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Hodges Lab

Hodges Lab Publications

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

Hansen TJ , Hodges E , ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome Genome research. 2022 Jul 20;

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

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
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

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

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 , 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
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

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
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

2006

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
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

2005

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
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

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