Journal Clubs are held monthly to advance interdisciplinary communication and integrate knowledge between math and biology.
Year 01 | Center Investigators will present foundational literature in developmental biology and mathematical biology.
September 28, 2018 | Presented by Richard Carthew
- Surface mechanics mediate pattern formation in the developing retina. Takashi Hayashi, and Richard W. Carthew. (2004) Nature. 431(7), 647-652. https://www.nature.com/articles/nature02952
- The emergence of geometric order in proliferating metazoan epithelia. Matthew C. Gibson, Ankit B. Patel, Radhika Nagpal, and Norbert Perrimon. (2006) Nature. 442(31), 1038-1041. https://www.nature.com/articles/nature05014
October 26, 2018 | Presented by William Kath
- On schemes of combinatorial transcription logic. Buchler, Nicolas E et al.Proceedings of the National Academy of Sciences of the United States of America vol. 100,9 (2003): 5136-41. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC404558/
- Dynamics in hybrid complex systems of switches and oscillators. Taylor, Dane et al. Chaos (Woodbury, N.Y.) vol. 23,3 (2013): 033142. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795755/
November 30, 2018 | Presented by Antonio (Tuca) Auffinger
- The energy landscapes and motions of proteins. H Frauenfelder, S G Sligar, P G Wolynes. Science. 1991 Dec 13;254(5038):1598-603. PMID: 1749933 https://www.ncbi.nlm.nih.gov/pubmed/1749933
- The Loss Surfaces of Multilayer Networks. A Choromanska, M Hena, M Mathieu, G B Arous, Y LeCun. arXiv:1412.0233v3 [cs.LG] 21 Jan 2015. http://proceedings.mlr.press/v38/choromanska15.pdf
- Mutations of Bacteria from Virus Sensitivity to Virus Resistance. S E Luria, M Delbrück. Genetics. November 20, 1943 vol. 28 no. 6 491-511. https://www.ncbi.nlm.nih.gov/pubmed/17247100
January 25, 2019 | Presented by Ji-Ping Wang
- Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Joseph Felsenstein. Evolution. 1985 Jul;39(4):783-791. doi: 10.1111/j.1558-5646.1985.tb00420.x PMID: 28561359 DOI: 10.1111/j.1558-5646.1985.tb00420.x
- Bootstrap confidence levels for phylogenetic trees. Bradley Efron, Elizabeth Halloran, Susan Holmes. Proc Natl Acad Sci U S A. 1996 Nov 12;93(23):13429-34. PMID: 8917608 PMCID: PMC24110 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC38940/
February 1, 2019 | Presented by Niall Mangan
- Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Bennett, B. D. et al. Nat. Chem. Biol. 5, 593–599 (2009).http://www.ncbi.nlm.nih.gov/pubmed/19561621
- Metabolomics and Isotope Tracing. Jang, C., Chen, L. & Rabinowitz, J. D. Cell 173, 822–837 (2018).https://doi.org/10.1016/j.cell.2018.03.055
February 22, 2019 | Presented by Ravi Allada
- Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes. Keegan KP, Pradhan S, Wang JP, Allada R. PLoS Comput Biol. 2007 Nov;3(11):e208. Epub 2007 Sep 11. PMID: 17983263 PMCID: PMC2098839 DOI: 10.1371/journal.pcbi.0030208
- A circadian gene expression atlas in mammals: implications for biology and medicine. Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):16219-24. doi: 10.1073/pnas.1408886111. Epub 2014 Oct 27. PMID: 25349387 PMCID: PMC4234565 DOI: 10.1073/pnas.1408886111
Friday, April 26, 2019 | Presented by Erik Andersen
- A maternal-effect selfish genetic element in Caenorhabditis elegans. Ben-David E, Burga A, Kruglyak L. Science. 2017;356(6342):1051–1055. doi:10.1126/science.aan0621 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251971/
Friday, May 17, 2019 | Presented by Rosemary Braun
- Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Tyson & et al. (2003). https://doi.org/10.1016/S0955-0674(03)00017-6
- Engineering stability in gene networks by autoregulation. Beckskei & Serrano (2000). https://www.nature.com/articles/35014651.pdf
- Multiscale effects of heating and cooling on genes and gene networks. Charlebois & et al (2018). https://doi.org/10.1073/pnas.1810858115
June 28, 2019 | Presented by Alec Wang
- A clonogenic common myeloid progenitor that gives rise to all myeloid lineages. Akashi K, Traver D, Miyamoto T, Weissman IL. Nature. 2000 Mar 9;404(6774):193-7. PMID: 10724173 DOI: 10.1038/35004599 https://www.nature.com/articles/35004599
- Clonal dynamics of native haematopoiesis. Sun J, Ramos A, Chapman B, et al. Nature. 2014;514(7522):322–327. PMID: 25296256 PMCID: PMC4408613 doi:10.1038/nature13824 https://www.nature.com/articles/nature13824
Year 02 | Center Scholars and Fellows will present recent literature of interest to the center projects in developmental biology and mathematical biology.
September 27, 2019 | Presented by Matt Hope
- Stem Cell Differentiation as a Non-Markov Stochastic Process. Stumpf PS et. al. Cell Systems 2017 5(03):268-282. https://www.ncbi.nlm.nih.gov/pubmed/28957659
October 25, 2019 | Presented by Marta Iwanaszko
- Temperature compensation and temperature sensation in the circadian clock. Philip B. Kidd, Michael W. Young, and Eric D. Siggia. PNAS November 17, 2015 112 (46) E6284-E6292; first published November 2, 2015 https://doi.org/10.1073/pnas.1511215112
November 22, 2019 | Presented by Gaotian Zhang
- Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Hyun Kim, Dong, Dominic Grün, and Alexander van Oudenaarden. Nature Genetics. 2013 Nov;45(11):1337-44. doi: 10.1038/ng.2763. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812263/
January 24, 2020 | Presented by Simon Freedman
- Universally sloppy parameter sensitivities in systems biology models. Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, et al. (2007) PLoS Comput Biol 3(10): e189. doi:10.1371/journal.pcbi.0030189
https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030189&type=printable
February 28, 2020 | Presented by Kevin Gallagher
- A dynamical model of ommatidial crystal formation. David K. Lubensky, Matthew W. Pennington, Boris I. Shraiman, and Nicholas E. Baker. PNAS July 5, 2011 108 (27) 11145-11150; https://doi.org/10.1073/pnas.1015302108
March 27, 2020 | Presented by Keren Li
- A genomic code for nucleosome positioning.Segal E, Fondufe-Mittendorf Y, Chen L, et al. Nature. 2006;442(7104):772–778. doi:10.1038/nature04979
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2623244/pdf/nihms-85676.pdf
April 24, 2020 | Presented by Andrew Liu
- Regulation of Anisotropic Tissue Growth by Two Orthogonal Signaling Centers. Barrio L, Milán M. Dev Cell. 2020;52(5):659–672.e3. doi:10.1016/j.devcel.2020.01.017 https:/www.sciencedirect.com/science/article/pii/S1534580720300496
May 22, 2020 | Presented by Elan Ness-Cohn
- Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator.Rust MJ, Golden SS, O’Shea EK. Science. 2011;331(6014):220‐ doi:10.1126/science.1197243 https://science.sciencemag.org/content/sci/331/6014/220.full.pdf
