Abstract 3134: Calling somatic variants from UG100 data using deep learning

Autor: Maya Levy, Doron Shem-Tov, Hila Benjamin, Sima Benjamin, Ilya Soifer, Shlomit Gilad, Danit Lebanony, Nika Iremadze, Eti Meiri, Doron Lipson, Omer Barad

Publikováno v: Cancer Research. 83:3134-3134

UG100 is a novel next-generation sequencing platform that combines high throughput with significantly lower sequencing cost. Previous studies have demonstrated broad applicability of UG100 data for whole-genome germline variant calling, single cell t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::ed0bbb47a95561be775a39f197e0f5fa
https://doi.org/10.1158/1538-7445.am2023-3134

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

Autor: Sean K. Simmons, Gila Lithwick-Yanai, Xian Adiconis, Florian Oberstrass, Nika Iremadze, Kathryn Geiger-Schuller, Pratiksha I. Thakore, Chris J. Frangieh, Omer Barad, Gilad Almogy, Orit Rozenblatt-Rosen, Aviv Regev, Doron Lipson, Joshua Z. Levin

Publikováno v: Nature biotechnology.

Here we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology. mnSBS uses mostly nat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::54eec09552604edae5585879e6851bdc
https://pubmed.ncbi.nlm.nih.gov/36109685

Next-generation sequencing-based QTL mapping for unravelling causative genes associated with melon fruit quality traits

Autor: Galil Tzuri, C. Jiao, Zhangjun Fei, Einat Bar, Efraim Lewinsohn, Amit Gur, Nadia Lombardi, Y. Burger, R. Harel-Beja, Adi Doron-Faigenboim, Guy Kol, L. Mao, M. Kenigswald, Yaakov Tadmor, U. Sa’ar, Shery Lev, Vitaly Portnoy, A. A. Schaffer, N. Katzir, Itay Gonda, Navot Galpaz, Elazar Fallik, Y. Xu, James J. Giovannoni, Omer Barad

Publikováno v: Acta horticulturae 1151 (2017): 9–16. doi:10.17660/ActaHortic.2017.1151.3
info:cnr-pdr/source/autori:Portnoy V., Gonda I., Galpaz N., Tzuri G., Lev S., Kenigswald M., Fei Z., Barad O., Harel-Beja R., Doron-Faigenboim A., Bar E., Sáar U., Xu Y., Lombardi N., Mao L., Jiao C., Kol G., Gur A., Fallik E., Tadmor Y., Burger Y., Schaffer A.A., Giovannoni J., Lewinsohn E., Katzir N./titolo:Next-generation sequencing-based QTL mapping for unravelling causative genes associated with melon fruit quality traits/doi:10.17660%2FActaHortic.2017.1151.3/rivista:Acta horticulturae/anno:2017/pagina_da:9/pagina_a:16/intervallo_pagine:9–16/volume:1151

High resolution QTL mapping of genetic factors affecting fruit quality traits in melon (Cucumis melo) was achieved in two projects. Next-generation sequencing (NGS), coupled with unique genetic materials, was used to attain high resolution mapping, i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a7329b16269282bcaf9568fbb832d7c0
https://doi.org/10.17660/actahortic.2017.1151.3

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

Autor: Alex B. Brohammer, Megan J. Bowman, Omer Barad, Shawn M. Kaeppler, Klaus L. Koehler, Kobi Baruch, Chris L. Wright, Mark A. Mikel, Alvaro G. Hernandez, Christopher J. Fields, Fei Lu, Nathan M. Springer, Edward S. Buckler, C. Robin Buell, Kevin L. Childs, Ilya Soifer, Candice N. Hirsch, Doron Shem-Tov, Cory D. Hirsch, Natalia de Leon

Publikováno v: The Plant Cell. 28:2700-2714

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1c4211342107d945f48055d71168d7af
https://doi.org/10.1105/tpc.16.00353

Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping

Autor: Arthur A. Schaffer, Ayala Meir, Yosef Burger, Adi Doron-Faigenboim, Uzi Saar, Linyong Mao, Navot Galpaz, Omer Barad, Amit Gur, Gil Ronen, Yaakov Tadmor, Zhangjun Fei, Galil Tzuri, Nadia Lombardi, Doron Shem-Tov, Eran Halperin, Yimin Xu, Vitaly Portnoy, Elazar Fallik, Efraim Lewinsohn, Nurit Katzir, Aaron Fait, Itay Gonda, Shery Lev, Oren Tzfadia, Merav Kenigswald, Rotem Harel-Beja, Guy Kol, James J. Giovannoni, Einat Bar, Chen Jiao

Publikováno v: Plant journal (Online) 94 (2018): 169–191. doi:10.1111/tpj.13838
info:cnr-pdr/source/autori:Galpaz N., Gonda I., Shem-Tov D., Barad O., Tzuri G., Lev S., Fei Z., Xu Y., Mao L., Jiao C., Harel-Beja R., Doron-Faigenboim A., Tzfadia O., Bar E., Meir A., Sa'ar U., Fait A., Halperin E., Kenigswald M., Fallik E., Lombardi N., Kol G., Ronen G., Burger Y., Gur A., Tadmor Y., Portnoy V., Schaffer A.A., Lewinsohn E., Giovannoni J.J., Katzir N./titolo:Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping/doi:10.1111%2Ftpj.13838/rivista:Plant journal (Online)/anno:2018/pagina_da:169/pagina_a:191/intervallo_pagine:169–191/volume:94

Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f6013385fae3dcb2b544c5d3633f8f3e
http://hdl.handle.net/11588/729395