User:Ahmad A. Mannan

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

Example of an image I uploaded and embedded into my Wiki.

• Date: THURSDAY 11TH FEBRUARY
• Time: 3-4PM
• Venue: HUXLEY 747

• Paper: Noise in Gene Expression is Coupled to Growth Rate

COMPILATION OF PAPERS TO READ

• Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism[1]

• Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations [2]

• Stress‐response balance drives the evolution of a network module and its host genome [3]

• Emergent genetic oscillations in a synthetic microbial consortium [4]

• Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms [5]

• A noisy linear map underlies oscillations in cell size and gene expression in bacteria [6]

• Replication of DNA in bacteria with heterogeneous generation times [7]

• Duplication of the bacterial cell and its initiation [8]

• Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size [9]

• A growth‐rate composition formula for the growth of E. coli on co‐utilized carbon substrates [10]

• Macromolecular Crowding as a Regulator of Gene Transcription [11]

• Cell Size and the Initiation of DNA Replication in Bacteria [12]

• How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximisation [13]

• Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations [14]

• Does evolutionary theory need a rethink? [15]

• A cross-chiral RNA polymerase ribozyme [16]

• Cell cycle: It takes three to find the exit [17]

• Loss of growth homeostasis by genetic decoupling of cell division from biomass growth: implication for size control mechanisms [18]

• Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation [19]

• Cell dynamics and gene expression control in tissue homeostasis and development [20]

• Quantitative evolutionary dynamics using high-resolution lineage tracking [21], with comment HERE

• Conditional density-based analysis of T cell signaling in single-cell data [22]

• Evolution of context dependent regulation by expansion of feast/famine regulatory proteins [23]

• Carbon source-dependent expansion of the genetic code in bacteria [24]

• Reducing the genetic code induces massive rearrangement of the proteome [25]

• Conserved codon composition of ribosomal protein coding genes inEscherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics [26]

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.

Publications

1. ISBN:9783527318742

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.