User:Ahmad A. Mannan

IMPERIAL BIOMATHS JOURNAL CLUB

We put together a journal club for sharing and discussing papers and problems (theory) of mathematical modelling of biological systems (both stochastically and deterministically).

NEXT GATHERING

• Date: THURSDAY 17th NOVEMBER
• Time: 4PM
• Venue: Huxley 747

• Paper: Synchronous long-term oscillations in a synthetic gene circuit

COMPILATION OF PAPERS TO READ

Academic Year 2015-2016

• [X] - Noise in Gene Expression is Coupled to Growth Rate[1]

• [X] - Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism[2]

• [X] - The quantitative and condition-dependent Escherichia coli proteome[3]

• [X] - Learning (from) the errors of a systems biology model[4]

• [X] - Dynamics of Epigenetic Regulation at the Single-Cell Level[5]

• [X] - Emergent genetic oscillations in a synthetic microbial consortium [6]

• [X] - Cell-Size Control and Homeostasis in Bacteria [7]

• [X] - Exploiting Nongenetic Cell-to-Cell Variation for Enhanced Biosynthesis [8] - Paper of the lab of Dr Fuzhong Zhang

• [X] - Constraints on Fluctuations in Sparsely Characterized Biological Systems [9]

• [X] - Stochastic Activation of a DNA Damage Response Causes Cell-to-Cell Mutation Rate Variation [10]

• [X] - Overflow metabolism in Escherichia coli results from efficient proteome allocation [11]

• [X] - Molecular circuits for dynamic noise filtering [12]

• [X] - Measurement of gene regulation in individual cells reveals rapid switching between promoter states [13]

• [X] - Cellular Growth Arrest and Persistence from Enzyme Saturation [14]

Academic Year 2016-2017

• [X] - Creating Single-Copy Genetic Circuits [15]

• [X] - The Cost of Protein Production [16]

• [] - Synchronous long-term oscillations in a synthetic gene circuit [17]

• [] - Bacterial persistence is an active σS stress response to metabolic flux limitation [18]

• [] - Sugar Synthesis from CO_2 in Escherichia coli [19]

• [] - Expression noise facilitates the evolution of gene regulation [20]

• [] - Complex Interplay of Physiology and Selection in the Emergence of Antibiotic Resistance [21]

• [] - Thresholds and ultrasensitivity from negative cooperativity [22]

• [] - Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized Systems [23] - Do on or after 23rd June

• [] - Synchronized mitochondrial and cytosolic translation programs [24] - Do on or after 23rd June

• [] - Glucose becomes one of the worst carbon sources for E.coli on poor nitrogen sources due to suboptimal levels of cAMP [25]

• Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations [26]

• Stress‐response balance drives the evolution of a network module and its host genome [27]

• Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms [28]

• A noisy linear map underlies oscillations in cell size and gene expression in bacteria [29]

• Replication of DNA in bacteria with heterogeneous generation times [30]

• Duplication of the bacterial cell and its initiation [31]

• Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size [32]

• A growth‐rate composition formula for the growth of E. coli on co‐utilized carbon substrates [33]

• Macromolecular Crowding as a Regulator of Gene Transcription [34]

• Cell Size and the Initiation of DNA Replication in Bacteria [35]

• How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximisation [36]

• Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations [37]

• Does evolutionary theory need a rethink? [38]

• A cross-chiral RNA polymerase ribozyme [39]

• Cell cycle: It takes three to find the exit [40]

• Loss of growth homeostasis by genetic decoupling of cell division from biomass growth: implication for size control mechanisms [41]

• Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation [42]

• Cell dynamics and gene expression control in tissue homeostasis and development [43]

• Quantitative evolutionary dynamics using high-resolution lineage tracking [44], with comment HERE

• Conditional density-based analysis of T cell signaling in single-cell data [45]

• Evolution of context dependent regulation by expansion of feast/famine regulatory proteins [46]

• Carbon source-dependent expansion of the genetic code in bacteria [47]

• Reducing the genetic code induces massive rearrangement of the proteome [48]

• Conserved codon composition of ribosomal protein coding genes inEscherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics [49]

CONTACT INFORMATION

Please feel free to e-mail me if you would like to suggest another paper to discuss at the group:

• Email me through OpenWetWare
• Visit the home page of our Lab from THIS link.

Useful Links

• Introductory tutorial
• OpenWetWare help pages
• Link to the tutorial on adjusting images in Wikis.
• Link to download the Wiki construction 'Cheat-Sheet' from my Dropbox. It details the simple commands needed to construct your Wiki pages.
• Further advanced level of editing Cheat-Sheets can be found HERE.
• Beware of copyright issues and fact that figures uploaded will fall under the Creative Commons license. Please see the following link.