User:Ahmad A. Mannan: Difference between revisions
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='''BIOMATHS JOURNAL CLUB'''= | ='''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). | 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 == | == NEXT GATHERING == | ||
[[Image:Screen Shot 2015-10-06 at 21.46.45.png|thumb|none|upright=2 | [[Image:Screen Shot 2015-10-06 at 21.46.45.png|thumb|none|upright=2]] | ||
THURSDAY | * Date: '''THURSDAY 17th NOVEMBER''' | ||
* Time: ''4PM'' | |||
* Venue: '''Huxley 747''' | |||
* Paper: [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19841.html '''''Synchronous long-term oscillations in a synthetic gene circuit'''''] | |||
[http:// | |||
== COMPILATION OF PAPERS TO READ == | == COMPILATION OF PAPERS TO READ == | ||
=== Academic Year 2015-2016 === | |||
* '''''[X]''''' - Noise in Gene Expression is Coupled to Growth Rate[http://genome.cshlp.org/content/early/2015/09/09/gr.191635.115.abstract] | |||
* '''''[X]''''' - Division in Escherichia coli is triggered by a size-sensing rather than a timing mechanism[http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-12-17] | |||
* | * '''''[X]''''' - The quantitative and condition-dependent Escherichia coli proteome[http://www.nature.com/nbt/journal/v34/n1/full/nbt.3418.html] | ||
* | |||
* [[ | * '''''[X]''''' - Learning (from) the errors of a systems biology model[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749970/] | ||
* '''''[X]''''' - Dynamics of Epigenetic Regulation at the Single-Cell Level[http://science.sciencemag.org/content/351/6274/720.full] | |||
* '''''[X]''''' - Emergent genetic oscillations in a synthetic microbial consortium [http://www.sciencemag.org/content/349/6251/986] | |||
* '''''[X]''''' - Cell-Size Control and Homeostasis in Bacteria [http://www.cell.com/current-biology/references/S0960-9822%2814%2901573-5] | |||
* '''''[X]''''' - Exploiting Nongenetic Cell-to-Cell Variation for Enhanced Biosynthesis [http://www.nature.com/nchembio/journal/v12/n5/full/nchembio.2046.html] - Paper of the lab of [http://zhang.eece.wustl.edu Dr Fuzhong Zhang] | |||
* '''''[X]''''' - Constraints on Fluctuations in Sparsely Characterized Biological Systems [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.058101] | |||
* '''''[X]''''' - Stochastic Activation of a DNA Damage Response Causes Cell-to-Cell Mutation Rate Variation [http://science.sciencemag.org/content/351/6277/1094] | |||
* '''''[X]''''' - Overflow metabolism in Escherichia coli results from efficient proteome allocation [http://www.nature.com/nature/journal/v528/n7580/abs/nature15765.html] | |||
* '''''[X]''''' - Molecular circuits for dynamic noise filtering [http://www.pnas.org/content/113/17/4729.short] | |||
* '''''[X]''''' - Measurement of gene regulation in individual cells reveals rapid switching between promoter states [http://science.sciencemag.org/content/351/6278/1218?utm_campaign=email-sci-toc&et_rid=49104479&et_cid=331862] | |||
* '''''[X]''''' - Cellular Growth Arrest and Persistence from Enzyme Saturation [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004825] | |||
=== Academic Year 2016-2017 === | |||
* '''''[X]''''' - Creating Single-Copy Genetic Circuits [http://www.sciencedirect.com/science/article/pii/S1097276516302362] | |||
* '''''[X]''''' - The Cost of Protein Production [http://www.sciencedirect.com/science/article/pii/S221112471501428X] | |||
* '''''[]''''' - Synchronous long-term oscillations in a synthetic gene circuit [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature19841.html] | |||
* '''''[]''''' - Bacterial persistence is an active σS stress response to metabolic flux limitation [http://msb.embopress.org/content/12/9/882?cpetoc] | |||
* '''''[]''''' - Sugar Synthesis from CO_2 in Escherichia coli [http://www.cell.com/cell/pdfExtended/S0092-8674(16)30668-7] | |||
* '''''[]''''' - Expression noise facilitates the evolution of gene regulation [https://elifesciences.org/content/4/e05856] | |||
* '''''[]''''' - Complex Interplay of Physiology and Selection in the Emergence of Antibiotic Resistance [http://www.sciencedirect.com/science/article/pii/S0960982216303372] | |||
* '''''[]''''' - Thresholds and ultrasensitivity from negative cooperativity [http://science.sciencemag.org/content/352/6288/990?utm_campaign=toc_sci-mag_2016-05-19&et_rid=49104479&et_cid=499312] | |||
* '''''[]''''' - Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized Systems [http://www.cell.com/cell-systems/fulltext/S2405-4712(16)30110-7] - Do on or after 23rd June | |||
* '''''[]''''' - Synchronized mitochondrial and cytosolic translation programs [http://www.nature.com/nature/journal/v533/n7604/full/nature18015.html] - 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 [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843011/] | |||
* Slow Protein Fluctuations Explain the Emergence of Growth Phenotypes and Persistence in Clonal Bacterial Populations [http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054272] | |||
* Stress‐response balance drives the evolution of a network module and its host genome [http://msb.embopress.org/content/11/8/827] | |||
* Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms [http://www.nature.com/nrg/journal/v16/n8/full/nrg3922.html?WT.ec_id=NRG-201508&spMailingID=49120140&spUserID=MjQyMjM5ODg1ODIS1&spJobID=722171134&spReportId=NzIyMTcxMTM0S0] | |||
* A noisy linear map underlies oscillations in cell size and gene expression in bacteria [http://www.nature.com/nature/journal/v523/n7560/full/nature14562.html] | |||
* Replication of DNA in bacteria with heterogeneous generation times [http://www.sciencedirect.com/science/article/pii/0022519368901689] | |||
* Duplication of the bacterial cell and its initiation [http://www.sciencedirect.com/science/article/pii/S0022519369800214] | |||
* Dilution of the cell cycle inhibitor Whi5 controls budding-yeast cell size [http://www.nature.com/nature/journal/v526/n7572/full/nature14908.html] | |||
* A growth‐rate composition formula for the growth of E. coli on co‐utilized carbon substrates [http://msb.embopress.org/content/11/4/801?cpetoc] | |||
* Macromolecular Crowding as a Regulator of Gene Transcription [http://ac.els-cdn.com/S0006349514002252/1-s2.0-S0006349514002252-main.pdf?_tid=b9ed6474-f5b7-11e4-94fc-00000aacb362&acdnat=1431113197_efa850dca9a5b6af11f5934d25ea6ad8] | |||
* Cell Size and the Initiation of DNA Replication in Bacteria [http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002549] | |||
* How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximisation [http://www.ncbi.nlm.nih.gov/pubmed/25754869] | |||
* Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations [http://www.nature.com/nature/journal/v513/n7518/full/nature13469.html?WT.ec_id=NATURE-20140918] | |||
* Does evolutionary theory need a rethink? [http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080] | |||
* A cross-chiral RNA polymerase ribozyme [http://www.nature.com/nature/journal/v515/n7527/full/nature13900.html?WT.ec_id=NATURE-20141120] | |||
* Cell cycle: It takes three to find the exit [http://www.nature.com/nature/journal/v517/n7532/full/nature14080.html] | |||
* Loss of growth homeostasis by genetic decoupling of cell division from biomass growth: implication for size control mechanisms [http://msb.embopress.org/content/10/12/769?cpetoc] | |||
* Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation [http://msb.embopress.org/content/10/12/770?cpetoc] | |||
* Cell dynamics and gene expression control in tissue homeostasis and development [http://msb.embopress.org/content/11/2/792?cpetoc] | |||
* Quantitative evolutionary dynamics using high-resolution lineage tracking [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14279.html?WT.ec_id=NATURE-20150226], with comment [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14207.html?WT.ec_id=NATURE-20150226 HERE] | |||
* Conditional density-based analysis of T cell signaling in single-cell data [http://www.sciencemag.org/content/346/6213/1250689.full.pdf?keytype=ref&siteid=sci&ijkey=Ng%2FJai9AuY2kc] | |||
* Evolution of context dependent regulation by expansion of feast/famine regulatory proteins [http://www.biomedcentral.com/1752-0509/8/122] | |||
* Carbon source-dependent expansion of the genetic code in bacteria [http://www.ncbi.nlm.nih.gov/pubmed/23185002] | |||
* Reducing the genetic code induces massive rearrangement of the proteome [http://www.ncbi.nlm.nih.gov/pubmed/25404328] | |||
* Conserved codon composition of ribosomal protein coding genes inEscherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC117187/] | |||
== | == CONTACT INFORMATION == | ||
Please feel free to e-mail me if you would like to suggest another paper to discuss at the group: | |||
* [[Special:Emailuser/Ahmad A. Mannan|Email me through OpenWetWare]] | |||
* <span style="color:red;">Visit the home page of our Lab from [http://www.imperial.ac.uk/people/d.oyarzun THIS] link.</span> | |||
==Useful Links== | ==Useful Links== |
Latest revision as of 06:54, 16 November 2016
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
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]
- 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.