Signal Recovery Using a Spiked Mixture Model

Authors: Delacour, Paul-Louis, Wahls, Sander, Spraggins, Jeffrey M., Migas, Lukasz, Van de Plas, Raf

Subject Terms: Statistics - Machine Learning, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2501.01840

Virtual Staining of Label-Free Tissue in Imaging Mass Spectrometry

Authors: Zhang, Yijie, Huang, Luzhe, Pillar, Nir, Li, Yuzhu, Migas, Lukasz G., Van de Plas, Raf, Spraggins, Jeffrey M., Ozcan, Aydogan

Subject Terms: Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Physics - Medical Physics, Physics - Optics

Access URL: http://arxiv.org/abs/2411.13120

Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data

Authors: Bialy, Nikki, Alber, Frank, Andrews, Brenda, Angelo, Michael, Beliveau, Brian, Bintu, Lacramioara, Boettiger, Alistair, Boehm, Ulrike, Brown, Claire M., Maina, Mahmoud Bukar, Chambers, James J., Cimini, Beth A., Eliceiri, Kevin, Errington, Rachel, Faklaris, Orestis, Gaudreault, Nathalie, Germain, Ronald N., Goscinski, Wojtek, Grunwald, David, Halter, Michael, Hanein, Dorit, Hickey, John W., Lacoste, Judith, Laude, Alex, Lundberg, Emma, Ma, Jian, Malacrida, Leonel, Moore, Josh, Nelson, Glyn, Neumann, Elizabeth Kathleen, Nitschke, Roland, Onami, Shuichi, Pimentel, Jaime A., Plant, Anne L., Radtke, Andrea J., Sabata, Bikash, Schapiro, Denis, Schöneberg, Johannes, Spraggins, Jeffrey M., Sudar, Damir, Vierdag, Wouter-Michiel Adrien Maria, Volkmann, Niels, Wählby, Carolina, Siyuan, Wang, Yaniv, Ziv, Strambio-De-Castillia, Caterina

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2401.13022

Super-resolution multi-contrast unbiased eye atlases with deep probabilistic refinement

Authors: Lee, Ho Hin, Saunders, Adam M., Kim, Michael E., Remedios, Samuel W., Remedios, Lucas W., Tang, Yucheng, Yang, Qi, Yu, Xin, Bao, Shunxing, Cho, Chloe, Mawn, Louise A., Rex, Tonia S., Schey, Kevin L., Dewey, Blake E., Spraggins, Jeffrey M., Prince, Jerry L., Huo, Yuankai, Landman, Bennett A.

Source: J. Med. Imag. 11(6), 064004 (2024)

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2401.03060

Multi-Contrast Computed Tomography Atlas of Healthy Pancreas

Authors: Zhou, Yinchi, Lee, Ho Hin, Tang, Yucheng, Yu, Xin, Yang, Qi, Bao, Shunxing, Spraggins, Jeffrey M., Huo, Yuankai, Landman, Bennett A.

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2306.01853

Uncovering lipid dynamics in Staphylococcus aureus osteomyelitis using multimodal imaging mass spectrometry

Authors: Good, Christopher J. ^{1, 2}, Butrico, Casey E. ³, Colley, Madeline E. ^{1, 4}, Emmerson, Lauren N. ^{1, 5}, Gibson-Corley, Katherine N. ³, Cassat, James E. ^{3, 6, 7, 8}, Spraggins, Jeffrey M. ^{1, 2, 3, 4, 8, 9, 12, ∗}, Caprioli, Richard M. ^{1, 2, 4, 10, 11}

Source: In Cell Chemical Biology 17 October 2024 31(10):1852-1868

New views of old proteins: clarifying the enigmatic proteome

Authors: Functional, Participants in a NIH Workshop on, Proteomics, Integrative, Johnson, Kristin E. Burnum, Conrads, Thomas P., Drake, Richard R., Herr, Amy E., Iyengar, Ravi, Kelly, Ryan T., Lundberg, Emma, MacCoss, Michael J., Naba, Alexandra, Nolan, Garry P., Pevzner, Pavel A., Rodland, Karin D., Sechi, Salvatore, Slavov, Nikolai, Spraggins, Jeffrey M., Van Eyk, Jennifer E., Vidal, Marc, Vogel, Christine, Walt, David R., Kelleher, Neil L.

Subject Terms: Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2108.07660

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

Authors: Hickey, John W., Neumann, Elizabeth K., Radtke, Andrea J., Camarillo, Jeannie M., Beuschel, Rebecca T., Albanese, Alexandre, McDonough, Elizabeth, Hatler, Julia, Wiblin, Anne E., Fisher, Jeremy, Croteau, Josh, Small, Eliza C., Sood, Anup, Caprioli, Richard M., Angelo, R. Michael, Nolan, Garry P., Chung, Kwanghun, Hewitt, Stephen M., Germain, Ronald N., Spraggins, Jeffrey M., Lundberg, Emma, Snyder, Michael P., Kelleher, Neil L., Saka, Sinem K.

Subject Terms: Quantitative Biology - Tissues and Organs

Access URL: http://arxiv.org/abs/2107.07953

Multi-Contrast Computed Tomography Healthy Kidney Atlas

Authors: Lee, Ho Hin, Tang, Yucheng, Xu, Kaiwen, Bao, Shunxing, Fogo, Agnes B., Harris, Raymond, de Caestecker, Mark P., Heinrich, Mattias, Spraggins, Jeffrey M., Huo, Yuankai, Landman, Bennett A.

Subject Terms: Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition

Access URL: http://arxiv.org/abs/2012.12432

Construction and Usage of a Human Body Common Coordinate Framework Comprising Clinical, Semantic, and Spatial Ontologies

Authors: Börner, Katy, Quardokus, Ellen M., Herr II, Bruce W., Cross, Leonard E., Record, Elizabeth G., Ju, Yingnan, Bueckle, Andreas D., Sluka, James P., Silverstein, Jonathan C., Browne, Kristen M., Jain, Sanjay, Wasserfall, Clive H., Jorgensen, Marda L., Spraggins, Jeffrey M., Patterson, Nathan H., Musen, Mark A., Weber, Griffin M.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Computation and Language, Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2007.14474

Imaging mass spectrometry reveals complex lipid distributions across Staphylococcus aureus biofilm layers

Authors: Rivera, Emilio S., Weiss, Andy, Migas, Lukasz G., Freiberg, Jeffrey A., Djambazova, Katerina V., Neumann, Elizabeth K., Van de Plas, Raf, Spraggins, Jeffrey M., Skaar, Eric P., Caprioli, Richard M.

Source: In Journal of Mass Spectrometry and Advances in the Clinical Lab November 2022 26:36-46

New Views of Old Proteins: Clarifying the Enigmatic Proteome

Authors: Burnum-Johnson, Kristin E., Conrads, Thomas P., Drake, Richard R., Herr, Amy E., Iyengar, Ravi, Kelly, Ryan T., Lundberg, Emma, MacCoss, Michael J., Naba, Alexandra, Nolan, Garry P., Pevzner, Pavel A., Rodland, Karin D., Sechi, Salvatore, Slavov, Nikolai, Spraggins, Jeffrey M., Van Eyk, Jennifer E., Vidal, Marc, Vogel, Christine, Walt, David R., Kelleher, Neil L.

Source: In Molecular & Cellular Proteomics July 2022 21(7)

Multi-contrast computed tomography healthy kidney atlas

Authors: Lee, Ho Hin, Tang, Yucheng, Xu, Kaiwen, Bao, Shunxing, Fogo, Agnes B., Harris, Raymond, de Caestecker, Mark P., Heinrich, Mattias, Spraggins, Jeffrey M., Huo, Yuankai, Landman, Bennett A.

Source: In Computers in Biology and Medicine July 2022 146

Zn-regulated GTPase metalloprotein activator 1 modulates vertebrate zinc homeostasis

Authors: Weiss, Andy, Murdoch, Caitlin C., Edmonds, Katherine A., Jordan, Matthew R., Monteith, Andrew J., Perera, Yasiru R., Rodríguez Nassif, Aslin M., Petoletti, Amber M., Beavers, William N., Munneke, Matthew J., Drury, Sydney L., Krystofiak, Evan S., Thalluri, Kishore, Wu, Hongwei, Kruse, Angela R.S., DiMarchi, Richard D., Caprioli, Richard M., Spraggins, Jeffrey M., Chazin, Walter J., Giedroc, David P., Skaar, Eric P.

Source: In Cell 9 June 2022 185(12):2148-2163

Automated biomarker candidate discovery in imaging mass spectrometry data through spatially localized Shapley additive explanations

Authors: Tideman, Leonoor E.M., Migas, Lukasz G., Djambazova, Katerina V., Patterson, Nathan Heath, Caprioli, Richard M., Spraggins, Jeffrey M., Van de Plas, Raf

Source: In Analytica Chimica Acta 8 September 2021 1177

Cadherin-11, Sparc-related modular calcium binding protein-2, and Pigment epithelium-derived factor are promising non-invasive biomarkers of kidney fibrosis

Authors: Knight, Richard, Lecker, Stewart H., Stillman, Isaac, Bogen, Steve, Amodu, Afolarin A., Ilori, Titlayo, Maikhor, Shana, Schmidt, Insa M., Beck, Laurence H., Henderson, Joel M., Onul, Ingrid, Verma, Ashish, McMahon, Gearoid M., Valerius, M. Todd, Waikar, Sushrut, Weins, Astrid, Colona, Mia R., Greka, Anna, Hacohen, Nir, Hoover, Paul J., Marshall, Jamie L., Aulisio, Mark, Chen, Yijiang M., Janowczyk, Andrew, Jayapandian, Catherine, Viswanathan, Vidya S., Bush, William S., Crawford, Dana C., Madabhushi, Anant, Bush, Lakeshia, Cooperman, Leslie, Gonzalez-Vicente, Agustin, Herlitz, Leal, Jolly, Stacey, Nguyen, Jane, O’toole, John, Palmer, Ellen, Poggio, Emilio, Sedor, John, Sendrey, Dianna, Spates-Harden, Kassandra, Taliercio, Jonathan, Bjornstad, Petter M., Pyle, Laura, Vinovskis, Carissa, Appelbaum, Paul, Balderes, Olivia, Barasch, Jonathan M., Bomback, Andrew S., Canetta, Pietro A., D’Agati, Vivette D., Kiryluk, Krzysztof, Kudose, Satoru, Mehl, Karla, Shang, Ning, Bansal, Shweta, Alexandrov, Theodore, Rennke, Helmut, El-Achkar, Tarek M., Barwinska, Daria, Bledso, Sharon, Borner, Katy, Bueckle, Andreas, Cheng, Yinghua, Dagher, Pierre C., Dunn, Kenneth W., Eadon, Michael T., Ferkowicz, Michael J., Herr, Bruce W., Kelly, Katherine J., Ferreira, Ricardo Melo, Quardokus, Ellen M., Record, Elizabeth, Rivera, Marcelino, Su, Jing, Sutton, Timothy A., Williams, James C., Jr., Winfree, Seth, Jain, Yashvardhan, Menez, Steven, Parikh, Chirag R., Rosenberg, Avi, Corona-Villalobos, Celia P., Wen, Yumeng, Johansen, Camille, Rosas, Sylvia E., Roy, Neil, Sun, Jennifer, Williams, Mark, Azeloglu, Evren U., Hansen, Jens, He, Cijang, Iyengar, Ravi, Xiong, Yuguang, Prasad, Pottumarthi, Srivastava, Anand, Madhavan, Sethu M., Parikh, Samir, Rovin, Brad, Shapiro, John P., Anderton, Christopher R., Lukowski, Jessica, Pasa-Tolic, Ljiljana, Velickovic, Dusan, Oliver, George (Holt), Ardayfio, Joseph, Bebiak, Jack, Brown, Keith, Campbell, Taneisha, Campbell, Catherine E., Hayashi, Lynda, Jefferson, Nichole, Roberts, Glenda V., Saul, John, Shpigel, Anna, Stutzke, Christy, Koewler, Robert, Pinkeney, Roy, Sealfon, Rachel, Troyanskaya, Olga, Wong, Aaron, Tuttle, Katherine R., Pollack, Ari, Goltsev, Yury, Ginley, Brandon, Lucarelli, Nicholas, Lutnick, Brendon, Sarder, Pinaki, Lake, Blue B., Zhang, Kun, Boada, Patrick, Laszik, Zoltan G., Nolan, Garry, Anjani, Kavya, Sarwal, Minnie, Mukatash, Tariq, Sigdel, Tara, Alloway, Rita R., Burg, Ashley R., Lee, Paul J., Rike, Adele, Shi, Tiffany, Woodle, E. Steve, Ascani, Heather, Balis, Ulysses G.J., Blanc, Victoria M., Conser, Ninive C., Eddy, Sean, Frey, Renee, He, Yougqun, Hodgin, Jeffrey B., Kretzler, Matthias, Lienczewski, Chrysta, Luo, Jinghui, Mariani, Laura H., Menon, Rajasree, Otto, Edgar, Schaub, Jennifer, Steck, Becky, Elder, Michele M., Gilliam, Matthew, Hall, Daniel E., Murugan, Raghavan, Palevsky, Paul M., Randhawa, Parmjeet, Rosengart, Matthew, Tublin, Mitchell, Vita, Tina, Winters, James, Kellum, John A., Alpers, Charles E., Berglund, Ashley, Berry, Brooke, Blank, Kristina N., Carson, Jonas, Daniel, Stephen, De Boer, Ian H., Dighe, Ashveena L., Dowd, Frederick, Grewenow, Stephanie M., Himmelfarb, Jonathan, Hoofnagle, Andrew N., Limonte, Christine, McClelland, Robyn L., Mooney, Sean D., Rezaei, Kasra, Shankland, Stuart, Snyder, Jamie, Wang, Ruikang, Wilcox, Adam, Williams, Kayleen, Park, Christopher, Montellano, Richard, Pamreddy, Annapurna, Sharma, Kumar, Venkatachalam, Manjeri, Ye, Hongping, Zhang, Guanshi, Basit, Mujeeb, Hedayati, S. Susan, Kermani, Asra, Lee, Simon C., Lu, Christopher Y., Miller, R. Tyler, Moe, Orson W., Patel, Jiten, Pillai, Anil, Sambandam, Kamalanathan, Torrealba, Jose, Toto, Robert D., Vazquez, Miguel, Wang, Nancy, Wen, Natasha, Zhang, Dianbo, Park, Harold, Caprioli, Richard M., Patterson, Nathan, Sharman, Kavya, Spraggins, Jeffrey M., Van de Plas, Raf, Basta, Jeanine, Diettman, Sabine M., Gaut, Joseph P., Jain, Sanjay, Rauchman, Michael I., Vijayan, Anitha, Cantley, Lloyd G., Kakade, Vijaykumar R., Moledina, Dennis, Shaw, Melissa M., Ugwuowo, Ugochukwu, Wilson, Francis P., Arora, Tanima, Kestenbaum, Bryan R., Alexopoulos, Leonidas G., Palsson, Ragnar, Liu, Jing, Stillman, Isaac E., Rennke, Helmut G., Vaidya, Vishal S., Wu, Haojia, Humphreys, Benjamin D., Waikar, Sushrut S.

Source: In Kidney International September 2021 100(3):672-683

Modulating Isoprenoid Biosynthesis Increases Lipooligosaccharides and Restores Acinetobacter baumannii Resistance to Host and Antibiotic Stress

Authors: Palmer, Lauren D., Minor, Keaton E., Mettlach, Joshua A., Rivera, Emilio S., Boyd, Kelli L., Caprioli, Richard M., Spraggins, Jeffrey M., Dalebroux, Zachary D., Skaar, Eric P.

Source: In Cell Reports 8 September 2020 32(10)

Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features

Authors: Islam, Mirazul, Chen, Bob, Spraggins, Jeffrey M., Kelly, Ryan T., Lau, Ken S.

Source: In Gastroenterology August 2020 159(2):453-466

Staphylococcus aureus exhibits heterogeneous siderophore production within the vertebrate host

Authors: Perry, William J., Spraggins, Jeffrey M., Sheldon, Jessica R., Grunenwald, Caroline M., Heinrichs, David E., Cassat, James E., Skaar, Eric P., Caprioli, Richard M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2019 Oct . 116(44), 21980-21982.

Access URL: https://www.jstor.org/stable/26859833

Integrated molecular imaging technologies for investigation of metals in biological systems: A brief review

Authors: Perry, William J., Weiss, Andy, Van de Plas, Raf, Spraggins, Jeffrey M., Caprioli, Richard M., Skaar, Eric P.

Source: In Current Opinion in Chemical Biology April 2020 55:127-135