Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Justin P. Sandoval"'
Autor:
Chongyuan Luo, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, Joseph R. Nery, António Pinto-Duarte, Brian Bui, Conor Fitzpatrick, Carolyn O’Connor, Seth Ruga, Marc E. Van Eden, David A. Davis, Deborah C. Mash, M. Margarita Behrens, Joseph R. Ecker
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-6 (2018)
Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.
Externí odkaz:
https://doaj.org/article/b58554dbcada4f7c8aeb1384ced312c3
Autor:
Todd P. Michael, Florian Jupe, Felix Bemm, S. Timothy Motley, Justin P. Sandoval, Christa Lanz, Olivier Loudet, Detlef Weigel, Joseph R. Ecker
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-8 (2018)
Long-read sequencing technologies facilitate efficient and high quality genome assembly. Here Michael et al. achieve a fast reference assembly for Arabidopsis thaliana KBS-Mac-74 accession using the handheld Oxford Nanopore MinION sequencer and consu
Externí odkaz:
https://doaj.org/article/ad6bc43df0404861ae63cd85f221e0b0
Autor:
April R Kriebel, Joshua D. Welch, Chao Gao, Sebastian Preissl, Joseph R. Ecker, Angeline Rivkin, Rosa Castanon, Justin P. Sandoval, Bing Ren, M. Margarita Behrens, Jialin Liu, Joseph R. Nery, Chongyuan Luo
Publikováno v:
Nature Biotechnology. 39:1000-1007
Integrating large single-cell gene expression, chromatin accessibility and DNA methylation datasets requires general and scalable computational approaches. Here we describe online integrative non-negative matrix factorization (iNMF), an algorithm for
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2804762e06021b3116650e1dc71d8790
https://doi.org/10.1038/s41587-021-00867-x
https://doi.org/10.1038/s41587-021-00867-x
Autor:
Todd P, Michael, Evan, Ernst, Nolan, Hartwick, Philomena, Chu, Douglas, Bryant, Sarah, Gilbert, Stefan, Ortleb, Erin L, Baggs, K Sowjanya, Sree, Klaus J, Appenroth, Joerg, Fuchs, Florian, Jupe, Justin P, Sandoval, Ksenia V, Krasileva, Ljudmylla, Borisjuk, Todd C, Mockler, Joseph R, Ecker, Robert A, Martienssen, Eric, Lam
Publikováno v:
Genome Res
Rootless plants in the genus Wolffia are some of the fastest growing known plants on Earth. Wolffia have a reduced body plan, primarily multiplying through a budding type of asexual reproduction. Here, we generated draft reference genomes for Wolffia
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::12ad80f542ebe5a0bbdba6377d043bb0
https://pubmed.ncbi.nlm.nih.gov/33361111
https://pubmed.ncbi.nlm.nih.gov/33361111
Autor:
Klaus-J. Appenroth, Douglas W. Bryant, Nolan Hartwick, Stefan Ortleb, K. Sowjanya Sree, Justin P. Sandoval, Joerg Fuchs, Florian Jupe, Todd C. Mockler, Erin Baggs, Ljudmylla Borisjuk, Ksenia V. Krasileva, Todd P. Michael, Sarah Gilbert, Philomena Chu, Eric Lam, Evan Ernst, Robert A. Martienssen, Joseph R. Ecker
Wolffia is the fastest growing plant genus on Earth with a recorded doubling time of less than a day. Wolffia has a dramatically reduced body plan, primarily growing through a continuous, budding-type asexual reproduction with no obvious phase transi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c04e2cbd68235cf5ecba88896faca26e
Autor:
M. Margarita Behrens, Rosa Castanon, Bing Ren, Joshua D. Welch, Justin P. Sandoval, Chongyuan Luo, Angeline Rivkin, Joseph R. Ecker, Sebastian Preissl, Chao Gao, Joseph R. Nery
Recent experimental advances have enabled high-throughput single-cell measurement of gene expression, chromatin accessibility and DNA methylation. We previously used integrative non-negative matrix factorization (iNMF) to jointly learn interpretable
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e103a9dd6df8c786376d39daaf319df5
https://doi.org/10.1101/2020.01.16.909861
https://doi.org/10.1101/2020.01.16.909861
Autor:
Angeline Rivkin, Antonio Pinto-Duarte, Joseph R. Nery, M. Margarita Behrens, Joseph R. Ecker, Conor Fitzpatrick, Brian Bui, Chongyuan Luo, Seth Ruga, Jingtian Zhou, Rosa Castanon, Carolyn O’Connor, Jacinta Lucero, Marc E. Van Eden, David A. Davis, Laurie Kurihara, Justin P. Sandoval, Deborah C. Mash
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-6 (2018)
Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. H
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b4d78bcaa234d61de934a8550bcb3634
https://pubmed.ncbi.nlm.nih.gov/30237449
https://pubmed.ncbi.nlm.nih.gov/30237449
Autor:
Laurie Kurihara, Joseph R. Ecker, Eran A. Mukamel, M. Margarita Behrens, Yupeng He, Justin P. Sandoval, Christopher L. Keown, Joseph R. Nery, Chongyuan Luo, Terrence J. Sejnowski, Rosa Castanon, Timothy T. Harkins, Jun-Hao Li, Jacinta Lucero, Brian Bui, Jingtian Zhou
Publikováno v:
Science (New York, N.Y.). 357(6351)
The mammalian brain contains diverse neuronal types, yet we lack single-cell epigenomic assays that are able to identify and characterize them. DNA methylation is a stable epigenetic mark that distinguishes cell types and marks regulatory elements. W
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a377bf7a7b73e9bd17d328a3d1a70088
https://pubmed.ncbi.nlm.nih.gov/28798132
https://pubmed.ncbi.nlm.nih.gov/28798132
Autor:
Florian Jupe, Angeline C Rivkin, Todd P Michael, Mark Zander, S Timothy Motley, Justin P Sandoval, R Keith Slotkin, Huaming Chen, Rosa Castanon, Joseph R Nery, Joseph R Ecker
Publikováno v:
PLoS Genetics, Vol 15, Iss 1, p e1007819 (2019)
The bacterium Agrobacterium tumefaciens has been the workhorse in plant genome engineering. Customized replacement of native tumor-inducing (Ti) plasmid elements enabled insertion of a sequence of interest called Transfer-DNA (T-DNA) into any plant g
Externí odkaz:
https://doaj.org/article/95ab8fb90c2041d8ab9f191a2f75b785