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Items: 19

1.

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.

Liu D, Davila-Velderrain J, Zhang Z, Kellis M.

Nucleic Acids Res. 2019 Aug 22;47(14):7235-7246. doi: 10.1093/nar/gkz538.

2.

Author Correction: Single-cell transcriptomic analysis of Alzheimer's disease.

Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, Tsai LH.

Nature. 2019 Jul;571(7763):E1. doi: 10.1038/s41586-019-1329-6.

PMID:
31209304
3.

Single-cell transcriptomic analysis of Alzheimer's disease.

Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, Menon M, He L, Abdurrob F, Jiang X, Martorell AJ, Ransohoff RM, Hafler BP, Bennett DA, Kellis M, Tsai LH.

Nature. 2019 Jun;570(7761):332-337. doi: 10.1038/s41586-019-1195-2. Epub 2019 May 1. Erratum in: Nature. 2019 Jun 17;:.

PMID:
31042697
4.

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use.

Liu M, Jiang Y, Wedow R, Li Y, Brazel DM, Chen F, Datta G, Davila-Velderrain J, McGuire D, Tian C, Zhan X; 23andMe Research Team; HUNT All-In Psychiatry, Choquet H, Docherty AR, Faul JD, Foerster JR, Fritsche LG, Gabrielsen ME, Gordon SD, Haessler J, Hottenga JJ, Huang H, Jang SK, Jansen PR, Ling Y, Mägi R, Matoba N, McMahon G, Mulas A, Orrù V, Palviainen T, Pandit A, Reginsson GW, Skogholt AH, Smith JA, Taylor AE, Turman C, Willemsen G, Young H, Young KA, Zajac GJM, Zhao W, Zhou W, Bjornsdottir G, Boardman JD, Boehnke M, Boomsma DI, Chen C, Cucca F, Davies GE, Eaton CB, Ehringer MA, Esko T, Fiorillo E, Gillespie NA, Gudbjartsson DF, Haller T, Harris KM, Heath AC, Hewitt JK, Hickie IB, Hokanson JE, Hopfer CJ, Hunter DJ, Iacono WG, Johnson EO, Kamatani Y, Kardia SLR, Keller MC, Kellis M, Kooperberg C, Kraft P, Krauter KS, Laakso M, Lind PA, Loukola A, Lutz SM, Madden PAF, Martin NG, McGue M, McQueen MB, Medland SE, Metspalu A, Mohlke KL, Nielsen JB, Okada Y, Peters U, Polderman TJC, Posthuma D, Reiner AP, Rice JP, Rimm E, Rose RJ, Runarsdottir V, Stallings MC, Stančáková A, Stefansson H, Thai KK, Tindle HA, Tyrfingsson T, Wall TL, Weir DR, Weisner C, Whitfield JB, Winsvold BS, Yin J, Zuccolo L, Bierut LJ, Hveem K, Lee JJ, Munafò MR, Saccone NL, Willer CJ, Cornelis MC, David SP, Hinds DA, Jorgenson E, Kaprio J, Stitzel JA, Stefansson K, Thorgeirsson TE, Abecasis G, Liu DJ, Vrieze S.

Nat Genet. 2019 Feb;51(2):237-244. doi: 10.1038/s41588-018-0307-5. Epub 2019 Jan 14.

5.

Modeling the Epigenetic Landscape in Plant Development.

Davila-Velderrain J, Caldu-Primo JL, Martinez-Garcia JC, Alvarez-Buylla ER.

Methods Mol Biol. 2018;1819:357-383. doi: 10.1007/978-1-4939-8618-7_17.

PMID:
30421413
6.

Structural robustness of mammalian transcription factor networks reveals plasticity across development.

Caldu-Primo JL, Alvarez-Buylla ER, Davila-Velderrain J.

Sci Rep. 2018 Sep 17;8(1):13922. doi: 10.1038/s41598-018-32020-1.

7.

Case Studies.

Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME.

Adv Exp Med Biol. 2018;1069:135-209. doi: 10.1007/978-3-319-89354-9_3.

PMID:
30076567
8.

Modeling Procedures.

Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME.

Adv Exp Med Biol. 2018;1069:35-134. doi: 10.1007/978-3-319-89354-9_2. Review.

PMID:
30076566
9.

Medical Systems Biology.

Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME.

Adv Exp Med Biol. 2018;1069:1-33. doi: 10.1007/978-3-319-89354-9_1.

PMID:
30076565
10.

Gene regulatory network underlying the immortalization of epithelial cells.

Méndez-López LF, Davila-Velderrain J, Domínguez-Hüttinger E, Enríquez-Olguín C, Martínez-García JC, Alvarez-Buylla ER.

BMC Syst Biol. 2017 Feb 16;11(1):24. doi: 10.1186/s12918-017-0393-5.

11.

Transcription factors YY1, Sp1 and Sp3 modulate dystrophin Dp71 gene expression in hepatic cells.

Peñuelas-Urquides K, Becerril-Esquivel C, Mendoza-de-León LC, Silva-Ramírez B, Dávila-Velderrain J, Cisneros B, de León MB.

Biochem J. 2016 Jul 1;473(13):1967-76. doi: 10.1042/BCJ20160163. Epub 2016 May 3.

PMID:
27143785
12.

Dynamic network modelling to understand flowering transition and floral patterning.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

J Exp Bot. 2016 Apr;67(9):2565-72. doi: 10.1093/jxb/erw123. Epub 2016 Mar 28.

PMID:
27025221
13.

Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates.

Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER.

BMC Syst Biol. 2015 May 13;9:20. doi: 10.1186/s12918-015-0166-y.

14.

Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

Front Genet. 2015 Apr 23;6:160. doi: 10.3389/fgene.2015.00160. eCollection 2015. Review.

15.

Descriptive vs. mechanistic network models in plant development in the post-genomic era.

Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER.

Methods Mol Biol. 2015;1284:455-79. doi: 10.1007/978-1-4939-2444-8_23.

PMID:
25757787
16.

XAANTAL2 (AGL14) Is an Important Component of the Complex Gene Regulatory Network that Underlies Arabidopsis Shoot Apical Meristem Transitions.

Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N, Ugartechea-Chirino Y, Villajuana-Bonequi M, de Folter S, Azpeitia E, Dávila-Velderrain J, Cruz-Sánchez D, Garay-Arroyo A, Sánchez Mde L, Estévez-Palmas JM, Álvarez-Buylla ER.

Mol Plant. 2015 May;8(5):796-813. doi: 10.1016/j.molp.2015.01.017. Epub 2015 Jan 28.

17.

Gene regulatory network models for floral organ determination.

Azpeitia E, Davila-Velderrain J, Villarreal C, Alvarez-Buylla ER.

Methods Mol Biol. 2014;1110:441-69. doi: 10.1007/978-1-4614-9408-9_26.

PMID:
24395275
18.

Molecular evolution constraints in the floral organ specification gene regulatory network module across 18 angiosperm genomes.

Davila-Velderrain J, Servin-Marquez A, Alvarez-Buylla ER.

Mol Biol Evol. 2014 Mar;31(3):560-73. doi: 10.1093/molbev/mst223. Epub 2013 Nov 21.

PMID:
24273325
19.

Comparison of gene expression profiles between pansensitive and multidrug-resistant strains of Mycobacterium tuberculosis.

Peñuelas-Urquides K, González-Escalante L, Villarreal-Treviño L, Silva-Ramírez B, Gutiérrez-Fuentes DJ, Mojica-Espinosa R, Rangel-Escareño C, Uribe-Figueroa L, Molina-Salinas GM, Dávila-Velderrain J, Castorena-Torres F, Bermúdez de León M, Said-Fernández S.

Curr Microbiol. 2013 Sep;67(3):362-71. doi: 10.1007/s00284-013-0376-8. Epub 2013 May 7.

PMID:
23649743

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