13 papers · ranked by Valyu relevance
Weiyi Li, Darach Miller, Xianan Liu, Lorenzo Tosi + 6 more
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid…
Nicolai von Kügelgen, Valeria Fernandez Vallone, Katarzyna A. Ludwik, Mariia Babaeva + 3 more
Human pluripotent stem cells (hPSCs) and other continuously cultured cell lines are prone to acquiring mutations and genomic aberrations over time, even when derived from well-characterized cell banks. To ensure experimental reproducibility and maintain cell line integrity, routine monitoring for genomic abnormalities…
Vivek Kumar, Robert R Klein, Benjamin Kaufman, Noah D Winans + 13 more
The development of accessible and cost-effective genotyping platforms is essential to accelerate genetic gain in crop improvement. To address the U.S. sorghum community’s need for a standardized, mid-density genotyping resource, we developed and validated a targeted single-nucleotide polymorphism (SNP) array using the…
Christopher I. Cooper, Delia Yao, Dorota H. Sendorek, Takafumi N. Yamaguchi + 8 more
Platform-specific error profiles necessitate confirmatory studies where predictions made on data generated using one technology are additionally verified by processing the same samples on an orthogonal technology. In disciplines that rely heavily on high-throughput data generation, such as genomics, reducing the impact…
Sisi Wang, Freek van Ede
Finding what you are looking for is a ubiquitous task in everyday life that relies on a two-way comparison between what is currently viewed and internal search goals held in memory. Yet, despite a wealth of studies tracking visual verification behavior among the external contents of perception, complementary processes…
Mika Sakurai-Yageta, Kazuki Kumada, Chinatsu Gocho, Satoshi Makino + 18 more
Increasing the power of genome-wide association studies in diverse populations is important for understanding the genetic determinants of disease risks, and large-scale genotype data are collected by genome cohort and biobank projects all over the world. In particular, ethnic-specific SNP arrays are becoming more…
Zachary C. Stevenson, Megan J. Moerdyk-Schauwecker, Brennen Jamison, Patrick C. Phillips
Precision genome editing for model organisms has revolutionized functional analysis and validation of a wide variety of molecular systems. To date, the capacity to insert transgenes into the model nematode Caenorhabditis elegans has focused on utilizing either transposable elements or CRISPR-based safe harbor…
Franjo Ivankovic, Dongmei Yu, James Shen, Lingyu Zhan + 9 more
Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to call CNVs, which can be used in association tests, such as association between CNV number and disease status. Unlike genotypes, CNV…
Johannes Geibel, Christian Reimer, Steffen Weigend, Annett Weigend + 2 more
Single nucleotide polymorphisms (SNPs), genotyped with SNP arrays, have become the most widely used marker types in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased…
Céline Hernandez, Morgane Thomas-Chollier, Aurélien Naldi, Denis Thieffry
At the crossroad between biology and mathematical modelling, computational systems biology can contribute to a mechanistic understanding of high-level biological phenomenon. But as our knowledge accumulates, the size and complexity of mathematical models increase, calling for the development of efficient dynamical…
Jenna E Gallegos, Sergei Hayrynen, Neil Adames, Jean Peccoud
Laboratory strains, cell lines, and other genetic materials change hands frequently in the life sciences. Despite evidence that such materials are subject to mix-ups, contamination, and accumulation of secondary mutations, verification of strains and samples is not an established part of many experimental workflows.…
Emilee Holtzapple, Brent Cochran, Natasa Miskov-Zivanov
Signaling network models are usually assembled from information in literature and expert knowledge or inferred from data. The goal of modeling is to gain mechanistic understanding of key signaling pathways and provide predictions on how perturbations affect large-scale processes such as disease progression. For…
Russell L. Lagore, Matt Waks, Timothy Hasapopoulos, Thomas Mercer + 5 more
To quantify parasitic losses in ultra-high field (UHF) magnetic resonance imaging (MRI) receive coils and determine how they contribute to the mismatch between numerically predicted and experimentally realized signal-to-noise ratio (SNR), with the goal of guiding receive-array designs toward ultimate intrinsic SNR…