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Items: 33

1.

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.

Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Yanju Z, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T.

Bioinformatics. 2018 Mar 14. doi: 10.1093/bioinformatics/bty155. [Epub ahead of print]

PMID:
29547915
2.

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences.

Chen Z, Zhao P, Li F, Leier A, Marquez-Lago TT, Wang Y, Webb GI, Smith AI, Daly RJ, Chou KC, Song J.

Bioinformatics. 2018 Mar 8. doi: 10.1093/bioinformatics/bty140. [Epub ahead of print]

PMID:
29528364
3.

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.

Song J, Li F, Leier A, Marquez-Lago TT, Akutsu T, Haffari G, Chou KC, Webb GI, Pike RN, Hancock J.

Bioinformatics. 2018 Feb 15;34(4):684-687. doi: 10.1093/bioinformatics/btx670.

PMID:
29069280
4.

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.

Wang J, Yang B, Revote J, Leier A, Marquez-Lago TT, Webb G, Song J, Chou KC, Lithgow T.

Bioinformatics. 2017 Sep 1;33(17):2756-2758. doi: 10.1093/bioinformatics/btx302.

PMID:
28903538
5.

Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection.

Botta D, Fuller MJ, Marquez-Lago TT, Bachus H, Bradley JE, Weinmann AS, Zajac AJ, Randall TD, Lund FE, León B, Ballesteros-Tato A.

Nat Immunol. 2017 Nov;18(11):1249-1260. doi: 10.1038/ni.3837. Epub 2017 Sep 11.

6.

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.

Wang Y, Song J, Marquez-Lago TT, Leier A, Li C, Lithgow T, Webb GI, Shen HB.

Sci Rep. 2017 Jul 18;7(1):5755. doi: 10.1038/s41598-017-06219-7.

7.

ESCRT-mediated vesicle concatenation in plant endosomes.

Buono RA, Leier A, Paez-Valencia J, Pennington J, Goodman K, Miller N, Ahlquist P, Marquez-Lago TT, Otegui MS.

J Cell Biol. 2017 Jul 3;216(7):2167-2177. doi: 10.1083/jcb.201612040. Epub 2017 Jun 7.

8.

Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.

Zhou Z, Liu Y, Chang Z, Wang H, Leier A, Marquez-Lago TT, Ma Y, Li J, Song J.

Appl Microbiol Biotechnol. 2017 Apr;101(7):2919-2929. doi: 10.1007/s00253-016-7994-6. Epub 2016 Dec 27.

PMID:
28028551
9.

Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling.

You C, Marquez-Lago TT, Richter CP, Wilmes S, Moraga I, Garcia KC, Leier A, Piehler J.

Sci Adv. 2016 Dec 2;2(12):e1600452. eCollection 2016 Dec.

10.

Asymmetrical Inheritance of Plasmids Depends on Dynamic Cellular Geometry and Volume Exclusion Effects.

Denton JA, Ghosh A, Marquez-Lago TT.

PLoS One. 2015 Oct 15;10(10):e0139443. doi: 10.1371/journal.pone.0139443. eCollection 2015.

11.

Delay chemical master equation: direct and closed-form solutions.

Leier A, Marquez-Lago TT.

Proc Math Phys Eng Sci. 2015 Jul 8;471(2179):20150049.

12.

Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries.

Ghosh A, Marquez-Lago TT.

PLoS One. 2015 Jul 31;10(7):e0133401. doi: 10.1371/journal.pone.0133401. eCollection 2015.

13.

Role reversal in a predator-prey interaction.

Sánchez-Garduño F, Miramontes P, Marquez-Lago TT.

R Soc Open Sci. 2014 Oct 1;1(2):140186. doi: 10.1098/rsos.140186. eCollection 2014 Oct.

14.

The Spatial Chemical Langevin Equation and Reaction Diffusion Master Equations: moments and qualitative solutions.

Ghosh A, Leier A, Marquez-Lago TT.

Theor Biol Med Model. 2015 Feb 27;12:5. doi: 10.1186/s12976-015-0001-6.

15.

Exact probability distributions of selected species in stochastic chemical reaction networks.

López-Caamal F, Marquez-Lago TT.

Bull Math Biol. 2014 Sep;76(9):2334-61. doi: 10.1007/s11538-014-9985-z. Epub 2014 Aug 26.

16.

Order reduction of the chemical master equation via balanced realisation.

López-Caamal F, Marquez-Lago TT.

PLoS One. 2014 Aug 14;9(8):e103521. doi: 10.1371/journal.pone.0103521. eCollection 2014.

17.

The long and viscous road: uncovering nuclear diffusion barriers in closed mitosis.

Zavala E, Marquez-Lago TT.

PLoS Comput Biol. 2014 Jul 17;10(7):e1003725. doi: 10.1371/journal.pcbi.1003725. eCollection 2014 Jul.

18.

Exact model reduction with delays: closed-form distributions and extensions to fully bi-directional monomolecular reactions.

Leier A, Barrio M, Marquez-Lago TT.

J R Soc Interface. 2014 Apr 2;11(95):20140108. doi: 10.1098/rsif.2014.0108. Print 2014 Jun 6.

19.

A selection criterion for patterns in reaction-diffusion systems.

Marquez-Lago TT, Padilla P.

Theor Biol Med Model. 2014 Jan 29;11:7. doi: 10.1186/1742-4682-11-7.

20.

Delays induce novel stochastic effects in negative feedback gene circuits.

Zavala E, Marquez-Lago TT.

Biophys J. 2014 Jan 21;106(2):467-78. doi: 10.1016/j.bpj.2013.12.010.

21.

Reduction of chemical reaction networks through delay distributions.

Barrio M, Leier A, Marquez-Lago TT.

J Chem Phys. 2013 Mar 14;138(10):104114. doi: 10.1063/1.4793982.

PMID:
23514472
22.

Anomalous diffusion and multifractional Brownian motion: simulating molecular crowding and physical obstacles in systems biology.

Marquez-Lago TT, Leier A, Burrage K.

IET Syst Biol. 2012 Aug;6(4):134-42. doi: 10.1049/iet-syb.2011.0049.

PMID:
23039694
23.

Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis.

Boettcher B, Marquez-Lago TT, Bayer M, Weiss EL, Barral Y.

J Cell Biol. 2012 Jun 25;197(7):921-37. doi: 10.1083/jcb.201112117. Epub 2012 Jun 18. Erratum in: J Cell Biol. 2012 Jul 9;198(1):143.

24.

Correction factors for boundary diffusion in reaction-diffusion master equations.

Leier A, Marquez-Lago TT.

J Chem Phys. 2011 Oct 7;135(13):134109. doi: 10.1063/1.3634003.

PMID:
21992284
25.

Integrative physical oncology.

Hatzikirou H, Chauviere A, Bauer AL, Leier A, Lewis MT, Macklin P, Marquez-Lago TT, Bearer EL, Cristini V.

Wiley Interdiscip Rev Syst Biol Med. 2012 Jan-Feb;4(1):1-14. doi: 10.1002/wsbm.158. Epub 2011 Aug 18. Review.

26.

Autonomous synchronization of chemically coupled synthetic oscillators.

Lang M, Marquez-Lago TT, Stelling J, Waldherr S.

Bull Math Biol. 2011 Nov;73(11):2678-706. doi: 10.1007/s11538-011-9642-8. Epub 2011 Mar 4.

PMID:
21373974
27.

Stochastic adaptation and fold-change detection: from single-cell to population behavior.

Marquez-Lago TT, Leier A.

BMC Syst Biol. 2011 Feb 3;5:22. doi: 10.1186/1752-0509-5-22.

28.

A novel approach to modelling water transport and drug diffusion through the stratum corneum.

Marquez-Lago TT, Allen DM, Thewalt J.

Theor Biol Med Model. 2010 Aug 17;7:33. doi: 10.1186/1742-4682-7-33.

29.

Counter-intuitive stochastic behavior of simple gene circuits with negative feedback.

Marquez-Lago TT, Stelling J.

Biophys J. 2010 May 19;98(9):1742-50. doi: 10.1016/j.bpj.2010.01.018.

30.

Probability distributed time delays: integrating spatial effects into temporal models.

Marquez-Lago TT, Leier A, Burrage K.

BMC Syst Biol. 2010 Mar 4;4:19. doi: 10.1186/1752-0509-4-19.

31.

A tunable synthetic mammalian oscillator.

Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M.

Nature. 2009 Jan 15;457(7227):309-12. doi: 10.1038/nature07616.

PMID:
19148099
32.

Generalized binomial tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise.

Leier A, Marquez-Lago TT, Burrage K.

J Chem Phys. 2008 May 28;128(20):205107. doi: 10.1063/1.2919124.

PMID:
18513050
33.

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

Marquez-Lago TT, Burrage K.

J Chem Phys. 2007 Sep 14;127(10):104101.

PMID:
17867731

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