Emily C. Hodges, Ph.D.

Assistant Professor

emily.hodges@vanderbilt.edu

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Faculty Appointments
Assistant Professor of Biochemistry
Education
Ph.D., Medical Science, Karolinska Institutet, Stockholm, SwedenB.A., French and Biology, Rhodes College, Memphis, Tennessee
Office Address
673B Light Hall
Nashville, TN 37232-0146
Research Description
Research in the Hodges Lab strives to understand how epigenetic features shape human genomes. Our work aims to dissect the relationship between DNA methylation and gene regulation, particularly with respect to the gene regulatory activity of non-coding functional elements. We study this relationship on two levels; first, we are interested in how DNA methylation states are established in differentiating cells. Second, we are interested in the relationship between genotype and DNA methylation state (epitype).
Research Keywords
DNA methylation and non-coding gene regulatory variation in evolution, development and disease
Publications
Chang D, Knapp M, Enk J, Lippold S, Kircher M, Lister A, MacPhee RD, Widga C, Czechowski P, Sommer R, Hodges E, Stümpel N, Barnes I, Dalén L, Derevianko A, Germonpré M, Hillebrand-Voiculescu A, Constantin S, Kuznetsova T, Mol D, Rathgeber T, Rosendahl W, Tikhonov AN, Willerslev E, Hannon G, Lalueza-Fox C, Joger U, Poinar H, Hofreiter M, Shapiro B. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci Rep. 2017 Mar 3/22/2017; 7: 44585. PMID: 28327635, PII: srep44585, DOI: 10.1038/srep44585, ISSN: 2045-2322.

McFadden DG, Politi K, Bhutkar A, Chen FK, Song X, Pirun M, Santiago PM, Kim-Kiselak C, Platt JT, Lee E, Hodges E, Rosebrock AP, Bronson RT, Socci ND, Hannon GJ, Jacks T, Varmus H. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2016 Oct 10/18/2016; 113(42): E6409-E6417. PMID: 27702896, PMCID: PMC5081629, PII: 1613601113, DOI: 10.1073/pnas.1613601113, ISSN: 1091-6490.

Dos Santos CO, Dolzhenko E, Hodges E, Smith AD, Hannon GJ. An epigenetic memory of pregnancy in the mouse mammary gland. Cell Rep [print-electronic]. 2015 May 5/19/2015; 11(7): 1102-9. PMID: 25959817, PMCID: PMC4439279, PII: S2211-1247(15)00390-3, DOI: 10.1016/j.celrep.2015.04.015, ISSN: 2211-1247.

Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, Bernardo DV, DeGiorgio M, Duggan AT, Bastos M, Wang Y, Stenderup J, Moreno-Mayar JV, Brunak S, Sicheritz-Ponten T, Hodges E, Hannon GJ, Orlando L, Price TD, Jensen JD, Nielsen R, Heinemeier J, Olsen J, Rodrigues-Carvalho C, Lahr MM, Neves WA, Kayser M, Higham T, Stoneking M, Pena SD, Willerslev E. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil [letter]. Curr. Biol [print-electronic]. 2014 Nov 11/3/2014; 24(21): R1035-7. PMID: 25455029, PMCID: PMC4370112, PII: S0960-9822(14)01274-3, DOI: 10.1016/j.cub.2014.09.078, ISSN: 1879-0445.

Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 2014 Jul 7/15/2014; 28(14): 1544-9. PMID: 25030694, PMCID: PMC4102761, PII: 28/14/1544, DOI: 10.1101/gad.244350.114, ISSN: 1549-5477.

Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E. De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome Res [print-electronic]. 2013 Oct; 23(10): 1601-14. PMID: 23811145, PMCID: PMC3787258, PII: gr.157271.113, DOI: 10.1101/gr.157271.113, ISSN: 1549-5469.

Wiggs JL, Howell GR, Linkroum K, Abdrabou W, Hodges E, Braine CE, Pasquale LR, Hannon GJ, Haines JL, John SW. Variations in COL15A1 and COL18A1 influence age of onset of primary open angle glaucoma. Clin. Genet [print-electronic]. 2013 Aug; 84(2): 167-74. PMID: 23621901, PMCID: PMC3771394, DOI: 10.1111/cge.12176, ISSN: 1399-0004.

Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD. Site identification in high-throughput RNA-protein interaction data. Bioinformatics [print-electronic]. 2012 Dec 12/1/2012; 28(23): 3013-20. PMID: 23024010, PMCID: PMC3509493, PII: bts569, DOI: 10.1093/bioinformatics/bts569, ISSN: 1367-4811.

Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, Smith AD. Genomic landscape of human allele-specific DNA methylation. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2012 May 5/8/2012; 109(19): 7332-7. PMID: 22523239, PMCID: PMC3358917, PII: 1201310109, DOI: 10.1073/pnas.1201310109, ISSN: 1091-6490.

Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell [print-electronic]. 2011 Oct 10/7/2011; 44(1): 17-28. PMID: 21924933, PMCID: PMC3412369, PII: S1097-2765(11)00676-9, DOI: 10.1016/j.molcel.2011.08.026, ISSN: 1097-4164.

Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell. 2011 Sep 9/16/2011; 146(6): 1029-41. PMID: 21925323, PMCID: PMC3205962, PII: S0092-8674(11)00942-1, DOI: 10.1016/j.cell.2011.08.016, ISSN: 1097-4172.

Albert FW, Hodges E, Jensen JD, Besnier F, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Good JM, Green RE, Burbano HA, Plyusnina IZ, Trut L, Andersson L, Schöneberg T, Carlborg O, Hannon GJ, Pääbo S. Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection. Heredity (Edinb) [print-electronic]. 2011 Sep; 107(3): 205-14. PMID: 21304545, PMCID: PMC3183948, PII: hdy20114, DOI: 10.1038/hdy.2011.4, ISSN: 1365-2540.

Erlich Y, Edvardson S, Hodges E, Zenvirt S, Thekkat P, Shaag A, Dor T, Hannon GJ, Elpeleg O. Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis. Genome Res [print-electronic]. 2011 May; 21(5): 658-64. PMID: 21487076, PMCID: PMC3083082, PII: gr.117143.110, DOI: 10.1101/gr.117143.110, ISSN: 1549-5469.

Lachke SA, Alkuraya FS, Kneeland SC, Ohn T, Aboukhalil A, Howell GR, Saadi I, Cavallesco R, Yue Y, Tsai AC, Nair KS, Cosma MI, Smith RS, Hodges E, Alfadhli SM, Al-Hajeri A, Shamseldin HE, Behbehani A, Hannon GJ, Bulyk ML, Drack AV, Anderson PJ, John SW, Maas RL. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science. 2011 Mar 3/25/2011; 331(6024): 1571-6. PMID: 21436445, PMCID: PMC3279122, PII: 331/6024/1571, DOI: 10.1126/science.1195970, ISSN: 1095-9203.

Igartua C, Turner EH, Ng SB, Hodges E, Hannon GJ, Bhattacharjee A, Rieder MJ, Nickerson DA, Shendure J. Targeted enrichment of specific regions in the human genome by array hybridization. Curr Protoc Hum Genet. 2010 Jul; Chapter 18: Unit 18.3. PMID: 20582915, PMCID: PMC2910258, DOI: 10.1002/0471142905.hg1803s66, ISSN: 1934-8258.

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z, Rooks M, Bhattacharjee A, Brizuela L, Albert FW, de la Rasilla M, Fortea J, Rosas A, Lachmann M, Hannon GJ, Pääbo S. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 May 5/7/2010; 328(5979): 723-5. PMID: 20448179, PMCID: PMC3140021, PII: 328/5979/723, DOI: 10.1126/science.1188046, ISSN: 1095-9203.

Rosa-Rosa JM, Gracia-Aznárez FJ, Hodges E, Pita G, Rooks M, Xuan Z, Bhattacharjee A, Brizuela L, Silva JM, Hannon GJ, Benitez J. Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS ONE. 2010; 5(4): e9976. PMID: 20368986, PMCID: PMC2848842, DOI: 10.1371/journal.pone.0009976, ISSN: 1932-6203.

Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila [letter]. Nat. Genet. 2010 Jan; 42(1): 6-9; author reply 9. PMID: 20037610, PMCID: PMC4136759, PII: ng0110-6, DOI: 10.1038/ng0110-6, ISSN: 1546-1718.

Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. Updates to the RMAP short-read mapping software. Bioinformatics [print-electronic]. 2009 Nov 11/1/2009; 25(21): 2841-2. PMID: 19736251, PMCID: PMC2895571, PII: btp533, DOI: 10.1093/bioinformatics/btp533, ISSN: 1367-4811.

Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res [print-electronic]. 2009 Sep; 19(9): 1593-605. PMID: 19581485, PMCID: PMC2752124, PII: gr.095190.109, DOI: 10.1101/gr.095190.109, ISSN: 1549-5469.

Hodges E, Rooks M, Xuan Z, Bhattacharjee A, Benjamin Gordon D, Brizuela L, Richard McCombie W, Hannon GJ. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc [print-electronic]. 2009; 4(6): 960-74. PMID: 19478811, PMCID: PMC2990409, PII: nprot.2009.68, DOI: 10.1038/nprot.2009.68, ISSN: 1750-2799.

Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, Grützner F, Stark A, Hannon GJ. Conservation of small RNA pathways in platypus. Genome Res [print-electronic]. 2008 Jun; 18(6): 995-1004. PMID: 18463306, PMCID: PMC2413167, PII: gr.073056.107, DOI: 10.1101/gr.073056.107, ISSN: 1088-9051.

Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature [print-electronic]. 2008 May 5/22/2008; 453(7194): 534-8. PMID: 18404147, PMCID: PMC2981145, PII: nature06904, DOI: 10.1038/nature06904, ISSN: 1476-4687.

Mi S, Cai T, Hu Y, Chen Y, Hodges E, Ni F, Wu L, Li S, Zhou H, Long C, Chen S, Hannon GJ, Qi Y. Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell [print-electronic]. 2008 Apr 4/4/2008; 133(1): 116-27. PMID: 18342361, PMCID: PMC2981139, PII: S0092-8674(08)00285-7, DOI: 10.1016/j.cell.2008.02.034, ISSN: 1097-4172.

Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR. Genome-wide in situ exon capture for selective resequencing. Nat. Genet [print-electronic]. 2007 Dec; 39(12): 1522-7. PMID: 17982454, PII: ng.2007.42, DOI: 10.1038/ng.2007.42, ISSN: 1546-1718.

Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M. Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res [print-electronic]. 2007 Dec; 17(12): 1865-79. PMID: 17989255, PMCID: PMC2099594, PII: gr.6593807, DOI: 10.1101/gr.6593807, ISSN: 1088-9051.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, , , Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 2007 Nov 11/8/2007; 450(7167): 219-32. PMID: 17994088, PMCID: PMC2474711, PII: nature06340, DOI: 10.1038/nature06340, ISSN: 1476-4687.

Available Postdoctoral Position Details
Posted: 3/27/2017

Postdoctoral Position - Epigenomics and Gene Regulation

A postdoctoral position is immediately available at the Vanderbilt University Genetics Institute and Department of Biochemistry. Our group is interested in the role of non-coding sequence variation in complex disease. Research in the Hodges Lab strives to understand how epigenetic features shape human genomes. Our work aims to dissect the relationship between DNA methylation and gene regulation, particularly with respect to the gene regulatory activity of non-coding functional elements. We study this relationship on two levels; first, we are interested in how DNA methylation states are established in differentiating cells. Second, we are interested in the relationship between genotype and DNA methylation state (epitype). Projects in our lab address these questions utilizing innovative biochemical, functional genomic and bioinformatic approaches. The successful candidate will have a strong molecular biology background. Experience with next-generation sequencing, statistical genetics, and bioinformatics is a priority. Please send CVs along with contact info for three references to emily.hodges"at"vanderbilt.edu