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Displaying 1 - 25 of 1140

Multi'omic Characterization of Human Whole Stool RGTMs

September 8, 2023
Amanda L. Bayless, Sandra M. Da Silva, Clay Davis, Abraham Kuri Cruz, Tracey Schock, Stephanie Servetas, Paulina Piotrowski
The gut microbiome plays a critical role in a vast and disparate set of health and disease states, including cancer and obesity. Human fecal is a complex mixture including microbes, proteins, undigested plant matter and fat content according to the diet

National Institute of Standards and Technology Environmental Scan 2023: Societal and Technology Landscape to Inform Science and Technology Research

August 23, 2023
Ashley Boggs-Russell, Kerrianne Buchanan, David W. Griffith, Heather Evans, Dimitrios Meritis, Lisa Ng, Anna Sberegaeva, Michelle Stephens
The 2023 National Institute of Standards and Technology Environmental Scan provides an analysis of key external factors that could impact NIST and the fulfillment of its mission in coming years. The analyses were conducted through three separate lenses

The complete sequence of a human Y chromosome

August 23, 2023
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah Hoyt, Dylan Taylor, Nathanael David Olson, Justin Zook, Adam Phillippy
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1,2,3. As a result, more than half of the Y chromosome is

A Draft Human Pangenome Reference

May 10, 2023
Wen-Wei Liao, Mobin Asri, Jana Ebler, Jennifer McDaniel, Nathanael David Olson, Justin Wagner, Justin Zook, Erik Garrison, Tobias Marschall, Ira Hall, Heng Li, Benedict Paten
Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the

Mechanical Regulation of Oral Epithelial Barrier Function

April 25, 2023
Eun Jin Lee, Yoontae Kim, Paul Salipante, Anthony Kotula, Dana Graves, Stella Alimperti
Epithelial cell function is modulated by mechanical forces imparted by the extracellular environment. The transmission of forces onto the cytoskeleton by modalities such as mechanical stress and matrix stiffness is necessary to address by the development

Variant calling and benchmarking in an era of complete human genome sequences

April 14, 2023
Nathanael David Olson, Justin Wagner, Nathan Dwarshuis, Karen Miga, Marc L. Salit, Justin Zook
Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Sequencing technologies and variant-calling methods have advanced rapidly, routinely providing reliable variant calls in most of

The emerging landscape of single-molecule protein sequencing technologies

April 11, 2023
Zvi Kelman, John Marino
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe

Three-dimensional, label-free cell viability measurements in tissue engineering scaffolds using optical coherence tomography

March 14, 2023
Greta Babakhanova, Anant Agrawal, Deepika Arora, Allison Horenberg, Jagat Budhathoki, Joy Dunkers, Joe Chalfoun, Peter Bajcsy, Carl Simon Jr.
In the field of tissue engineering, 3D scaffolds and cells are often combined to yield constructs that are used as therapeutics to repair or restore tissue function in patients. Viable cells are required to achieve the intended mechanism of action for the

Inhibition of human APE1 and MTH1 DNA repair proteins by dextran-coated g-Fe2O3 ultrasmall superparamagnetic iron oxide nanoparticles

February 28, 2023
Erdem Coskun, Pawel Jaruga, Miral M. Dizdar, Bryant C. Nelson, Neenu Singh, Leona Scanlan, Shareen Doak
Aim: To quantitatively evaluate the inhibition of human DNA repair proteins APE1 and MTH1 by dextran-coated γ-Fe2O3 ultrasmall superparamagnetic iron oxide nanoparticles (dUSPIONs). Materials & methods: Liquid chromatography–tandem mass spectrometry with

FixItFelix: improving genomic analysis by fixing reference errors

February 21, 2023
Sairam Behera, Jonathan LeFaive, Peter Orchard, Justin Zook, Fritz Sedlazeck
The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical

Biglycan regulates bone development and regeneration

February 16, 2023
Reut Shainer, Vardit Kram, Tina Kilts, Andrew Doyle, Inbal Shainer, Carl Simon Jr., Jinyang Zeng-Brouwers, Liliana Schaefer, Marian Young
Endochondral bone development and regeneration relies on activation and proliferation of periosteum derived cells (PDCs). Biglycan (Bgn), an extracellular matrix component, is known to be expressed in bone and cartilage, however little is known about its

Iron-sulfur clusters are involved in post-translational arginylation

January 28, 2023
Verna Van, Janae Brown, Corin R. O'Shea, Hannah Rosenbach, Ijaz Mohamed, Nna-Emeka Ejimogu, Toan Bui, Veronika Szalai, Kelly Chacon, Ingrid Span, Aaron T. Smith
Eukaryotic arginylation is an essential post-translational modification that both modulates protein stability and regulates protein half-life through the N-degron pathway. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA

Design and characterization of a protein fold switching network

January 26, 2023
David Travis Gallagher, Biao Ruan, Yanan He, Yingwei Chen, Eun Jung Choi, Yihong Chen, Dana Motabar, Tsega Solomon, Richard Simmerman, Thomas Kauffman, John Orban, Philip Bryan
Protein sequences encoding three common small folds (3-alpha, beta-grasp, and alpha/beta plait) were connected in a network of mutational pathways that intersect at high-identity sequences, termed nodes. The structures of proteins around nodes were

ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics

January 24, 2023
Tobias Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Magnus Palmblad, Ben Neely, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric Deutsch
Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and

Measuring Dimensionality of Cell-Scaffold Contacts of Primary Human Bone Marrow Stromal Cells Cultured on Electrospun Fiber Scaffolds

January 1, 2023
Carl Simon Jr., Peter Bajcsy, Joe Chalfoun, Michael Paul Majurski, Mary C. Brady, Mylene Simon, Nathan Hotaling, Nick Schaub, Allison Horenberg, Piotr Szczypinski, Dongbo Wang, Veronica DeFelice, Soweon Yoon, Stephanie Florczyk
The properties and structure of the cellular microenvironment can influence cell behavior. Sites of cell adhesion to the extracellular matrix (ECM) initiate intracellular signaling that direct cell functions such as proliferation, differentiation and
Displaying 1 - 25 of 1140