Publications
Articles submitted for peer-review, arXiv publications and abstracts/presentations are not included here.
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Journal Publications
Wang, J., Li, J., Hou, Y., Dai, W., Xie, R., Marquez-Lago, T.T., Leier, A., Zhou, T., Torres, V., Hay, I., Stubenrauch, C., Zhang, Y., Song, J., Lithgow, T. (2021).
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria
Nucleic Acids Research gkaa899
Wang, Y., Li, F., Bharathwaj, M., Rosas, N.C., Leier, A., Akutsu, T., Webb, G.I., Marquez-Lago, T.T., Li, J., Lithgow, T., Song, J. (2021).
DeepBL: a deep learning method for in silico discovery of betalactamases.
Briefings in Bioinformatics bbaa301
Boi, S.K., Orlandella, R.M., Gibson, J.T., Turbitt, W.J., Wald, G., Thomas, L., Rosean, C.B., Norris, K.E., Bing, M., Bertrand, L., Gross, B.P., Makkouk, A., Starenki, D., Farag, K.I., Sorge, R.E., Brown, J.A., Gordetsky, J., Yasin, H., Garje, R., Nandagopal, L., Weiner, G.J., Lubaroff, D.M., Arend, R.C., Li, P., Zakharia, Y., Yang, E., Salem, A.K., Nepple, K., Marquez-Lago, T.T., Norian, L.A. (2020)
Obesity diminishes response to PD-1-based immunotherapies in renal cancer
J Immunotherapy Cancer 8(2): e000725
Chen, Z., Zhao, P., Li, F., Marquez-Lago, T.T., Leier, A., Revote, J., Powell, D.R., Akutsu, T., Webb, G.I., Smith, I.A., Chou, K-C, Daly, R.J., Song, J. (2020)
iLearn: An integrated platform and meta-learner for feature engineering, machine learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings in Bioinformatics bbz041
Wang, J.*, Yang, B.*, An, Y.*, Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G.I., Strugnell, R.A., Song, J., Lithgow, T. (2019)
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches
Briefings in Bioinformatics. bbx164
*Co-first authors
Li, F., Wang, Y., Li, C., Marquez-Lago, T.T., Leier, A., Rawlings, N.D., Haffari, G., Revote, J., Akutsu, T., Chou, K.C., Purcell, A.W., Pike, R.N., Webb, G.I., Smith, A.I., Lithgow, T., Daly, R.J., Whisstock, J.C. and Jiangning Song (2019)
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods
Briefings in Bioinformatics
Botta, D., Fuller, M.J., Marquez-Lago, T.T., Bachus, H., Bradley, J.E., Weinmann, A.S., Zajac, A.J., Randall, T.D., Lund, F.E., Leon, B., Ballesteros-Tato A. (2017)
Dynamic regulation of T follicular regulatory cell responses by interleukin 2 during influenza infection.
Nature Immunology 18, 1249-1260
Song, J., Wang, H., Wang, J., Leier, A., Marquez-Lago, T., Yang, B., Zhang, Z., Akutsu, T., Webb, G., Daly R. (2017)
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection.
Scientific Reports 7:6862
Buono, R.A. , Leier, A. , Paez-Valencia, J., Pennington, J.G., Goodman, K., Miller, N., Ahlquist, P., Marquez-Lago, T. and Otegui M. (2017)
ESCRT-mediated vesicle concatenation in plant endosomes.
J. Cell Biol. Vol 216, No. 7
** Article featured in JCB Research Highlights
Faculty of 1000 rated: Link
Boettcher, B. *, Marquez-Lago, T. *, Bayer, M., Weiss, E., Barral, Y. (2012)
Nuclear envelope morphology constrains diffusion and promotes asymmetric protein segregation in closed mitosis.
J. Cell Biol. Vol. 197, Number 7: 921-937
** Article featured in JCB Research Highlights
Article included in JCB's most-read list
Faculty of 1000 rated: Link
* Co-first authors
Marquez-Lago, T., Leier, A., and Burrage, K. (2012)
Anomalous diffusion and multifractional Brownian motion: simulating molecular crowding and physical obstacles in Systems Biology.
IET Systems Biology 6(4):134-142
** Article appearing in special issue (Modelling Noise in Biochemical Reaction Networks)
Leier, A., and Marquez-Lago, T. (2011)
Correction factors for boundary diffusion and bimolecular reactions in reaction-diffusion master equations.
J. Chem. Phys. 135, 134109
** Article selected for JCP focus in Biochemical Physics, Volume 5, Issue 10: Link
Marquez-Lago, T., Allen, D.M. and Thewalt, J. (2010)
A novel approach to modelling water transport and drug diffusion through the stratum corneum.
Theoretical Biology and Medical Modelling 7:33
Marquez-Lago, T., and Stelling, J. (2010)
Counter-intuitive stochastic behavior of simple gene circuits with negative feedbacks.
Biophysical J. 98(9):1742-1750
** Article commented in Nature (News and Views): PDF link
Tigges, M., Marquez-Lago, T., Stelling, J. and Fussenegger, M. (2009)
A tunable synthetic mammalian oscillator.
Nature 457: 309-312
** Article featured in Nature (News and Views): PDF link
Nature podcast: 15 January 2009. Link
Nature webfocus (Synthetic systems biology). Link
Faculty of 1000 rated: Link
Leier, A., Marquez-Lago, T., Burrage, K. (2008)
Generalized binomial tau-leap method for biochemical processes incorporating both delay and intrinsic noise.
J. Chem. Phys. 128, 205107
** Article selected for JCP focus in Biochemical Physics, Volume 2, Issue 5: Link
Marquez-Lago, T., Burrage, K. (2007)
Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.
J. Chem. Phys. 127, 104101
** Article selected for JCP focus in Biochemical Physics, Volume 1, Issue 9: Link
Book Chapters
Keeling, K.M., Leier, A., Bedwell, D.M., Chen A.T., Kesterson, R.A. Marquez-Lago, T.T., Muller, U.F., Zhou, J., Popplewell, L., and Wallis, D. (2022)
Targeted Therapeutics for Rare Disorders. In: Comprehensive Precision Medicine (Elsevier).
Chen, Z., Liu, X., Li, F., Li C., Marquez-Lago, T.T., Leier, A., Webb, G.I., Xu, D., Akutsu, T., and Song, J. (2022)
Systematic Characterization of Lysine Post-Translational Modification sites Using MUscADEL. In: Computational Methods for Predicting Post-Translational Modification Sites (Springer).
Burrage, K., Burrage, P., Leier, A. and Marquez-Lago, T.T. (2017)
A review of stochastic and delay simulation approaches in both time and space in Computational Cell Biology. In Stochastic Dynamical Systems in Cellular Biology: Multiscale modeling, asymptotics and numerical methods (Springer). Holcman, D. (Ed.) > In press
Burrage, K., Burrage, P., Leier, A., Marquez-Lago, T.T. and Nicolau, D.V. (2011)
Stochastic simulation for spatial modelling of dynamic processes in a living cell. In Design and Analysis of Bio-molecular Circuits (Springer Verlag). Koeppl, H., Setti, G. di Bernardo, M. and Densmore, D. (Eds.) > PDF link
Marquez-Lago, T.T. and Marchisio M.A. (2010)
Synthetic Biology: dynamic modeling and construction of cell systems. In Dynamic Process Modelling (Wiley-VCH). Banga, J., Georgiadis, M. and Pistikopoulos, S. (Eds.) > PDF link
Barrio, M., Burrage, K., Burrage, P., Leier, A. and Marquez-Lago, T. (2009)
Computational Approaches for Modeling Intrinsic Noise and Delays in Genetic Regulatory Networks. In Computational Methodologies in Gene Regulatory Networks. Das, S., Caragea, D., Hsu, W. H. and Welch, S. M. (Eds.). > PDF link
Lopez-Aguilar, F., Marquez-Lago, T. (2007)
El colapso de un altepetl. Trayectoria de Itzmiquilpan despues de la conquista. In Antropologia Fractal. Lopez Aguilar, F., Brambila Paz, F. (Eds.), pp. 141-164.CIMAT and Sociedad Matematica Mexicana (first edition), Insituto Nacional de Antropologia e Historia (second edition).
Conference Proceedings
Xu, Y., Leier, A., Marquez-Lago, T.T., Xie, J., Whisstock, J., Wilson, C., Song, J. (2020)
Explainable prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning
American Medical Informatics Association (AMIA) Proceedings > PDF link
Xu, Y., Wilson, C., Leier, A., Marquez-Lago, T.T., Whisstock, J., Song, J. (2020)
PhosTransfer: a deep transfer learning-based predictor for phosphorylation sites in hierarchy
Proceedings of thee Pacific-Asia Conference on Knowledge Discovery and Data Mining > PDF link
Burrage, K., Lythe, G., Marquez-Lago, T.T.* (2020)
Recent developments in mathematical and computational biomedicine
BIRS bulletin > PDF link
Marquez-Lago, T.T.* (2020)
Bioengineering human milk through the metabolomemicrobiome, AI and the Chemical Master Equation
American Institute of Physics Conference Proceedings > PDF link
Xu, Y., Wilson, C., Leier, A., Marquez-Lago, T.T., Whisstock, J., Song, J. (2020)
PhosTransfer: a deep transfer learning-based predictor for phosphorylation sites in hierarchy.
Proceedings of the Pacific-Asia Conference on Knowledge Discovery and Data Mining > PDF link
Burrage, K., Burrage, P., Leier, A., Marquez-Lago, T. (2008)
Stochastic delay models for molecular clocks and somite formation.
Proc. SPIE. Complex Systems II, 68020Z, Vol. 6802 > PDF link
Leslie, K.K., Marquez-Lago, T., Slepoy, A., Plimpton, S., Oliver, J., and Steinberg, S. (2005)
ChemCell mathematical modeling defines a biologically relevant lower limit of progesterone receptors in endometrial cancer. Reproductive Sciences, Vol. 12: pp. 22A - 82A.
Bohun, S. et al. (2001)
Modelling InSb Czochralski Growth.
Proc. 5th PIMS-IPSW > PDF link
Anderson, P. et al. (2001)
Locating watchtowers in terrains.
Proc. 4th PIMS-GIMMC > PDF link