CS6404: Reading List (Spring 2006)

Note: This list is not a complete list of related topics. It mostly reflects the instructor’s personal research interest. Thus this list serves as a guideline for beginners to get familiar with this area. For student with certain background in this area, you may want to choose your own reading and project source. However, reading at least five papers in this list is required so that you can at least broaden your view of this area. Please do not try to finish reading all of them during a semester.

1.     H. Kitano, Computational systems biology, Nature, 420, 206-210, Nov. 14, 2002

2.     Hasty J, McMillen D, Collins JJ, Engineered gene circuits, NATURE 420 (6912): 224-230 NOV 14 2002

3.     Endy D, Brent R Modelling cellular behaviour NATURE 409 (6818): 391-395 JAN 18 2001

4.     Gardner TS, Cantor CR, Collins JJ, Construction of a genetic toggle switch in Escherichia coli, NATURE 403 (6767): 339-342 JAN 20 2000

5.     Elowitz MB, Levine AJ, Siggia ED, et al. Stochastic gene expression in a single cell SCIENCE 297 (5584): 1183-1186 AUG 16 2002

6.     Wall ME, Hlavacek WS, Savageau MA, Design of gene circuits: Lessons from bacteria, NATURE REVIEWS GENETICS 5 (1): 34-42 JAN 2004

7.     Rao CV, Wolf DM, Arkin AP, Control, exploitation and tolerance of intracellular noise NATURE 420 (6912): 231-237 NOV 14 2002

8.     Kobayashi H, Kaern M, Araki M, et al., Programmable cells: Interfacing natural and engineered gene networks, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (22): 8414-8419 JUN 1 2004

9.     Strogatz SH, Exploring complex networks, NATURE 410 (6825): 268-276 MAR 8 2001

10.  Kitano H, Funahashi A, Matsuoka Y, et al., Using process diagrams for the graphical representation of biological networks, NATURE BIOTECHNOLOGY 23 (8): 961-966 AUG 2005

11.  Becskei A, Seraphin B, Serrano L, Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion, EMBO JOURNAL 20 (10): 2528-2535 MAY 15 2001

12.  McAdams HH, Srinivasan B, Arkin AP, The evolution of genetic regulatory systems in bacteria, NATURE REVIEWS GENETICS 5 (3): 169-178 MAR 2004

13.  McAdams HH, Arkin A, Gene regulation: Towards a circuit engineering discipline, CURRENT BIOLOGY 10 (8): R318-R320 APR 20 2000

14.  McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale, TRENDS IN GENETICS 15 (2): 65-69 FEB 1999

15.  Arkin A, Ross J, McAdams HH, Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells, GENETICS 149 (4): 1633-1648 AUG 1998

16.  McAdams HH, Arkin A, Simulation of prokaryotic genetic circuits, ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 27: 199-224 1998 (accessible through Web of Science)

17.  McAdams HH, Arkin A. Stochastic mechanisms in gene expression, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 94 (3): 814-819 FEB 4 1997

18.  Ozbudak EM, Thattai M, Kurtser I, et al. Regulation of noise in the expression of a single gene NATURE GENETICS 31 (1): 69-73 MAY 2002

19.  Kierzek AM, Zaim J, Zielenkiewicz P, The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression JOURNAL OF BIOLOGICAL CHEMISTRY 276 (11): 8165-8172 MAR 16 2001

20.  Goldbeter A, Computational approaches to cellular rhythms, NATURE 420 (6912): 238-245 NOV 14 2002

21.  Leloup JC, Goldbeter A Toward a detailed computational model for the mammalian circadian clock PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 100 (12): 7051-7056 JUN 10 2003

22.  Gonze D, Halloy J, Leloup JC, et al. Stochastic models for circadian rhythms: effect of molecular noise on periodic and chaotic behaviour COMPTES RENDUS BIOLOGIES 326 (2): 189-203 FEB 2003

23.  Leloup JC, Goldbeter A Modeling the mammalian circadian clock: Sensitivity analysis and multiplicity of oscillatory mechanisms JOURNAL OF THEORETICAL BIOLOGY 230 (4): 541-562 OCT 21 2004

24.  Endy D, You LC, Yin J, et al. Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 97 (10): 5375-5380 MAY 9 2000

25.  Endy D, Kong D, Yin J Intracellular kinetics of a growing virus: A genetically structured simulation for bacteriophage T7 BIOTECHNOLOGY AND BIOENGINEERING 55 (2): 375-389 JUL 20 1997

26.  SCHOLEY JM Cell division NATURE 422 : 746 2003

27.  Bowerman B Cell division - Timing the machine NATURE 430 (7002): 840-842 AUG 19 2004

28.  Paulson J Summing up the noise in gene networks NATURE 427 (6973): 415-418 JAN 29 2004

29.  BECSKEI A Engineering stability in gene networks by autoregulation NATURE 405 : 590 2000

30.  El-Samad H, Kurata H, Doyle JC, et al. Surviving heat shock: Control strategies for robustness and performance  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (8): 2736-2741 FEB 22 2005

31.  Kitano H Opinon - Cancer as a robust system: implications for anticancer therapy  NATURE REVIEWS CANCER 4 (3): 227-235 MAR 2004

32.  SHEA MA, ACKERS GK THE OR CONTROL-SYSTEM OF BACTERIOPHAGE-LAMBDA - A PHYSICAL-CHEMICAL MODEL FOR GENE-REGULATION JOURNAL OF MOLECULAR BIOLOGY 181 (2): 211-230 1985 (This paper is not accessible from online and I only have a hard copy of it. You may copy it from library. It described the gene expression mechanism of lambda phage, which was later applied by A. Arkin. )

33.  Kiehl TR, Mattheyses RM, Simmons MK Hybrid simulation of cellular behavior  BIOINFORMATICS 20 (3): 316-322 FEB 12 2004

34.  Korobkova E, Emonet T, Vilar JMG, et al. From molecular noise to behavioural variability in a single bacterium NATURE 428 (6982): 574-578 APR 1 2004

35.  Tyson JJ, Hong CI, Thron CD, et al. A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM BIOPHYSICAL JOURNAL 77 (5): 2411-2417 NOV 1999

36.  Morton-Firth CJ, Bray D Predicting temporal fluctuations in an intracellular signalling pathway JOURNAL OF THEORETICAL BIOLOGY 192 (1): 117-128 MAY 7 1998    

37.  GILLESPIE DT, GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS JOURNAL OF COMPUTATIONAL PHYSICS 22 (4): 403-434 1976. (This paper is not accessible online. I have a pdf file of it and you can copy it from the class link. )

38.  GILLESPIE DT, EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS JOURNAL OF PHYSICAL CHEMISTRY 81 (25): 2340-2361 1977.

39.  GILLESPIE DT Approximate accelerated stochastic simulation of chemically reacting systems JOURNAL OF CHEMICAL PHYSICS 115 : 1716 2001

40.  Vilar JMG, Kueh HY, Barkai N, et al.Mechanisms of noise-resistance in genetic oscillators PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 99 (9): 5988-5992 APR 30 2002

41.  Kepler TB, Elston TC Stochasticity in transcriptional regulation: Origins, consequences, and mathematical epresentations BIOPHYICAL JOURNAL 81 (6): 3116-3136 DEC 2001

42.  Angeli D, Ferrell JE, Sontag ED Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feed back systems PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101 (7): 1822-1827 FEB 17 2004

43.  Srivastava R, You L, Summers J, et al. Stochastic vs. deterministic modeling of intracellular viral kinetics JOURNAL OF THEORETICAL BIOLOGY 218 (3): 309-321 OCT 7 2002

44.  Isaacs FJ, Blake WJ, Collins JJ Signal processing in single cells SCIENCE 307 (5717): 1886-1888 MAR 25 2005

45.  Swain PS, Elowitz MB, Siggia ED Intrinsic and extrinsic contributions to stochasticity in gene expression PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 99 (20): 12795-12800 OCT 1 2002

46.  Samoilov M, Plyasunov S, Arkin AP Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (7): 2310-2315 FEB 15 2005

47.  Wolf DM, Vazirani VV, Arkin AP Diversity in times of adversity: probabilistic strategies in microbial survival games JOURNAL OF THEORETICAL BIOLOGY 234 (2): 227-253 MAY 21 2005

48.  Blake WJ, Collins JJ And the noise played on: Stochastic gene expression and HIV-1 infection CELL 122 (2): 147-149 JUL 29 2005

49.  Blake WJ, Kaern M, Cantor CR, et al. Noise in eukaryotic gene expression NATURE 422 (6932): 633-637 APR 10 2003

50.  Raser JM, O'Shea EK Control of stochasticity in eukaryotic gene expression SCIENCE 304 (5678): 1811-1814 JUN 18 2004

51.  Rosenfeld N, Young JW, Alon U, et al. Gene regulation at the single-cell level SCIENCE 307 (5717): 1962-1965 MAR 25 2005

52.  Weinberger LS, Burnett JC, Toettcher JE, et al. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity CELL 122 (2): 169-182 JUL 29 2005

53.  Kaern M, Elston TC, Blake WJ, et al. Stochasticity in gene expression: From theories to phenotypes NATURE REVIEWS GENETICS 6 (6): 451-464 JUN 2005

54.  Tyson JJ, Csikasz-Nagy A, Novak B The dynamics of cell cycle regulation BIOESSAYS 24 (12): 1095-1109 DEC 2002

55.  Hasty J, Isaacs F, Dolnik M, et al. Designer gene networks: Towards fundamental cellular control CHAOS 11 (1): 207-220 MAR 2001

56.  Battogtokh D, Tyson JJ Bifurcation analysis of a model of the budding yeast cell cycle CHAOS 14 (3): 653-661 SEP 2004

57.  Judd EM, Laub MT, McAdams HH Toggles and oscillators: new genetic circuit designs BIOESSAYS 22 (6): 507-509 JUN 2000

58.  Pedraza JM, van Oudenaarden A Noise propagation in gene networks SCIENCE 307 (5717): 1965-1969 MAR 25 2005

59.  Thattai M, van Oudenaarden A Intrinsic noise in gene regulatory networks PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 98 (15): 8614-8619 JUL 17 2001

60.  Kobayashi H, Kaern M, Araki M, et al. Programmable cells: Interfacing natural and engineered gene networks PNAS 101 (22): 8414-8419 JUN 1 2004

61.  Korobkova E, Emonet T, Vilar JMG, et al. From molecular noise to behavioural variability in a single bacterium NATURE 428 (6982): 574-578 APR 1 2004