Qbio honours programme

tree of life

QBio Journal club

In the QBio journal club we read Quantitative Biology papers. This is a monthly journal club starting at 17:30h in N507 of the Kruytbuilding.

The upcoming schedule is:


15-6-2017 (Rob de Boer): Manukyan L, Montandon SA, Fofonjka A, Smirnov S, Milinkovitch MC. A living mesoscopic cellular automaton made of skin scales. Nature. 2017 Apr 12;544(7649):173-179. doi: 10.1038/nature22031. PubMed PMID: 28406206.

We have already read and discussed the following papers:

18-5-2017 (Rutger Hermsen): Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: origins and consequences. Science. 2010 Nov 19;330(6007):1099-102. doi: 10.1126/science.1192588. PubMed PMID: 21097934.

20-4-2017 (Marvin Tanenbaum): Hongtao Chena, Miki Fujioka, and Thomas Gregor. Direct visualization of transcriptional activation by physical enhancer{promoter proximity. bioRxiv preprint first posted online Jan. 11, 2017; doi: http://dx.doi.org/10.1101/099523.

16-3-2017 (Kirsten ten Tusscher): van den Berg T, Korver RA, Testerink C, Ten Tusscher KH. Modeling halotropism: a key role for root tip architecture and reflux loop remodeling in redistributing auxin. Development. 2016 Sep 15;143(18):3350-62. doi: 10.1242/dev.135111. PubMed PMID: 27510970; PubMed Central PMCID: PMC5047658.

16-2-2017 (Harold MacGillavry): Santamaria F, Gonzalez J, Augustine GJ, Raghavachari S. Quantifying the effects of elastic collisions and non-covalent binding on glutamate receptor trafficking in the post-synaptic density. PLoS Comput Biol. 2010 May 13;6(5):e1000780. doi: 10.1371/journal.pcbi.1000780. PubMed PMID: 20485563; PubMed Central PMCID: PMC2869312.

19-1-2017 (Sander van den Heuvel & Mike Boxem): Sailer A, Anneken A, Li Y, Lee S, Munro E. Dynamic Opposition of Clustered Proteins Stabilizes Cortical Polarity in the C. elegans Zygote. Dev Cell. 2015 Oct 12;35(1):131-42. doi: 10.1016/j.devcel.2015.09.006. PubMed PMID: 26460948.

15-12-2016 (Bas Dutihl): Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. Uncovering Earth's virome. Nature. 2016 Aug 25;536(7617):425-30. PubMed PMID: 27533034.

17-11-2016 (Berend Snel): Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS. Genome evolution in the allotetraploid frog Xenopus laevis. Nature. 2016 Oct 19;538(7625):336-343. doi: 10.1038/nature19840. PubMed PMID: 27762356.

27-10-2016 (Rob de Boer): Novkovic M, Onder L, Cupovic J, Abe J, Bomze D, Cremasco V, Scandella E, Stein JV, Bocharov G, Turley SJ, Ludewig B. Topological Small-World Organization of the Fibroblastic Reticular Cell Network Determines Lymph Node Functionality. PLoS Biol. 2016 Jul 14;14(7):e1002515. doi: 10.1371/journal.pbio.1002515. PubMed PMID: 27415420, and Textor J, Mandl JN, de Boer RJ. The Reticular Cell Network: A Robust Backbone for Immune Responses. PLoS Biol. 2016 Oct 11;14(10):e2000827. doi: 10.1371/journal.pbio.2000827. PubMed PMID: 27727272.

16-6-2016 (Marvin Tanenbaum): Wu B, Buxbaum AR, Katz ZB, Yoon YJ, Singer RH. Quantifying Protein-mRNA Interactions in Single Live Cells. Cell. 2015 Jul 2;162(1):211-20. doi: 10.1016/j.cell.2015.05.054. PubMed PMID: 26140598.

19-5-2016 (Istvan Kleijn): Kiviet DJ, Nghe P, Walker N, Boulineau S, Sunderlikova V, Tans SJ. Stochasticity of metabolism and growth at the single-cell level. Nature. 2014 Oct 16;514(7522):376-9. doi: 10.1038/nature13582. Epub 2014 Sep 3. PubMed PMID: 25186725.

21-4-2016 (Rob de Boer): Halle S, Keyser KA, Stahl FR, Busche A, Marquardt A, Zheng X, Galla M, Heissmeyer V, Heller K, Boelter J, Wagner K, Bischoff Y, Martens R, Braun A, Werth K, Uvarovskii A, Kempf H, Meyer-Hermann M, Arens R, Kremer M, Sutter G, Messerle M, Förster R. In Vivo Killing Capacity of Cytotoxic T Cells Is Limited and Involves Dynamic Interactions and T Cell Cooperativity. Immunity. 2016 Feb 16;44(2):233-45. doi: 10.1016/j.immuni.2016.01.010. Epub 2016 Feb 9. PubMed PMID: 26872694.

17-3-2016 (Bas Dutilh): Pittis AA, Gabaldón T. Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. Nature. 2016 Mar 3;531(7592):101-4. doi: 10.1038/nature16941. Epub 2016 Feb 3. PubMed PMID: 26840490; PubMed Central PMCID: PMC4780264.

18-2-2016 (Anna Akhmanova): Bieling P, Telley IA, Surrey T. A minimal midzone protein module controls formation and length of antiparallel microtubule overlaps. Cell. 2010 Aug 6;142(3):420-32. doi: 10.1016/j.cell.2010.06.033. PubMed PMID: 20691901.

21-1-2016 (Casper Hoogenraad): Xu K, Zhong G, Zhuang X. Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science. 2013 Jan 25;339(6118):452-6. doi: 10.1126/science.1232251. Epub 2012 Dec 13. PubMed PMID: 23239625; PubMed Central PMCID: PMC3815867.

10-12-2015 (Geert Geeven): Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science. 2013 Nov 22;342(6161):948-53. doi: 10.1126/science.1236083. Epub 2013 Nov 7. PubMed PMID: 24200812; PubMed Central PMCID: PMC4040465.

16-11-2015 (Rob de Boer): Kidd PB, Young MW, Siggia ED. Temperature compensation and temperature sensation in the circadian clock. Proc Natl Acad Sci U S A. 2015 Nov 17;112(46):E6284-92. doi: 10.1073/pnas.1511215112. Epub 2015 Nov 2. PubMed PMID: 26578788; PubMed Central PMCID: PMC4655526.

29-10-2015 (Berend Snel & Bas Dutilh): Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM. Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Science. 2015 May 22;348(6237):921-5. doi: 10.1126/science.aaa0769. PubMed PMID: 25999509.

25-6-2015 (Lukas Kapitein): Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Jülicher F, Hyman AA. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science. 2009 Jun 26;324(5935):1729-32. doi: 10.1126/science.1172046. Epub 2009 May 21. PubMed PMID: 19460965. and Spatial organization of the cell cytoplasm by position-dependent phase separation. Lee CF, Brangwynne CP, Gharakhani J, Hyman AA, Jülicher F. Phys Rev Lett. 2013 Aug 23;111(8):088101. Epub 2013 Aug 20.

28-5-2015 (Rob de Boer & Sander van den Heuvel): Lee TJ, Yao G, Bennett DC, Nevins JR, You L. Stochastic E2F activation and reconciliation of phenomenological cell-cycle models. PLoS Biol. 2010 Sep 21;8(9). pii: e1000488. doi: 10.1371/journal.pbio.1000488. PubMed PMID: 20877711; PubMed Central PMCID: PMC2943438.

30-4-2015 (Rob de Boer & Sjoerd Verduijn Lunel) Sandler O, Mizrahi SP, Weiss N, Agam O, Simon I, Balaban NQ. Lineage correlations of single cell division time as a probe of cell-cycle dynamics. Nature. 2015 Mar 26;519(7544):468-71. doi: 10.1038/nature14318. Epub 2015 Mar 11. PubMed PMID: 25762143.