Dr. Pablo Mier

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ORCID iD icon
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[December 2024] I moved to Universidad Pablo de Olavide (Spain). My new email account is pmiemun@upo.es.

The web page of my new research group is this.


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Bio & Research interest
My research is mostly based on low complexity regions and protein evolution. As a result of many of my research projects, I developed dedicated web tools / repositories to give other researchers the opportunity to reuse my codes and data. These are usually focused on being easy-to-use and minimizing the required input data and parameters.

I am accredited in Spain by the National Agency of Assessment, Quality and Certification (ANECA) as:
  • Professor ("Profesor Contratado Doctor"),
  • Assistant lecturer ("Profesor Ayudante Doctor"),
  • Private University Professor ("Profesor de Universidad Privada").
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Tools & Repositories
Developed by me:

In which I participated:
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Publications
Overview
Published 54
(As first author) 28 (+2 with same contribution as first author)
(As last author) 2
(As corresponding author) 28

    2024

  1. Mier P*, Andrade-Navarro MA. Predicting the involvement of polyQ- and polyA in protein-protein interactions by their amino acid context. Heliyon (2024). PMID:39323775.
  2. Mier P*, Andrade-Navarro MA, Morett E. Homorepeat variability within the human population. NAR Genom Bioinform 6(2024), lqae053. PMID:38774515.
  3. Mac Donagh J, Marchesini A, Spiga A, Fallico MJ, Arrias PN, Monzon AM, Vagiona A-C, Goncalves-Kulik M, Mier P, Andrade-Navarro MA. Structured tandem repeats in protein interactions. International Journal of Molecular Sciences 25(2024), 2994. PMID:38474241.

    4. 2023

  4. Mier P*, Andrade-Navarro MA. The nucleotide landscape of polyXY regions. Comput Struct Biotechnol J 21(2023), 5408-5412. PMID:38022702.
  5. Elena Real CA+, Mier P+, Sibille N, Andrade-Navarro MA, Bernadó P. Structure-function relationships in protein homorepeats. Curr Opin Struct Biol 83(2023), 102726. PMID:37924569.
  6. Monzon AM, Arrias PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE*. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol 215(2023), 108023. PMID:37652396.
  7. Mier P*, Andrade-Navarro MA. Evolutionary study of protein Short Tandem Repeats in protein families. Biomolecules 13(2023), 1116. PMID:37509152.
  8. Schumbera E+, Mier P+, Andrade-Navarro MA*. Phase separating Rho: a widespread regulatory function of disordered regions in proteins revealed in bacteria. Signal Transduction and Targeted Therapy 8(2023), 253. PMID:37344523.
  9. Erdozain S, Barrionuevo E, Ripoll L, Mier P, Andrade-Navarro MA. Protein repeats evolve and emerge in giant viruses. Journal of Structural Biology 215(2023), 107962. PMID:37031868.

    10. 2022

  10. Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA*. Functional tuning of intrinsically disordered regions in human proteins by composition bias. Biomolecules 12(2022), 1486. PMID:36291695.
  11. Mier P*, Andrade-Navarro MA. Regions with two amino acids in protein sequences: a step forward from homorepeats into the low complexity landscape. Comput Struct Biotechnol J 20(2022), 5516-5523. PMID:36249567.
  12. Mier P*, Elena-Real C, Cortés J, Bernadó P, Andrade-Navarro MA. The sequence context in poly-Alanine regions: Structure, function and conservation. Bioinformatics 38(2022), 4851-4858. PMID:36106994.
  13. Goncalves-Kulik M, Mier P, Kastano K, Cortés J, Bernadó P, Schmid F, Andrade-Navarro MA*. Low complexity induces structure in protein regions predicted as intrinsically disordered. Biomolecules 12(2022), 1098. PMID:36008992.
  14. Vagiona AC, Mier P, Petrakis S, Andrade-Navarro MA*. Analysis of Huntington’s disease modifiers using the hyperbolic mapping of the protein interaction network. Int J Mol Sci 10(2022), 5853. PMID:35628660.
  15. Mier P*, Fontaine JF, Stoldt M, Libbrecht R, Martelli C, Foitzik S, Andrade-Navarro MA. Annotation and analysis of 3902 odorant receptor protein sequences from 21 insect species provide insights into the evolution of odorant receptor gene families in solitary and social insects. Genes 13(2022), 919. PMID:35627304.
  16. Mier P* and Andrade-Navarro MA. PolyX2: fast detection of homorepeats in large protein datasets. Genes 13(2022), 758. PMID:35627143.

    17. 2021

  17. Mier P* and Andrade-Navarro MA. Between Interactions and Aggregates: The PolyQ Balance. Genome Biology and Evolution 13(2021), evab246. PMID:34791220.
  18. Kamel M, Kastano, Mier P, Andrade-Navarro MA*. REP2: a web server to detect common tandem repeats in protein sequences. Journal of Molecular Biology 433(2021), 166895. PMID:33972020.
  19. Mier P* and Andrade-Navarro MA. The conservation of low complexity regions in bacterial proteins depends on the pathogenicity of the strain and subcellular location of the protein. Genes 12(2021), 451. PMID:33809982.
  20. Mier P* and Andrade-Navarro MA. Avoided Motifs: short amino acid strings missing from protein datasets. Biological Chemistry 402(2021), 945-951. PMID:33660494.
  21. Kastano K, Mier P, Andrade-Navarro MA*. The role of low complexity regions in protein interaction modes: an illustration in Huntingtin. International Journal of Molecular Sciences 22(2021), 1727. PMID:33572172.

    22. 2020

  22. Mier P* and Andrade-Navarro MA. Assessing the low complexity of protein sequences via the low complexity triangle. PLoS ONE (2020). doi: 10.1371/journal.pone.0239154. PMID:33378336.
  23. Rubio A, Mier P, Andrade-Navarro MA, Garzón A, Jiménez J, Pérez-Pulido AJ*. CRISPR sequences are sometimes erroneously translated and can contaminate public databases with spurious proteins containing spaced repeats. Database (2020). doi: 10.1093/database/baaa088. PMID:33206958.
  24. Kastano K, Erdős G, Mier P, Alanis-Lobato G, Promponas VJ, Dosztányi Z, Andrade-Navarro MA*. Evolutionary study of disorder in protein sequences. Biomolecules 10(2020), 1413. PMID:33036302.
  25. Paladin L, Necci M, Piovesan D, Mier P, Andrade-Navarro MA, Tosatto SCE*. A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication. J Struct Biol 212(2020), 107608. PMID:32896658.
  26. Mier P* and Andrade-Navarro MA. The features of polyglutamine regions depend on their evolutionary stability. BMC Evol Biol 20(2020), 59. PMID:32448113.
  27. Mier P* and Andrade-Navarro MA. MAGA: A Supervised Method to Detect Motifs From Annotated Groups in Alignments. Evol Bioinform Online 16(2020). PMID:32425492.
  28. Jarnot P, Ziemska-Legiecka J, Dobson L, Merski M, Mier P, Andrade-Navarro M.A., Hancock J.M., Dosztanyi Z, Paladin L, Necci M, Piovesan D, Tosatto S.C.E., Promponas V.J., Grynberg M., Gruca A*. PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins. Nucleic Acids Res 48(2020), W77-W84. PMID:32421769.
  29. Urbanek A, Popovic K, Morató A, Estaña A, Elena-Real CA, Mier P, Fournet A, Allemand F, Delbecq S, Andrade-Navarro MA, Cortés J, Sibille N, Bernadó P*. Flanking Regions Determine the Structure of the Poly-Glutamine in Huntingtin through Mechanisms Common among Glutamine-Rich Human Proteins. Structure 28(2020), 733-746. PMID:32402249.
  30. Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY*. The 18S ribosomal RNA m6A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 21(2020), e49443. PMID:32350990.
  31. Mier P, Elena Real C, Urbanek A, Bernadó P, Andrade-Navarro MA*. The importance of definitions in the study of polyQ regions: a tale of thresholds, impurities and sequence context. Comput Struct Biotechnol J 18(2020), 306-313. PMID:32071707.
  32. Mier P*, Paladin L, Tamana S, Petrosian S, Hajdu-Soltész B, Urbanek A, Gruca A, Plewczynski D, Grynberg M, Bernadó P, Gáspári Z, Ouzounis C, Promponas VJ, Kajava AV, Hancock JM, Tosatto SCE, Dosztanyi Z, Andrade-Navarro MA. Disentangling the complexity of low complexity proteins. Brief Bioinform 21(2020), 458-472. PMID:30698641.

    33. 2019

  33. Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D*. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 47(2019), 10994-11006. PMID:31584084.
  34. Brown P, RELISH Consortium, Zhou Y*. Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database (2019), 1-67. PMID:33326193.
  35. Kamel M, Mier P, Tari A, Andrade-Navarro MA*. Repeatability in protein sequences. J Struct Biol 208(2019), 86-91. PMID:31408700.
  36. Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jiménez J, Pérez-Pulido AJ*. AnABlast, re-searching for protein-coding sequences in genomic regions. Methods Mol Biol 1962(2019), 207-214. PMID:31020562. ISBN: 978-1-4939-9172-3.
  37. Mier P* and Andrade-Navarro MA. Traitpedia: a collaborative effort to gather species traits. Bioinformatics 35(2019), 1079-1081. PMID:30165582.
  38. Mier P* and Andrade-Navarro MA. Toward completion of the Earth’s proteome: an update a decade later. Brief Bioinform 20(2019), 463:470. PMID:29040399.

    39. 2018

  39. Mier P*, Pérez-Pulido AJ, Andrade-Navarro MA. Automated selection of homologs to track the evolutionary history of proteins. BMC Bioinform 1(2018), 431. PMID:30453878.
  40. Alanis-Lobato G*, Mier P, Andrade-Navarro MA*. The latent geometry of the human protein interaction network. Bioinformatics 34(2018), 2826-2834. PMID:29635317.
  41. Mier P* and Andrade-Navarro MA. Glutamine codon usage and polyQ evolution in primates depend on the Q stretch length. Genome Biol Evol 10(2018), 816-825. PMID:29608721.
  42. Brüne D, Andrade-Navarro MA, Mier P*. Proteome-wide comparison between the amino acid composition of domains and linkers. BMC Res Notes 11(2018). PMID:29426365.

    43. 2017

  43. Totzeck F, Andrade-Navarro MA, Mier P*. The Protein Structure Context of PolyQ Regions. PLoS ONE 12(2017): e0170801. PMID:28125688.
  44. Mier P*, Alanis-Lobato G, Andrade-Navarro MA. Context characterization of amino acid homorepeats using evolution, position, and order. Proteins: Structure, Function and Bioinformatics 85(2017), 709-719. PMID:28097686.
  45. Mier P*, Pérez-Pulido AJ, Reynaud EG, Andrade-Navarro MA. Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family. PLoS ONE 12(2017): e0169750. PMID:28072865.
  46. Mier P* and Andrade-Navarro MA. dAPE: a web server to detect homorepeats and follow their evolution. Bioinformatics 33(2017), 1221-1223. PMID:28031183.
  47. Mier P*, Alanis-Lobato G, Andrade-Navarro MA. Protein-protein interactions can be predicted using coiled coil co-evolution patterns. Journal of Theoretical Biology 412(2017), 198-203. PMID:27832945.

    48. 2016

  48. Alanis-Lobato G*, Mier P, Andrade-Navarro MA. Manifold learning and maximum likelihood estimation for hyperbolic network embedding. Applied Network Science 1(2016). PMID:30533502.
  49. Alanis-Lobato G*, Mier P, Andrade-Navarro MA. Efficient embedding of complex networks to hyperbolic space via their Laplacian. Scientific Reports 6(2016). PMID:27445157.
  50. Mier P* and Andrade-Navarro MA. CABRA: Cluster and Annotate Blast Results Algorithm. BMC Res Notes 9(2016). PMID:27129717.
  51. Mier P* and Andrade-Navarro MA. FastaHerder2: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases. Journal of Computational Biology 23(2016), 270-278. PMID:26828375.

    52. 2015

  52. Mier P, Andrade-Navarro MA, Pérez-Pulido AJ*. orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins. PLoS ONE 10(2015): e0143906. PMID:26624019.

    53. 2012

  53. Muñoz-Centeno MC, Martín-Guevara C, Flores A, Pérez-Pulido A, Antúnez-Rodríguez C, Castillo A, Sánchez-Durán M, Mier P, Bejarano E*. Mpg2 interacts and cooperates with Mpg1 to maintain yeast glycosylation. FEMS Yeast Research 12(2012), 511-520. PMID:22416758.
  54. Mier P, Pérez-Pulido AJ*. Fungal Smn and Spf30 homologues are mainly present in filamentous fungi and genomes with many introns: Implications for Spinal Muscular Atrophy. Gene 491(2012), 135-141. PMID:22020225.
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(Co-)/Organization of scientific events
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Editorial work
  • Editorial Board Member of journal BMC Methods. ISSN 3004-8729, June 2024 – current.
  • Editorial Board Member of journal BMC Bioinformatics. ISSN 1471-2105, March 2024 – June 2024.
  • Guest Editor of Special Issue Bioinformatics in Protein Evolution, in journal Biomolecules. ISSN 2218-273X, June 2023.
  • Reviewer Board Member of journal BioTech. ISSN 2673-6284, June 2022 – current.
  • Associate editor of number 2 of journal Biosaia. ISSN 2254-3821, April 2013.
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Teaching
  • [2015-2024] Support for teaching of protein bioinformatics. Johannes Gutenberg University (Mainz, Germany).
  • [2019-2024] Professor of subject “Linux operating system and high-performance computing”. Postgraduate course “Diploma of Specialization in Bioinformatics Analysis”. Universidad Pablo de Olavide (Seville, Spain).
  • [2015-2017, 2019-2024] Professor of subject “Handling molecular sequences”. Postgraduate course “Diploma of Specialization in Bioinformatics Analysis”. Universidad Pablo de Olavide (Seville, Spain).
  • [2015-2017] Professor of subject “Gene functional annotation and biological enrichment”. Postgraduate course “Diploma of Specialization in Bioinformatics Analysis”. Universidad Pablo de Olavide (Seville, Spain).
  • [2011-2013] Professor of subject “Bioinformatics”. Bachelor degree: Biotechnology. Universidad Pablo de Olavide (Seville, Spain).
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Education
  • [2020] Entry-Level Python Programmer, certified by the Python Institute. Exam Version: PCEP-30-01 [NP]. Digital certification.
  • [2013-2014] PhD in “Bioinformatics in Biotechnology and Biomedicine”. Dissertation title: “Development of biocomputing protocols and tools for the search of orthologous proteins and its application in evolutionary analyses”.
  • [2011-2013] M.Sc. degree in “Health Biotechnology”. Universidad Pablo de Olavide (Seville, Spain). Grades: 9.3/10.
  • [2006-2011] B.Sc. degree in "Biotechnology". Universidad Pablo de Olavide (Seville, Spain). Grades: 8.23/10.
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Languages

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