Research output per year
Research output per year
- 1 - 50 out of 594 results
Search results
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2024
Activation of coagulation FXI promotes endothelial inflammation and amplifies platelet activation in a nonhuman primate model of hyperlipidemia
Kohs, T. C. L., Vu, H. H., Jordan, K. R., Parra-Izquierdo, I., Hinds, M. T., Shatzel, J. J., Kievit, P., Morgan, T. K., Yunga, S. T., Ngo, T. T. M., Aslan, J. E., Wallisch, M., Lorentz, C. U., Tucker, E. I., Gailani, D., Lindner, J. R., Puy, C. & McCarty, O. J. T., Jan 2024, In: Research and Practice in Thrombosis and Haemostasis. 8, 1, 102276.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Automatically pre-screening patients for the rare disease aromatic L-amino acid decarboxylase deficiency using knowledge engineering, natural language processing, and machine learning on a large EHR population
Cohen, A. M., Kaner, J., Miller, R., Kopesky, J. W. & Hersh, W., Mar 1 2024, In: Journal of the American Medical Informatics Association. 31, 3, p. 692-704 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Autotaxin–lysolipid signaling suppresses a CCL11–eosinophil axis to promote pancreatic cancer progression
Bhattacharyya, S., Oon, C., Diaz, L., Sandborg, H., Stempinski, E. S., Saoi, M., Morgan, T., López, C. S., Cross, J. R. & Sherman, M., Feb 2024, In: Nature Cancer. 5, 2, p. 283-298 16 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Comparison of Immunotherapy versus Targeted Therapy Effectiveness in BRAF-Mutant Melanoma Patients and Use of cGAS Expression and Aneuploidy as Potential Prognostic Biomarkers
Garrison, Z., Clister, T., Bleem, E., Berry, E. G. & Kulkarni, R., Mar 2024, In: Cancers. 16, 5, 1027.Research output: Contribution to journal › Article › peer-review
Open Access -
DESP demixes cell-state profiles from dynamic bulk molecular measurements
Youssef, A., Paul, I., Crovella, M. & Emili, A., Mar 25 2024, In: Cell Reports Methods. 4, 3, 100729.Research output: Contribution to journal › Article › peer-review
Open Access -
Essentials of Theranostics: A Guide for Physicians and Medical Physicists
Sedlack, A. J. H., Meyer, C., Mench, A., Winters, C., Barbon, D., Obrzut, S. & Mallak, N., Jan 2024, In: Radiographics. 44, 1, e230097.Research output: Contribution to journal › Article › peer-review
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From Average Transient Transporter Currents to Microscopic Mechanism─A Bayesian Analysis
George, A. & Zuckerman, D. M., Feb 29 2024, In: Journal of Physical Chemistry B. 128, 8, p. 1830-1842 13 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments
Jokela, T. A., Dane, M. A., Smith, R. L., Devlin, K. L., Shalabi, S., Lopez, J. C., Miyano, M., Stampfer, M. R., Korkola, J. E., Gray, J. W., Heiser, L. M. & LaBarge, M. A., Jan 2024, In: Cellular Signalling. 113, 110958.Research output: Contribution to journal › Article › peer-review
Open Access -
High-throughput methylome analysis reveals differential methylation for early and late onset preeclampsia for mothers and their children
Layman, C. E., Ward, S., Davis, B. A., Nevonen, K. A., Okhovat, M., Rincon, M., Valent, A., Carbone, L. & Thornburg, K. L., Mar 2024, In: Physiological genomics. 56, 3, p. 276-282 7 p.Research output: Contribution to journal › Article › peer-review
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Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia
Pino, J. C., Posso, C., Joshi, S. K., Nestor, M., Moon, J., Hansen, J. R., Hutchinson-Bunch, C., Gritsenko, M. A., Weitz, K. K., Watanabe-Smith, K., Long, N., McDermott, J. E., Druker, B. J., Liu, T., Tyner, J. W., Agarwal, A., Traer, E., Piehowski, P. D., Tognon, C. E., Rodland, K. D., & 1 others, Jan 16 2024, In: Cell Reports Medicine. 5, 1, 101359.Research output: Contribution to journal › Article › peer-review
Open Access -
Nerve Visualization using Phenoxazine-Based Near-Infrared Fluorophores to Guide Prostatectomy
Wang, L. G., Montaño, A. R., Masillati, A. M., Jones, J. A., Barth, C. W., Combs, J. R., Kumarapeli, S. U., Shams, N. A., van den Berg, N. S., Antaris, A. L., Galvis, S. N., McDowall, I., Rizvi, S. Z. H., Alani, A. W. G., Sorger, J. M. & Gibbs, S. L., Apr 18 2024, In: Advanced Materials. 36, 16, 2304724.Research output: Contribution to journal › Article › peer-review
Open Access -
NETosis Is Induced by Complement Component 5a: Implications in the Pathogenesis of Pyoderma Gangrenosum
Wang, Z., Hornick, N., Vague, M., Yang, D., Keller, J., Kody, S., Leachman, S., Ortega-Loayza, A. G. & Liu, Y., Jan 2024, In: Journal of Investigative Dermatology. 144, 1, p. 184-188.e2Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
Night and Day, Why Radiologists Need Play
Averill, S. L., Gomez, E. N., Belfi, L. M., Hui, J., Mallak, N. & Chetlen, A., Feb 2024, In: Academic radiology. 31, 2, p. 360-370 11 p.Research output: Contribution to journal › Article › peer-review
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Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project
Zhang, Z., Shafer, A., Johnson-Camacho, K., Adey, A., Anur, P., Brown, K. A., Conrad, C., Crist, R., Farris, P. E., Harrington, C. A., Marriott, L. K., Mitchell, A., O'Roak, B., Serrato, V., Richards, C. S., Spellman, P. T. & Shannon, J., Jan 19 2024, In: Journal of Clinical and Translational Science. 8, 1, e32.Research output: Contribution to journal › Article › peer-review
Open Access -
Optimization of Tissue Digestion Methods for Characterization of Photoaged Skin by Single Cell RNA Sequencing Reveals Preferential Enrichment of T Cell Subsets
Clister, T., Fey, R. M., Garrison, Z. R., Valenzuela, C. D., Bar, A., Leitenberger, J. J. & Kulkarni, R. P., Feb 2024, In: Cells. 13, 3, 266.Research output: Contribution to journal › Article › peer-review
Open Access -
Predicting transcription factor activity using prior biological information
Yashar, W. M., Estabrook, J., Holly, H. D., Somers, J., Nikolova, O., Babur, O., Braun, T. & Demir, E., Mar 15 2024, In: iScience. 27, 3, 109124.Research output: Contribution to journal › Article › peer-review
Open Access -
RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration
Olson, H. M., Maxfield, A., Calistri, N. L., Heiser, L. M., Qian, W., Knaut, H. & Nechiporuk, A. V., Jan 2024, In: Development (Cambridge). 151, 1, dev201898.Research output: Contribution to journal › Article › peer-review
Open Access -
Second site reversion of HIV-1 envelope protein baseplate mutations maps to the matrix protein
Alfadhli, A., Romanaggi, C. A., Barklis, R. L. & Barklis, E., Feb 2024, In: Journal of virology. 98, 2Research output: Contribution to journal › Article › peer-review
Open Access -
Structurally divergent and recurrently mutated regions of primate genomes
Mao, Y., Harvey, W. T., Porubsky, D., Munson, K. M., Hoekzema, K., Lewis, A. P., Audano, P. A., Rozanski, A., Yang, X., Zhang, S., Yoo, D. A., Gordon, D. S., Fair, T., Wei, X., Logsdon, G. A., Haukness, M., Dishuck, P. C., Jeong, H., del Rosario, R., Bauer, V. L., & 14 others, Mar 14 2024, In: Cell. 187, 6, p. 1547-1562.e13Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
The Reactome Pathway Knowledgebase 2024
Milacic, M., Beavers, D., Conley, P., Gong, C., Gillespie, M., Griss, J., Haw, R., Jassal, B., Matthews, L., May, B., Petryszak, R., Ragueneau, E., Rothfels, K., Sevilla, C., Shamovsky, V., Stephan, R., Tiwari, K., Varusai, T., Weiser, J., Wright, A., & 4 others, Jan 5 2024, In: Nucleic acids research. 52, D1, p. D672-D678Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility
Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A. C. & Cusanovich, D. A., Dec 2024, In: Genome biology. 25, 1, 78.Research output: Contribution to journal › Article › peer-review
Open Access -
Uterine Uptake of Estrogen and Progestogen-Based Radiotracers in Rhesus Macaques with Endometriosis
Wilson, R. C., Link, J. M., Lee, Y. Z., Oldan, J. D., Young, S. L. & Slayden, O. D., Apr 2024, In: Molecular Imaging and Biology. 26, 2, p. 334-343 10 p.Research output: Contribution to journal › Article › peer-review
Open Access -
2023
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
Dommer, A., Casalino, L., Kearns, F., Rosenfeld, M., Wauer, N., Ahn, S. H., Russo, J., Oliveira, S., Morris, C., Bogetti, A., Trifan, A., Brace, A., Sztain, T., Clyde, A., Ma, H., Chennubhotla, C., Lee, H., Turilli, M., Khalid, S., Tamayo-Mendoza, T., & 32 others, Jan 2023, In: International Journal of High Performance Computing Applications. 37, 1, p. 28-44 17 p.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility
Queitsch, K., Moore, T. W., O'Connell, B. L., Nichols, R. V., Muschler, J. L., Keith, D., Lopez, C., Sears, R. C., Mills, G. B., Yardımcı, G. G. & Adey, A. C., Nov 20 2023, In: Cell Reports Methods. 3, 11, 100625.Research output: Contribution to journal › Article › peer-review
Open Access -
Allele-Specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha-Mutant Endometrial Cancer
Blanchard, Z., Rush, C. M., Arnesen, S., Vahrenkamp, J. M., Rodriguez, A. C., Jarboe, E. A., Brown, C., Chang, M. E. K., Flory, M. R., Mohammed, H., Modzelewska, K., Lum, D. H. & Gertz, J., Oct 1 2023, In: Molecular Cancer Research. 21, 10, p. 1023-1036 14 p.Research output: Contribution to journal › Article › peer-review
Open Access -
An altered extracellular matrix–integrin interface contributes to Huntington’s disease-associated CNS dysfunction in glial and vascular cells
Hernandez, S. J., Lim, R. G., Onur, T., Dane, M. A., Smith, R., Wang, K., Jean, G. E. H., Reyes-Ortiz, A., Devlin, K., Miramontes, R., Wu, J., Casale, M., Kilburn, D., Heiser, L. M., Korkola, J. E., Van Vactor, D., Botas, J., Thompson-Peer, K. L. & Thompson, L. M., May 1 2023, In: Human molecular genetics. 32, 9, p. 1483-1496 14 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects
Gross, S. M., Mohammadi, F., Sanchez-Aguila, C., Zhan, P. J., Liby, T. A., Dane, M. A., Meyer, A. S. & Heiser, L. M., Dec 2023, In: Nature communications. 14, 1, 3450.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
A phosphoinositide switch mediates exocyst recruitment to multivesicular endosomes for exosome secretion
Liu, D. A., Tao, K., Wu, B., Yu, Z., Szczepaniak, M., Rames, M., Yang, C., Svitkina, T., Zhu, Y., Xu, F., Nan, X. & Guo, W., Dec 2023, In: Nature communications. 14, 1, 6883.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors
Braun, T. P., Estabrook, J., Schonrock, Z., Curtiss, B. M., Darmusey, L., Macaraeg, J., Enright, T., Coblentz, C., Callahan, R., Yashar, W., Taherinasab, A., Mohammed, H., Coleman, D. J., Druker, B. J., Demir, E., Lusardi, T. A. & Maxson, J. E., Feb 2023, In: Leukemia. 37, 2, p. 478-487 10 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
O’Connell, B. L., Nichols, R. V., Pokholok, D., Thomas, J., Acharya, S. N., Nishida, A., Thornton, C. A., Co, M., Fields, A. J., Steemers, F. J. & Adey, A. C., 2023, In: Genome Research. 33, 2, p. 208-217 10 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Automated deep-learning system in the assessment of MRI-visible prostate cancer: comparison of advanced zoomed diffusion-weighted imaging and conventional technique
Hu, L., Fu, C., Song, X., Grimm, R., von Busch, H., Benkert, T., Kamen, A., Lou, B., Huisman, H., Tong, A., Penzkofer, T., Choi, M. H., Shabunin, I., Winkel, D., Xing, P., Szolar, D., Coakley, F., Shea, S., Szurowska, E., Guo, J. Y., & 3 others, Dec 2023, In: Cancer Imaging. 23, 1, 6.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease
Burkhart, J. G., Wu, G., Song, X., Raimondi, F., McWeeney, S., Wong, M. H. & Deng, Y., Jul 14 2023, In: Patterns. 4, 7, 100758.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma
Thieme, E., Bruss, N., Sun, D., Dominguez, E. C., Coleman, D., Liu, T., Roleder, C., Martinez, M., Garcia-Mansfield, K., Ball, B., Pirrotte, P., Wang, L., Xia, Z. & Danilov, A. V., Dec 2023, In: Molecular Cancer. 22, 1, 64.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Characterization of extracellular matrix deposited by segmental trabecular meshwork cells
Raghunathan, V. K., Nartey, A., Dhamodaran, K., Baidouri, H., Staverosky, J. A., Keller, K. E., Zientek, K., Reddy, A., Acott, T. & Vranka, J. A., Sep 2023, In: Experimental Eye Research. 234, 109605.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells
McClatchy, J., Strogantsev, R., Wolfe, E., Lin, H. Y., Mohammadhosseini, M., Davis, B. A., Eden, C., Goldman, D., Fleming, W. H., Conley, P., Wu, G., Cimmino, L., Mohammed, H. & Agarwal, A., Dec 2023, In: Nature communications. 14, 1, 8102.Research output: Contribution to journal › Article › peer-review
Open Access -
Comparison and validation of the 2022 European LeukemiaNet guidelines in acute myeloid leukemia
Lachowiez, C. A., Long, N., Saultz, J., Gandhi, A., Newell, L. F., Hayes-Lattin, B., Maziarz, R. T., Leonard, J., Bottomly, D., McWeeney, S., Dunlap, J., Press, R., Meyers, G., Swords, R., Cook, R. J., Tyner, J. W., Druker, B. J. & Traer, E., May 9 2023, In: Blood Advances. 7, 9, p. 1899-1909 11 p.Research output: Contribution to journal › Article › peer-review
Open Access25 Scopus citations -
Cytogenetically Cryptic Acute Promyelocytic Leukemia: A Diagnostic Challenge
Mohebnasab, M., Li, P., Hong, B., Dunlap, J., Traer, E., Fan, G., Press, R. D., Moore, S. R. & Xie, W., Sep 2023, In: International journal of molecular sciences. 24, 17, 13075.Research output: Contribution to journal › Article › peer-review
Open Access -
Deciphering spatially distinct immune microenvironments in glioblastoma using ferumoxytol and gadolinium-enhanced and FLAIR hyperintense MRI phenotypes
Stoller, J., Kersch, C. N., Muldoon, L., Ambady, P., Harrington, C. A., Fu, R., Raslan, A. M., Dogan, A., Neuwelt, E. A. & Barajas, R. F., Jan 1 2023, In: Neuro-Oncology Advances. 5, 1, vdad148.Research output: Contribution to journal › Article › peer-review
Open Access -
Deletion of the mRNA stability factor ELAVL1 (HuR) in pancreatic cancer cells disrupts the tumor microenvironment integrity
McCarthy, G. A., Di Niro, R., Finan, J. M., Jain, A., Guo, Y., Wyatt, C. R., Guimaraes, A. R., Waugh, T. A., Keith, D., Morgan, T. K., Sears, R. C. & Brody, J. R., Jun 1 2023, In: NAR Cancer. 5, 2, zcad016.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Yashar, W. M., Curtiss, B. M., Coleman, D. J., VanCampen, J., Kong, G., Macaraeg, J., Estabrook, J., Demir, E., Long, N., Bottomly, D., McWeeney, S. K., Tyner, J. W., Druker, B. J., Maxson, J. E. & Braun, T. P., Jul 1 2023, In: Molecular Cancer Research. 21, 7, p. 631-647 17 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
the COVID-19 Disease Map Community, 2023, In: Frontiers in immunology. 14, 1282859.Research output: Contribution to journal › Article › peer-review
Open Access -
Dual probe difference specimen imaging for prostate cancer margin assessment
Kwon, M. J., House, B. J., Barth, C. W., Solanki, A., Jones, J. A., Davis, S. C. & Gibbs, S. L., Aug 1 2023, In: Journal of biomedical optics. 28, 8, 082806.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Dynamic remodeling of Escherichia coli interactome in response to environmental perturbations
Youssef, A., Bian, F., Paniikov, N. S., Crovella, M. & Emili, A., Nov 2023, In: Proteomics. 23, 21-22, 2200404.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Early Detection of Prostate Cancer: AUA/SUO Guideline Part II: Considerations for a Prostate Biopsy
Wei, J. T., Barocas, D., Carlsson, S., Coakley, F., Eggener, S., Etzioni, R., Fine, S. W., Han, M., Kim, S. K., Kirkby, E., Konety, B. R., Miner, M., Moses, K., Nissenberg, M. G., Pinto, P. A., Salami, S. S., Souter, L., Thompson, I. M. & Lin, D. W., Jul 2023, In: Journal of Urology. 210, 1, p. 54-63 10 p.Research output: Contribution to journal › Article › peer-review
20 Scopus citations -
Early Detection of Prostate Cancer: AUA/SUO Guideline Part I: Prostate Cancer Screening
Wei, J. T., Barocas, D., Carlsson, S., Coakley, F., Eggener, S., Etzioni, R., Fine, S. W., Han, M., Kim, S. K., Kirkby, E., Konety, B. R., Miner, M., Moses, K., Nissenberg, M. G., Pinto, P. A., Salami, S. S., Souter, L., Thompson, I. M. & Lin, D. W., Jul 2023, In: Journal of Urology. 210, 1, p. 46-53 8 p.Research output: Contribution to journal › Article › peer-review
45 Scopus citations -
Effect of antiplatelet agents and tyrosine kinase inhibitors on oxLDL-mediated procoagulant platelet activity
Zheng, T. J., Kohs, T. C. L., Mueller, P. A., Pang, J., Reitsma, S. E., Parra-Izquierdo, I., Melrose, A. R., Yang, L., Choi, J., Zientek, K. D., Sviridov, D. O., Larson, M. K., Williams, C. D., Pamir, N., Shatzel, J. J., Reddy, A. P., Kievit, P., Remaley, A. T., Stevens, J. F., Hinds, M. T., & 2 others, Apr 25 2023, In: Blood Advances. 7, 8, p. 1366-1378 13 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Enhancement of dielectrophoresis-based particle collection from high conducting fluids due to partial electrode insulation
Luna, R., Heineck, D., Hinestrosa, J. P., Dobrovolskaia, I., Hamilton, S., Malakian, A., Gustafson, K. T., Huynh, K. T., Kim, S., Ware, J., Stimson, E., Ross, C., Schutt, C. E. & Ibsen, S. D., Aug 2023, In: ELECTROPHORESIS. 44, 15-16, p. 1234-1246 13 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Evaluating Receptor-Specific Fresh Specimen Staining for Tumor Margin Detection in Clinical Breast Specimens
Byrd, B. K., Wells, W. A., Strawbridge, R. R., Barth, C. W., Samkoe, K. S., Gibbs, S. L. & Davis, S. C., Oct 2023, In: Molecular Imaging and Biology. 25, 5, p. 911-922 12 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Experimental design considerations for studies of human tear proteins
Harkness, B. M., Hegarty, D. M., Saugstad, J. A., Behrens, H., Betz, J., David, L. L., Lapidus, J. A., Chen, S., Stutzman, R., Chamberlain, W., Perez-Blanco, M., Galor, A. & Aicher, S. A., Apr 2023, In: Ocular Surface. 28, p. 58-78 21 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Flexible Cyclic Immunofluorescence (cyCIF) Using Oligonucleotide Barcoded Antibodies
McMahon, N. P., Jones, J. A., Anderson, A. N., Dietz, M. S., Wong, M. H. & Gibbs, S. L., Feb 2023, In: Cancers. 15, 3, 827.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations