Efficient assembly of nanopore reads via highly accurate and intact error correction

Autor: Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao

Publikováno v: Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)

Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopor

Externí odkaz: https://doaj.org/article/38b07015c4a4482d87dff528f09c3e09

MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification

Autor: Yao-Xin Wang, Siqian Yang, Ying Chen, Qi Dai

Publikováno v: Frontiers in Genetics, Vol 11 (2020)
Frontiers in Genetics

DNA N6-methyladenine (6mA) modification has been discovered as the most prevalent DNA modification in prokaryotes and eukaryotes, involving gene expression, DNA replication and repair, and host-pathogen interactions. Single-molecule real-time sequenc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::36c23df2dd920939eca0c33b2b6ef13d
https://www.frontiersin.org/article/10.3389/fgene.2020.00269/full

Cytogenetic prognostication within medulloblastoma subgroups.

Autor: Shih DJ; David J.H. Shih, Marc Remke, Vijay Ramaswamy, Betty Luu, Yuan Yao, Xin Wang, Adrian M. Dubuc, Livia Garzia, John Peacock, Stephen C. Mack, Xiaochong Wu, Adi Rolider, A. Sorana Morrissy, Florence M.G. Cavalli, Claudia C. Faria, Stephen W. Scherer, Uri Tabori, Cynthia E. Hawkins, David Malkin, Eric Bouffet, James T. Rutka, and Michael D. Taylor, Hospital for Sick Children; David J.H. Shih, Marc Remke, Vijay Ramaswamy, Yuan Yao, Xin Wang, Adrian M. Dubuc, John Peacock, Stephen C. Mack, and Michael D. Taylor, University of Toronto, Toronto; Boleslaw Lach, McMaster University, Hamilton, Ontario; Jennifer A. Chan, University of Calgary, Calgary, Alberta; Steffen Albrecht, Adam Fontebasso, and Nada Jabado, McGill University, Montreal, Quebec, Canada; Paul A. Northcott, Andrey Korshunov, Marcel Kool, David T.W. Jones, and Stefan M. Pfister, German Cancer Research Center; Stefan M. Pfister, University Hospital Heidelberg, Heidelberg; Ulrich Schüller, Ludwig-Maximilians-University, Munich; Stefan Rutkowski, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Karel Zitterbart, Masaryk University School of Medicine; Karel Zitterbart and Leos Kren, University Hospital Brno, Brno, Czech Republic; Toshihiro Kumabe and Teiji Tominaga, Tohoku University Graduate School of Medicine, Sendai, Japan; Young Shin Ra, University of Ulsan, Asan Medical Center; Ji-Yeoun Lee, Byung-Kyu Cho, Seung-Ki Kim, and Kyu-Chang Wang, Seoul National University Children's Hospital, Seoul; Shin Jung, Chonnam National University Research Institute of Medical Sciences, Chonnam National University Hwasun Hospital and Medical School, Chonnam, South Korea; Peter Hauser and Miklós Garami, Semmelweis University, Budapest; László Bognár and Almos Klekner, University of Debrecen, Medical and Health Science Centre, Debrecen, Hungary; Shenandoah Robinson, Boston Children's Hospital; Scott L. Pomeroy, Harvard Medical School, Boston, MA; Ali G. Saad, University of Arkansas for Medical Sciences, Little, Northcott PA, Remke M, Korshunov A, Ramaswamy V, Kool M, Luu B, Yao Y, Wang X, Dubuc AM, Garzia L, Peacock J, Mack SC, Wu X, Rolider A, Morrissy AS, Cavalli FM, Jones DT, Zitterbart K, Faria CC, Schüller U, Kren L, Kumabe T, Tominaga T, Shin Ra Y, Garami M, Hauser P, Chan JA, Robinson S, Bognár L, Klekner A, Saad AG, Liau LM, Albrecht S, Fontebasso A, Cinalli G, De Antonellis P, Zollo M, Cooper MK, Thompson RC, Bailey S, Lindsey JC, Di Rocco C, Massimi L, Michiels EM, Scherer SW, Phillips JJ, Gupta N, Fan X, Muraszko KM, Vibhakar R, Eberhart CG, Fouladi M, Lach B, Jung S, Wechsler-Reya RJ, Fèvre-Montange M, Jouvet A, Jabado N, Pollack IF, Weiss WA, Lee JY, Cho BK, Kim SK, Wang KC, Leonard JR, Rubin JB, de Torres C, Lavarino C, Mora J, Cho YJ, Tabori U, Olson JM, Gajjar A, Packer RJ, Rutkowski S, Pomeroy SL, French PJ, Kloosterhof NK, Kros JM, Van Meir EG, Clifford SC, Bourdeaut F, Delattre O, Doz FF, Hawkins CE, Malkin D, Grajkowska WA, Perek-Polnik M, Bouffet E, Rutka JT, Pfister SM, Taylor MD

Publikováno v: Journal of clinical oncology : official journal of the American Society of Clinical Oncology [J Clin Oncol] 2014 Mar 20; Vol. 32 (9), pp. 886-96. Date of Electronic Publication: 2014 Feb 03.