Leveraging Genomics, Transcriptomics, and Epigenomics to Understand the Biology and Chemoresistance of Ovarian Cancer by Sandra Muñoz-Galván, Amancio Carnero

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Epigenome-wide association study of metabolic syndrome in African-American adults by Tomi Akinyemiju, Anh N. Do, Amit Patki, Stella Aslibekyan, Degui Zhi, Bertha Hidalgo, Hemant K. Tiwari, Devin Absher, Xin Geng, Donna K. Arnett, Marguerite R. Irvin

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Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution by Jacob R. Leistico, Priyanka Saini, Christopher R. Futtner, Miroslav Hejna, Yasuhiro Omura, Pritin N. Soni, Poorva Sandlesh, Magdy Milad, Jian-Jun Wei, Serdar Bulun, J. Brandon Parker, Grant D. Barish, Jun S. Song, Debabrata Chakravarti

Subjects: “…epigenomics…”
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Deconvolution of the Genomic and Epigenomic Interaction Landscape of Triple-Negative Breast Cancer by Jiande Wu, Tarun Karthik Kumar Mamidi, Lu Zhang, Chindo Hicks

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Perinatal Nutritional Reprogramming of the Epigenome Promotes Subsequent Development of Nonalcoholic Steatohepatitis by Luz Helena Gutierrez Sanchez, Kyoko Tomita, Qianqian Guo, Kunimaro Furuta, Husam Alhuwaish, Petra Hirsova, Saurabh Baheti, Bonnie Alver, Ryan Hlady, Keith D. Robertson, Samar H. Ibrahim

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Functional Variants Identified Efficiently through an Integrated Transcriptome and Epigenome Analysis by Fanlin Meng, Guohong Yuan, Xiurui Zhu, Yiming Zhou, Dong Wang, Yong Guo

“…Here, we proposed a new strategy termed integrated transcriptome and epigenome analysis (iTEA) to identify functional genetic variants in non-coding elements. …”
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Epigenomic signature of major congenital heart defects in newborns with Down syndrome by Julia S. Mouat, Shaobo Li, Swe Swe Myint, Benjamin I. Laufer, Philip J. Lupo, Jeremy M. Schraw, John P. Woodhouse, Adam J. de Smith, Janine M. LaSalle

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CUT&Tag for efficient epigenomic profiling of small samples and single cells by Hatice S. Kaya-Okur, Steven J. Wu, Christine A. Codomo, Erica S. Pledger, Terri D. Bryson, Jorja G. Henikoff, Kami Ahmad, Steven Henikoff

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Influence of pathogens on host genome and epigenome in development of head and neck cancer by Sanket Desai

“…This review focuses on the effect of opportunistic pathogens on the host genome and epigenome, which contributes to the disease progression. …”
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Comparison of Genomic and Epigenomic Expression in Monozygotic Twins Discordant for Rett Syndrome. by Kunio Miyake, Chunshu Yang, Yohei Minakuchi, Kenta Ohori, Masaki Soutome, Takae Hirasawa, Yasuhiro Kazuki, Noboru Adachi, Seiko Suzuki, Masayuki Itoh, Yu-Ichi Goto, Tomoko Andoh, Hiroshi Kurosawa, Mitsuo Oshimura, Masayuki Sasaki, Atsushi Toyoda, Takeo Kubota

“…Here, we report the genomic and epigenomic sequences in skin fibroblasts of a discordant monozygotic twin pair with Rett syndrome, an X-linked neurodevelopmental disorder characterized by autistic features, epileptic seizures, gait ataxia and stereotypical hand movements. …”
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Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF. by Xiaogang Cheng, Ancy Joseph, Victor Castro, Alice Chen-Liaw, Zachary Skidmore, Takaharu Ueno, Jun-Ichi Fujisawa, Daniel A Rauch, Grant A Challen, Michael P Martinez, Patrick Green, Malachi Griffith, Jacqueline E Payton, John R Edwards, Lee Ratner

“…The integrated provirus includes a single binding site for the epigenomic insulator, CCCTC-binding protein (CTCF), but its function remains unclear. …”
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PEGR: a flexible management platform for reproducible epigenomic and genomic research by Danying Shao, Gretta D. Kellogg, Ali Nematbakhsh, Prashant K. Kuntala, Shaun Mahony, B. Franklin Pugh, William K. M. Lai

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Residential surrounding greenness and DNA methylation: An epigenome-wide association study by Rongbin Xu, Shuai Li, Shanshan Li, Ee Ming Wong, Melissa C. Southey, John L. Hopper, Michael J. Abramson, Yuming Guo

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Next-Generation Sequencing and Epigenomics Research: A Hammer in Search of Nails by Shrutii Sarda, Sridhar Hannenhalli

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An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer by Evanguelos Xylinas, Melanie R. Hassler, Dazhong Zhuang, Martin Krzywinski, Zeynep Erdem, Brian D. Robinson, Olivier Elemento, Thomas Clozel, Shahrokh F. Shariat

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Epigenomics of being bullied: changes in DNA methylation following bullying exposure by Rosa H. Mulder, Esther Walton, Alexander Neumann, Lotte C. Houtepen, Janine F. Felix, Marian J. Bakermans-Kranenburg, Matthew Suderman, Henning Tiemeier, Marinus H. van IJzendoorn, Caroline L. Relton, Charlotte A. M. Cecil

“…However, little is known about the biological pathways that change after exposure to bullying. Epigenome-wide changes in DNA methylation in peripheral blood were studied from pre- to post measurement of bullying exposure, in a longitudinal study of the population-based Generation R Study and Avon Longitudinal Study of Parents and Children (combined n = 1,352). …”
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Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity by Wen Fong Ooi, Manjie Xing, Chang Xu, Xiaosai Yao, Muhammad Khairul Ramlee, Mei Chee Lim, Fan Cao, Kevin Lim, Deepak Babu, Lai-Fong Poon, Joyce Lin Suling, Aditi Qamra, Astrid Irwanto, James Qu Zhengzhong, Tannistha Nandi, Ai Ping Lee-Lim, Yang Sun Chan, Su Ting Tay, Ming Hui Lee, James O. J. Davies, Wai Keong Wong, Khee Chee Soo, Weng Hoong Chan, Hock Soo Ong, Pierce Chow, Chow Yin Wong, Sun Young Rha, Jianjun Liu, Axel M. Hillmer, Jim R. Hughes, Steve Rozen, Bin Tean Teh, Melissa Jane Fullwood, Shang Li, Patrick Tan

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Genomics and Epigenomics in the Molecular Biology of Melanoma—A Prerequisite for Biomarkers Studies by Daniela Luminita Zob, Iolanda Augustin, Lavinia Caba, Monica-Cristina Panzaru, Setalia Popa, Alina Delia Popa, Laura Florea, Eusebiu Vlad Gorduza

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MESIA: multi-epigenome sample integration approach for precise peak calling by Seung Gwa Park, Woo-Jin Kim, Jae-I Moon, Ki-Tae Kim, Hyun-Mo Ryoo

“…MESIA is a shell-script-based open-source code that provides researchers involved in the epigenome with comprehensive insights.…”
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Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag by Steven Henikoff, Jorja G. Henikoff, Kami Ahmad, Ronald M. Paranal, Derek H. Janssens, Zachary R. Russell, Frank Szulzewsky, Sita Kugel, Eric C. Holland

“…However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. …”
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