Search Results - "Longabaugh, William J. R."

Interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology by Gorman, Chris, Punzo, Davide, Octaviano, Igor, Pieper, Steven, Longabaugh, William J. R., Clunie, David A., Kikinis, Ron, Fedorov, Andrey Y., Herrmann, Markus D.

“…The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and…”
Get full text

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning by Vokes, Steven A, Ji, Hongkai, McCuine, Scott, Tenzen, Toyoaki, Giles, Shane, Zhong, Sheng, Longabaugh, William J R, Davidson, Eric H, Wong, Wing H, McMahon, Andrew P

“…Sonic hedgehog (Shh) acts as a morphogen to mediate the specification of distinct cell identities in the ventral neural tube through a Gli-mediated (Gli1-3)…”
Get full text

Combing the hairball with BioFabric: a new approach for visualization of large networks by Longabaugh, William J R

“…The analysis of large, complex networks is an important aspect of ongoing biological research. Yet there is a need for entirely new, scalable approaches for…”
Get full text

The TP53 Database: transition from the International Agency for Research on Cancer to the US National Cancer Institute by de Andrade, Kelvin César, Lee, Elaine E., Tookmanian, Elise M., Kesserwan, Chimene A., Manfredi, James J., Hatton, Jessica N., Loukissas, Jennifer K., Zavadil, Jiri, Zhou, Lei, Olivier, Magali, Frone, Megan N., Shahzada, Owais, Longabaugh, William J. R., Kratz, Christian P., Malkin, David, Hainaut, Pierre, Savage, Sharon A.

Get full text

gene regulatory network armature for T lymphocyte specification by Georgescu, Constantin, Longabaugh, William J.R, Scripture-Adams, Deirdre D, David-Fung, Elizabeth-Sharon, Yui, Mary A, Zarnegar, Mark A, Bolouri, Hamid, Rothenberg, Ellen V

“…Choice of a T lymphoid fate by hematopoietic progenitor cells depends on sustained Notch-Delta signaling combined with tightly regulated activities of multiple…”
Get full text

BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks by Longabaugh, William J R

“…BioTapestry is an open source, freely available software tool that has been developed to handle the -challenges of modeling genetic regulatory networks (GRNs)…”
Get more information

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks by Longabaugh, William J.R., Davidson, Eric H., Bolouri, Hamid

“…Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on…”
Get full text

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo by Su, Yi-Hsien, Li, Enhu, Geiss, Gary K., Longabaugh, William J.R., Krämer, Alexander, Davidson, Eric H.

“…The current gene regulatory network (GRN) for the sea urchin embryo pertains to pregastrular specification functions in the endomesodermal territories. Here we…”
Get full text

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis by Gillespie, Mark A., Palii, Carmen G., Sanchez-Taltavull, Daniel, Shannon, Paul, Longabaugh, William J.R., Downes, Damien J., Sivaraman, Karthi, Espinoza, Herbert M., Hughes, Jim R., Price, Nathan D., Perkins, Theodore J., Ranish, Jeffrey A., Brand, Marjorie

“…Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs). However, despite years of studies,…”
Get full text

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network by Longabaugh, William J. R., Zeng, Weihua, Zhang, Jingli A., Hosokawa, Hiroyuki, Jansen, Camden S., Li, Long, Romero-Wolf, Maile, Liu, Pentao, Kueh, Hao Yuan, Mortazavi, Ali, Rothenberg, Ellen V.

“…T-cell development from hematopoietic progenitors depends on multiple transcription factors, mobilized and modulated by intrathymic Notch signaling. Key…”
Get full text

NCI Imaging Data Commons by Fedorov, Andrey, Longabaugh, William J R, Pot, David, Clunie, David A, Pieper, Steve, Aerts, Hugo J W L, Homeyer, André, Lewis, Rob, Akbarzadeh, Afshin, Bontempi, Dennis, Clifford, William, Herrmann, Markus D, Höfener, Henning, Octaviano, Igor, Osborne, Chad, Paquette, Suzanne, Petts, James, Punzo, Davide, Reyes, Madelyn, Schacherer, Daniela P, Tian, Mi, White, George, Ziegler, Erik, Shmulevich, Ilya, Pihl, Todd, Wagner, Ulrike, Farahani, Keyvan, Kikinis, Ron

“…The National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) aims to establish a national cloud-based data science infrastructure. Imaging Data…”
Get full text

National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence by Fedorov, Andrey, Longabaugh, William J R, Pot, David, Clunie, David A, Pieper, Steven D, Gibbs, David L, Bridge, Christopher, Herrmann, Markus D, Homeyer, André, Lewis, Rob, Aerts, Hugo J W L, Krishnaswamy, Deepa, Thiriveedhi, Vamsi Krishna, Ciausu, Cosmin, Schacherer, Daniela P, Bontempi, Dennis, Pihl, Todd, Wagner, Ulrike, Farahani, Keyvan, Kim, Erika, Kikinis, Ron

“…The remarkable advances of artificial intelligence (AI) technology are revolutionizing established approaches to the acquisition, interpretation, and analysis…”
Get full text

The NCI Imaging Data Commons as a platform for reproducible research in computational pathology by Schacherer, Daniela P., Herrmann, Markus D., Clunie, David A., Höfener, Henning, Clifford, William, Longabaugh, William J.R., Pieper, Steve, Kikinis, Ron, Fedorov, Andrey, Homeyer, André

“…•The Imaging Data Commons (IDC) is a new repository of FAIR cancer image collections.•Introduction to using the IDC for reproducible research in computational…”
Get full text

A high-resolution network model for global gene regulation in Mycobacterium tuberculosis by Peterson, Eliza J R, Reiss, David J, Turkarslan, Serdar, Minch, Kyle J, Rustad, Tige, Plaisier, Christopher L, Longabaugh, William J R, Sherman, David R, Baliga, Nitin S

“…The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments…”
Get full text

The NCI Imaging Data Commons as a platform for reproducible research in computational pathology by Schacherer, Daniela P, Herrmann, Markus D, Clunie, David A, Höfener, Henning, Clifford, William, Longabaugh, William J. R, Pieper, Steve, Kikinis, Ron, Fedorov, Andrey, Homeyer, André

“…Comput Methods Programs Biomed (2023) Background and Objectives: Reproducibility is a major challenge in developing machine learning (ML)-based solutions in…”
Get full text

Slim: interoperable slide microscopy viewer and annotation tool for imaging data science and computational pathology by Gorman, Chris, Punzo, Davide, Octaviano, Igor, Pieper, Steve, Longabaugh, William J. R, Clunie, David A, Kikinis, Ron, Fedorov, Andrey Y, Herrmann, Markus D

“…The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and…”
Get full text

Computational representation of developmental genetic regulatory networks by Longabaugh, William J.R., Davidson, Eric H., Bolouri, Hamid

“…Developmental genetic regulatory networks (GRNs) have unique architectural characteristics. They are typically large-scale, multi-layered, and organized in a…”
Get full text

BioTapestry now provides a web application and improved drawing and layout tools by Paquette, Suzanne M, Leinonen, Kalle, Longabaugh, William J R

“…Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of…”
Get full text