Breakage fusion bridge cycles drive high oncogene number with moderate intratumoural heterogeneity

Authors: Siavash Raeisi Dehkordi, Ivy Tsz-Lo Wong, Jing Ni, Jens Luebeck, Kaiyuan Zhu, Gino Prasad, Lena Krockenberger, Guanghui Xu, Biswanath Chowdhury, Utkrisht Rajkumar, Ann Caplin, Daniel Muliaditan, Aditi Gnanasekar, Ceyda Coruh, Qiushi Jin, Kristen Turner, Shu Xian Teo, Andy Wing Chun Pang, Ludmil B. Alexandrov, Christelle En Lin Chua, Frank B. Furnari, John Maciejowski, Thomas G. Paulson, Julie A. Law, Howard Y. Chang, Feng Yue, Ramanuj DasGupta, Jean Zhao, Paul S. Mischel, Vineet Bafna

Source: Nature Communications, Vol 16, Iss 1, Pp 1-19 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

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Chromatin activity identifies differential gene regulation across human ancestries

Authors: Kade P. Pettie, Maxwell Mumbach, Amanda J. Lea, Julien Ayroles, Howard Y. Chang, Maya Kasowski, Hunter B. Fraser

Source: Genome Biology, Vol 25, Iss 1, Pp 1-23 (2024)

Subject Terms: HiChIP, Activity-by-Contact, Cis-regulation, Enhancer, bQTL, Gene expression, Biology (General), QH301-705.5, Genetics, QH426-470

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Relation: https://doaj.org/toc/1474-760X

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Charge-altering releasable transporters enhance mRNA delivery in vitro and exhibit in vivo tropism

Authors: Zhijian Li, Laura Amaya, Ruoxi Pi, Sean K. Wang, Alok Ranjan, Robert M. Waymouth, Catherine A. Blish, Howard Y. Chang, Paul A. Wender

Source: Nature Communications, Vol 14, Iss 1, Pp 1-15 (2023)

Subject Terms: Science

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Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/9e61f17a635449b78342282fbc40e058

Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature

Authors: Eloise Berson, Anjali Sreenivas, Thanaphong Phongpreecha, Amalia Perna, Fiorella C. Grandi, Lei Xue, Neal G. Ravindra, Neelufar Payrovnaziri, Samson Mataraso, Yeasul Kim, Camilo Espinosa, Alan L. Chang, Martin Becker, Kathleen S. Montine, Edward J. Fox, Howard Y. Chang, M. Ryan Corces, Nima Aghaeepour, Thomas J. Montine

Source: Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/05827f0fc6bd405d8f51032b99aead11

The AAV capsid can influence the epigenetic marking of rAAV delivered episomal genomes in a species dependent manner

Authors: Adriana Gonzalez-Sandoval, Katja Pekrun, Shinnosuke Tsuji, Feijie Zhang, King L. Hung, Howard Y. Chang, Mark A. Kay

Source: Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/d62aaf6b8f6e41b794d5bf3b8b68ef81

Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer’s disease

Authors: Min Yu, Yage Nie, Jiawen Yang, Shilun Yang, Rui Li, Varsha Rao, Xiaoyan Hu, Cheng Fang, Simeng Li, Dengpan Song, Fuyou Guo, Michael P. Snyder, Howard Y. Chang, Calvin J. Kuo, Jin Xu, Junlei Chang

Source: Cell Reports, Vol 42, Iss 11, Pp 113392- (2023)

Subject Terms: CP: Neuroscience, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124723014043; https://doaj.org/toc/2211-1247

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The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1

Authors: Bahareh Haddad Derafshi, Tamas Danko, Soham Chanda, Pedro J. Batista, Ulrike Litzenburger, Qian Yi Lee, Yi Han Ng, Anu Sebin, Howard Y. Chang, Thomas C. Südhof, Marius Wernig

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-28 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/f6144c8eb12747dd9d2726213f094bb0

KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress

Authors: Jan-Renier Moonen, James Chappell, Minyi Shi, Tsutomu Shinohara, Dan Li, Maxwell R. Mumbach, Fan Zhang, Ramesh V. Nair, Joseph Nasser, Daniel H. Mai, Shalina Taylor, Lingli Wang, Ross J. Metzger, Howard Y. Chang, Jesse M. Engreitz, Michael P. Snyder, Marlene Rabinovitch

Source: Nature Communications, Vol 13, Iss 1, Pp 1-16 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/dd0de669b721470b8265ca8d188386af

Locus specific epigenetic modalities of random allelic expression imbalance

Authors: Lucile Marion-Poll, Benjamin Forêt, Dina Zielinski, Florian Massip, Mikael Attia, Ava C. Carter, Laurène Syx, Howard Y. Chang, Anne-Valerie Gendrel, Edith Heard

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/b793b4a1019a4a6fa1acd10a7e4751c8

Chromatin accessibility associates with protein-RNA correlation in human cancer

Authors: Akshay Sanghi, Joshua J. Gruber, Ahmed Metwally, Lihua Jiang, Warren Reynolds, John Sunwoo, Lisa Orloff, Howard Y. Chang, Maya Kasowski, Michael P. Snyder

Source: Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

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Structural modularity of the XIST ribonucleoprotein complex

Authors: Zhipeng Lu, Jimmy K. Guo, Yuning Wei, Diana R. Dou, Brian Zarnegar, Qing Ma, Rui Li, Yang Zhao, Fan Liu, Hani Choudhry, Paul A. Khavari, Howard Y. Chang

Source: Nature Communications, Vol 11, Iss 1, Pp 1-14 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/ce192c166d4848879fbe0c187c228701

Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis

Authors: Qian Liu, Lisa C. Zaba, Ansuman T. Satpathy, Michelle Longmire, Wen Zhang, Kun Li, Jeffrey Granja, Chuang Guo, Jun Lin, Rui Li, Karen Tolentino, Gabriela Kania, Oliver Distler, David Fiorentino, Lorinda Chung, Kun Qu, Howard Y. Chang

Source: Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/136a9ffc01a74f60ae540dd0b3a7288f

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications

Authors: Jingwen Fang, Qing Ma, Ci Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Erisse Martin Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang

Source: Genome Biology, Vol 20, Iss 1, Pp 1-21 (2019)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/5122f9dc0f75472ca820e5eee9f8092a

Functional significance of U2AF1 S34F mutations in lung adenocarcinomas

Authors: Mohammad S. Esfahani, Luke J. Lee, Young-Jun Jeon, Ryan A. Flynn, Henning Stehr, Angela B. Hui, Noriko Ishisoko, Eric Kildebeck, Aaron M. Newman, Scott V. Bratman, Matthew H. Porteus, Howard Y. Chang, Ash A. Alizadeh, Maximilian Diehn

Source: Nature Communications, Vol 10, Iss 1, Pp 1-13 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/0437a662c77043ed87f4f0be71eb3a88

GWAS for systemic sclerosis identifies multiple risk loci and highlights fibrotic and vasculopathy pathways

Authors: Elena López-Isac, Marialbert Acosta-Herrera, Martin Kerick, Shervin Assassi, Ansuman T. Satpathy, Jeffrey Granja, Maxwell R. Mumbach, Lorenzo Beretta, Carmen P. Simeón, Patricia Carreira, Norberto Ortego-Centeno, Ivan Castellvi, Lara Bossini-Castillo, F. David Carmona, Gisela Orozco, Nicolas Hunzelmann, Jörg H. W. Distler, Andre Franke, Claudio Lunardi, Gianluca Moroncini, Armando Gabrielli, Jeska de Vries-Bouwstra, Cisca Wijmenga, Bobby P. C. Koeleman, Annika Nordin, Leonid Padyukov, Anna-Maria Hoffmann-Vold, Benedicte Lie, European Scleroderma Group, Susanna Proudman, Wendy Stevens, Mandana Nikpour, Australian Scleroderma Interest Group (ASIG), Timothy Vyse, Ariane L. Herrick, Jane Worthington, Christopher P. Denton, Yannick Allanore, Matthew A. Brown, Timothy R. D. J. Radstake, Carmen Fonseca, Howard Y. Chang, Maureen D. Mayes, Javier Martin

Source: Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/2c83b5b19dd94142a96da7824aa29e78

Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions

Authors: Rajarshi P. Ghosh, Quanming Shi, Linfeng Yang, Michael P. Reddick, Tatiana Nikitina, Victor B. Zhurkin, Polly Fordyce, Timothy J. Stasevich, Howard Y. Chang, William J. Greenleaf, Jan T. Liphardt

Source: Nature Communications, Vol 10, Iss 1, Pp 1-16 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/c785b7867538444e850f8a448f988344

fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins

Authors: Meredith Corley, Ryan A. Flynn, Steven M. Blue, Brian A. Yee, Howard Y. Chang, Gene W. Yeo

Source: STAR Protocols, Vol 2, Iss 3, Pp 100762- (2021)

Subject Terms: Genomics, RNAseq, Molecular Biology, Antibody, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166721004688; https://doaj.org/toc/2666-1667

Access URL: https://doaj.org/article/9b2ac54000f94ebe9fde6319b126b28e

Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE

Authors: Lu Chen, Howard Y. Chang, Steven E. Artandi

Source: STAR Protocols, Vol 2, Iss 2, Pp 100477- (2021)

Subject Terms: Cell separation/fractionation, Sequencing, RNA-seq, Molecular Biology, Gene Expression, CRISPR, Science (General), Q1-390

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666166721001842; https://doaj.org/toc/2666-1667

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Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity

Authors: Rebecca Leylek, Marcela Alcántara-Hernández, Jeffrey M. Granja, Michael Chavez, Kimberly Perez, Oscar R. Diaz, Rui Li, Ansuman T. Satpathy, Howard Y. Chang, Juliana Idoyaga

Source: Cell Reports, Vol 32, Iss 12, Pp 108180- (2020)

Subject Terms: ATAC-seq, human, dendritic cells, plasmacytoid dendritic cells, pDCs, transitional dendritic cells, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124720311694; https://doaj.org/toc/2211-1247

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QS25. Conservation of the Fibroblast Programming Response to Solid Organ Tumors Suggests Novel Treatment Strategies Targeting the Mgp and Cd26 Surface Receptors

Authors: Michael Januszyk, MD, PhD, Deshka S. Foster, MD, PhD, Kathryn E. Yost, PhD, Malini Chinta, BS, Nicholas Guardino, BS, Kellen Chen, PhD, Dominic Henn, MD, Daniel Delitto, MD, PhD, Derrick C. Wan, MD, Jeffrey A. Norton, MD, Howard Y. Chang, MD PhD, Geoffrey C. Gurtner, MD, Michael T. Longaker, MD

Source: Plastic and Reconstructive Surgery, Global Open, Vol 10, Iss 6S, Pp 105-105 (2022)

Subject Terms: Surgery, RD1-811

File Description: electronic resource

Relation: http://journals.lww.com/prsgo/fulltext/10.1097/01.GOX.0000842952.70200.36; https://doaj.org/toc/2169-7574

Access URL: https://doaj.org/article/159fce26513943a09c3d49320e905e13