Author Archives: Alex

The haplotype-resolved T2T carnation (Dianthus caryophyllus) genome reveal the correlation between genome architecture and gene expression

November 2023 Authors: Lan Lan, Luhong Leng, Weichao, Yonglin Ren, Wayne Reeve, Xiaopeng Fu, Zhiqiang Wu, Xiaoni Zhang Abstract: “Carnation (Dianthus caryophyllus) is one of the most valuable commercial 45 flowers, due to its richness of colour and form, and … more »

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“Range+T “ for Tight Sizing of HMW Libraries

Range+T Size Selection Note: Range + T is available for all PippinHT instruments. However, only BluePippins with serial numbers 2700 and above will run the method. Sage’s DNA size selection technology has been used to help improve PacBio sequencing, particularly … more »

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Cut the Big Stuff: >50kb High Pass DNA Size Selection on the HLS2

We have been getting quite a few inquiries of late from researchers who would like to size select DNA fragments above 50kb. This may be due in no small part to our friends at Grandomics, China, who have been citing … more »

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The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

May 2023 Authors: Shinichi Morita, Tomoko F. Shibata, Tomoaki Nishiyama, Yuuki Kobayashi, Katsushi Yamaguchi, Kouhei Toga, Takahiro Ohde, Hiroki Gotoh, Takaaki Kojima, Jesse N. Weber, Marco Salvemini, Takahiro Bino, Mutsuki Mase, Moe Nakata, Tomoko Mori, Shogo Mori, Richard Cornette, Kazuki … more »

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Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method

March 2023 Authors: Veronika Mikhaylova, Madison Rzepka, Tetsuya Kawamura1, Yu Xia, Peter L. Chang, Shiguo Zhou, Long Pham, Naisarg Modi, Likun Yao, Adrian Perez-Agustin, Sara Pagans, T. Christian Boles , Ming Lei, Yong Wang, Ivan Garcia-Bassets, and Zhoutao Chen Abstract: … more »

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AGBT23 Roundup!

Well, we have another fabulous AGBT behind us that we were happy to attend.   Our take home messages? A. Spatial transcriptomics is the exciting new frontier.  B.  True human WGS  has been accomplished and is moving into population-scale work. And … more »

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Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification

February 2023 Authors: Zenaida V.Magbanua, Chuan-YuHsu, OlgaPechanova, Mark Arick II, Corrinne E.Grover, Daniel G.Peterson Abstract: “We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral … more »

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Utility of long-read sequencing for All of Us

January 2023 Authors: M. Mahmoud, Y. Huang, K. Garimella, P. A. Audano, W. Wan, N. Prasad, R. E. Handsaker, S. Hall, A. Pionzio, M. C. Schatz, M. E. Talkowski, E. E. Eichler, S. E. Levy, F. J. Sedlazeck Abstract: “The … more »

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Significance of HLA in the development of Graves’ orbitopathy

January 2023 Authors: Magdalena Stasiak, Katarzyna Zawadzka-Starczewska, Bogusław Tymoniuk, Bartłomiej Stasiak, Andrzej Lewiński Abstract: “Graves’ disease (GD), similarly to most autoimmune disease, is triggered by environmental factors in genetically predisposed individuals. Particular HLA alleles increase or decrease GD risk. No … more »

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Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands

January 2023 Authors: Natalia Musiał, Aleksandra Bogucka, Dmitry Tretiakow, Andrzej Skorek, Jacek Ryl Gdańsk, Paulina Czaplewska Abstract: “Salivary stones, also known as sialoliths, are formed in a pathological situation in the salivary glands. So far, neither the mechanism of their … more »

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