Publications

Recent example systems biology publications from the University of Aberdeen

PIs from the University of Aberdeen Systems Biology Programme areindicated

Ramb R, Eichler M, Ing A, Thiel M, Weiller C, Grebogi C, Schwarzbauer C,
Timmer J, Schelter B. The impact of latent confounders in directed network
analysis in neuroscience. Philos Trans A Math Phys Eng Sci. 2013 Jul
15;371(1994):20110612. doi: 10.1098/rsta.2011.0612. Print 2013 Jul 13. PubMed
PMID: 23858480.

Radmaneshfar E, Kaloriti D, Gustin MC, Gow NA, Brown AJ, Grebogi C, Romano MC, Thiel M. From START to FINISH: The Influence of Osmotic Stress on the Cell Cycle. PLoS One. 2013 Jul 10;8(7):e68067. doi: 10.1371/journal.pone.0068067. Print 2013.

Ozyamak E, de Almeida C, de Moura AP, Miller S, Booth IR. Integrated stress
response of Escherichia coli to methylglyoxal: transcriptional readthrough from
the nemRA operon enhances protection through increased expression of glyoxalase
I. Mol Microbiol. 2013 Jun;88(5):936-50.

Ciandrini L, Stansfield I, Romano MC. Ribosome traffic on mRNAs maps to gene
ontology: genome-wide quantification of translation initiation rates and polysome
size regulation. PLoS Comput Biol. 2013;9(1):e1002866.

Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I. Regulation
of release factor expression using a translational negative feedback loop: a systems analysis. RNA. 2012 Dec;18(12):2320-34.

Kaloriti D, Tillmann A, Cook E, Jacobsen M, You T, Lenardon M, Ames L,
Barahona M, Chandrasekaran K, Coghill G, Goodman D, Gow NA, Grebogi C, Ho HL,
Ingram P, McDonagh A, de Moura AP, Pang W, Puttnam M, Radmaneshfar E, Romano MC, Silk D, Stark J, Stumpf M, Thiel M, Thorne T, Usher J, Yin Z, Haynes K, Brown AJ. Combinatorial stresses kill pathogenic Candida species. Med Mycol. 2012
Oct;50(7):699-709.

Heiland I, Bodenstein C, Hinze T, Weisheit O, Ebenhoeh O, Mittag M, Schuster
S. Modeling temperature entrainment of circadian clocks using the Arrhenius
equation and a reconstructed model from Chlamydomonas reinhardtii. J Biol Phys.
2012 Jun;38(3):449-64.

You T, Ingram P, Jacobsen MD, Cook E, McDonagh A, Thorne T, Lenardon MD, de
Moura AP, Romano MC, Thiel M, Stumpf M, Gow NA, Haynes K, Grebogi C, Stark J,
Brown AJ. A systems biology analysis of long and short-term memories of osmotic
stress adaptation in fungi. BMC Res Notes. 2012 May 25;5:258.

Sommerlade L, Thiel M, Platt B, Plano A, Riedel G, Grebogi C, Timmer J,
Schelter B. Inference of Granger causal time-dependent influences in noisy
multivariate time series. J Neurosci Methods. 2012 Jan 15;203(1):173-85.

Richard M, Fryett M, Miller S, Booth I, Grebogi C, Moura A. Optimality in DNA
repair. J Theor Biol. 2012 Jan 7;292:39-43.

Kartal O, Mahlow S, Skupin A, Ebenhoeh O. Carbohydrate-active enzymes
exemplify entropic principles in metabolism. Mol Syst Biol. 2011 Oct 25;7:542.

Davidson S, Lear M, Shanley L, Hing B, Baizan-Edge A, Herwig A, Quinn JP,
Breen G, McGuffin P, Starkey A, Barrett P, MacKenzie A. Differential activity by
polymorphic variants of a remote enhancer that supports galanin expression in the
hypothalamus and amygdala: implications for obesity, depression and alcoholism.
Neuropsychopharmacology. 2011 Oct;36(11):2211-21.

Karschau J, de Almeida C,Richard MC, Miller S, Booth IR, Grebogi C, de Moura
AP. A matter of life or death: modeling DNA damage and repair in bacteria.
Biophys J. 2011 Feb 16;100(4):814-21.

Ebenhoeh O, Houwaart T, Lokstein H, Schlede S, Tirok K. A minimal mathematical
model of nonphotochemical quenching of chlorophyll fluorescence. Biosystems. 2011
Feb;103(2):196-204.

Guseva K, Thiel M, Booth I, Miller S, Grebogi C, de Moura A. Collective
response of self-organized clusters of mechanosensitive channels. Phys Rev E Stat
Nonlin Soft Matter Phys. 2011 Feb;83(2 Pt 1):020901.

Sch?tte M, Skupin A, Segr? D, Ebenhoeh O. Modeling the complex dynamics of
enzyme-pathway coevolution. Chaos. 2010 Dec;20(4):045115.

Brackley CA, Ebenhoeh O, Grebogi C, Kurths J, de Moura A, Romano MC, Thiel M.
Introduction to focus issue: dynamics in systems biology. Chaos. 2010
Dec;20(4):045101. doi: 10.1063/1.3530126. PubMed PMID: 21198113.

Schotte M, Mutwil M, Persson S, Ebenhoeh O. Analyzing gene coexpression data
by an evolutionary model. Genome Inform. 2010 Jul;24(1):154-63.

Rato C, Amirova SR, Bates DG, Stansfield I, Wallace HM. Translational recoding
as a feedback controller: systems approaches reveal polyamine-specific effects on
the antizyme ribosomal frameshift. Nucleic Acids Res. 2011 Jun;39(11):4587-97.

Brackley CA, Romano MC, Thiel M. The dynamics of supply and demand in mRNA
translation. PLoS Comput Biol. 2011 Oct;7(10):e1002203.

You T, Stansfield I, Romano MC, Brown AJ, Coghill GM. Analysing GCN4
translational control in yeast by stochastic chemical kinetics modelling and
simulation. BMC Syst Biol. 2011 Aug 18;5:131.  

Basler G, Grimbs S, Ebenhöh O, Selbig J, Nikoloski Z. Evolutionary
significance of metabolic network properties. J R Soc Interface. 2011 Nov 30.

Brackley CA, Romano MC, Thiel M. Slow sites in an exclusion process with
limited resources. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Nov;82(5 Pt
1):051920.

Brackley CA, Romano MC, Grebogi C, Thiel M. Limited resources in a driven
diffusion process. Phys Rev Lett. 2010 Aug 13;105(7):078102.

Ciandrini L, Stansfield I, Romano MC. Role of the particle's stepping cycle in
an asymmetric exclusion process: a model of mRNA translation. Phys Rev E Stat
Nonlin Soft Matter Phys. 2010 May;81(5 Pt 1):051904.

Kartal O, Mahlow S, Skupin A, Ebenhöh O. Carbohydrate-active enzymes exemplify
entropic principles in metabolism. Mol Syst Biol. 2011 Oct 25;7:542. doi:
10.1038/msb.2011.76.

Pfau T, Christian N, Ebenhöh O. Systems approaches to modelling pathways and
networks. Brief Funct Genomics. 2011 Sep;10(5):266-79. doi: 10.1093/bfgp/elr022.

Basler G, Ebenhöh O, Selbig J, Nikoloski Z. Mass-balanced randomization of
metabolic networks. Bioinformatics. 2011 May 15;27(10):1397-403. Epub 2011 Mar
23.

Schütte M, Skupin A, Segrè D, Ebenhöh O. Modeling the complex dynamics of
enzyme-pathway coevolution. Chaos. 2010 Dec;20(4):045115. P

May P, Christian N, Ebenhöh O, Weckwerth W, Walther D. Integration of
proteomic and metabolomic profiling as well as metabolic modeling for the
functional analysis of metabolic networks. Methods Mol Biol. 2011;694:341-63.

Schütte M, Mutwil M, Persson S, Ebenhöh O. Analyzing gene coexpression data
by an evolutionary model. Genome Inform. 2010 Jul;24(1):154-63.

Tamura T, Christian N, Takemoto K, Ebenhöh O, Akutsu T. Analysis and
prediction of nutritional requirements using structural properties of metabolic
networks and support vector machines. Genome Inform. 2010 Jan;22:176-90.

Schütte M, Klitgord N, Segrè D, Ebenhöh O. Co-evolution of metabolism and
protein sequences. Genome Inform. 2010 Jan;22:156-66.

Witzel F, Götze J, Ebenhöh O. Slow deactivation of ribulose 1,5-bisphosphate
carboxylase/oxygenase elucidated by mathematical models. FEBS J. 2010
Feb;277(4):931-50.

Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S. Assembly of
an interactive correlation network for the Arabidopsis genome using a novel
heuristic clustering algorithm. Plant Physiol. 2010 Jan;152(1):29-43.

de Silva E, Krishnan J, Betney R, Stansfield I. (2010) A mathematical modelling framework for elucidating the role of feedback control in translation termination. J Theor Biol. 2010 Feb 20. [Epub ahead of print]

Kartal O, Ebenhöh O. Ground state robustness as an evolutionary design
principle in signaling networks. PLoS One. 2009 Dec 1;4(12):e8001.

Christian N, May P, Kempa S, Handorf T and Ebenhöh O. (2009) An integrative approach towards completing genome-scale metabolic networks. Molecular BioSystems, in press (2009).

May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J,
Recuenco-Munoz L, Ebenhöh O, Weckwerth W, Walther D. Metabolomics- and
proteomics-assisted genome annotation and analysis of the draft metabolic network
of Chlamydomonas reinhardtii. Genetics. 2008 May;179(1):157-66.

Coghill, GM Srinivasan A, and King RD (2008) Qualitative system identification from imperfect data. Journal of Artificial Intelligence Research, 32; 825 – 877.

Matthäus F, Salazar C and Ebenhöh O. (2008) Biosynthetic potentials of metabolites and their hierarchical organization. PLoS Comput Biol, 4:e1000049.

Nieduszynski CA, Knox Y, Donaldson AD. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 20:1874-9.

Romano MC, Thiel M, Stansfield I, and Grebogi C (2009) Queueing Phase Transition: Theory of Translation. Phys. Rev. Lett. 102: 198104

Schelin AB, Károlyi G, de Moura AP, Booth NA, Grebogi C.(2009) Chaotic advection in blood flow. Phys Rev E Stat Nonlin Soft Matter Phys. 80:016213.

Ullner E, Zaikin A, Volkov EI and Garcia-Ojalvo J (2007). Multistability and clustering in a population of synthetic genetic oscillators via phase- repulsive cell-to-cell communication. Phys. Rev. Lett. 99: 148103

Van Leeuwen P, Geue D, Thiel M, Cysarz D, Lange S, Romano MC, Wessel N, Kurths
J, Grönemeyer DH. Influence of paced maternal breathing on fetal-maternal heart
rate coordination. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13661-6.

Wulff P, Ponomarenko AA, Bartos M, Korotkova TM, Fuchs EC, Bähner F, Both M, Tort AB, Kopell NJ, Wisden W, Monyer H. (2009) Hippocampal theta rhythm and its coupling with gamma oscillations require fast inhibition onto parvalbumin-positive interneurons. Proc Natl Acad Sci U S A. 106:3561-3566.

You T, Coghill, GM and Brown, AJP (2007) A quantitative model for the translational control of GCN4 in yeast. Proc. Foundat. Sys. Biol. Engin. 2007: 121-126.