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Autor:
J Charalel, Marina Sirota, Katharine Yu, Christina Yau, Theodore C. Goldstein, Bin Chen, Denise M. Wolf, Atul J. Butte, Dvir Aran, L.J. van 't Veer
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Nature communications, vol 10, iss 1
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications
Cancer cell lines are a cornerstone of cancer research but previous studies have shown that not all cell lines are equal in their ability to model primary tumors. Here we present a comprehensive pan-cancer analysis utilizing transcriptomic profiles f
Autor:
Elior Rahmani, Lisa F. Barcellos, Saharon Rosset, Regev Schweiger, Brooke Rhead, Sriram Sankararaman, Eleazar Eskin, Eran Halperin, Lindsey A. Criswell
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Nature communications, vol 10, iss 1
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications
High costs and technical limitations of cell sorting and single-cell techniques currently restrict the collection of large-scale, cell-type-specific DNA methylation data. This, in turn, impedes our ability to tackle key biological questions that pert
Autor:
Mart Krupovic, Matthew B. Sullivan, Charlotte Guyomar, Carolina Megumi Mizuno, Francisco Rodriguez-Valera, Reynald Gillet, Régis Lavigne, Patrick Forterre, Simon Roux
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Nature Communications
Mizuno, CM; Guyomar, C; Roux, S; Lavigne, R; Rodriguez-Valera, F; Sullivan, M; et al.(2017). Numerous cultivated and uncultivated viruses encode ribosomal proteins. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/3mr361nf
Nature Communications, 2019, 10 (1), pp.752. ⟨10.1038/s41467-019-08672-6⟩
Nature communications, vol 10, iss 1
Nature Communications, Nature Publishing Group, 2019, 10 (1), pp.752. ⟨10.1038/s41467-019-08672-6⟩
Mizuno, Carolina M; Guyomar, Charlotte; Roux, Simon; Lavigne, Régis; Rodriguez-Valera, Francisco; Sullivan, Matthew B; et al.(2019). Numerous cultivated and uncultivated viruses encode ribosomal proteins.. Nature communications, 10(1), 752. doi: 10.1038/s41467-019-08672-6. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/8f0519r0
Nature Communications
Mizuno, CM; Guyomar, C; Roux, S; Lavigne, R; Rodriguez-Valera, F; Sullivan, M; et al.(2017). Numerous cultivated and uncultivated viruses encode ribosomal proteins. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/3mr361nf
Nature Communications, 2019, 10 (1), pp.752. ⟨10.1038/s41467-019-08672-6⟩
Nature communications, vol 10, iss 1
Nature Communications, Nature Publishing Group, 2019, 10 (1), pp.752. ⟨10.1038/s41467-019-08672-6⟩
Mizuno, Carolina M; Guyomar, Charlotte; Roux, Simon; Lavigne, Régis; Rodriguez-Valera, Francisco; Sullivan, Matthew B; et al.(2019). Numerous cultivated and uncultivated viruses encode ribosomal proteins.. Nature communications, 10(1), 752. doi: 10.1038/s41467-019-08672-6. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/8f0519r0
Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference
Autor:
Jaeson Calla, Elizabeth A. Winzeler, Alyaa Mohamed, Zaira Hellen Villa Galarce, Gregory LaMonte, Annie N. Cowell, Bing Yu Zou, Lawrence T. Wang, Joseph M. Vinetz, Justine Swann, Carlos Tong Rios, Pamela Orjuela-Sánchez, Shangzhong Li, Marta Moreno, Nathan E. Lewis
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-13 (2019)
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications
Nature communications, vol 10, iss 1
The exoerythrocytic stage of Plasmodium infection is a critical window for prophylactic intervention. Using genome-wide dual RNA sequencing of flow-sorted infected and uninfected hepatoma cells we show that the human mucosal immunity gene, mucin-13 (
Autor:
Zhonghua Zhang, Elisabet Johansson, Samriddha Ray, Lisa J. Martin, Kathryn A. Wikenheiser-Brokamp, Mariana L. Stevens, Hong Ji, Gurjit K. Khurana Hershey, Matthew T. Weirauch, Brandy P. Ruff, Arjun Kothari, Jocelyn M. Biagini Myers, Dorothy M. Supp, Amrita Jagpal, Hua He
Publikováno v:
Nature Communications
Nature communications, vol 11, iss 1
Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
Nature communications, vol 11, iss 1
Nature Communications, Vol 11, Iss 1, Pp 1-10 (2020)
Single nucleotide polymorphisms (SNPs) in the gene encoding kinesin family member 3A, KIF3A, have been associated with atopic dermatitis (AD), a chronic inflammatory skin disorder. We find that KIF3A SNP rs11740584 and rs2299007 risk alleles create c
Autor:
Travis J. Meyers, Jun Shan, Thomas J. Hoffmann, Donglei Hu, Rajdeep Das, Stephen K. Van Den Eeden, John S. Witte, Felix Y. Feng, Joshua D. Hoffman, Elad Ziv, Linda Kachuri, Nima C. Emami
Publikováno v:
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Here we train cis-regulatory models of prostate tissue gene expression and impute expression transcriptome-wide for 233,955 European ancestry men (14,616 prostate cancer (PrCa) cases, 219,339 controls) from two large cohorts. Among 12,014 genes evalu
Autor:
Diane Salamon, Eric H. Kim, Derek Gao, Nongluk Plongthongkum, Joseph P. Gaut, Ramakrishna Venkatesh, Amanda Knoten, Anitha Vijayan, Song Chen, Sanjay Jain, Blue B. Lake, Masato Hoshi, Kun Zhang
Publikováno v:
Nature Communications
Nature Communications, Vol 10, Iss 1, Pp 1-15 (2019)
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-15 (2019)
Nature communications, vol 10, iss 1
Defining cellular and molecular identities within the kidney is necessary to understand its organization and function in health and disease. Here we demonstrate a reproducible method with minimal artifacts for single-nucleus Droplet-based RNA sequenc
Autor:
Nikita Kadakia, Jian Yan, Joseph Avruch, Anthony Aylward, Dana Kramer, Kelly A. Frazer, Laura Regué, Jee Yun Han, Kyle J. Gaulton, David U. Gorkin, Liliana Minichiello, Nicholas Vinckier, Maike Sander, Ning Dai, Joshua Chiou, Mei-Lin Okino, Frauke Drees, Naoki Nariai, William W. Greenwald, Allen Wang, Bing Ren, Yunjiang Qiu
Publikováno v:
Nature Communications
Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)
Nature communications, vol 10, iss 1
Genetic variants affecting pancreatic islet enhancers are central to T2D risk, but the gene targets of islet enhancer activity are largely unknown. We generate a high-resolution map of islet chromatin loops using Hi-C assays in three islet samples an
Autor:
Moli Huang, Jonathan W. Said, Ling-Wen Ding, Mark Edward Puhaindran, Angela Pang, H. Phillip Koeffler, Yan-Yi Jiang, Boon Cher Goh, Sigal Gery, Tuan Zea Tan, Xin-Yu Ke, Deepika Kanojia, Pushkar Dakle, Liang Xu, Jianxiang Chen, Ye Chen, Anand Mayakonda, Ruby Yu-Tong Lin
Publikováno v:
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Nature Communications
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Nature Communications
Liposarcomas (LPSs) are a group of malignant mesenchymal tumors showing adipocytic differentiation. Here, to gain insight into the enhancer dysregulation and transcriptional addiction in this disease, we chart super-enhancer structures in both LPS ti
Autor:
Bong Hyun Sung, Bernhard O. Palsson, Jun Hyoung Lee, Sun Chang Kim, Donghui Choe, Minseob Yoo, Soonkyu Hwang, Suhyung Cho, Byung-Kwan Cho
Publikováno v:
Nature Communications
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Nature communications, vol 10, iss 1
Nature Communications, Vol 10, Iss 1, Pp 1-14 (2019)
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be under