publications
brain
biology & dysfuntion
Huang WC, Peng Z, Murdock MH, Liu L, Mathys H, Davila-Velderrain J, Jiang X, Chen M, Ng AP, Kim T, Abdurrob F. Lateral mammillary body neurons in mouse brain are disproportionately vulnerable in Alzheimer’s disease. Science Translational Medicine. 2023 Apr 19;15(692):eabq1019.
Blanchard JW*, Akay LA*, Davila-Velderrain J*, von Maydell D*, Mathys H, Davidson SM, Effenberger A, Chen CY, Maner-Smith K, Hajjar I, Ortlund EA. APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes. Nature. 2022 Nov 16:1-1. *equal contribution
Welch GM, Boix CA, Schmauch E, Davila-Velderrain J, Victor MB, Dileep V, Bozzelli PL, Su Q, Cheng JD, Lee A, Leary NS. Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration. Science Advances. 2022 Sep 28;8(39):eabo4662.
Singh N, Benoit MR, Zhou J, Das B, Davila-Velderrain J, Kellis M, Tsai LH, Hu X, Yan R. BACE-1 inhibition facilitates the transition from homeostatic microglia to DAM-1. Science Advances. 2022 Jun 17;8(24):eabo1286.
Barker SJ, Raju RM, Milman NE, Wang J, Davila-Velderrain J, Gunter-Rahman F, Parro CC, Bozzelli PL, Abdurrob F, Abdelaal K, Bennett DA. MEF2 is a key regulator of cognitive potential and confers resilience to neurodegeneration. Science translational medicine. 2021 Nov 3;13(618):eabd7695.
Lee H, Fenster RJ, Pineda SS, Gibbs WS, Mohammadi S, Davila-Velderrain J, Garcia FJ, Therrien M, Novis HS, Gao F, Wilkinson H. Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation. Neuron. 2020 Jul 17.
Blanchard JW, Bula M, Davila-Velderrain J, Akay LA, Zhu L, Frank A, Victor MB, Bonner JM, Mathys H, Lin YT, Ko T. Reconstruction of the human blood–brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. Nature Medicine. 2020 Jun 8:1-2.
Marco A, Meharena HS, Dileep V, Raju RM, Davila-Velderrain J, Zhang AL, Adaikkan C, Young JZ, Gao F, Kellis M, Tsai LH. Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble. Nature neuroscience. 2020 Dec;23(12):1606-17.
Mathys H*, Davila-Velderrain J*, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature. 2019 Jun 20;570(7761):332-7. *equal contribution
single-cell
biology
Mohammadi S*, Davila-Velderrain J*, Kellis M. A multiresolution framework to characterize single-cell state landscapes. Nature communications. 2020 Oct 26;11(1):5399. *equal contribution
Mohammadi S*, Davila-Velderrain J*, Kellis M. Reconstruction of cell-type-specific interactomes at single-cell resolution. Cell systems. 2019 Dec 18;9(6):559 *equal contribution
He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Communications biology. 2021 May 26;4(1):629.
Menon M*, Mohammadi S*, Davila-Velderrain J*, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nature communications. 2019 Oct 25;10(1):4902. *equal contribution
systems
biology
Dávila-Velderrain J, Caldú-Primo JL, Martínez-García JC, Álvarez-Buylla Roces ME. Gene Regulatory Network Dynamical Logical Models for Plant Development Plant development. InPlant Systems Biology: Methods and Protocols 2021 Nov 26 (pp. 59-77). New York, NY: Springer New York.
Caldu-Primo JL, Verduzco-Martínez JA, Alvarez-Buylla ER, Davila-Velderrain J. In vivo and in vitro human gene essentiality estimations capture contrasting functional constraints. NAR Genomics and Bioinformatics. 2021 Sep 1;3(3):lqab063.
Liu D, Davila-Velderrain J, Zhang Z, Kellis M. Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization. Nucleic acids research. 2019 Aug 22;47(14):7235-46.
Caldu-Primo JL, Alvarez-Buylla ER, Davila-Velderrain J. Structural robustness of mammalian transcription factor networks reveals plasticity across development. Scientific Reports. 2018 Sep 17;8(1):13922.
Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME. Modeling Methods for Medical Systems Biology: Regulatory Dynamics Underlying the Emergence of Disease Processes. Springer; 2018 Aug 3.
Caldu-Primo JL, Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Cancer in attractor landscape modeling: a systems biology perspective of the disease. In Cancer A Complex Disease:3.
Davila-Velderrain J, Caldu-Primo JL, Martinez-Garcia JC, Alvarez-Buylla ER. Modeling the epigenetic landscape in plant development. Computational Cell Biology: Methods and Protocols. 2018:357-83.
Méndez-López LF, Davila-Velderrain J, Domínguez-Hüttinger E, Enríquez-Olguín C, Martínez-García JC, Alvarez-Buylla ER. Gene regulatory network underlying the immortalization of epithelial cells. BMC systems biology. 2017 Dec;11:1-5.
Davila-Velderrain J, Martínez-García JC, Álvarez-Buylla ER. Boolean dynamic Modeling approaches to study plant gene regulatory networks: integration, validation, and prediction. Plant Gene Regulatory Networks: Methods and Protocols. 2017:297-315.
Álvarez-Buylla ER, Davila-Velderrain J, Martínez-García JC. Systems biology approaches to development beyond bioinformatics: nonlinear mechanistic models using plant systems. BioScience. 2016 May 1;66(5):371-83.
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Dynamic network modelling to understand flowering transition and floral patterning. Journal of Experimental Botany. 2016 Apr 1;67(9):2565-72.
Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER. Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates. BMC systems biology. 2015 Dec;9(1):1-4.
Perez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Davila-Velderrain J, Cruz-Sanchez D, Garay-Arroyo A, de la Paz Sánchez M. XAANTAL2 (AGL14) is an important component of the complex gene regulatory network that underlies Arabidopsis shoot apical meristem transitions. Molecular plant. 2015 May 4;8(5):796-813.
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development. Frontiers in genetics. 2015 Apr 23;6:160.
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Descriptive vs. mechanistic network models in plant development in the post-genomic era. Plant Functional Genomics: Methods and Protocols. 2015:455-79.
Azpeitia E, Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER. Gene regulatory network models for floral organ determination. Flower development: Methods and protocols. 2014:441-69.
evolution
Álvarez-Buylla ER, Davila-Velderrain J, Martínez García JC. Beyond (non) genetics: rethinking inheritance as a complex emergent process. Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, UNAM.
Alvarez-Buylla ER, Garay-Arroyo A, García-Ponce de León B, Sánchez MD, Gonzalez-Ortega E, Davila-Velderrain J, Martínez-García JC, Piñeyro-Nelson A. Developmental Evolutionary Ecology in Mexico. Revista mexicana de biodiversidad. 2017;88:14-26.
Davila-Velderrain J, Roces EA. Linear Causation Schemes in Post-genomic Biology: The Subliminal and Convenient One-to-one Genotype-Phenotype Mapping Assumption. Inter Disciplina. 2015;3(5):267-80.
Davila-Velderrain J, Servin-Marquez A, Alvarez-Buylla ER. Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes. Molecular biology and evolution. 2014 Mar 1;31(3):560-73.
Davila-Velderrain J, Alvarez-Buylla ER. Bridging the genotype and the phenotype: towards an epigenetic landscape approach to evolutionary systems biology. Frontiers in ecology, evolution and complexity. 2014:144-54.