Zobrazeno 1 - 8
of 8
pro vyhledávání: '"Maryam Ghareghani"'
Autor:
Mir Henglin, Maryam Ghareghani, William T. Harvey, David Porubsky, Sergey Koren, Evan E. Eichler, Peter Ebert, Tobias Marschall
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-26 (2024)
Abstract Haplotype information is crucial for biomedical and population genetics research. However, current strategies to produce de novo haplotype-resolved assemblies often require either difficult-to-acquire parental data or an intermediate haploty
Externí odkaz:
https://doaj.org/article/3512fe7340b944e4bcccd787429f9cff
Autor:
Peter Ebert, Peter A. Audano, Peter M. Lansdorp, Mark Chaisson, Maryam Ghareghani, Katherine M. Munson, Ashley D. Sanders, Charles Lee, Marina Haukness, Arvis Sulovari, Jana Ebler, Benedict Paten, Evan E. Eichler, Scott E. Devine, Jan O. Korbel, Melanie Sorensen, Tobias Marschall, William T. Harvey, David Porubsky, Mitchell R. Vollger, Pierre Marijon
Publikováno v:
Nature Biotechnology
Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::664704a0641e287e772e1b3e41ea2b2c
http://edoc.mdc-berlin.de/19711/7/19711suppl.zip
http://edoc.mdc-berlin.de/19711/7/19711suppl.zip
Autor:
Zepeng Mu, Jana Ebler, PingHsun Hsieh, Kai Ye, Marta Byrska-Bishop, William T. Harvey, Mark Gerstein, Chong Li, Bernardo Rodriguez-Martin, Tobias Rausch, Michael E. Talkowski, Rebecca Serra Mari, Allison Regier, Xinghua Shi, Arvis Sulovari, Weichen Zhou, Martin Santamarina, Hufsah Ashraf, Oliver Stegle, Scott E. Devine, Yu Chen, Xuefang Zhao, Jiadong Lin, Susan Fairley, Mark Chaisson, Wolfram Höps, Alexandra P. Lewis, Ira M. Hall, Benjamin Raeder, Feyza Yilmaz, Wayne E. Clarke, Aaron M. Wenger, Qihui Zhu, Xiaofei Yang, Ashley D. Sanders, Marc Jan Bonder, Junjie Chen, Maryam Ghareghani, Katherine M. Munson, Luke J. Tallon, Evan E. Eichler, Alex Hastie, Paul Flicek, Jose M. C. Tubio, Jan O. Korbel, Peter A. Audano, Jingwen Ren, Peter Ebert, Tobias Marschall, Nelson T. Chuang, David Porubsky, Anna O. Basile, Joyce V. Lee, Yang I. Li, Harrison Brand, André Corvelo, Michael C. Zody, Patrick Hasenfeld, Ryan E. Mills, Charles Lee, Zechen Chong, Haley J. Abel, Sushant Kumar
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent–child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::dc0b557d21456d6ebdcdea2f2663403f
https://doi.org/10.1101/2020.12.16.423102
https://doi.org/10.1101/2020.12.16.423102
Autor:
Tsung Yu Lu, Rebecca Serra Mari, Joyce V. Lee, Peter A. Audano, Susan Fairley, Mark Chaisson, Scott E. Devine, Ira M. Hall, Maryam Ghareghani, Sushant Kumar, Aaron M. Wenger, Jan O. Korbel, Hufsah Ashraf, Feyza Yilmaz, Tobias Marschall, Jana Ebler, Zechen Chong, Wolfram Höps, Paul Flicek, Kai Ye, Haley J. Abel, Katherine M. Munson, Jiadong Lin, Qihui Zhu, Weichen Zhou, Xiaofei Yang, Wayne E. Clarke, Michael C. Zody, Uday S. Evani, Xinghua Shi, Patrick Hasenfeld, Martin Santamarina, Bernardo Rodriguez-Martin, Tobias Rausch, Michael E. Talkowski, Jose M. C. Tubio, Luke J. Tallon, Yang I. Li, Yu Chen, Junjie Chen, André Corvelo, Zepeng Mu, PingHsun Hsieh, David Porubsky, Nelson T. Chuang, William T. Harvey, Alexandra P. Lewis, Marc Jan Bonder, Oliver Stegle, Benjamin Raeder, Xuefang Zhao, Alex Hastie, Harrison Brand, Allison A. Regier, Peter Ebert, Ryan E. Mills, Anna O. Basile, Marta Byrska-Bishop, Mark Gerstein, Chong Li, Arvis Sulovari, Jingwen Ren, Ashley D. Sanders, Charles Lee, Evan E. Eichler
Publikováno v:
Science
Resolving genomic structural variationMany human genomes have been reported using short-read technology, but it is difficult to resolve structural variants (SVs) using these data. These genomes thus lack comprehensive comparisons among individuals an
Autor:
Katherine M. Munson, Mark Chaisson, Jan O. Korbel, Tobias Marschall, Scott E. Devine, Benedict Paten, Ashley D. Sanders, Charles Lee, Evan E. Eichler, William T. Harvey, Marina Haukness, Maryam Ghareghani, Mitchell R. Vollger, Melanie Sorensen, P. Ebert, David Porubsky, Peter A. Audano, Peter M. Lansdorp, Arvis Sulovari
The prevailing genome assembly paradigm is to produce consensus sequences that “collapse” parental haplotypes into a consensus sequence. Here, we leverage the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing (
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::438393e952827894f32c182f859503b9
Autor:
Vladimir Benes, Jean-Pierre Bourquin, Paulina Richter-Pechanska, Beat Bornhauser, Joachim B. Kunz, Tobias Rausch, Andreas E. Kulozik, Balca R. Mardin, Ashley D. Sanders, Benjamin Raeder, Martin Schrappe, Maryam Ghareghani, Venla Kinanen, M. Alexandra C. C. van Vliet, Silvia Jenni, Hyobin Jeong, Sascha Meiers, Jan O. Korbel, Tobias Marschall, Jürgen Zimmermann, David Porubsky
Structural variation (SV), where rearrangements delete, duplicate, invert or translocate DNA segments, is a major source of somatic cell variation. It can arise in rapid bursts, mediate genetic heterogenity, and dysregulate cancer-related pathways. T
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18f147c8f889ee8b04ba017168506f36
https://doi.org/10.1101/849604
https://doi.org/10.1101/849604
Autor:
Jan O. Korbel, Maryam Ghareghani, Sascha Meiers, Ashley D. Sanders, Tobias Marschall, David Porubskỳ, Evan E. Eichler
Publikováno v:
Bioinformatics
ISMB 2018 Proceedings
ISMB 2018 Proceedings
Given file contains fastq formatted Strand-seq reads originating from 132 single-cell libraries. The fastq file was generated from mapped BAM files containing pair-end reads. In this file only first mate of each pair is reported and at the same time
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3e9780c594816bb4866072a660a9e51e
https://hdl.handle.net/21.11116/0000-0001-E5AA-D21.11116/0000-0001-E5AC-B
https://hdl.handle.net/21.11116/0000-0001-E5AA-D21.11116/0000-0001-E5AC-B
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing
Autor:
David Porubsky, Ashley D. Sanders, Martin Schrappe, Tobias Rausch, Jan O. Korbel, Beat Bornhauser, Joachim B. Kunz, Andreas E. Kulozik, Tobias Marschall, Benjamin Raeder, Davide Bolognini, Juergen Zimmermann, Balca R. Mardin, M. Alexandra C. C. van Vliet, Vladimir Benes, Hyobin Jeong, Maryam Ghareghani, Venla Kinanen, Jean-Pierre Bourquin, Paulina Richter-Pechanska, Sascha Meiers, Silvia Jenni, Gabriel M. C. Longo
Publikováno v:
Nature Biotechnology
Nat Biotechnol
Nat Biotechnol
Structural variation (SV), involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic SVs in si