Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

Autor: Alison D. Tang, Cameron M. Soulette, Marijke J. van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J. Wu, Angela N. Brooks

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

Long-read sequencing is useful in determining exon-connectivity of full-length mRNA isoforms. Here, by long-read nanopore sequencing, the authors report that intron retention is downregulated in SF3B1 mutant chronic lymphocytic leukemia cells than no

Externí odkaz: https://doaj.org/article/6a806ecaedad4c65b48bc9c6561be042

Common Workflow Language User Guide

Autor: Alain Domissy, Andrew Jesaitis, bamiwoaluko, Benjamin Carr, Michele Mastropietro, Emannuel Fernandes de Oliveira Carvalho, Eugene Miloslavsky, Robin Long, Ngumih Fien, Mary Gathoni, Henry Liu, Marijke J. van Baren, jessMaia, Bruno P. Kinoshita, Kaushik Ghose, Konstantin Taletskiy, Kushal Beniwal, Mark A. Jensen, Levai Mackenzie Ágbàrà, Manabu Ishii, medcelerate, Michael R. Crusoe, Ruth B. McCole, sersorrel, Adrian Sharma, Steffen Möller, Oghenemaro Akpobi, Stian Soiland-Reyes, Luka Stojanovic, Sarah Wait Zaranek, Peter Amstutz, Toby Hodges, Tomoya Tanjo, Daiki Tsuchiya, Wolfgang Gerlach, Zipho Mashologu

Common Workflow Language User Guide

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::680552fbb787d2ca291a50b85fd60749

Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla.

Autor: Peter H Waltman, Jian Guo, Emily Nahas Reistetter, Samuel Purvine, Charles K Ansong, Marijke J van Baren, Chee-Hong Wong, Chia-Lin Wei, Richard D Smith, Stephen J Callister, Joshua M Stuart, Alexandra Z Worden

Publikováno v: PLoS ONE, Vol 11, Iss 7, p e0155839 (2016)

Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote (

Externí odkaz: https://doaj.org/article/2584346cad1842d9bc0f7c2bc0019081

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

Autor: Andrew Lamb, David Haan, Mark Akeson, Thea Norman, Kyle Ellrott, John D. Watson, Jin Zhang, Yifan Wang, Hongjiu Zhang, Cu Nguyen, Yin Hu, Justin Guinney, Alex Buchanan, Dmitri V. Rozanov, Brian J. Haas, Miten Jain, Mehmet Eren Ahsen, Ryan Spangler, Gustavo Stolovitzky, Yuanfang Guan, Marijke J. van Baren, Christopher Sugai, Jing Woei Li, Paul C. Boutros, Joshua M. Stuart, Allison L. Creason, Alokkumar Jha, Cristian Caloian, Alexander Dobin, Christopher G. Maher, Sebastian Uhrig, Kristen K. Dang, Thomas Yu, M. Rick Rollins, Matthew Inkman, Kami E. Chiotti, Paul T. Spellman

Publikováno v: Cell Syst

The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ba6122c78673179e00de4168748d4a88
https://doi.org/10.1016/j.cels.2021.05.021

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

Autor: Emily Nahas Reistetter, Sebastian Sudek, Jane Grimwood, Jeremy Schmutz, Charles Bachy, Samuel O. Purvine, Camille Poirier, Richard D. Smith, Alan Kuo, Marijke J. van Baren, Chee Hong Wong, Thomas J. Deerinck, Igor V. Grigoriev, Hang Yu, Chia-Lin Wei, Alexandra Z. Worden, Stephen J. Callister

Publikováno v: BMC genomics, vol 17, iss 1
BMC Genomics, 17 (1). Art.Nr. 267.
van Baren, MJ; Bachy, C; Reistetter, EN; Purvine, SO; Grimwood, J; Sudek, S; et al.(2016). Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics, 17(1). doi: 10.1186/s12864-016-2585-6. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/4n11p2r6
BMC Genomics

Background Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a2d651bd1e6bf0645a094b276a6fc95c
https://escholarship.org/uc/item/4n11p2r6