18  A. Citri and Y. Yarden. EGF-ERBB signalling: towards the systems level. Nature Rev.Mol.Cell Biol. 7 (7):505-516, 2006. Get the big picture about receptor pathways. Post a PCRC.

SysBio15 Asgn_20B_Class_20_Article_17_2015_03_19

Cellular Noise: Read Article 17  N. Geva-Zatorsky, N. Rosenfeld, S. Itzkovitz, R. Milo, A. Sigal, E. Dekel, T. Yarnitzky, Y. Liron, P. Polak, G. Lahav, and U. Alon. Oscillations and variability in the p53 system. Mol.Sys.Biol. 2:2006.0033, 2006.. This sorts out the problem. Worth a careful read! Post a PCRC.

SysBio15 Asgn_20A_Class_20_Article_16_2015_03_19

Cellular Noise: Read Article 16  G. Lahav, N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A. J. Levine, M. B. Elowitz, and U. Alon. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat.Genet. 36 (2):147-150, 2004.. This is a very appealing paper, but not quite right. Post a PCRC.

SysBio15 Asgn_19A_Class_19_Article_15_2015_03_17

Cellular Noise: Read Article 15  M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain. Stochastic gene expression in a single cell. Science 297 (5584):1183-1186, 2002.. This is a classic . Read it carefully. Post a PCRC.

SysBio15 Asgn_12A_Class_12_Article_11_2015_02_17

Epigenetics, Attractors, and Noise: Read Article 11  S. Huang, G. Eichler, Y. Bar-Yam, and D. E. Ingber. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys.Rev.Lett. 94 (12):128701, 2005. This is an introduction to both cell reprogramming and data visualization. Post a PCRC.

SysBio15 Asgn_12B_Class_12_Article_12_2015_02_17

Epigenetics, Attractors, and Noise: Read Article 12  S. Huang. Reprogramming cell fates: reconciling rarity with robustness. BioEssays 31 (5):546-560, 2009. Study this carefully. Post a PCRC.

SysBio15 Asgn_13A_Class_13_Article_13_2015_02_19

Epigenetics, Attractors, and Noise: Read Article 13  S. Huang. The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology? BioEssays 34 (2):149-157, 2012. Study this carefully. Post a PCRC

SysBio15 Asgn_13B_Class_13_Article_14_2015_02_19

Epigenetics, Attractors, and Noise: Read Article 14  A.H. Lang,  et al., Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes PLoS-CB, 10: e1003734 (2014).. This is an actual implementation of the concept. Post a PCRC.

SysBio15 Asgn_8A_Class_08_Article_10_2015_01_29

Classical Network Models: Read Article 10  J. J. Tyson, A. Csikasz-Nagy, and B. Novak. The dynamics of cell cycle regulation. BioEssays 24 (12):1095-1109, 2002.. We will discuss this article in depth, which will take at least a full class. This should be a first reading to get an overview. Post a PCRC. We will have a second, more careful reading in a second class with a second PCRC.

SysBio15 Asgn_8B_Class_08_Article_11_2015_01_29

Classical Network Models: Read very carefully Article 11  J. J. Tyson, K. C. Chen, and B. Novak. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr.Opin.Cell Biol. 15 (2):221-231, 2003.. Also read PPT-10 for for a compact summary. We will discuss this article and the PPT in depth, which will take at least a full class. This should be a first reading to get an overview. Post a PCRC. We will have a second, more careful reading in a second class with a second PCRC for Thursday.

SysBio15 Asgn_8C_Class_08_Presentation_10_2015_01_29

Classical Network Models: Study Presentation 10  SysBio15-PPT-09_Tyson_Sniffers_2012_02_06_1407.ppt. and use this as a study guide for the important parts of Article 11.

SysBio15 Asgn_7C_Class_07_Short Presentation_03_2015_01_27

Genomics: Review Short Presentation 03  Oliver_SP-RNAseq_01.22.2014.pptx. in the Student_Short_Presentations folder in the VU-Box and figure out as much as you can on your own. Post a PCRC on the Blog, focusing on what you want explained in more detail.

SysBio15 Asgn_6B_Class_06_Presentation_07_2015_01_22

Control: Study Presentation 07  Examples_of_Control_2015_01_23_0521.ppt. We will discuss this presentation in depth. Be prepared to fill in the blank slides! Post a PCRC to guide the discussion.

SysBio15 Asgn_7A_Class_07_Short Presentation_01_2015_01_27

 Biohackers: Review Short Presentation 01  Jones_SP-igem_2015_01_20.pptx. in the Student_Short_Presentations folder in the VU-Box and figure out as much as you can on your own. Post a PCRC on the Blog, focusing on what you want explained in more detail.

SysBio15 Asgn_7B_Class_07_Short Presentation_02_2015_01_27

Computation: Review Short Presentation 02  Pino_SP-NP-complete_vs_np-hard_2015_01_20.pptx. in the Student_Short_Presentations folder in the VU-Box and figure out as much as you can on your own. Post a PCRC on the Blog, focusing on what you want explained in more detail.

SysBio15 Asgn_5A_Class_05_Article_07_2015_01_20

Systems Biology Dimensions and Challenges: Read Article 07  S. Huang and J. Wikswo. Dimensions of systems biology. In: Reviews of Physiology, Biochemistry and Pharmacology, edited by S. G. Amara, E. Bamberg, T. Gudermann, S. C. Hebert, R. Jahn, W. J. Lederer, R. Lill, A. Miyajima, and S. Offermanns, 2006, p. 81-104. Post a PCRC on the Blog

SysBio15 Asgn_5B_Class_05_Article_08_2015_01_20

Systems Biology Dimensions and Challenges: Read Article 08  J. P. Wikswo, A. Prokop, F. Baudenbacher, D. Cliffel, B. Csukas, and Momchil. Velkovsky. Engineering challenges of BioNEMS: the integration of microfluidics, and micro- and nanodevices, models, and external control for systems biology. IEE Proc.-Nanobiotechnol. 153 (4):81-101, 2006. Post a PCRC on the Blog

SysBio15 Asgn_6A_Class_06_Article_09_2015_01_22

Control: Read Article 09  P. R. LeDuc, W. C. Messner, and J. P. Wikswo. How do control-based approaches enter into biology? Annu.Rev.Biomed.Engr. 13:369-396, 2011.
This article addresses a problem central to much of existing biology, systems biology, and organs on a chip -- much of the work to date has been done in an open-loop manner, and hence does not adequately probe the system dynamics. Post a PCRC on the Blog.

SysBio15 Asgn_4A_Class_04_Article_04_2015_01_15

C. difficile and the Microbiome: Read Article 04  F. Bäckhed, R.E. Ley, J.L. Sonnenburg, D.A. Peterson and J.I. Gordon "Host-Bacterial Mutualism in the Human Intestine," Science, 307 (5717): 1915-1920 (2005).

Post a PCRC on the Blog.

SysBio15 Asgn_4B_Class_04_Article_05_2015_01_15

C. difficile and the Microbiome: Scan Article 05  R.E. Ley, D.A. Peterson, and J.I. Gordon, "Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine," Cell 124, 837–848 (2006).
Focus on Figure 1 and Table 1. Post a PCRC on the blog.

SysBio15 Asgn_4C_Class_04_Article_06_2015_01_15

C. difficile and the Microbiome: Read Article 06  M. Rupnik, M.H. Wilcox, and D.N. Gerding, "Clostridium difficile infection: new developments in epidemiology
and pathogenesis," Nature Revs Microbiol, 7: 526-536 (2009).
Post a PCRC on the Blog. Ultimately, the class will be focusing how to describe the mechanism of action of TCDA and TCDB, not the infection itself.

SysBio15 Asgn_3A_Class_03_Article_03_2015_01_13

Read Article 03  J. A. Mclean, W. B. Ridenour, and R. M. Caprioli. Profiling and imaging of tissues by imaging ion mobility-mass spectrometry. J.Mass Spectrom. 42 (8):1099-1105, 2007.. Read carefully - it is the future of biology. Post a PCRC on the Blog.

SysBio15 Asgn_3B_Class_03_Press Release_01_2015_01_13

Read Press Release 01  PR01_RTA_DARPA_2013_05_08.pdf. Read carefully - it is the future of biology. Post a PCRC on the Blog

SysBio15 Asgn_3C_Class_03_Presentation_05_2015_01_13

Study Presentation 05  P05_DARPA-SN-13-32-Proposers_Day_Slides.pdf. Look this over before class - it will be the topic of discussion for the second half of class. Post a PCRC on the Blog

SysBio15 Asgn_3D_Class_03_Presentation_06_2015_01_13

Play the PPT in presentation mode: Presentation 06  P06_TL308_IAS_T-Cell_2007_09_0906.ppt. An automated tool to create animations like of this is what I'm hoping to develop to provide a spatio-temporal cartoon of mechanism of action for RTA.  I'm looking for volunteers!

SysBio15 Asgn_2A_Class_02_Article_01_2015_01_08

Read Article 01  J.P. Wikswo. The relevance and potential roles of microphysiological systems in biology and medicine. Exp.Biol.Med. 239:1061-1072, 2014.. Post a PCRC on the Blog

SysBio15 Asgn_2B_Class_02_Article_02_2015_01_08

Read Article 02  J.P. Wikswo and A.P. Porter, Biology coming full circle: Joining the whole and the parts. Exp.Biol.Med. In Press, 2015.. Post a PCRC on the Blog

SysBio15 Asgn_2C_Class_02_Presentation_04_2015_01_08

Review Presentation 04  TL375_Princeton_2014_12_01_1512r1.pdf. Look this over before class - it will be the topic of discussion for the day. Post a PCRC on the Blog.

SysBio15 Asgn_1A_Class_01_TEDx Hamilton _V01_2015_01_06

 Watch TEDx Hamilton  V01  Your body in a microchip 
http://www.youtube.com/watch?v=cn9Q4c3dXGU. 
Post a PCRC on the Blog

The instructions are on the right side of the blog. You need five entries
      0. What I already knew (0. Knew: ...)

1. What I Learned (1. Learned: ...)

2. Most pressing questions? (2. Pressing ?: ...) 

3. Presentation topic (3. Presentation: ...)

4. Thoughts on class or systems biology, etc. (4. Thoughts: ...)

SysBio15 Asgn_1B_Class_01_TEDx Wikswo_V02_2015_01_06

Watch TEDx Wikswo V02  The Homunculi and I- Lessons from Building Organs on Chips
http://www.youtube.com/watch?v=4ht3m6p8iZ0. 
Post a PCRC on the Blog: 
The instructions are on the right side of the blog. You need five entries
      0. What I already knew (0. Knew: ...)

1. What I Learned (1. Learned: ...)

2. Most pressing questions? (2. Pressing ?: ...)

3. Presentation topic (3. Presentation: ...)

4. Thoughts on class or systems biology, etc. (4. Thoughts: ...)