Publications of Laurence Loewe
Scientific publications in population genetics, systems biology and computer science.
L27 Ehlert K & Loewe L (2014) “Lazy Updating increases the speed of stochastic simulations” Journal of Chemical Physics 141: 204109 http://dx.doi.org/10.1063/1.4901114
Introduces a new trick for speeding up stochastic simulations in the presence of hub-molecules like ATP.
Pre-review-submission-Link (2013): http://arxiv.org/abs/1310.2068 PDF
- L26 Watterson S, Guerriero M-L , Blanc M, Mazein A, Loewe L, Robertson KA, Gibbs H, Shui G, Wenk MR, Hillston J, Ghazal P (2013) "A
model of flux regulation in the cholesterol biosynthesis pathway:
Immune mediated graduated flux reduction versus statin-like led stepped
flux reduction". Biochimie 95:613–621
Link: http://dx.doi.org/10.1016/j.biochi.2012.05.024 PDF | DOI | Pubmed | Journal
- L25 McGaugh
S, Himmel TL, Noor, MAF
"Recombination Modulates How Selection Affects Linked Sites in Drosophila."
PLoS Biology 10(11):
Link: http://dx.doi.org/10.1371/journal.pbio.1001422 PDF | DOI | Pubmed | Journal
L24 Modrzynska K, Creasey A, Loewe L, Cezard T, Martinelli A, Borges
S, Cravo P, Blaxter M, CarterR, Hunt P (2012) “Genome-wide re-sequencing defines mutations of complex chloroquine
resistance in malaria”. BMC Genomics
Link: http://www.biomedcentral.com/1471-2164/13/106 PDF | DOI | Pubmed | Journal
- L23 Loewe L, (2012) “How evolutionary
systems biology will help understand adaptive landscapes and distributions of
mutational effects”. In: Soyer O, editor. Evolutionary Systems Biology:
Advances in Experimental Medicine and Biology vol. 751 pages 399-410. Springer.
Link: http://www.springerlink.com/content/t240h2n4v5j61735/ PDF | DOI | Pubmed | Journal
- L22 Loewe L, Guerriero ML, Watterson S, Moodie S, Ghazal P & Hillston J (2011) "Translation
from the quantified implicit process flow abstraction in SBGN-PD
diagrams to Bio-Pepa illustrated on the Cholesterol pathway". Transactions on Computational Systems Biology XIII, Priami, C et al. (eds), Lecture Notes in Bioinformatics LNBI 6575, pages 13-38.
Link: http://www.springerlink.com/content/4104145214nr746t/ PDF | DOI | ACM-DL | Journal
- L21 Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D,
Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto TD, Pain A, Blaxter M
& Cravo P (2010) “Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation
conferring artemisinin resistance in an isogenic lineage of malaria parasites”.
BMC Genomics 11:499 (13 pages).
Link: http://www.biomedcentral.com/1471-2164/11/499 PDF | DOI | Pubmed | Journal
- L20 Haddrill PR, Loewe L & Charlesworth B (2010) "Estimating the parameters of selection on nonsynonymous mutations in Drosophila pseudoobscura and D. miranda" Genetics 185:1381-1396
Applies the method in L6 to a much bigger dataset and compares it to other analyses.
Link: http://www.genetics.org/cgi/content/abstract/185/4/1381 DOI | Pubmed | Journal
- L19 Loewe L & Hill, WG (2010) “Introduction: The population genetics of mutations: good, bad and indifferent” Philosophical Transactions of the Royal Society B 365:1153-1167.
An overview of the population genetics of mutations that highlights future challenges.
Link: http://dx.doi.org/doi:10.1098/rstb.2009.0317 PDF | DOI | Journal abstract | Journal issue
- L18 Waxman D & Loewe L (2010) “A stochastic model for a single
click of Muller’s ratchet”. Journal of theoretical Biology 264:1120-1132
Explores a new approach to computing the rate of Muller's ratchet and compares it to evolution@home simulations.
Link: http://dx.doi.org/10.1016/j.jtbi.2010.03.014 PDF | DOI | Pubmed | Journal
- L17 Akman O, Guerriero ML, Loewe L & Troein C (2010) "Complementary approaches to understanding the plant circadian clock", in Proceedings of the "3rd Workshop From Biology To Concurrency and back" (FBTC 2010), http://disi.unitn.it/~fbtc2010/ Electronic Proceedings in Theoretical Computer Science EPTCS 19:1–19, DOI: 10.4204/EPTCS.19.1
Further steps towards an evolutionary systems biology model of a circadian clock with entrainment. I contributed the mutational robustness analyses. Builds loosely on [L13].
URL: http://arxiv.org/abs/1002.4661 PDF | Journal | Workshop page
- L16 Loewe L, Moodie S & Hillston J (2009) "Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA", Proceedings of the "2nd International Workshop on Computational Models for Cell Processes" (CompMod2009 workshop, http://combio.abo.fi/compmod09/), in Electronic Proceedings in Theoretical Computer Science EPTCS 6:93-107, DOI: 10.4204/EPTCS.6.7
This work builds a compiler that maps biochemical models from SBGN-PD to Bio-PEPA to build a bridge from visual model construction to automated simulations. See also [L7n].
Link: http://arxiv.org/abs/0910.1410 PDF | Workshop page | Journal
- L15 Duguid A, Gilmore S, Guerriero ML, Hillston J & Loewe L (2009) "Design and development of software tools for Bio-PEPA", pp. 956-967 in Proceedings of the 2009 Winter Simulation Conference (WSC'09 http://www.wintersim.org/),
edited by RMD Rossetti, RR Hill, B Johansson, A Dunkin &
RG Ingalls. Austin, Texas: IEEE Press.
A description of how the Bio-PEPA modelling tools are organised to facilitate the automatic conversion of models between different mathematical and other formalisms.
Link: http://www.informs-sim.org/wsc09papers/091.pdf PDF | Offical abstract | Offical PDF | PDF at CSBE
- L14 Loewe L (2009) "A framework for evolutionary systems biology", BMC Systems Biology 3:27 (34 pages, designated ‘highly accessed’ by BMC from continuous traffic).
This is the definitive reference for my new mechanistic framework for evolutionary systems biology that brings together systems biology and evolutionary genetics in order to help understand adaptive landscapes.
Link: http://www.biomedcentral.com/1752-0509/3/27/ Official PDF | PubMed | DOI | Journal | Enhanced PDF
- L13 Loewe L & Hillston J (2008) "The distribution of mutational effects
on fitness in a simple circadian clock", Proceedings of the 6th Conference on Computational Methods in Systems Biology 11-15 Oct 2008 Rostock, Germany,
CMSB08, published in: Lecture Notes in Bioinformatics 5307:156-175.
The first proof of concept for my new approach to evolutionary systems biology.
Link: http://dx.doi.org/10.1007/978-3-540-88562-7_14 PDF | DOI
- L12 Loewe L & Cutter A (2008) "On the potential for extinction by
Muller’s Ratchet in Caenorhabditis elegans", BMC Evolutionary Biology
8:125 (13 pages).
Here I combined my theory and evolution@home results with the expertise of my collaborator on the worm C. elegans. Builds on [L11].
Link: http://www.biomedcentral.com/1471-2148/8/125 PDF | Journal
- L11 Loewe L & Lamatsch, D (2008) "Quantifying the threat from Muller's ratchet in the Amazon molly (Poecilia formosa)", BMC Evolutionary Biology 8:88 (20 pages, designated ‘highly accessed’ by BMC, peak after news coverage).
Building on older work I also explain how Muller’s ratchet theory can be applied to selfing species.
Link: http://www.biomedcentral.com/1471-2148/8/88 PDF | Journal
- L10 Loewe L (2007) "Evolution@home: observations on participant choice, work unit variation and low-effort global computing". Software Practice & Experience 37:1289-1318.
This describes the semi-automated global computing by evolution@home and what needs to be improved. Builds on [L3].
Link: http://doi.wiley.com/10.1002/spe.806 DOI link
- L9 Loewe L & Charlesworth B (2007) "Background selection in single
genes may explain patterns of codon bias", Genetics 175:1381-1393.
Explores the patterns that deleterious mutations can produce within genes.
Link: http://www.genetics.org/cgi/content/abstract/175/3/1381 PDF | PubMed | DOI | Journal
- L8 Loewe L & Charlesworth B (2006) "Inferring the distribution of mutational effects on fitness in Drosophila", Biology Letters 2:426-430.
Compares different types of distributions and finds the log-normal type to perform best.
Link: http://dx.doi.org/DOI:10.1098/rsbl.2006.0481 PDF | ISI | PubMed | DOI | Journal
- L7 Loewe L (2006) "Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA" Genetics Research 87:133-159.
The most rigorous analysis so far of the potential for mutational meltdown in human mitochrondria, a good pointer to much of the work on Muller’s ratchet and the most comprehensive list so far of all the processes that might help to prevent meltdown.
Link: http://journals.cambridge.org/action/displayAbstract?aid=439711 PDF | ISI | PubMed | DOI | Journal
- L6 Loewe L & Charlesworth B, Bartolomé C & Nöel V (2006) "Estimating selection on non-synonymous mutations", Genetics 172:1079-1092.
We introduce a new approach to estimate the distribution of mutational effects from diversity data in two species that does not depend on ancient demography. We find most new mutations are effectively deleterious but have selection coefficients that are well below the thresholds of what can be detected directly in experiments.
Link: http://www.genetics.org/cgi/content/abstract/172/2/1079 PDF | ISI | PubMed | DOI | Journal | Poster
- L5 Loewe L (2004) "Response to comment on 'High deleterious genomic mutation rate in stationary phase of Escherichia coli'", Science 304:518-518.
I show that earlier criticism of L4 is unjustified and how bacteria might cooperate to be more flexible.
Link: http://www.sciencemag.org/cgi/content/full/304/5670/518d PDF | ISI | DOI | Journal
- L4 Loewe L, Textor V & Scherer S (2003) "High deleterious genomic mutation rate in stationary phase of Escherichia coli", Science 302:1558-1560.
The first mutation accumulation experiment in stationary phase. Like in all MA experiments, only large selection coefficients could be observed. This work uncovers complex evolutionary processes in stationary phase that have a wide range of implications that can only be explored in computational models that are yet to be built.
Link: http://www.sciencemag.org/cgi/content/abstract/302/5650/1558 PDF-core | PDF-collect | ISI | PubMed | DOI | Journal
- L3 Loewe L (2002) "evolution@home: Experiences with work units that span more than 7 orders of magnitude in computational complexity",
pp. 425-431. in Proceedings of the 2nd International Workshop on Global and Peer-to-Peer
Computing on Large Scale Distributed Systems at the 2nd IEEE/ACM
International Symposium on Cluster Computing and the Grid (CCGrid2002),
21-24 May, Berlin, Germany, IEEE Computer Society.
There are powerful normalising forces that get a wide range of tasks computed, if users are allowed to choose the complexity of tasks they want to compute (evolution@home is first to offer this option in global computing).
Link: http://doi.ieeecomputersociety.org/10.1109/CCGRID.2002.1017176 PDF | DOI | ConferenceProceedings
- L2 Loewe L (2002) "Global computing for bioinformatics", Briefings in Bioinformatics 3:377-388.
Reviews types of bioinformatics tasks can benefit from globally distributed computing.
Link: http://bib.oxfordjournals.org/cgi/content/abstract/3/4/377 PDF | PubMed | DOI | Journal
- L1 Loewe L & Scherer S (1997) "Mitochondrial Eve: The plot thickens", Trends in Ecology & Evolution 12:422-423.
Explores how archaeological data could be used to make inferences on mutation rates.
Edited special issues
Loewe L & Hill, WG; editors (2010) “The population genetics of mutations: good, bad and indifferent”, Philosophical Transactions of the Royal Society B volume 365, issue number 1544, pages 1149-1294, ISSN 0962-8436, ISBN: 978-0-85403-813-8. Table of contents | News item from evolution@home perspecive | The print issue can be
ordered from: http://rstb.royalsocietypublishing.org/site/2010/mutations.xhtml (for a discount enter special code TB 1544
when prompted). | Preface and Introduction are free.
This collection of papers by influential scientists highlights many of the challenges that we face when trying to understand the evolution of life with a special view on mutations. This is an excellent collection of papers for understanding the complex scientific questions that inspire the work behind evolution@home. Mostly written for reasonably informed professional biologists or experts, some of it can be challenging to understand for others. This issue is dedicated to Brian Charlesworth on the occasion of his 65th birthday for his many contributions to population genetics.
I have served as a reviewer for PLoS Biology, Proceedings of the National Academy of Sciences of the USA, Proceedings of the Royal Society of London Series Biological Sciences, Philosophical Transactions of the Royal Society B, Biology Letters, Evolution, Genetics, Molecular Biology & Evolution, Genetical Research, Journal of theoretical Biology, BMC Bioinformatics, BMC Evolutionary Biology, Fundamental and Applied Limnology, BioSilico, TheScientificWorldJournal and BioTechniques.
- L10n Ehlert K & Loewe L (2013) “Lazy Updating increases the speed of stochastic simulations” arXiv:1310.2068 [q-bio.QM] Introduces a new trick for speeding up stochastic simulations in the presence of hub-molecules like ATP.
- L9n Loewe L & Hill, WG (2010) “Preface: Mutations and Brian Charlesworth” Philosophical Transactions of the Royal Society B 365:1151-1151.
Honours Brian Charlesworth’s contributions to population genetics.
- L8n Loewe L & Viglas S (2010) “SQL vs NoSQL for simulation data management”, http://forum.idea.ed.ac.uk/ ; iDEA contribution; poster presented at
“idea Lab lunch” 23 Feb 2010, School of Informatics, Uni Edinburgh.
This work explores approaches for building extremely scalable simulation results databases, as needed for the analysis of very complex computational models.
- L7n Loewe L, Moodie S & Hillston J (2009) "Technical Report: Defining a textual representation for SBGN Process Diagrams and translating it to Bio-PEPA for quantitative analysis of the MAPK signal transduction cascade", Technical Report EDI-INF-RR-1334, School for Informatics, University of Edinburgh.
This work defines a textual representation for the systems biology graphical notation process diagrams and explains how this can be augmented by quantitative information to facilitate automated simulations.
Link: http://www.inf.ed.ac.uk/publications/report/1334.html Original report | Software available at CSBE site
- L6n Loewe L & Hillston J (2008) "Meeting report: Computational models in systems biology", Genome Biology 9:328. (3 pages).
Building models is the art of capturing the essence of systems. This invited meeting report gives examples for some of the essence capturing abstractions used in systems biology.
Link: http://genomebiology.com/2008/9/12/328 PDF | Pubmed | DOI | Journal
- L5n Loewe L (2008) “Designing a Front-End for Bio-PEPA”, (5 pages) in: Gilmore S,
editor. Proceedings of the 7th Workshop on Process Algebra and Stochastically Timed
Activities, 30-31 July 2008, Edinburgh, UK.
A design prototype for a biologist-friendly model implementation language is presented.
Link: http://pastaworkshop.org/proceedings/loewe-pasta2008.pdf PDF | Workshop site
- L4n Loewe L (2008) "Evolution@home: The first global computing system for evolutionary biology", invited chapter in the book "Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities" edited by M. Weber, Rechenkraft.net.
- L3n Loewe L (2008) “Negative Selection”, Nature Education 1(1), Short
introduction as invited by the editors of the “Evolutionary Genetics”
section of the new “Nature Education” initiative.
Stable Link: http://www.nature.com/scitable/topicpage/Negative-Selection-1136
- L2n Loewe L (2008) “Genetic Mutation”, Nature Education 1(1), Short
introduction as invited by the of the “Evolutionary Genetics” section
of the new “Nature Education” initiative.
Stable Link: http://www.nature.com/scitable/topicpage/Genetic-Mutation-1127
- L1n Loewe L (2006) “Population Genetics Group Meeting 2006”, Meeting report, Genetics Society News, Issue 57, pp. 22-25.
Link: http://www.genetics.org.uk/files/pdf/Genetics%20soc%20issue%2057.pdf PDF of the issue
- L0n Loewe L (2005) "Evolution@home: Global computing quantifies evolution
due to Muller's ratchet", BMC Bioinformatics 2005, vol. 6, suppl 3,
p.18-18. Abstract of a poster presented at BioSysBio: Bioinformatics and Systems Biology Conference, Edinburgh, UK. 14–15 July 2005. Poster won a prize.
Link: http://www.biomedcentral.com/1471-2105/6/S3/P18 | PDF | Journal