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Center for Models of Life
Niels Bohr Institute
University of Copenhagen
Blegdamsvej 17
2100 Copenhagen Ř
Mail:  cmolnbi.dk

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Ala Trusina

Ala Trusina
Position: Assistant Prof.
Email: trusinanbi.dk
www: http://alatrusina.eu
Phone: 0045 52701296

Life is a collection of processes on so many scales: miliseconds to centuries, nanome- ters to kilometers. And as our capacity for information processing is finite we naturally zoom in and out between these scales to build our mental model of the world: We pick up a few key elements and coarse-grain the details. In my research I am advocating a similar approach of a coarse-grained modeling to capture the key interactions at the core of a biological process.

The main focus of my research is on understanding the logic behind stress responses. What mechanisms did cells and organisms evolve to deal with the insults that perturb their normal function (stresses)? What are the differences and similarities between the stress responses? (Both at the level of regulatory network and the dynamics of its components). With this knowledge and with the help of mathematical modeling the hope is to outline the "core circuits" that govern a given process of interest.

Part of my current focus is on the stress response processes that are directly in- volved in diseases: Dynamics of NF-kB meditated inflammatory response in tissue (Inflammation); Unfolded protein response (Diabetes); DNA damage and response to genotoxic stresses, telomeres dynamics (Aging, Cancer). These are mainly theoretical projects in collaboration with experimentalists.

We have also started a number of experimental projects in single cell organisms: heat shock response in E.coli and H2O2 oxidative stress response in S. Pombi. With the help of fluorescent time-lapse microscopy we are investigating the dynamics of these responses and how they differ from cell-to-cell. Inspired by our study of inflammatory response in tissue, I am now expanding my activities more into the the area of cell-cell communication and how this process forms and orchestrating tissue responses.

You can learn more about our porjects here


Publications:
Silas Boye Nissen, Marta Perera, Javier Martin Gonzalez, Sophie M. Morgani, Mogens H. Jensen, Kim Sneppen, Joshua M. Brickman, Ala Trusina
Four simple rules that are sufficient to generate the mammalian blastocyst
Plos Biology 15:e2000737 (2017)

Thomas Holst-Hansen, Elena Abad, Aura Muntasell, Miguel Lopez-Botet, Mogens H. Jensen, Ala Trusina, Jordi Garcia-Ojalvo
Impact of Zygosity on Bimodal Phenotype Distributions
Biophysical Journal 113:148 (2017)

Michaela J. Obersriebnig, Emil M. H. Pallesen, Kim Sneppen, Ala Trusina and Genevičve Thon
Nucleation and spreading of a heterochromatic domain in fission yeast
Nature Communications 7:11518 (2016)

Sřren Vedel, Harry Nunns, Andrej Košmrlj, Szabolcs Semsey, Ala Trusina
Asymmetric Damage Segregation Constitutes an Emergent Population-Level Stress Response
Cell Systems 3:187 (2016)

Ala Trusina
Stress induced telomere shortening: longer life with less mutations?
BMC Systems Biology 8: (2014)

Kristian Moss Bendtsen, Martin Borch Jensen, Alfred May, Lene Juel Rasmussen, Ala Trusina, Vilhelm A. Bohr, Mogens H. Jensen
Dynamics of the DNA repair proteins WRN and BLM in the nucleoplasm and nucleoli
European Biophysics Journal 0: (2014)

Sirin W. Gangstad, Cilie W. Feldager, Jeppe Juul, and Ala Trusina
Noisy transcription factor NF-κB oscillations stabilize and sensitize cytokine signaling in space
Phys. Rev. E 87: 022702 (2013)

akočiūnas T, Holm LR, Verhein-Hansen J, Trusina A, Thon G
Two portable recombination enhancers direct donor choice in fission yeast heterochromatin
PLoS Genetics 9:e1003762 (2013)

Benedicte Mengel, Sandeep Krishna, Mogens H. Jensen, Ala Trusina
Nested feedback loops in gene regulation
Physica A 391:100 (2012)

Ilaria Cataudella, Ala Trusina, Kim Sneppen, Kenn Gerdes, and Namiko Mitarai
Conditional cooperativity in toxin–antitoxin regulation prevents random toxin activation and promotes fast translational recovery
Nuc. Acids Res. 40:6424 (2012)

Kristian Moss Bendtsen, Jeppe Juul, Ala Trusina
Fragile DNA Repair Mechanism Reduces Ageing in Multicellular Model
PLoS ONE 7:e36018 (2012)

A. G. Lerner,J-P Upton,P.V.K. Praveen,R. Ghosh,Y. Nakagawa,A. Igbaria,S. Shen,V. Nguyen,B.J. Backes,M. Heiman,N. Heintz,P. Greengard,S. Hui,Q. Tang, A. Trusina,S. A. Oakes,F. R. Papa
IRE1α Induces Thioredoxin-Interacting Protein to Activate the NLRP3 Inflammasome and Promote Programmed Cell Death under Irremediable ER Stress
Cell Metabolism 6:250 (2012)

Masayo Inoue, Namiko Mitarai, and Ala Trusina.
Circuit architecture explains functional similarity of bacterial heat shock responses
Phys. Biol. 9:066003 (2012)
1209.2504

J.O. Haerter, A. Trusina, K. Sneppen
Bacterial CRISPR defense system buffers phage diversity
Journal of Virology 85:10554 (2011)

Joachim Mathiesen, Namiko Mitarai, Kim Sneppen, and Ala Trusina
Ecosystems with mutually exclusive interactions self-organize to a state of high diversity
Phys. Rev. Lett. 107 107:188101 (2011)
1108.2011

Pernille Yde, Benedicte Mengel, Mogens H Jensen, Sandeep Krishna and Ala Trusina
Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue
BMC Systems Biology 5:115 (2011)

Pernille Yde, Mogens Hogh Jensen, and Ala Trusina
Analyzing inflammatory response as excitable media
Phys. Rev. E 84:051913 (2011)

Benedicte Mengel, Alexander Hunziker, Lykke Pedersen, Ala Trusina, Mogens H Jensen and Sandeep Krishna
Modeling oscillatory control in NF-κB, p53 and Wnt signaling
Current Opinion in Genetics & Development 20:571 (2010)

Sneppen K, Trusina A, Jensen MH, and Bornholdt S
A minimal model for multiple epidemics and immunity spreading.
Plos One 5:e13326 (2010)

Ala Trusina and Chao Tang
The unfolded protein response and translation attenuation: a modelling approach
Diabetes, Obesity and Metabolism 12: (2010)

W. Ma, A. Trusina, H. El-Samad,W. Lim and C. Tang
Defining Network Topologies that Can Achieve Biochemical Adaptation
Cell 138:760 (2009)

P. Merksamer, A. Trusina, F. Papa
Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions
Cell 135:933 (2008)

A. Trusina, F. Papa, C. Tang
Rationalizing translation attenuation in the network architecture of the unfolded protein response
PNAS 105:20280 (2008)

Ala Trusina, Feroz Papa and Chao Tang
Translation Attenuation Mechanism in Unfolded Protein Response
Evolution from Cellular to Social Scales NATO Science for Peace and Security Series B: Physics and Biophysics 0:83 (2008)

M. T Borup , A. Trusina, A. Andersson
Aging mechanism as the "down side" of adaptation: A network approach
J Theor Biol. 250:66 (2007)

Jacob Bock Axelsen, Sebastian Bernhardsson, Martin Rosvall, Kim Sneppen, Ala Trusina
Degree Landscapes in Scale-Free Networks
Phys. Rev. E 74:036119 (2006)
physics/0512075

M. Rosvall, A. Trusina, P. Minnhagen, K. Sneppen
Networks and Cities: An Information Perspective
Phys. Rev. Lett 94:28701 (2005)
cond-mat/0407054

K. Sneppen, A. Trusina, M. Rosvall
Hide and Seek on Complex Networks
Europhys. Lett. 69:853 (2005)
cond-mat/0407055

Beom Jun Kim, Petter Minhagen, Ala Trusina og Kim Sneppen
Scale Free networks from Aggregation and Creation of Vertices
European Physical Journal B 43:369 (2005)

Ala Trusina, Kim Sneppen, I.B. Dodd, K.E. Shearwin and J.B. Egan.
Functional alignment of regulatory networks: A study of temerate phages
Plos Computational Biology 1:7 (2005)
q-bio.MN/0511047

A. Trusina, M. Rosvall, K. Sneppen
Communication Boundaries in Networks
Phys. Rev. Lett. 94:238701 (2004)
cond-mat/0412064

Ala Trusina, Sergei Maslov, Petter Minnhagen, Kim Sneppen
Hierarchy and Anti-Hierarchy in Real and Scale Free networks
Phys. Rev. Lett. 92:178702 (2004)
cond-mat/0308339

Beom Jun Kim, Ala Trusina, Petter Minnhagen, Kim Sneppen
Self Organized Scale-Free Networks from Mergin and Regeneration
: (2004)
nlin.AO/0403006

K. Sneppen, M. Rosvall, A. Trusina and P. Minnhagen
A simple model for self organization of bipartite networks
Europhys. Lett. 67:394 (2004)

P. Minnhagen, M. Rosvall, K. Sneppen and A. Trusina.
Self-organization of structures and networks from merging and small-scale fluctuations
Physica A 340:724 (2004)
cond-mat/0406752