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 Spring 2012

Date Presenter Topic/Reading
Jan 23 Organizational Meeting
Jan 31 Taylor Southwick S Kaplan, A Bren, and U Alon. "The incoherent feed-forward loop can generate non-monotonic input functions for genes." Molecular Systems Biology 4:203, 2008.
Feb 7 Shuxiang Ruan L Goentoro, O Shoval, M Kirschner, and U Alon. "The incoherent feedforward loop can provide fold-change detection in gene regulation." Molecular Cell 36:894-899, 2009.
Feb 14 Kiersten Ruff PJ Ingram, MPH Stumpf, and J Stark. "Network motifs: structure does not determine function." BMC Genomics 7:108, 2006.
Feb 21 Zane Goodwin G Lahav, N Rosenfeld, A Sigal, N Geva-Zatorsky, AJ Levine, MB Elowitz, and U Alon. "Dynamics of the p53-Mdm2 feedback loop in individual cells." Nature Genetics 36:147-150, 2004.
Feb 28 Hemangi Chaudari S Basu, Y Gerchman, CH Collins, FH Arnold, and R Weiss. "A synthetic multicellular system for programmed pattern formation." Nature 434:1130-1134, 2005.
Mar 6 Sathish Subramanian M Paulsen, S Legewie, R Eils, E Karaulanov, and C Niehrs. "Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development." PNAS 108:10202-10207, 2011.
Mar 13 Spring Break
Mar 20 Arthur Lee AD Economou, A Ohazama, T Porntaveetus, PT Sharpe, S Kondo, MA Basson, A Gritli-Linde, MT Cobourne, and JBA Green. "Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate." Nature Genetics 44:348-351, 2012.
Mar 27 Zeke Maier A Goldbeter and O Pourquie. "Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt, and FGF signaling pathways." Journal of Theoretical Biology 252:574-585, 2008.
Apr 3 Shuxiang Ruan MF Berger, AA Philippakis, AM Qureshi, FS He, PW Estep III, and ML Bulyk. "Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities." Nature Biotechnology 24:1429-1435, 2006.
Apr 10 Molly Gibson Y Zhao, D Granas, and GD Stormo. "Inferring binding energies from selected binding sites." PLoS Computational Biology 5(12):e1000590, 2009.
Apr 17 Temidayo Adebiyi MM Chen, LC Chou, TT Hsieh, DD Lee, KW Liu, CY Yu, YJ Oyang, HK Tsai, and CY Chen. "De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae." Bioinformatics 28:701-708, 2012.

Some Prior Editions of the Journal Club