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3. Author Correction: Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) were mistakenly omitted from the ENCODE Project Consortium author list. The original Article has been corrected online.

Published
2022

4. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author

Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
ENCODE Project Consortium, General Science & Technology
Abstract

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article.

Published
2022

8. Subtype-specific 3D genome alteration in acute myeloid leukaemia

Author

Xu, Jie, Song, Fan, Lyu, Huijue, Kobayashi, Mikoto, Zhang, Baozhen, Zhao, Ziyu, Hou, Ye, Wang, Xiaotao, Luan, Yu, Jia, Bei, Stasiak, Lena, Wong, Josiah Hiu-yuen, Wang, Qixuan, Jin, Qi, Jin, Qiushi, Fu, Yihao, Yang, Hongbo, Hardison, Ross C., Dovat, Sinisa, Platanias, Leonidas C., Diao, Yarui, Yang, Yue, Yamada, Tomoko, Viny, Aaron D., Levine, Ross L., Claxton, David, Broach, James. R., Zheng, Hong, and Yue, Feng

Published
2022
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9. CTCF blocks antisense transcription initiation at divergent promoters

Author

Luan, Jing, Vermunt, Marit W., Syrett, Camille M., Coté, Allison, Tome, Jacob M., Zhang, Haoyue, Huang, Anran, Luppino, Jennifer M., Keller, Cheryl A., Giardine, Belinda M., Zhang, Shiping, Dunagin, Margaret C., Zhang, Zhe, Joyce, Eric F., Lis, John T., Raj, Arjun, Hardison, Ross C., and Blobel, Gerd A.

Published
2022
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11. The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Author

He, Peng, Williams, Brian A, Trout, Diane, Marinov, Georgi K, Amrhein, Henry, Berghella, Libera, Goh, Say-Tar, Plajzer-Frick, Ingrid, Afzal, Veena, Pennacchio, Len A, Dickel, Diane E, Visel, Axel, Ren, Bing, Hardison, Ross C, Zhang, Yu, and Wold, Barbara J

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Cancer Genomics, Cancer, Biotechnology, Pediatric, Stem Cell Research, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Cell Differentiation, Cell Lineage, Chromatin, Embryo, Mammalian, Embryonic Development, Enhancer Elements, Genetic, Epigenomics, Extremities, Female, Gene Expression Regulation, Developmental, Male, Mice, Poly A, Promoter Regions, Genetic, RNA-Seq, Single-Cell Analysis, Transcription Factors, Transcriptome, General Science & Technology
Abstract

During mammalian embryogenesis, differential gene expression gradually builds the identity and complexity of each tissue and organ system1. Here we systematically quantified mouse polyA-RNA from day 10.5 of embryonic development to birth, sampling 17 tissues and organs. The resulting developmental transcriptome is globally structured by dynamic cytodifferentiation, body-axis and cell-proliferation gene sets that were further characterized by the transcription factor motif codes of their promoters. We decomposed the tissue-level transcriptome using single-cell RNA-seq (sequencing of RNA reverse transcribed into cDNA) and found that neurogenesis and haematopoiesis dominate at both the gene and cellular levels, jointly accounting for one-third of differential gene expression and more than 40% of identified cell types. By integrating promoter sequence motifs with companion ENCODE epigenomic profiles, we identified a prominent promoter de-repression mechanism in neuronal expression clusters that was attributable to known and novel repressors. Focusing on the developing limb, single-cell RNA data identified 25 candidate cell types that included progenitor and differentiating states with computationally inferred lineage relationships. We extracted cell-type transcription factor networks and complementary sets of candidate enhancer elements by using single-cell RNA-seq to decompose integrative cis-element (IDEAS) models that were derived from whole-tissue epigenome chromatin data. These ENCODE reference data, computed network components and IDEAS chromatin segmentations are companion resources to the matching epigenomic developmental matrix, and are available for researchers to further mine and integrate.

Published
2020

12. Perspectives on ENCODE

Author

Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Biotechnology, Human Genome, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Animals, Binding Sites, Chromatin, DNA Methylation, Databases, Genetic, Gene Expression Regulation, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Molecular Sequence Annotation, Quality Control, Regulatory Sequences, Nucleic Acid, Transcription Factors, ENCODE Project Consortium, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

13. Expanded encyclopaedias of DNA elements in the human and mouse genomes

Author

Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Chromatin, DNA, DNA Footprinting, DNA Methylation, DNA Replication Timing, Databases, Genetic, Deoxyribonuclease I, Genome, Genome, Human, Genomics, Histones, Humans, Mice, Mice, Transgenic, Molecular Sequence Annotation, RNA-Binding Proteins, Registries, Regulatory Sequences, Nucleic Acid, Transcription, Genetic, Transposases, ENCODE Project Consortium, General Science & Technology
Abstract

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Published
2020

14. Expanded encyclopaedias of DNA elements in the human and mouse genomes.

Author

ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, and Weng, Zhiping

Subjects
ENCODE Project Consortium, Chromatin, Animals, Mice, Transgenic, Humans, Mice, Deoxyribonuclease I, Transposases, RNA-Binding Proteins, Histones, DNA, Registries, DNA Footprinting, Genomics, DNA Methylation, DNA Replication Timing, Transcription, Genetic, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Databases, Genetic, Molecular Sequence Annotation, Human Genome, HIV/AIDS, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Published
2020

15. Perspectives on ENCODE.

Author

ENCODE Project Consortium, Snyder, Michael P, Gingeras, Thomas R, Moore, Jill E, Weng, Zhiping, Gerstein, Mark B, Ren, Bing, Hardison, Ross C, Stamatoyannopoulos, John A, Graveley, Brenton R, Feingold, Elise A, Pazin, Michael J, Pagan, Michael, Gilchrist, Daniel A, Hitz, Benjamin C, Cherry, J Michael, Bernstein, Bradley E, Mendenhall, Eric M, Zerbino, Daniel R, Frankish, Adam, Flicek, Paul, and Myers, Richard M

Subjects
ENCODE Project Consortium, Chromatin, Animals, Humans, Mice, Histones, Transcription Factors, Genomics, DNA Methylation, Gene Expression Regulation, Binding Sites, Regulatory Sequences, Nucleic Acid, Genome, Genome, Human, Quality Control, Databases, Genetic, Molecular Sequence Annotation, Human Genome, Vaccine Related, Biotechnology, Genetics, Immunization, Vaccine Related (AIDS), Prevention, 1.1 Normal biological development and functioning, Generic health relevance, General Science & Technology
Abstract

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Published
2020

22. A map of cis-regulatory elements and 3D genome structures in zebrafish

Author

Yang, Hongbo, Luan, Yu, Liu, Tingting, Lee, Hyung Joo, Fang, Li, Wang, Yanli, Wang, Xiaotao, Zhang, Bo, Jin, Qiushi, Ang, Khai Chung, Xing, Xiaoyun, Wang, Juan, Xu, Jie, Song, Fan, Sriranga, Iyyanki, Khunsriraksakul, Chachrit, Salameh, Tarik, Li, Daofeng, Choudhary, Mayank N. K., Topczewski, Jacek, Wang, Kai, Gerhard, Glenn S., Hardison, Ross C., Wang, Ting, Cheng, Keith C., and Yue, Feng

Published
2020
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24. Genome folding principles revealed in condensin-depleted mitotic chromosomes

Author

Zhao, Han, primary, Lin, Yinzhi, additional, Lin, En, additional, Liu, Fuhai, additional, Shu, Lirong, additional, Jing, Dannan, additional, Wang, Baiyue, additional, Wang, Manzhu, additional, Shan, Fengnian, additional, Zhang, Lin, additional, Lam, Jessica, additional, Midla, Susannah, additional, Giardine, Belinda, additional, Keller, Cheryl, additional, Hardison, Ross, additional, Blobel, Gerd, additional, and Zhang, Haoyue, additional

Published
2023
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30. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Author

Mortazavi, Ali, Pepke, Shirley, Jansen, Camden, Marinov, Georgi K, Ernst, Jason, Kellis, Manolis, Hardison, Ross C, Myers, Richard M, and Wold, Barbara J

Subjects
Cell Line, K562 Cells, Chromatin, Humans, Histones, Transcription Factors, Chromosome Mapping, Computational Biology, Algorithms, User-Computer Interface, Promoter Regions, Genetic, Data Mining, Human Umbilical Vein Endothelial Cells, Gene Ontology, Vaccine Related, Biotechnology, Human Genome, HIV/AIDS, Genetics, Underpinning research, 1.5 Resources and infrastructure (underpinning), Generic health relevance, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

We tested whether self-organizing maps (SOMs) could be used to effectively integrate, visualize, and mine diverse genomics data types, including complex chromatin signatures. A fine-grained SOM was trained on 72 ChIP-seq histone modifications and DNase-seq data sets from six biologically diverse cell lines studied by The ENCODE Project Consortium. We mined the resulting SOM to identify chromatin signatures related to sequence-specific transcription factor occupancy, sequence motif enrichment, and biological functions. To highlight clusters enriched for specific functions such as transcriptional promoters or enhancers, we overlaid onto the map additional data sets not used during training, such as ChIP-seq, RNA-seq, CAGE, and information on cis-acting regulatory modules from the literature. We used the SOM to parse known transcriptional enhancers according to the cell-type-specific chromatin signature, and we further corroborated this pattern on the map by EP300 (also known as p300) occupancy. New candidate cell-type-specific enhancers were identified for multiple ENCODE cell types in this way, along with new candidates for ubiquitous enhancer activity. An interactive web interface was developed to allow users to visualize and custom-mine the ENCODE SOM. We conclude that large SOMs trained on chromatin data from multiple cell types provide a powerful way to identify complex relationships in genomic data at user-selected levels of granularity.

Published
2013

33. Integrative annotation of chromatin elements from ENCODE data

Author

Hoffman, Michael M, Ernst, Jason, Wilder, Steven P, Kundaje, Anshul, Harris, Robert S, Libbrecht, Max, Giardine, Belinda, Ellenbogen, Paul M, Bilmes, Jeffrey A, Birney, Ewan, Hardison, Ross C, Dunham, Ian, Kellis, Manolis, and Noble, William Stafford

Subjects
Human Genome, Genetics, Generic health relevance, Chromatin, Enhancer Elements, Genetic, Genome, Human, Genome-Wide Association Study, Humans, Insulator Elements, Molecular Sequence Annotation, Promoter Regions, Genetic, Proteins, Regulatory Elements, Transcriptional, Terminator Regions, Genetic, Transcription, Genetic, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape.

Published
2013

34. Integrative detection and analysis of structural variation in cancer genomes

Author

Dixon, Jesse R., Xu, Jie, Dileep, Vishnu, Zhan, Ye, Song, Fan, Le, Victoria T., Yardımcı, Galip Gürkan, Chakraborty, Abhijit, Bann, Darrin V., Wang, Yanli, Clark, Royden, Zhang, Lijun, Yang, Hongbo, Liu, Tingting, Iyyanki, Sriranga, An, Lin, Pool, Christopher, Sasaki, Takayo, Rivera-Mulia, Juan Carlos, Ozadam, Hakan, Lajoie, Bryan R., Kaul, Rajinder, Buckley, Michael, Lee, Kristen, Diegel, Morgan, Pezic, Dubravka, Ernst, Christina, Hadjur, Suzana, Odom, Duncan T., Stamatoyannopoulos, John A., Broach, James R., Hardison, Ross C., Ay, Ferhat, Noble, William Stafford, Dekker, Job, Gilbert, David M., and Yue, Feng

Published
2018
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35. Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Author

Xiang, Guanjue, primary, He, Xi, additional, Giardine, Belinda M., additional, Weaver, Kathryn J., additional, Taylor, Dylan J., additional, McCoy, Rajiv C., additional, Jansen, Camden, additional, Keller, Cheryl A., additional, Wixom, Alexander Q., additional, Cockburn, April, additional, Miller, Amber, additional, Qi, Qian, additional, He, Yanghua, additional, Li, Yichao, additional, Lichtenberg, Jens, additional, Heuston, Elisabeth F., additional, Anderson, Stacie M., additional, Luan, Jing, additional, Vermunt, Marit W., additional, Yue, Feng, additional, Sauria, Michael E.G., additional, Schatz, Michael C., additional, Taylor, James, additional, Göttgens, Berthold, additional, Hughes, Jim R., additional, Higgs, Douglas R., additional, Weiss, Mitchell J., additional, Cheng, Yong, additional, Blobel, Gerd A., additional, Bodine, David, additional, Zhang, Yu, additional, Li, Qunhua, additional, Mahony, Shaun, additional, and Hardison, Ross C., additional

Published
2023
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36. Gene silencing dynamics are modulated by transiently active regulatory elements

Author

Vermunt, Marit W., primary, Luan, Jing, additional, Zhang, Zhe, additional, Thrasher, A. Josephine, additional, Huang, Anran, additional, Saari, Megan S., additional, Khandros, Eugene, additional, Beagrie, Robert A., additional, Zhang, Shiping, additional, Vemulamada, Pranay, additional, Brilleman, Matilda, additional, Lee, Kiwon, additional, Yano, Jennifer A., additional, Giardine, Belinda M., additional, Keller, Cheryl A., additional, Hardison, Ross C., additional, and Blobel, Gerd A., additional

Published
2023
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44. Mechanisms of Polycomb Group Protein-Mediated Fetal Hemoglobin Silencing

Author

Qin, Kunhua, primary, Huang, Peng, additional, Lan, Xianjiang, additional, Saari, Megan S., additional, Khandros, Eugene, additional, Abdulmalik, Osheiza Y., additional, Keller, Cheryl A., additional, Giardine, Belinda M., additional, Hardison, Ross C., additional, Shi, Junwei, additional, and Blobel, Gerd A., additional

Published
2022
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47. A genome-editing strategy to treat [beta]-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition

Author

Traxler, Elizabeth A, Yao, Yu, Wang, Yong-Dong, Woodard, Kaitly J, Kurita, Ryo, Nakamura, Yukio, Hughes, Jim R, Hardison, Ross C, Blobel, Gerd A, Li, Chunliang, and Weiss, Mitchell J

Subjects
Genetic engineering -- Methods, Hemoglobinopathies -- Genetic aspects -- Diagnosis -- Care and treatment, Gene mutation -- Identification and classification, Biological sciences, Health
Abstract

Author(s): Elizabeth A Traxler [1, 2]; Yu Yao [1]; Yong-Dong Wang [3]; Kaitly J Woodard [1]; Ryo Kurita [4]; Yukio Nakamura [4, 5]; Jim R Hughes [6]; Ross C Hardison [...]

Published
2016
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48. Abstract 2953: Subtype-specific and structure variation induced 3D genome alteration in acute myeloid leukemia

Author

Xu, Jie, primary, Song, Fan, additional, Zhang, Baozhen, additional, Lyu, Huijue, additional, Kobayashi, Mikoto, additional, Zhao, Ziyu, additional, Hou, Ye, additional, Wang, Xiaotao, additional, Luan, Yu, additional, Jia, Bei, additional, Stasiak, Lena, additional, Wang, Qixuan, additional, Jin, Qi, additional, Jin, Qiushi, additional, Fu, Yihao, additional, Hardison, Ross C., additional, Dovat, Sinisa, additional, Platanias, Leonidas C., additional, Yang, Yue, additional, Yamada, Tomoko, additional, Viny, Aaron D., additional, Levine, Ross L., additional, Claxton, David F., additional, Broach, James R., additional, Zheng, Hong, additional, and Yue, Feng, additional

Published
2022
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49. Comparative Genomics

Author

Hardison, Ross C., Speicher, Michael R., editor, Motulsky, Arno G., editor, and Antonarakis, Stylianos E., editor

Published
2010
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