BIOL 5496/CSE 7800: Computational Molecular Biology Journal Club

Welcome to the home page for BIOL 5496/CSE 7800, the Computational Molecular Biology Journal Club. The Journal Club meets Tuesdays, 4-5 PM in 4444 Forest Park, Room 6404.

Your course masters are Jeremy Buhler and Barak Cohen.

Participants in the Journal Club present recent published research in the areas of computational molecular biology, systems biology, and bioinformatics. Every student receiving credit for participation, except for DBBS Computational and Systems Biology students in their first semester, must present a paper at one meeting of the Journal Club and must otherwise participate as described in the course overview. Other students, postdocs, faculty, and staff are welcome to attend and participate.

Schedule of Presentations for Fall 2011

Date Presenter Topic/Reading
Sep 6 Organizational Meeting
Sep 13 Molly Gibson D Bray, RB Bourret, and MI Simon. "Computer Simulation of the Phosphorylation Cascade Controlling Bacterial Chemotaxis." Molecular Biology of the Cell 4:469-482, 1993.
Sep 20 Brett Maricque N Barkai and S Leibler. "Robustness in simple biochemical networks." Nature 387:913-917, 1997.
Sep 27 Zeke Maier R Bonneau, DJ Reiss, P Shannon, M Facciotti, L Hood, NS Baliga, and V Thorsson. "The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo." Genome Biology 7(5):R36, 2006.
Oct 4 Chris Schlosberg KC Chen, L Calzone, A Csikasz-Nagy, FR Cross, B Novak, and JJ Tyson. "Integrative analysis of cell cycle control in budding yeast." Molecular Biology of the Cell 15(8):3841-3862, 2004.
Oct 11 Adnan Elhammali JM Raser and EK O'Shea. "Control of Stochasticity in Eukaryotic Gene Expression." Science 304:1811-1814, 2004.
Oct 18 Mark Charbonneau DM Suter, N Molina, D Gatfield, K Schneider, U Schibler, and F Naef. "Mammalian genes are transcribed with widely different bursting kinetics." Science 332:472-474, 2011.
Oct 25 Igor Nikolskiy T-L To and N Maheshri. "Noise can induce bimodality in positive transcriptional feedback loops without bistability." Science 327:1142-1145, 2010.
Nov 1 Vasavi Sundaram PB Gupta, CM Fillmore, G Jiang, SD Shapira, K Tao, C Kuperwasser, and ES Lander. "Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells." Cell 146:633-634, 2011.
Nov 8 Nicholas Ho Rui Yuan R Drmanac, AB Sparks, MJ Callow, AL Halpern et al. "Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays." Science 327:78-81, 2009.
Nov 15 Ben Borgo JM Rothberg, W Hinz, TM Rearick, J Schultz, et al. "An integrated semiconductor device enabling non-optical genome sequencing." Nature 475:348-352, 2011.
Nov 29 Brett Maricque J Clarke, H-C Wu, L Jayasinghe, A Patel, S Reid, and H Bayley. "Continuous base identification for single-moluecule nanopore DNA sequencing." Nature Nanotechnology 4:265-270, 2009.
Dec 6 Kevin Chen B McNally, A Singer, Z Yu, Y Sun, Z Weng, and A Meller. "Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays." Nano Letters 10(6):2237-2244, 2010.

Some Prior Editions of the Journal Club