Selected publications

Articles submitted for peer-review, arXiv publications and abstracts/presentations are not included here.

List includes UAB SOM team and Lab head publications prior to UAB.

* Click on image to access publication *

Journal Publications

Smith, M.D., Seleme, M., Marquez-Lago, T.T., Chen J-W., Mach, M., Britt, W.J. (2025).

Early control of cochlear viral load limits cochlear inflammation and prevents virus-induced sensorineural hearing loss

Journal of Neuroinflammation 22:92

Weiner, E., Berryman, E., Frey, F., Gonzalez-Solis, A., Leier, A., Marquez-Lago, T.T., Saric A., Otegui, M.S.., (2024).

Endosomal membrane budding patterns in plants

PNAS 121(44) e2409407121

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., Wallis, D. (2024).

Targeted therapeutics for rare disorders

Comprehensive Precision Medicine 1: 249-271

Chen, C., Jiang, J., Tejeshwar, C.R., Marquez-Lago, T.T., Frank S.J., Leier, A., (2023).

A role for JAK2 in mediating cell surface GHR-PRLR interaction

eLife 89890.1

Chen, J-W., Shrestha, L., Green, G., Leier, A., Marquez-Lago, T.T. (2023).

The hitchhikers' guide to RNA sequencing and functional analysis

Briefings in Bioinformatics bbac529

Marquez-Lago, T.T., Steinberg, S. (2022).

Stochastic model of ERK-mediated progesterone receptor translocation, clustering and transcriptional activity

Scientific Reports 12: 11791

Chen, J., Li, F., Wang, M., Li, J., Marquez-Lago, T.T., Leier, A., Revote, J., Li, S., Liu, Q., Song, J., Lithgow, T. (2022).

BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data

Frontiers in Big Data Volume 4

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

Xu, J., Li, F., Leier, A., Xiang, D., Shen, H., Marquez Lago, T.T, Li, J., Yu, D., Song, J. (2021)

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides

Briefings in Bioinformatics bbaa083

Zhang, Y., Sun, Y., Wang, J., Marquez-Lago, T.T., Leier, A., Xie, R., Jiang, Q., Lithgow, T., Song, J. (2021)

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

Briefings in Bioinformatics bbaa125

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

Leier, A., Bedwell D.M., Chen, A.T., Dickson, G., Keeling, K.M., Kesterson, R.A., Korf, B.R., Marquez-Lago, T.T., Müller, U.F., Popplewell, L., Zhou, J., Wallis, D. (2020)

Mutation Directed Therapeutics for Neurofibromatosis Type I

Molecular Therapy-Nucleic Acids Vol 20: 739-753

Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T.T., Wang, Y., Webb, G.I., Baggag, A., Bensmail, H., Song, J. (2020)

PROSPECT: a web server for predicting protein histidine phosphorylation sites in bacteria

Journal of Bioinformatics and Computational Biology

Li, F., Leier, A., Liu, Q., Wang, Y., Xiang, D., Akutsu, T., Webb, G.I., Smith, A.I., Marquez-Lago, T.T.*, Song, J.* (2020)

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information

Genomics, Proteomics & Bioinformatics 18(1): 52-64

Li, F., Chen, J., Leier, A., Marquez-Lago, T.T., Liu, Q., Revote, J., Wang, Y., Akutsu, T., Smith, A.I., Webb, G.I., Kurgan, L., Song, J. (2020)

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.

Bioinformatics btz721

Zhang, Y., Yu, F., Xie, R., Li, J., Leier, A., Marquez-Lago, T.T., Akustsu, T., Smith. A.I., Ge, Z., Wang, J., Lithgow, T., Song, J. (2020)

PenGaRoo: a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.

Bioinformatics btz629

Li, F., Fan, C., Marquez-Lago, T.T., Leier, A., Revote, J., Jia, C., Wei, L., Smith, I.A., Chou, K-C, Liu, Q., Song, J. (2020)

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.

Briefings in Bioinformatics bbz050

Mei, S., Li, F., Marquez-Lago, T.T., Leier, A., Giam, K., Croft, N.P., Smith, I.A., Chou, K-C, Rossjohn, J., Li, J., Purcell, A.W., Song, J. (2020)

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide binding prediction.

Briefings in Bioinformatics bbz051

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

Zhang, M., Li, F., Marquez-Lago, T.T., Leier, A., Fan, C., Kwoh, C.K. Chou, K-C., Song, J., Jia, C. (2019)

MULTiPLy: a novel multi-layer predictor for discovering general and specific types of promoters

Bioinformatics btz016

Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T.T., Leier, A., Hayashida, M., Akutsu, T., Zhang, J., Chou, K-C, Selkrig, J., Zhou, T., Song, J. and Trevor Lithgow (2019)

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

Bioinformatics

Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T.T., Leier, A., Akutsu, T., Smith, I., Webb, G.I., Li, L., Chou, K-C and Jiangning Song (2019)

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Briefings in Bioinformatics

Bachus, H., Kaur, K., Papilllon, A.M., Marquez-Lago, T.T., Yu, Z., Ballesteros-Tato, A., Matalon, S. and Beatriz Leon (2019)

Impaired Tumor-Necrosis-Factor-alpha-driven Dendritic Cell Activation Limits Lipopolysaccharide-Induced Protection from Allergic Inflammation in Infants

Immunity 50:1-16

Zhang, Y., Xie, R., Wang, J., Leier, A., Marquez-Lago, T.T., Akutsu, T., Webb, G.I., Chou, K-C and Jiangning Song (2019)

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

Briefings in Bioinformatics

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

Li, F., Li, C., Marquez-Lago, T.T., Leier, A., Akutsu, T., Purcell, A.W., Lithgow, T., Daly, R.J., Song, J. and Kuo-Chen Chou (2018)

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

Bioinformatics 34(24): 4223-4231

Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K-C, Strugnell, R.A., Song, J. and Trevor Lithgow (2018)

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

Bioinformatics bty155

Song, J., Li, F., Leier, A., Marquez-Lago, T.T., Akutsu, T., Haffari, G., Chou, K.C., Webb, G.I., Pike, R.N. (2018)

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

Bioinformatics 34(4): 684–687

An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G.I., Song, J. and Lithgow, T. (2018)

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.

Briefings in Bioinformatics bbw100:1-14

Chen, Z.*, Zhao, P.*, Li, F., Leier, A., Marquez-Lago, T., Wang, Y., Webb, G.I., Daly, R.J., Chou, K-C, Song, J. (2018)

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

Bioinformatics bty 140

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

Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G., Shen H. (2017)

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

Scientific Reports 7:5755

Wang, J., Yang B., Revote J., Leier, A., Marquez-Lago, T., Webb, G.I., Song, J., Chou K-C. and Lithgow, T. (2017)

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

Bioinformatics Vol 33, Issue 17, Pages 2756–2758

You, C., Marquez-Lago, T., Richter, C.P, Wilmes, S., Moraga, I., Garcia, K.C., Leier, A. and Piehler, J. (2016)

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

Science Advances Vol. 2, No. 12, e1600452

Zhou, A., Liu, Y., Chang, Z., Wang, H., Leier, A., Marquez-Lago, T., Ma, Y., Li, J. and Song, J. (2016)

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

Applied Microbiology and Biotechnology Vol. 101, Issue 7, pp 2919

Denton, J., Ghosh, A. and Marquez-Lago, T. (2015)

Asymmetrical inheritance of plasmids depends on dynamic cellular geometry and volume exclusion effects.

PLoS ONE 10(10):e0139443

Ghosh, A. and Marquez-Lago, T. (2015)

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

PLoS ONE 10(7):e0133401

Leier, A. and Marquez-Lago, T. (2015)

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

Proc. Royal Society A 471:20150049

Ghosh, A., Leier, A. and Marquez-Lago, T. (2015)

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

Theoretical Biology and Medical Modelling 12:5

Sanchez-Garduno, F., Miramontes, P. and Marquez-Lago, T. (2014)

Role reversal in a predator-prey interaction.

Royal Society Open Science 1: 140186

Lopez-Caamal, F. and Marquez-Lago, T. (2014)

Order Reduction of the Chemical Master Equation via Balanced Realisation.

PLoS ONE 9(8): e103521

Zavala, E. and Marquez-Lago, T. (2014)

The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis.

PLoS Computational Biology 10(7): e1003725

Lopez-Caamal, F. and Marquez-Lago, T. (2014)

Exact Probability Distributions of Selected Species in Stochastic Chemical Reaction Networks.

Bull. Math. Biol. 76:2334

Leier, A., Barrio, M. and Marquez-Lago, T. (2014)

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

J. Royal Society Interface 11: 20140108

Marquez-Lago, T. and Padilla, P. (2014)

A selection criterion for patterns in reaction-diffusion systems.

Theoretical Biology and Medical Modelling 11:7

Zavala, E. and Marquez-Lago, T. (2014)

Delays Induce Novel Stochastic Effects in Negative Feedback Gene Circuits.

Biophysical J. Vol. 106, Issue 2: 467-478

Barrio, M.*, Leier, A.*, and Marquez-Lago, T.* (2013)

Reduction of chemical reaction networks through delay distributions.

J. Chem. Phys. 138, 104114

* All authors contributed equally

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)

Hatzikirou, H., Chauviere, A., Bauer, A., Leier, A., Lewis, M., Macklin, P., Marquez-Lago, T., Bearer, E., Cristini, V. (2012)

Integrative Physical Oncology.

WIREs Systems Biology and Medicine Vol. 4, Issue 1, Pages 1-14

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. and Leier, A. (2011)

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

BMC Systems Biology 5:22

Lang, M., Marquez-Lago, T., Stelling, J., and Waldherr, S. (2011)

Autonomous synchronization of chemically coupled synthetic oscillators.

Bull. Math. Biol. Vol. 73, Number 11: 2678

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

Marquez-Lago, T., Leier, A., and Burrage, K. (2010)

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

BMC Systems Biology 4:19

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

Leier, A., Marquez-Lago, T., Burrage, K., Burrage, P. (2008)

Modelling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells.

J. Mult. Comp. Eng. Vol. 6, Issue 1: 77-86

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.)

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

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