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An Introduction To Systems Biology Pdf Uri Alon Lab

Design principles of biological circuits. Possibly explaining why only a few circuit designs recur across biology. Cell Systems. Mayo, Uri Alon. An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical and Computational Biology) [Uri Alon] on. Search this site. An Introduction to Systems Biology by Uri Alon. The origin of bursts and heavy tail in human dynamics.pdf (344k).

Uri Alon
Born1969 (age 49–50)[1]
Alma materHebrew University of Jerusalem
Weizmann Institute of Science
Known forNetwork motifs
AwardsOverton Prize (2004)
Scientific career
InstitutionsWeizmann Institute of Science
Princeton University
Doctoral advisorDavid Mukamel[2]
Other academic advisors
Websitewww.weizmann.ac.il/mcb/UriAlon

Uri Alon (Hebrew: אורי אלון; born 1969) is a Professor and Systems Biologist at the Weizmann Institute of Science.[4] His highly cited[5] research investigates gene expression,[6]network motifs[7][8] and the design principles of biological networks[9] in Escherichia coli and other organisms using both computational biology and traditional experimental wet laboratory techniques.[10]

Education[edit]

Alon earned his bachelor's and master's degrees from the Hebrew University of Jerusalem and his Ph.D. in Theoretical Physics[2][11] from the Weizmann Institute of Science.

Career[edit]

After having his interest in biology sparked, Alon headed to Princeton University for his postdoctoral work in experimental biology. He returned to the Weizmann Institute as a professor.

History Of Systems Biology

Alon features in several popular videos on YouTube such as Sunday at the Lab (with Michael Elowitz)[12] and How to Give a Good Talk.[13] As of 2011, he is the author of the most highly bookmarked scientific paper on CiteULike[14]How To Choose a Good Scientific Problem[15] and How to Build a Motivated Research Group.[16]

An Introduction To Systems Biology Uri Alon

Awards[edit]

In 2004 Alon was awarded the Overton Prize[3] for 'outstanding accomplishment by a scientist in the early to mid stage of his or her career' by the International Society for Computational Biology. Alon has also been awarded:

  • Moore Fellowship, California Institute of Technology (2000)
  • EMBO Young Investigator Award (2001)
  • IBM Faculty Award (2003)
  • Minerva Junior Research Group on Biological Computation (2003)
  • Morris L. Levinson Award in Biology (2003)
  • Teva Founders Prize (2005)
  • European Molecular Biology Organization membership (2007),[17]
  • Radcliffe Institute for Advanced Study fellow 2009[18]
  • HFSP Nakasone Award (2014)[19]

References[edit]

  1. ^'Wis-Find: Author Search Results'. weizmann.ac.il.
  2. ^ abAlon, U.; Evans, M.; Hinrichsen, H.; Mukamel, D. (1996). 'Roughening Transition in a One-Dimensional Growth Process'. Physical Review Letters. 76 (15): 2746–2749. arXiv:cond-mat/9512069. Bibcode:1996PhRvL.76.2746A. doi:10.1103/PhysRevLett.76.2746. PMID10060778.
  3. ^ ab'ISCB Newsletter 7-3'. iscb.org.
  4. ^'Homepage - Uri Alon'. weizmann.ac.il.
  5. ^Uri Alon publications indexed by Google Scholar
  6. ^Alon, U.; Barkai, N.; Notterman, D. A.; Gish, K.; Ybarra, S.; Mack, D.; Levine, A. J. (1999). 'Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays'. Proceedings of the National Academy of Sciences. 96 (12): 6745–6750. Bibcode:1999PNAS..96.6745A. doi:10.1073/pnas.96.12.6745. PMC21986. PMID10359783.
  7. ^Milo, R.; Shen-Orr, S.; Itzkovitz, S.; Kashtan, N.; Chklovskii, D.; Alon, U. (2002). 'Network Motifs: Simple Building Blocks of Complex Networks'. Science. 298 (5594): 824–827. Bibcode:2002Sci..298.824M. CiteSeerX10.1.1.225.8750. doi:10.1126/science.298.5594.824. PMID12399590.
  8. ^Shen-Orr, S. S.; Milo, R.; Mangan, S.; Alon, U. (2002). 'Network motifs in the transcriptional regulation network of Escherichia coli'. Nature Genetics. 31 (1): 64–68. doi:10.1038/ng881. PMID11967538.
  9. ^Uri Alon (2007). An introduction to systems biology: design principles of biological circuits. Boca Raton: Chapman & Hall/CRC. ISBN978-1-58488-642-6.
  10. ^List of publications from Microsoft Academic
  11. ^'arXiv.org Search'. arxiv.org.
  12. ^'Uri Alon's Song - Sunday at the Lab co-written with Elowitz' on YouTube
  13. ^' How to Give a Good Talk by Uri Alon' on YouTube
  14. ^'CiteULike CiteGeist: Popular Papers'. Retrieved 2011-06-09.
  15. ^Alon, U. (2009). 'How to Choose a Good Scientific Problem'(PDF). Molecular Cell. 35 (6): 726–728. doi:10.1016/j.molcel.2009.09.013. PMID19782018.
  16. ^Alon, U. (2010). 'How to Build a Motivated Research Group'(PDF). Molecular Cell. 37 (2): 151–152. doi:10.1016/j.molcel.2010.01.011. PMID20122395.
  17. ^'Uri Alon'. f1000.com.
  18. ^Radcliffe Fellows
  19. ^'2014 HFSP Nakasone Award goes to Uri Alon'. hfsp.org.
Introduction to systems biology

External links[edit]

  • Uri Alon at TED
Retrieved from 'https://en.wikipedia.org/w/index.php?title=Uri_Alon&oldid=890102310'
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Systems Biology

系統生物學 Systems Biology


教學網頁http://syslab.nchu.edu.tw/

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授課老師:劉俊吉老師 陳盈璁老師

上課時間:週三 5, 6 (1:10pm ~ 3:00pm)

上課教室:703 (劉俊吉老師 研究室)


Textbook:


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An Introduction to Systems Biology: Design Principles of Biological Circuits

Author: Uri Alon

Publisher: Chapman and Hall/CRC


References:

  • Systems biology course 2014 Uri Alon - lecture 1 [youtube]
  • Coursera https://www.coursera.org/[ted]
  • Salman Khan: Let's use video to reinvent education [ted]. Salman Khan talks about how and why he created the remarkable Khan Academy, a carefully structured series of educational videos offering complete curricula in math and, now, other subjects. You can learn math from Khan Academy https://www.khanacademy.org/
    • Introduction to differential calculus [khanacademy]
    • The derivative of f(x)=x^2 for any x [khanacademy]
    • Differential equation introduction [khanacademy]
  • COPASI: Biochemical System Simulator http://www.copasi.org/
    • COPASI Video Tutorialshttp://copasi.org/Support/Video_Tutorials/
    • COPASI Tutorialshttp://anna.fi.muni.cz/~xsafran1/vyuka/PB050/tutorial/tutorial-3/index.htm
  • The Ping-Pong Algorithm R package https://rdrr.io/cran/isa2/man/ppa.html

Syllabus:

  • Microarray data analysis (ppt)
  1. Transcription networks (ppt)
  2. Autoregulation (ppt)
  3. The Feed-Forward Loop Network Motif (ppt)
  4. Temporal Programs and the Global Structure (ppt)
  5. Network Motifs (ppt)
  6. Discovering regulatory and signaling circuits in molecular interaction (ppt)
  7. Discovery of multi-dimensional modules (ppt)
  8. Bayesian Probabilistic model(ppt)
  9. Label propagation algorithm (ppt)
  10. A human phenome-interactome network of protein complexes (ppt)
  11. Hidden Markov Models
  12. Baum-Welch Algorithm
  13. Bayesian Network

Homework 1 (Due: Oct 11)


Homework 2 (Due: Nov 1)

1. Design anetwork motif.
2. Write the equations with production and removal rates.
3. Run COPASI to generate the simulated data.
4. Explain your simulated data.


Homework 3 (Due: Nov 29)
  1. Select a time-course dataset from NCBI GEO ( >10 time points) http://www.ncbi.nlm.nih.gov/geo/
  2. For example,
    • GDS2350 (25 time points) http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2350
    • GDS2318 (13 time points) http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2318
    • GDS1752 (13 time points) http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS1752
  3. Use Win-RAR to unzip data (http://www.winrar.com/)
  4. Write a program to search temporal programs.
  5. You can refer to the R program (txt).
  6. Output a temporal program.
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