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Items: 37

1.

Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Wang J, Li J, Yang B, Xie R, Marquez-Lago TT, Leier A, Hayashida M, Akutsu T, Zhang Y, Chou KC, Selkrig J, Zhou T, Song J, Lithgow T.

Bioinformatics. 2018 Nov 2. doi: 10.1093/bioinformatics/bty914. [Epub ahead of print]

PMID:
30388198
2.

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.

Zhang Y, Xie R, Wang J, Leier A, Marquez-Lago TT, Akutsu T, Webb GI, Chou KC, Song J.

Brief Bioinform. 2018 Aug 24. doi: 10.1093/bib/bby079. [Epub ahead of print]

PMID:
30351377
3.

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.

Li F, Wang Y, Li C, Marquez-Lago TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J.

Brief Bioinform. 2018 Aug 29. doi: 10.1093/bib/bby077. [Epub ahead of print]

PMID:
30184176
4.

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.

Li F, Li C, Marquez-Lago TT, Leier A, Akutsu T, Purcell AW, Smith AI, Lithgow T, Daly RJ, Song J, Chou KC.

Bioinformatics. 2018 Jun 27. doi: 10.1093/bioinformatics/bty522. [Epub ahead of print]

PMID:
29947803
5.

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, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T.

Bioinformatics. 2018 Aug 1;34(15):2546-2555. doi: 10.1093/bioinformatics/bty155.

PMID:
29547915
6.

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 Jul 15;34(14):2499-2502. doi: 10.1093/bioinformatics/bty140.

PMID:
29528364
7.

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
8.

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
9.

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.

10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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
26.

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
27.

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.

28.

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
29.

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.

30.

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
31.

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.

32.

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.

33.

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.

34.

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.

35.

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
36.

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
37.

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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