Publications

1. A method to predict the response to directional selection using a Kalman filter.

Milocco L, Salazar-Ciudad I. Proc Natl Acad Sci U S A. 2022 Jul 12;119(28):e2117916119. doi: 10.1073/pnas.2117916119. Epub 2022 Jul 6. PMID: 35867739 Free PMC article.

2. Evolution of the G Matrix under Nonlinear Genotype-Phenotype Maps.

Milocco L, Salazar-Ciudad I. Am Nat. 2022 Mar;199(3):420-435. doi: 10.1086/717814. Epub 2022 Jan 11. PMID: 35175900

3. Correction: On the evolution and development of morphological complexity: A view from gene regulatory networks.

Hagolani PF, Zimm R, Vroomans R, Salazar-Ciudad I. PLoS Comput Biol. 2021 Dec 10;17(12):e1009686. doi: 10.1371/journal.pcbi.1009686. eCollection 2021 Dec. PMID: 34890397 Free PMC article.

4. Mechano-chemical feedback mediated competition for BMP signalling leads to pattern formation.

Toddie-Moore DJ, Montanari MP, Tran NV, Brik EM, Antson H, Salazar-Ciudad I, Shimmi O. Dev Biol. 2022 Jan;481:43-51. doi: 10.1016/j.ydbio.2021.09.006. Epub 2021 Sep 20. PMID: 34555363 Free article.

5. On the evolution and development of morphological complexity: A view from gene regulatory networks.

Hagolani PF, Zimm R, Vroomans R, Salazar-Ciudad I. PLoS Comput Biol. 2021 Feb 24;17(2):e1008570. doi: 10.1371/journal.pcbi.1008570. eCollection 2021 Feb. PMID: 33626036 Free PMC article.

6. Why call it developmental bias when it is just development?

Salazar-Ciudad I. Biol Direct. 2021 Jan 9;16(1):3. doi: 10.1186/s13062-020-00289-w. PMID: 33422150 Free PMC article.

7. Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps.

Milocco L, Salazar-Ciudad I. Evolution. 2020 Feb;74(2):230-244. doi: 10.1111/evo.13907. Epub 2020 Jan 3. PMID: 31883344

8. Cell signaling stabilizes morphogenesis against noise.

Hagolani PF, Zimm R, Marin-Riera M, Salazar-Ciudad I. Development. 2019 Oct 18;146(20):dev179309. doi: 10.1242/dev.179309. PMID: 31628213

9. Adaptation and Conservation throughout the Drosophila melanogaster Life-Cycle.

Coronado-Zamora M, Salvador-Martínez I, Castellano D, Barbadilla A, Salazar-Ciudad I. Genome Biol Evol. 2019 May 1;11(5):1463-1482. doi: 10.1093/gbe/evz086. PMID: 31028390 Free PMC article.

10. Bracketing phenogenotypic limits of mammalian hybridization.

Savriama Y, Valtonen M, Kammonen JI, Rastas P, Smolander OP, Lyyski A, Häkkinen TJ, Corfe IJ, Gerber S, Salazar-Ciudad I, Paulin L, Holm L, Löytynoja A, Auvinen P, Jernvall J. R Soc Open Sci. 2018 Nov 28;5(11):180903. doi: 10.1098/rsos.180903. eCollection 2018 Nov. PMID: 30564397 Free PMC article.

11. Quantitative Morphological Variation in the Developing Drosophila Wing.

Matamoro-Vidal A, Huang Y, Salazar-Ciudad I, Shimmi O, Houle D. G3 (Bethesda). 2018 Jul 2;8(7):2399-2409. doi: 10.1534/g3.118.200372. PMID: 29844017 Free PMC article.

12. Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study.

Marin-Riera M, Moustakas-Verho J, Savriama Y, Jernvall J, Salazar-Ciudad I. PLoS Comput Biol. 2018 Feb 26;14(2):e1005981. doi: 10.1371/journal.pcbi.1005981. eCollection 2018 Feb. PMID: 29481561 Free PMC article.

13. Mapping Selection within Drosophila melanogaster Embryo's Anatomy.

Salvador-Martínez I, Coronado-Zamora M, Castellano D, Barbadilla A, Salazar-Ciudad I. Mol Biol Evol. 2018 Jan 1;35(1):66-79. doi: 10.1093/molbev/msx266. PMID: 29040697

14. Mechanical constraint from growing jaw facilitates mammalian dental diversity.

Renvoisé E, Kavanagh KD, Lazzari V, Häkkinen TJ, Rice R, Pantalacci S, Salazar-Ciudad I, Jernvall J. Proc Natl Acad Sci U S A. 2017 Aug 29;114(35):9403-9408. doi: 10.1073/pnas.1707410114. Epub 2017 Aug 14. PMID: 28808032 Free PMC article.

15. How complexity increases in development: An analysis of the spatial-temporal dynamics of Gene expression in Ciona intestinalis.

Salvador-Martínez I, Salazar-Ciudad I. Mech Dev. 2017 Apr;144(Pt B):113-124. doi: 10.1016/j.mod.2017.02.001. Epub 2017 Feb 9. PMID: 28189795 Free article.

16. A set of simple cell processes is sufficient to model spiral cleavage.

Brun-Usan M, Marín-Riera M, Grande C, Truchado-Garcia M, Salazar-Ciudad I. Development. 2017 Jan 1;144(1):54-62. doi: 10.1242/dev.140285. Epub 2016 Nov 25. PMID: 27888194

17. Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model.

Marin-Riera M, Brun-Usan M, Zimm R, Välikangas T, Salazar-Ciudad I. Bioinformatics. 2016 Jan 15;32(2):219-25. doi: 10.1093/bioinformatics/btv527. Epub 2015 Sep 5. PMID: 26342230

18. Patterned Anchorage to the Apical Extracellular Matrix Defines Tissue Shape in the Developing Appendages of Drosophila.

Ray RP, Matamoro-Vidal A, Ribeiro PS, Tapon N, Houle D, Salazar-Ciudad I, Thompson BJ. Dev Cell. 2015 Aug 10;34(3):310-22. doi: 10.1016/j.devcel.2015.06.019. Epub 2015 Jul 16. PMID: 26190146 Free PMC article.

19. How complexity increases in development: An analysis of the spatial-temporal dynamics of 1218 genes in Drosophila melanogaster.

Salvador-Martínez I, Salazar-Ciudad I. Dev Biol. 2015 Sep 15;405(2):328-39. doi: 10.1016/j.ydbio.2015.07.003. Epub 2015 Jul 14. PMID: 26187198 Free article.

20. Making quantitative morphological variation from basic developmental processes: Where are we? The case of the Drosophila wing.

Matamoro-Vidal A, Salazar-Ciudad I, Houle D. Dev Dyn. 2015 Sep;244(9):1058-1073. doi: 10.1002/dvdy.24255. Epub 2015 Mar 31. PMID: 25619644 Free PMC article. Review.

21. On the effect of phenotypic dimensionality on adaptation and optimality.

Brun-Usan M, Marin-Riera M, Salazar-Ciudad I. J Evol Biol. 2014 Dec;27(12):2614-28. doi: 10.1111/jeb.12516. Epub 2014 Oct 9. PMID: 25303021 Free article.

22. Replaying evolutionary transitions from the dental fossil record.

Harjunmaa E, Seidel K, Häkkinen T, Renvoisé E, Corfe IJ, Kallonen A, Zhang ZQ, Evans AR, Mikkola ML, Salazar-Ciudad I, Klein OD, Jernvall J. Nature. 2014 Aug 7;512(7512):44-8. doi: 10.1038/nature13613. Epub 2014 Jul 30. PMID: 25079326 Free PMC article.

23. The origin and loss of periodic patterning in the turtle shell.

Moustakas-Verho JE, Zimm R, Cebra-Thomas J, Lempiäinen NK, Kallonen A, Mitchell KL, Hämäläinen K, Salazar-Ciudad I, Jernvall J, Gilbert SF. Development. 2014 Aug;141(15):3033-9. doi: 10.1242/dev.109041. PMID: 25053434

24. Adaptive dynamics under development-based genotype-phenotype maps.

Salazar-Ciudad I, Marín-Riera M. Nature. 2013 May 16;497(7449):361-4. doi: 10.1038/nature12142. Epub 2013 May 1. PMID: 23636325

25. The Causality Horizon and Developmental bases of Morphological Evolution.

Salazar-Ciudad I.* and Jernvall, J. Biol. Theory 8:286-292. doi.org/10.1007/s13752-013-0121-3

26. Evolution in Biological and Non-Biological Systems: The Origins of Life.

Salazar-Ciudad I.*.. Biol. Theory 7:26-37. doi.org/10.1007/s13752-012-0066-y

27. Tooth patterning and evolution.

Salazar-Ciudad I. Curr Opin Genet Dev. 2012 Dec;22(6):585-92. doi: 10.1016/j.gde.2012.10.006. Epub 2012 Dec 19. PMID: 23266218 Review.

28. A two level mutation-selection model of cultural evolution and diversity.

Salazar-Ciudad I. J Theor Biol. 2010 Nov 21;267(2):171-85. doi: 10.1016/j.jtbi.2010.08.021. Epub 2010 Aug 26. PMID: 20800601

29. A computational model of teeth and the developmental origins of morphological variation.

Salazar-Ciudad I, Jernvall J. Nature. 2010 Mar 25;464(7288):583-6. doi: 10.1038/nature08838. Epub 2010 Mar 10. PMID: 20220757

30. Morphological evolution and embryonic developmental diversity in metazoa.

Salazar-Ciudad I. Development. 2010 Feb;137(4):531-9. doi: 10.1242/dev.045229. PMID: 20110318 Review.

31. Looking at the origin of phenotypic variation from pattern formation gene networks.

Salazar-Ciudad I. J Biosci. 2009 Oct;34(4):573-87. doi: 10.1007/s12038-009-0075-6. PMID: 19920342 Free article. Review.

32. Evolution in biological and nonbiological systems under different mechanisms of generation and inheritance.

Salazar-Ciudad I. Theory Biosci. 2008 Nov;127(4):343-58. doi: 10.1007/s12064-008-0052-x. Epub 2008 Oct 23. PMID: 18946696

33. Tooth morphogenesis in vivo, in vitro, and in silico.

Salazar-Ciudad I. Curr Top Dev Biol. 2008;81:341-71. doi: 10.1016/S0070-2153(07)81012-X. PMID: 18023734 Review.

34. On the origins of morphological variation, canalization, robustness, and evolvability.

Salazar-Ciudad I. Integr Comp Biol. 2007 Sep;47(3):390-400. doi: 10.1093/icb/icm075. Epub 2007 Jul 26. PMID: 21672847

35. The economy of tinkering mammalian teeth.

Jernvall J, Salazar-Ciudad I. Novartis Found Symp. 2007;284:207-16; discussion 216-24. doi: 10.1002/9780470319390.ch14. PMID: 17710855 Review.

36. Commonalities in fly embryogenesis and mammalian pituitary patterning.

Veitia RA, Salazar-Ciudad I. Trends Endocrinol Metab. 2007 Sep;18(7):261-5. doi: 10.1016/j.tem.2007.08.002. Epub 2007 Aug 10. PMID: 17693094 Review.

37. Continuous tooth generation in mouse is induced by activated epithelial Wnt/beta-catenin signaling.

Järvinen E, Salazar-Ciudad I, Birchmeier W, Taketo MM, Jernvall J, Thesleff I. Proc Natl Acad Sci U S A. 2006 Dec 5;103(49):18627-32. doi: 10.1073/pnas.0607289103. Epub 2006 Nov 22. PMID: 17121988 Free PMC article.

38.On the origins of morphological disparity and its diverse developmental bases.

Salazar-Ciudad I. Bioessays. 2006 Nov;28(11):1112-22. doi: 10.1002/bies.20482. PMID: 17041901

39. Developmental constraints vs. variational properties: How pattern formation can help to understand evolution and development.

Salazar-Ciudad I. J Exp Zool B Mol Dev Evol. 2006 Mar 15;306(2):107-25. doi: 10.1002/jez.b.21078. PMID: 16254986 Review.

40. Graduality and innovation in the evolution of complex phenotypes: insights from development.

Salazar-Ciudad I, Jernvall J. J Exp Zool B Mol Dev Evol. 2005 Nov 15;304(6):619-31. doi: 10.1002/jez.b.21058. PMID: 16032700

41. How different types of pattern formation mechanisms affect the evolution of form and development.

Salazar-Ciudad I, Jernvall J. Evol Dev. 2004 Jan-Feb;6(1):6-16. doi: 10.1111/j.1525-142x.2004.04002.x. PMID: 15108813

42. Mechanisms of pattern formation in development and evolution.

Salazar-Ciudad I, Jernvall J, Newman SA. Development. 2003 May;130(10):2027-37. doi: 10.1242/dev.00425. PMID: 12668618 Review.

43. A gene network model accounting for development and evolution of mammalian teeth.

Salazar-Ciudad I, Jernvall J. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8116-20. doi: 10.1073/pnas.132069499. Epub 2002 Jun 4. PMID: 12048258 Free PMC article.

44. Phenotypic and dynamical transitions in model genetic networks. II. Application to the evolution of segmentation mechanisms.

Salazar-Ciudad I, Solé RV, Newman SA. Evol Dev. 2001 Mar-Apr;3(2):95-103. doi: 10.1046/j.1525-142x.2001.003002095.x. PMID: 11341678

45. Phenotypic and dynamical transitions in model genetic networks. I. Emergence of patterns and genotype-phenotype relationships.

Salazar-Ciudad I, Newman SA, Solé RV. Evol Dev. 2001 Mar-Apr;3(2):84-94. doi: 10.1046/j.1525-142x.2001.003002084.x. PMID: 11341677

46. Gene network dynamics and the evolution of development.

Solé RV, Salazar-Ciudad I I, Newman SA. Trends Ecol Evol. 2000 Dec 1;15(12):479-480. doi: 10.1016/s0169-5347(00)02000-0. PMID: 11114427 No abstract available.

47. Gene networks capable of pattern formation: from induction to reaction-diffusion.

Salazar-Ciudad I, Garcia-Fernández J, Solé RV. J Theor Biol. 2000 Aug 21;205(4):587-603. doi: 10.1006/jtbi.2000.2092. PMID: 10931754