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Author Archives: Alex
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 »
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 »
Posted in Citation
Tagged HiFi, PacBio, PippinHT, whole genome sequencing
Comments Off on Utility of long-read sequencing for All of Us
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 »
Posted in Citation
Tagged Graves Disease, HLA, MHC, Pippin Prep
Comments Off on Significance of HLA in the development of Graves’ orbitopathy
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 »
Posted in Citation
Tagged Protein Mass Spec, SageELF
Comments Off on Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands
Large Cancer Pedigree Involving Multiple Cancer Genes including Likely Digenic MSH2 and MSH6 Lynch Syndrome (LS) and an Instance of Recombinational Rescue from LS
January 2023 Authors: Ingrid P. Vogelaar, Stephanie Greer, Fan Wang, GiWon Shin, Billy Lau, Yajing H, Sigurdis Haraldsdottir, Rocio Alvarez, Dennis Hazelett, Peter Nguyen, Francesca P. Aguirre, Maha Guindi, Andrew Hendifar, Jessica Balcom, Anna Leininger, Beth Fairbank, Hanlee Ji, Megan … more »
Optimising ddRAD sequencing for population genomic studies with ddgRADer
October 2022 Authors: Aparna Lajmi, Felix Glinka, Eyal Privman Info: In this preprint, the authors describe an online webtool that they have developed for designing ddRAD-seq experiments. This webtool assists in the recommendation of restriction enzyme pairs and size-selection criteria. … more »
Posted in Citation
Tagged BluePippin, ddRADseq, Pippin Prep
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Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients
September 2022 Authors: Elsie Cheruba, Ramya Viswanathan, Pui-Mun Wong, Howard John Womersley, Shuting Han, Brenda Tay, Yiting Lau, Anna Gan, Polly S. Y. Poon, Anders Skanderup, Sarah B. Ng, Aik Yong Chok, Dawn Qingqing Chong, Iain Beehuat Tan, Lih Feng … more »
Posted in Citation
Tagged bisulfite sequencing, BluePippin, cell-free DNA, Illumina, methylation
Comments Off on Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients
rDNA array length is a major determinant of replicative lifespan in budding yeast
April 2022 Authors: Manuel Hotz, Nathaniel H. Thayer, David G. Hendrickson, Elizabeth L. Schinski, Jun Xu, and Daniel E. Gottschling Info: The authors propose a new mechanism for aging and lifespan determination in budding yeast. The researchers “discovered a previously … more »
Posted in Citation
Tagged ATAC-seq, Pippin Prep
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An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing
Feb 2022 Authors: Catherine D. Aimone, Steen Hoyer, Anna E. Dye, David O. Deppong, Siobain Duffy, Ignazio Carbone, Linda Hanley-Bowdoin Info: The authors provide a protocol for analyzing single stranded DNA (ssDNA) from begomoviruses, which cause significant damage to many … more »
Posted in Citation
Tagged BluePippin, ssDNA
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High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads
September 2021 Authors: Bo Wang, Xiaofei Yang, Yanyan Jia, Yu Xu, Peng Jia, Ningxin Dang, Songbo Wang, Tun Xu, Xixi Zhao, Shenghan Gao, Quanbin Dong, Kai Ye Info: The authors report on a high quality genome assembly of the model … more »
Posted in Citation
Tagged BluePippin, HiFi, HLS, oxford nanopore, PacBio
Comments Off on High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads