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Recent Posts
- The haplotype-resolved T2T carnation (Dianthus caryophyllus) genome reveal the correlation between genome architecture and gene expression
- “Range+T “ for Tight Sizing of HMW Libraries
- Cut the Big Stuff: >50kb High Pass DNA Size Selection on the HLS2
- The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation
- Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method
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Author Archives: Alex
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
Comments Off on Optimising ddRAD sequencing for population genomic studies with ddgRADer
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
Comments Off on rDNA array length is a major determinant of replicative lifespan in budding yeast
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
Comments Off on An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing
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
High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
July 2021 Authors: Ashley Jones ,Cynthia Torkel,David Stanley,Jamila Nasim,Justin Borevitz,Benjamin Schwessinger Info: The authors provide a protocol for preparing high molecular weight DNA sequencing libraries with a particular focus on difficult plant and fungal tissues, and also can be used … more »
Posted in Citation
Tagged oxford nanopore, PacBio, PippinHT
Comments Off on High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing
Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes
June 2021 Authors: Eric S Tvedte, Mark Gasser, Benjamin C Sparklin, Jane Michalski, Carl E Hjelmen, J Spencer Johnston, Xuechu Zhao, Robin Bromley, Luke J Tallon, Lisa Sadzewicz, David A Rasko, Julie C Dunning Hotopp Info: This side-by-side comparison of … more »
Posted in Citation
Tagged BluePippin, oxford nanopore, PacBio
Comments Off on Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes
Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
April 2021 Authors: Multiple authors, the SEQC2 Oncopanel Sequencing Working Group Info: A multi-site and cross-platform evaluation of circulating tumor DNA (ctDNA) NGS assays was conducted by the SEQC2 Oncopanel Sequencing Working Group and reported on in this comprehensive study. … more »
Posted in Citation
Tagged cell-free DNA, circulation tumor DNA, ctDNA, Pippin Prep
Comments Off on Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
May 2021 Authors: Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D Clark, Richard M Leggett Info: Oxford Nanopore adaptive sampling is a real-time sequencing method with which analysis software identifies several hundred sequence bases as they pass through … more »
Posted in Citation
Tagged BluePippin, High Pass, oxford nanopore
Comments Off on Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples