Zobrazeno 1 - 10
of 141
pro vyhledávání: '"Timothy Daley"'
Autor:
Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, Xi Chen, Zhana Duren, Alicia Schep, William J. Greenleaf, Wing Hung Wong
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-8 (2018)
Single cell ATAC-seq (scATAC-seq) data reveals cellular level epigenetic heterogeneity but its application in delineating distinct subpopulations is still challenging. Here, the authors develop scABC, a statistical method for unsupervised clustering
Externí odkaz:
https://doaj.org/article/981f5451f9b94168a52a12c4a38b1aab
Autor:
Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff, Jose Rodriguez Santana, Erez Y. Levanon, Prescott G. Woodruff, Esteban Burchard, Max A. Seibold, Sagiv Shifman, Eleazar Eskin, Noah Zaitlen
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-12 (2018)
Abstract High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Or
Externí odkaz:
https://doaj.org/article/d5953314c54a44c1a89d0b7809960987
Publikováno v:
Annual Review of Biomedical Data Science. 3:137-162
Large-scale CRISPR-Cas pooled screens have shown great promise to investigate functional links between genotype and phenotype at the genome-wide scale. In addition to technological advancement, there is a need to develop computational methods to anal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c75c0fe4afc070b8fc87f32d73bf0423
https://doi.org/10.1146/annurev-biodatasci-020520-113523
https://doi.org/10.1146/annurev-biodatasci-020520-113523
Publikováno v:
J Comput Biol
For many types of high-throughput sequencing experiments, success in downstream analysis depends on attaining sufficient coverage for individual positions in the genome. For example, when identifying single-nucleotide variants de novo, the number of
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7ebd033ef742b19a937bad7f3f4690bd
https://doi.org/10.1089/cmb.2019.0264
https://doi.org/10.1089/cmb.2019.0264
Publikováno v:
Genome Biology, Vol 21, Iss 1, Pp 1-13 (2020)
Genome Biology
Genome Biology
Genome-wide pooled CRISPR-Cas-mediated knockout, activation, and repression screens are powerful tools for functional genomic investigations. Despite their increasing importance, there is currently little guidance on how to design and analyze CRISPR-
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::58cb1f74e93d3696dfc73ca7cb20d22d
http://link.springer.com/article/10.1186/s13059-020-01972-x
http://link.springer.com/article/10.1186/s13059-020-01972-x
Publikováno v:
Annual Review of Biomedical Data Science. 2:39-67
High-throughput sequencing technologies have evolved at a stellar pace for almost a decade and have greatly advanced our understanding of genome biology. In these sampling-based technologies, there is an important detail that is often overlooked in t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::58ad98c6a9da3030b32e69cac48c1f36
https://doi.org/10.1146/annurev-biodatasci-072018-021339
https://doi.org/10.1146/annurev-biodatasci-072018-021339
Publikováno v:
Statist. Sci. 35, no. 1 (2020), 2-13
Unsupervised methods, including clustering methods, are essential to the analysis of single-cell genomic data. Model-based clustering methods are under-explored in the area of single-cell genomics, and have the advantage of quantifying the uncertaint
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e2af765a89302d5630b29cb46fd6ac63
https://doi.org/10.1214/19-sts714
https://doi.org/10.1214/19-sts714
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-13 (2018)
Genome Biology
Genome Biology
Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly fo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::268467425330de9e4e677dc7533e3239
http://link.springer.com/article/10.1186/s13059-018-1538-6
http://link.springer.com/article/10.1186/s13059-018-1538-6
Autor:
Cydney Rios, Hagit T. Porath, Timothy Daley, Max A. Seibold, Serghei Mangul, Andrew D. Smith, Prescott G. Woodruff, Kevin Hsieh, Jose Rodriguez Santana, Celeste Eng, Harry Taegyun Yang, Nicolas Strauli, Agata Wesolowska-Andersen, Esteban G. Burchard, Eleazar Eskin, Sagiv Shifman, Linus Chen, Stephanie A. Christenson, Franziska Gruhl, Erez Y. Levanon, Roberto Spreafico, Roel A. Ophoff, Ryan D. Hernandez, Noah Zaitlen
Publikováno v:
Genome Biology, Vol 19, Iss 1, Pp 1-12 (2018)
Genome biology, vol 19, iss 1
Genome Biology, vol. 19, no. 1, pp. 36
Genome Biology
Genome biology, vol 19, iss 1
Genome Biology, vol. 19, no. 1, pp. 36
Genome Biology
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Prot
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f21c064ff6dc859f0bfc3f29617197a4
http://link.springer.com/article/10.1186/s13059-018-1403-7
http://link.springer.com/article/10.1186/s13059-018-1403-7
Autor:
Haifeng Wang, Albert C. Lo, Lei S. Qi, Cordelia Yu, Timothy Daley, Dehua Zhao, Cindy M. Nguyen, Muneaki Nakamura, Marie La Russa, Yanxia Liu
Visualizing the real-time dynamics of genome rearrangement in single living cells is core to studying genomics and diagnostics. Here, we report a robust, versatile approach named CRISPRLive-cell fluorescentinsituhybridization (LiveFISH) for multi-loc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e04490685034c14cc3051a8a26ed73fa
https://doi.org/10.1101/734483
https://doi.org/10.1101/734483
