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Displaying 101 - 125 of 802

A Diploid Assembly-based Benchmark for Variants in The Major Histocompatibility Complex

September 22, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Chen-Shan Chin, Qiandong Zeng, Alexander Dilthey, Tobias Marschall, Mikko Rautiainen, Erik Garrison, Shilpa Garg
Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct accurate, phased de novo assemblies. We focus on a medically important, highly variable, 5

Improving patient outcomes with regenerative medicine: How to move the needle forward in cell manufacturing, standards, 3D bioprinting, AI enabled automation, education and training

June 17, 2020
Author(s)
Carl Simon Jr., Josh Hunsberger, Claudia Zylberberg, Preveen Ramamoorthy, Thomas Tubon, Crystal Ruff, Ram Bedi, Kurt Gielen, Lynn Fisher, Jed Johnson, Priya Barankiak, Behzad Mahdavi, Michael Hadjisavas, Shannon Eaker, Cameron Miller
Regenerative Medicine Manufacturing Society (RMMS), is the first and only professional society dedicated specifically towards advancing manufacturing solutions for the field of regenerative medicine. RMMS' vision is to provide greater patient access to

Expression of a germline variant in the N-terminal domain of the human DNA glycosylase NTHL1 induces cellular transformation without impairing enzymatic function or substrate specificity

June 16, 2020
Author(s)
Carolyn G. Marsden, Pawel Jaruga, Erdem Coskun, Robyn L. Maher, David S. Pederson, Miral M. Dizdar, Joann B. Sweasy
Oxidatively-induced DNA damage, widely accepted as a key player in the onset of cancer, is predominantly repaired by base excision repair (BER). BER is initiated by DNA glycosylases, which locate and remove damaged bases from DNA. NTHL1 is a bifunctional

A robust benchmark for detection of germline large deletions and insertions

June 15, 2020
Author(s)
Justin Zook, Nathanael David Olson, Marc Salit, Fritz Sedlazeck
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and comprehensiveness. To help translate these methods to routine research and clinical practice, we developed a

Assembly and annotation of an Ashkenazi human reference genome

June 2, 2020
Author(s)
Justin M. Zook, Justin M. Wagner, Nathanael D. Olson, Steven L. Salzberg, Alaina Shumate, Aleksey V. Zimin, Daniela Puiu, Mihaela Pertea, Marc Salit
Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very small sample of the human population. There is a

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

May 4, 2020
Author(s)
Justin M. Zook, Kishwar Shafin, Trevor Pesout, Ryan Lorig-Roach, Marina Haukness, Hugh E. Olsen, Miten Jain, Benedict Paten
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and

Ion-beam radiation damage to DNA by investigation of free radical formation and base damage

March 1, 2020
Author(s)
Melis Kant, Pawel Jaruga, Erdem Coskun, Samuel Ward, Alexander Stark, David Becker, Amitav Adhikary, Michael Sevilla, Miral M. Dizdar
This work investigated the physicochemical processes and DNA base products involved in Ne-22 ion- beam (ca. 1.4 GeV) radiation damage to hydrated (12 waters/nucleotide) highly polymerized salmon sperm DNA. For this purpose, approximately 12 small (ca. 10

Measurement of PARP1 in human tissues by liquid chromatography tandem mass spectrometry

March 1, 2020
Author(s)
Erdem Coskun, Gamze Tuna, Pawel Jaruga, Alessandro Tona, Onur Erdem, Miral M. Dizdar
Poly(ADP ribose) polymerase 1 (PARP1) is a multifunctional DNA repair protein of the base excision repair pathway and plays a major role in the repair of DNA strand breaks and in replication and transcriptional regulation among other functions. Mounting

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di- heptamer macromolecular assembly

January 14, 2020
Author(s)
Xingjian Xu, Raquel Ruiz, Kaylin Adipietro, Christopher Peralta, Danya Ben-Hail, Kristen Varney, Mary Cook, Braden Roth, Paul Wilder, Thomas Cleveland, Alexander Grishaev, Heather Neu, Sarah Michel, Wenbo Yu, Dorothy Beckett, Richard Rustandi, Alex MacKerell, Amedee des Georges, Edwin Pozharski, David Weber
Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in

Measurement of Airborne Emissions from Extinguished Cigarettes: Final Report

December 16, 2019
Author(s)
Dustin G. Poppendieck
Three series of experiments were conducted in this study. First, studies were performed to the determine the relative distributions of the target chemicals in freshly smoked butts by analyzing six types of samples consisting of different parts of the butts

Understanding the characteristics of sequence-based single-source DNA profiles

November 9, 2019
Author(s)
Sarah Riman, Hariharan K. Iyer, Lisa A. Borsuk, Peter M. Vallone
The sequencing of STR markers provides additional information present in the underlying sequence variation that is typically masked by traditional fragment-based genotyping. However, the interpretation of STR profiles generated by targeted sequencing

Metabolomics Test Materials for Quality Control: A Study of a Urine Materials Suite

November 7, 2019
Author(s)
Dan Bearden, David A. Sheen, Yamil Simon, Bruce A. Benner Jr., Werickson Fortunato de Carvalho Rocha, Niksa Blonder, Katrice A. Lippa, Richard Beger, Laura Schnackenberg, Jinchun Sun, Khyati Mehta, Amrita Cheema, Haiwei Gu, Ramesh Marupaka, Nagana Gowda, Daniel Raftery
There is a lack of experimental reference materials and standards for metabolomics measurements, such as urine, plasma, and other human fluid samples. Reasons include difficulties with supply, distribution, and dissemination of information about the

Recognition of DNA adducts by edited and unedited forms of DNA glycosylase NEIL1

November 2, 2019
Author(s)
Irina G. Minko, Vladimir Vartanian, Naoto Tozaki, Erdem Coskun, Sanem Hosbas Coskun, Pawel Jaruga, J Yeo, M.P. Stone, M Egli, Miral M. Dizdar, Amanda K. McCullough, R S. Lloyd
Pre-mRNA encoding human NEIL1 undergoes editing by adenosine deaminase ADAR1 that converts a single adenosine to inosine, and this conversion results in an amino acid change of lysine 242 to arginine. Previous investigations of the catalytic efficiencies

An updated protocol based on CLSI document C37 for preparation of off-the-clot serum from individual units for use alone or to prepare commutable pooled serum reference materials

October 30, 2019
Author(s)
Johanna Camara, Uliana Danilenko, Hubert W. Vesper, Gary L. Myers, Patric A. Clapshaw, W. Greg Miller
Manufacturers of in-vitro diagnostic medical devices, clinical laboratories, research laboratories and calibration laboratories require commutable reference materials that can be used in the calibration hierarchies of medical laboratory measurement

Primary standardization of Ra-224 activity by liquid scintillation counting

October 11, 2019
Author(s)
Denis E. Bergeron, Jeffrey T. Cessna, Ryan P. Fitzgerald, Brian E. Zimmerman, Lizbeth Laureano-Perez, Ronald Colle, Leticia S. Pibida, Elisa Napoli
A standard for 224Ra activity has been developed, based on triple-to-double coincidence ratio (TDCR) liquid scintillation (LS) counting. The standard was confirmed by efficiency tracing and 4παβ(LS)-γ(NaI(Tl)) anticoincidence counting, as well as by 4πγ

NIST Fatty Acid Quality Assurance Program 2017 Final Report

October 1, 2019
Author(s)
Bruce A. Benner Jr., Jacolin A. Murray
At the request of the National Institutes of Health’s (NIH’s) Office of Dietary Supplements (ODS) and in conjunction with the Centers for Disease Control and Prevention (CDC), in 2017 the National Institute of Standards and Technology (NIST) conducted the
Displaying 101 - 125 of 802