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Publications

2025

Chalkley ML, Guerin LN, Iyer T, Mallahan S, Nelson S, Sahin M, Hodges E, Ess KC, Ihrie RA, Human TSC2 mutant cells exhibit aberrations in early neurodevelopment accompanied by changes in the DNA Methylome Human molecular genetics. 2025 Apr 6; 34 (8) 684-698
Guerin LN, Scott TJ, Yap JA, Johansson A, Puddu F, Charlesworth T, Yang Y, Simmons AJ, Lau KS, Ihrie RA, Hodges E, Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification Cell reports. 2025 May 9; 44 (5) 115680

2024

Ye X, Guerin LN, Chen Z, Rajendren S, Dunker W, Zhao Y, Zhang R, Hodges E, Karijolich J, Enhancer-promoter activation by the Kaposi sarcoma-associated herpesvirus episome maintenance protein LANA Cell reports. 2024 Feb 27; 43 (3) 113888
Gu G, Brown M, Agan V, Nevills S, Hu R, Simmons A, Xu Y, Yang Y, Yagan M, Najam S, Dadi P, Sampson L, Magnuson M, Jacobson D, Lau K, Hodges E, Endocrine islet β-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients Research square. 2024 Mar 07;
Chalkley ML, Guerin LN, Iyer T, Mallahan S, Nelson S, Sahin M, Hodges E, Ess KC, Ihrie RA, Human TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome bioRxiv : the preprint server for biology. 2024 Jun 06;
Miranda AX, Kemp J, Davidson BA, Bellomo SE, Miranda VE, Manoni A, Marchiò C, Croessmann S, Park BH, Hodges E, Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations BMC genomics. 2024 May 27; 25 (1) 519

2023

Bomber ML, Wang J, Liu Q, Barnett KR, Layden HM, Hodges E, Stengel KR, Hiebert SW, Human SMARCA5 is continuously required to maintain nucleosome spacing Molecular cell. 2023 Jan 10; 83 (4) 507-522.e6
James JL, Taylor BC, Axelrod ML, Sun X, Guerin LN, Gonzalez-Ericsson PI, Wang Y, Sanchez V, Fahey CC, Sanders ME, Xu Y, Hodges E, Johnson DB, Balko JM, Polycomb repressor complex 2 suppresses interferon-responsive MHC-II expression in melanoma cells and is associated with anti-PD-1 resistance Journal for immunotherapy of cancer. 2023 Nov 20; 11 (11)
Scott TJ, Hansen TJ, McArthur E, Hodges E, Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development BMC genomics. 2023 Oct 19; 24 (1) 623

2022

2021

Guerin LN, Barnett KR, Hodges E, Dual detection of chromatin accessibility and DNA methylation using ATAC-Me Nature protocols. 2021 Oct 18; 16 (12) 5377-5397
Yang Z, Wu XS, Wei Y, Polyanskaya SA, Iyer SV, Jung M, Lach FP, Adelman ER, Klingbeil O, Milazzo JP, Kramer M, Demerdash OE, Chang K, Goodwin S, Hodges E, McCombie WR, Figueroa ME, Smogorzewska A, Vakoc CR, Transcriptional Silencing of Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia Cancer discovery. 2021 Apr 23; 11 (9) 2300-2315
Wei Y, Huang YH, Skopelitis DS, Iyer SV, Costa ASH, Yang Z, Kramer M, Adelman ER, Klingbeil O, Demerdash OE, Polyanskaya SA, Chang K, Goodwin S, Hodges E, McCombie WR, Figueroa ME, Vakoc CR, SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia Cancer discovery. 2021 Sep 16;

2020

Barnett KR, Decato BE, Scott TJ, Hansen TJ, Chen B, Attalla J, Smith AD, Hodges E, ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions Molecular cell. 2020 Jan 17;

2019

Hodges E, Sequencing in High Definition Drives a Changing Worldview of the Epigenome Cold Spring Harbor perspectives in medicine. 2019 Jun 03; 9 (6)
Boothby MR, Hodges E, Thomas JW, Molecular regulation of peripheral B cells and their progeny in immunity Genes & development. 2019 Jan 1; 33 (1-2) 26-48
Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G, Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity Developmental cell. 2019 Jan 7; 48 (1) 49-63.e7

2017

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 Scientific reports. 2017 Mar 22; 7 44585
Qu J, Hodges E, Molaro A, Gagneux P, Dean MD, Hannon GJ, Smith AD, Evolutionary expansion of DNA hypomethylation in the mammalian germline genome Genome research. 2017 Dec 19; 28 (2) 145-158
Stengel KR, Barnett KR, Wang J, Liu Q, Hodges E, Hiebert SW, Bhaskara S, Deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B-cel… Proceedings of the National Academy of Sciences of the United States of America. 2017 Jul 24;

2016

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 ade… Proceedings of the National Academy of Sciences of the United States of America. 2016 Oct 18; 113 (42) E6409-E6417

2015

Dos Santos CO, Dolzhenko E, Hodges E, Smith AD, Hannon GJ, An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland. Cell reports. 2015 May 6;

2014

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 & development. 2014 Jul 15; 28 (14) 1544-9
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. Current biology : CB. 2014 Nov 3; 24 (21) R1035-7

2013

Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E, De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome research. 2013 Oct 23 (10) 1601-14

2012

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 (Oxford, England). 2012 Dec 1; 28 (23) 3013-20
Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, Smith AD, Genomic landscape of human allele-specific DNA methylation. Proceedings of the National Academy of Sciences of the United States of America. 2012 May 8; 109 (19) 7332-7

2011

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 16; 146 (6) 1029-41
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… Molecular cell. 2011 Oct 7; 44 (1) 17-28
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 he… Genome research. 2011 May 21 (5) 658-64
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 (New York, N.Y.). 2011 Mar 25; 331 (6024) 1571-6

2010

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. Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.]. 2010 Jul Chapter 18 Unit 18.3
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 (New York, N.Y.). 2010 May 7; 328 (5979) 723-5
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, analy… PloS one. 2010 5 (4) e9976
Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC, Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nature genetics. 2010 Jan 42 (1) 6-9; author reply 9-10

2009

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 bisulfit… Genome research. 2009 Sep 19 (9) 1593-605
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 (Oxford, England). 2009 Nov 1; 25 (21) 2841-2
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… Nature protocols. 2009 4 (6) 960-74

2008

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. 2008 Apr 4; 133 (1) 116-27
Stark A, Bushati N, Jan CH, Kheradpour P, Hodges E, Brennecke J, Bartel DP, Cohen SM, Kellis M, A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes & development. 2008 Jan 1; 22 (1) 8-13
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 research. 2008 Jun 18 (6) 995-1004
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. 2008 May 22; 453 (7194) 534-8

2007

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. Nature genetics. 2007 Dec 39 (12) 1522-7
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 8; 450 (7167) 219-32
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 research. 2007 Dec 17 (12) 1865-79

2006

Wu W, Hodges E, Höög C, Thorough validation of siRNA-induced cell death phenotypes defines new anti-apoptotic protein. Nucleic acids research. 2006 34 (2) e13
Kemmer D, Podowski RM, Arenillas D, Lim J, Hodges E, Roth P, Sonnhammer EL, Höög C, Wasserman WW, NovelFam3000–uncharacterized human protein domains conserved across model organisms. BMC genomics. 2006 7 48

2005

Tamas I, Hodges E, Dessi P, Johnsen R, Vaz Gomes A, A combined approach exploring gene function based on worm-human orthology. BMC genomics. 2005 6 65
Hodges E, Redelius JS, Wu W, Höög C, Accelerated discovery of novel protein function in cultured human cells. Molecular & cellular proteomics : MCP. 2005 Sep 4 (9) 1319-27

2004

Wu W, Hodges E, Redelius J, Höög C, A novel approach for evaluating the efficiency of siRNAs on protein levels in cultured cells. Nucleic acids research. 2004 32 (2) e17
Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer EL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, Höög C, Agarwal P, Wasserman WW, Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of … Comparative and functional genomics. 2004 5 (8) 584-95