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Employment (1)

Vanderbilt University: Nashville, TN, US

2015-01-01 to present (Biochemistry)
Employment
Source: Self-asserted source
Emily Hodges

Education and qualifications (2)

Cold Spring Harbor Laboratory: Cold Spring Harbor, NY, US

2006-10-01 to 2014-12-01 | Postdoctoral Fellowship
Education
Source: Self-asserted source
Emily Hodges

Karolinska Institutet: Stockholm, Stockholm County, SE

2002-01-01 to 2006-06-09 | PhD (Dept. of Cell and Molecular Biology, Programme in Functional Genomics and Bioinformatics)
Education
Source: Self-asserted source
Emily Hodges

Professional activities (4)

New York Academy of Sciences: New York, NY, US

Membership
Source: Self-asserted source
Emily Hodges

American Society of Human Genetics: Bethesda, Maryland, US

Membership
Source: Self-asserted source
Emily Hodges

American Association for Cancer Research: Philadelphia, PA, US

Membership
Source: Self-asserted source
Emily Hodges

Cold Spring Harbor Laboratory: Cold Spring Harbor, New York, US

2014 to present | Instructor - The Genome Access Course
Service
Source: Self-asserted source
Emily Hodges

Funding (2)

Bridging Epigenomics and Patient Data to Detect Enhanceropathies in Cancer

2018-10-01 to 2019-09-01 | Grant
Congressionally Directed Medical Research Programs (Frederick, US)
URL: https://app.dimensions.ai/details/grant/grant.9289980
GRANT_NUMBER:

W81XWH-20-1-0522
Source: Self-asserted source
Emily Hodges via DimensionsWizard

Dissecting Genetic and Epigenetic variation in the Cancer Regulome

2015-01-01 to 2018-05-31 | Grant
National Cancer Institute (Bethesda, US)
URL: https://app.dimensions.ai/details/grant/grant.3858590
GRANT_NUMBER: K22CA184308
Source: Self-asserted source
Emily Hodges via DimensionsWizard

Works (50 of 54)

Items per page:
Page 1 of 2

Human TSC2 Mutant Cells Exhibit Aberrations in Early Neurodevelopment Accompanied by Changes in the DNA Methylome

2024-06-06 | Preprint
DOI: 10.1101/2024.06.04.597443
Contributors: Mary-Bronwen L. Chalkley; Lindsey N. Guerin; Tenhir Iyer; Samantha Mallahan; Sydney Nelson; Mustafa Sahin; Emily Hodges; Kevin C. Ess; Rebecca A. Ihrie
Source: check_circle
Crossref

Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans

Cell Genomics
2024-04 | Journal article
DOI: 10.1016/j.xgen.2024.100536
Contributors: Tyler J. Hansen; Sarah L. Fong; Jessica K. Day; John A. Capra; Emily Hodges
Source: check_circle
Crossref

Genomic dissection and mutation-specific target discovery for breast cancerPIK3CAhotspot mutations

2024-01-04 | Preprint
DOI: 10.1101/2024.01.03.574067
Contributors: Adam X. Miranda; Justin Kemp; Brad Davidson; Sara Erika Bellomo; Verda Agan; Alexandra Manoni; Caterina Marchiò; Sarah Croessmann; Ben H. Park; Emily Hodges
Source: check_circle
Crossref

Human gene regulatory evolution is driven by the divergence of regulatory element function in bothcisandtrans

2023-02-15 | Preprint
DOI: 10.1101/2023.02.14.528376
Contributors: Tyler Hansen; Sarah Fong; John A. Capra; Emily Hodges
Source: check_circle
Crossref

Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development

2022-12-16 | Preprint
DOI: 10.1101/2022.12.15.520535
Contributors: Timothy J. Scott; Tyler J. Hansen; Evonne McArthur; Emily Hodges
Source: check_circle
Crossref

Genes associated with depression and coronary artery disease are enriched for inflammation and cardiomyopathy-associated pathways

2022-10-26 | Preprint
DOI: 10.1101/2022.10.25.22280854
Contributors: Kritika Singh; Hyunjoon Lee; Julia M Sealock; Tyne Miller-Flemming; Peter Straub; Nancy J. Cox; Quinn S. Wells; Jordan W. Smoller; Emily C. Hodges; Lea K. Davis
Source: check_circle
Crossref

ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome

Genome Research
2022-08 | Journal article
DOI: 10.1101/gr.276766.122
Contributors: Tyler J. Hansen; Emily Hodges
Source: check_circle
Crossref

Identifying transcription factor-bound activators and silencers in the chromatin accessible human genome using ATAC-STARR-seq

2022-03-28 | Preprint
DOI: 10.1101/2022.03.25.485870
Contributors: Tyler J. Hansen; Emily Hodges
Source: check_circle
Crossref

Dual detection of chromatin accessibility and DNA methylation using ATAC-Me

Nature Protocols
2021-12 | Journal article
DOI: 10.1038/s41596-021-00608-z
Contributors: Lindsey N. Guerin; Kelly R. Barnett; Emily Hodges
Source: check_circle
Crossref

Transcriptional silencing of ALDH2 confers a dependency on Fanconi anemia proteins in acute myeloid leukemia.

Cancer discovery
2021-04 | Journal article
DOI: 10.1158/2159-8290.cd-20-1542
PMID: 33893150
Contributors: Yang Z; Wu XS; Wei Y; Polyanskaya SA; Iyer SV; Jung M; Lach FP; Adelman ER; Klingbeil O; Milazzo JP et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Transcriptional silencing of ALDH2 in acute myeloid leukemia confers a dependency on Fanconi anemia proteins

2020-10 | Preprint
DOI: 10.1101/2020.10.23.352070
PPR: PPR229850
Contributors: Yang Z; Wei Y; Wu XS; Iyer SV; Jung M; Adelman ER; Klingbeil O; Kramer M; Demerdash OE; Chang K et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.

Nature ecology & evolution
2020-07 | Journal article
DOI: 10.1038/s41559-020-1261-z
PMID: 32719451
PMC: PMC7529911
Contributors: Rinker DC; Simonti CN; McArthur E; Shaw D; Hodges E; Capra JA
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions

Molecular Cell
2020-03 | Journal article
DOI: 10.1016/j.molcel.2020.01.004
Contributors: Kelly R. Barnett; Benjamin E. Decato; Timothy J. Scott; Tyler J. Hansen; Bob Chen; Jonathan Attalla; Andrew D. Smith; Emily Hodges
Source: check_circle
Crossref

Sequencing in High Definition Drives a Changing Worldview of the Epigenome.

Cold Spring Harbor perspectives in medicine
2019-06 | Journal article
DOI: 10.1101/cshperspect.a033076
PMID: 30201789
PMC: PMC6546039
Contributors: Hodges E
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Molecular regulation of peripheral B cells and their progeny in immunity.

Genes & development
2019-01 | Journal article
DOI: 10.1101/gad.320192.118
PMID: 30602439
PMC: PMC6317321
Contributors: Boothby MR; Hodges E; Thomas JW
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity.

Developmental cell
2019-01 | Journal article
DOI: 10.1016/j.devcel.2018.11.048
PMID: 30620902
PMC: PMC6327977
Contributors: Liu J; Banerjee A; Herring CA; Attalla J; Hu R; Xu Y; Shao Q; Simmons AJ; Dadi PK; Wang S et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck

2019-01-29 | Other
DOI: 10.1101/533257
Contributors: David C. Rinker; Corinne N. Simonti; Evonne McArthur; Douglas Shaw; Emily Hodges; John A. Capra
Source: check_circle
Crossref

Corrigendum: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome

Genome Research
2018-05 | Journal article
DOI: 10.1101/gr.236885.118
Part of ISSN: 1088-9051
Contributors: Jianghan Qu; Emily Hodges; Antoine Molaro; Pascal Gagneux; Matthew D. Dean; Gregory J. Hannon; Andrew D. Smith
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Evolutionary expansion of DNA hypomethylation in the mammalian germline genome

Genome Research
2017 | Journal article
DOI: 10.1101/gr.225896.117
Part of ISSN: 1088-9051
Contributors: Jianghan Qu; Emily Hodges; Antoine Molaro; Pascal Gagneux; Matthew D. Dean; Gregory J. Hannon; Andrew D. Smith
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Deacetylase activity of histone deacetylase 3 is required for productiveVDJrecombination and B-cell development

Proceedings of the National Academy of Sciences
2017-07 | Journal article
DOI: 10.1073/pnas.1701610114
Part of ISSN: 0027-8424
Contributors: Kristy R. Stengel; Kelly R. Barnett; Jing Wang; Qi Liu; Emily Hodges; Scott W. Hiebert; Srividya Bhaskara
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

Scientific reports
2017-03 | Journal article
DOI: 10.1038/srep44585
PMID: 28327635
PMC: PMC5361112
Contributors: Chang D; Knapp M; Enk J; Lippold S; Kircher M; Lister A; MacPhee RD; Widga C; Czechowski P; Sommer R et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma

2016-04-11 | Other
DOI: 10.1101/048058
Contributors: David McFadden; Katerina Politi; Arjun Bhutkar; Frances K Chen; Xiaoling Song; Mono Pirun; Philip M Santiago; Caroline Kim; James T Platt; Emily Lee et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

An Epigenetic Memory of Pregnancy in the Mouse Mammary Gland

Cell Reports
2015-05 | Journal article
DOI: 10.1016/j.celrep.2015.04.015
Part of ISSN: 2211-1247
Contributors: Camila O. dos Santos; Egor Dolzhenko; Emily Hodges; Andrew D. Smith; Gregory J. Hannon
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.

Current biology : CB
2014-10 | Journal article
DOI: 10.1016/j.cub.2014.09.078
PMID: 25455029
PMC: PMC4370112
Contributors: Malaspinas AS; Lao O; Schroeder H; Rasmussen M; Raghavan M; Moltke I; Campos PF; Sagredo FS; Rasmussen S; Gonçalves VF et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Two waves of de novo methylation during mouse germ cell development.

Genes & development
2014-07 | Journal article
DOI: 10.1101/gad.244350.114
PMID: 25030694
PMC: PMC4102761
Contributors: Molaro A; Falciatori I; Hodges E; Aravin AA; Marran K; Rafii S; McCombie WR; Smith AD; Hannon GJ
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

Genome Research
2013-06 | Journal article
DOI: 10.1101/gr.157271.113
Part of ISSN: 1088-9051
Contributors: F. Schlesinger; A. D. Smith; T. R. Gingeras; G. J. Hannon; E. Hodges
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Variations in COL15A1 and COL18A1 influence age of onset of primary open angle glaucoma.

Clinical genetics
2013-05 | Journal article
DOI: 10.1111/cge.12176
PMID: 23621901
PMC: PMC3771394
Contributors: Wiggs JL; Howell GR; Linkroum K; Abdrabou W; Hodges E; Braine CE; Pasquale LR; Hannon GJ; Haines JL; John SW
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Site identification in high-throughput RNA–protein interaction data

Bioinformatics
2012-09 | Journal article
DOI: 10.1093/bioinformatics/bts569
Part of ISSN: 1367-4803
Contributors: Philip J. Uren; Emad Bahrami-Samani; Suzanne C. Burns; Mei Qiao; Fedor V. Karginov; Emily Hodges; Gregory J. Hannon; Jeremy R. Sanford; Luiz O. F. Penalva; Andrew D. Smith
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Genomic landscape of human allele-specific DNA methylation.

Proceedings of the National Academy of Sciences of the United States of America
2012-04 | Journal article
DOI: 10.1073/pnas.1201310109
PMID: 22523239
PMC: PMC3358917
Contributors: Fang F; Hodges E; Molaro A; Dean M; Hannon GJ; Smith AD
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

Molecular Cell
2011-10 | Journal article
DOI: 10.1016/j.molcel.2011.08.026
Part of ISSN: 1097-2765
Contributors: Emily Hodges; Antoine Molaro; Camila O. Dos Santos; Pramod Thekkat; Qiang Song; Philip J. Uren; Jin Park; Jason Butler; Shahin Rafii; W. Richard McCombie et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

Cell
2011-09 | Journal article
DOI: 10.1016/j.cell.2011.08.016
Part of ISSN: 0092-8674
Contributors: Antoine Molaro; Emily Hodges; Fang Fang; Qiang Song; W. Richard McCombie; Gregory J. Hannon; Andrew D. Smith
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis.

Genome research
2011-04 | Journal article
DOI: 10.1101/gr.117143.110
PMID: 21487076
PMC: PMC3083082
Contributors: Erlich Y; Edvardson S; Hodges E; Zenvirt S; Thekkat P; Shaag A; Dor T; Hannon GJ; Elpeleg O
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Mutations in the RNA granule component TDRD7 cause cataract and glaucoma.

Science (New York, N.Y.)
2011-03 | Journal article
DOI: 10.1126/science.1195970
PMID: 21436445
PMC: PMC3279122
Contributors: Lachke SA; Alkuraya FS; Kneeland SC; Ohn T; Aboukhalil A; Howell GR; Saadi I; Cavallesco R; Yue Y; Tsai AC et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Targeted resequencing of a genomic region influencing tameness and aggression reveals multiple signals of positive selection.

Heredity
2011-02 | Journal article
DOI: 10.1038/hdy.2011.4
PMID: 21304545
PMC: PMC3183948
Contributors: Albert FW; Hodges E; Jensen JD; Besnier F; Xuan Z; Rooks M; Bhattacharjee A; Brizuela L; Good JM; Green RE et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Targeted Enrichment of Specific Regions in the Human Genome by Array Hybridization

Current Protocols in Human Genetics
2010-07 | Journal article
DOI: 10.1002/0471142905.hg1803s66
Part of ISSN: 1934-8266
Contributors: Catherine Igartua; Emily H. Turner; Sarah B. Ng; Emily Hodges; Gregory J. Hannon; Arindam Bhattacharjee; Mark J. Rieder; Deborah A. Nickerson; Jay Shendure
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Targeted investigation of the Neandertal genome by array-based sequence capture.

Science (New York, N.Y.)
2010-05 | Journal article
DOI: 10.1126/science.1188046
PMID: 20448179
PMC: PMC3140021
Contributors: Burbano HA; Hodges E; Green RE; Briggs AW; Krause J; Meyer M; Good JM; Maricic T; Johnson PL; Xuan Z et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Deep Sequencing of Target Linkage Assay-Identified Regions in Familial Breast Cancer: Methods, Analysis Pipeline and Troubleshooting

PLoS ONE
2010-04-02 | Journal article
DOI: 10.1371/journal.pone.0009976
Part of ISSN: 1932-6203
Contributors: Juan Manuel Rosa-Rosa; Francisco Javier Gracia-Aznárez; Emily Hodges; Guillermo Pita; Michelle Rooks; Zhenyu Xuan; Arindam Bhattacharjee; Leonardo Brizuela; José M. Silva; Gregory J. Hannon et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Evolutionary flux of canonical microRNAs and mirtrons in Drosophila

Nature Genetics
2010-01 | Journal article
DOI: 10.1038/ng0110-6
Part of ISSN: 1061-4036
Contributors: Eugene Berezikov; Na Liu; Alex S Flynt; Emily Hodges; Michelle Rooks; Gregory J Hannon; Eric C Lai
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Updates to the RMAP short-read mapping software

Bioinformatics
2009-09-07 | Journal article
DOI: 10.1093/bioinformatics/btp533
Part of ISSN: 1367-4803
Contributors: A. D. Smith; W.-Y. Chung; E. Hodges; J. Kendall; G. Hannon; J. Hicks; Z. Xuan; M. Q. Zhang
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.

Genome research
2009-07 | Journal article
DOI: 10.1101/gr.095190.109
PMID: 19581485
PMC: PMC2752124
Contributors: Hodges E; Smith AD; Kendall J; Xuan Z; Ravi K; Rooks M; Zhang MQ; Ye K; Bhattacharjee A; Brizuela L et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

Nature Protocols
2009-05 | Journal article
DOI: 10.1038/nprot.2009.68
Part of ISSN: 1754-2189
Contributors: Emily Hodges; Michelle Rooks; Zhenyu Xuan; Arindam Bhattacharjee; D Benjamin Gordon; Leonardo Brizuela; W Richard McCombie; Gregory J Hannon
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Conservation of small RNA pathways in platypus

Genome Research
2008-05-07 | Journal article
DOI: 10.1101/gr.073056.107
Part of ISSN: 1088-9051
Contributors: E. P. Murchison; P. Kheradpour; R. Sachidanandam; C. Smith; E. Hodges; Z. Xuan; M. Kellis; F. Grutzner; A. Stark; G. J. Hannon
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

Cell
2008-04 | Journal article
DOI: 10.1016/j.cell.2008.02.034
Part of ISSN: 0092-8674
Contributors: Shijun Mi; Tao Cai; Yugang Hu; Yemiao Chen; Emily Hodges; Fangrui Ni; Liang Wu; Shan Li; Huanyu Zhou; Chengzu Long et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

Nature
2008-04-10 | Journal article
DOI: 10.1038/nature06904
Part of ISSN: 0028-0836
Contributors: Oliver H. Tam; Alexei A. Aravin; Paula Stein; Angelique Girard; Elizabeth P. Murchison; Sihem Cheloufi; Emily Hodges; Martin Anger; Ravi Sachidanandam; Richard M. Schultz et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.

Genes & development
2008-01 | Journal article
DOI: 10.1101/gad.1613108
PMID: 18172160
PMC: PMC2151017
Contributors: Stark A; Bushati N; Jan CH; Kheradpour P; Hodges E; Brennecke J; Bartel DP; Cohen SM; Kellis M
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

Genome Research
2007 | Journal article
DOI: 10.1101/gr.6593807
Part of ISSN: 1088-9051
Contributors: A. Stark; P. Kheradpour; L. Parts; J. Brennecke; E. Hodges; G. J. Hannon; M. Kellis
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Nature
2007-11 | Journal article
DOI: 10.1038/nature06340
PMID: 17994088
PMC: PMC2474711
Contributors: Stark A; Lin MF; Kheradpour P; Pedersen JS; Parts L; Carlson JW; Crosby MA; Rasmussen MD; Roy S; Deoras AN et al.
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Genome-wide in situ exon capture for selective resequencing

Nature Genetics
2007-11-04 | Journal article
DOI: 10.1038/ng.2007.42
Part of ISSN: 1061-4036
Contributors: Emily Hodges; Zhenyu Xuan; Vivekanand Balija; Melissa Kramer; Michael N Molla; Steven W Smith; Christina M Middle; Matthew J Rodesch; Thomas J Albert; Gregory J Hannon et al.
Source: Self-asserted source
Emily Hodges via Crossref Metadata Search

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

BMC genomics
2006-03 | Journal article
DOI: 10.1186/1471-2164-7-48
PMID: 16533400
PMC: PMC1440326
Contributors: Kemmer D; Podowski RM; Arenillas D; Lim J; Hodges E; Roth P; Sonnhammer EL; Höög C; Wasserman WW
Source: Self-asserted source
Emily Hodges via Europe PubMed Central

Thorough validation of siRNA-induced cell death phenotypes defines new anti-apoptotic protein.

Nucleic acids research
2006-01 | Journal article
DOI: 10.1093/nar/gnj015
PMID: 16432257
PMC: PMC1345702
Contributors: Wu W; Hodges E; Höög C
Source: Self-asserted source
Emily Hodges via Europe PubMed Central
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Peer review (2 reviews for 2 publications/grants)

Review activity for Molecular cell. (1)
Review activity for Nature (1)
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