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2020

Androgen receptor-binding sites are highly mutated in prostate cancer

Morova, T., McNeill, D. R., Lallous, N., Gönen, M., Dalal, K., Wilson, D. M., Gürsoy, A., Keskin, Ö. & Lack, N. A., Dec 1 2020, In : Nature communications. 11, 1, 832.

Research output: Contribution to journalArticle

Open Access

A prospective prediction tool for understanding Crimean–Congo haemorrhagic fever dynamics in Turkey

Ak, Ergönül & Gönen, M., Jan 2020, In : Clinical Microbiology and Infection. 26, 1, p. 123.e1-123.e7

Research output: Contribution to journalArticle

1 Scopus citations

Assessment of neonatal, cord, and adult platelet granule trafficking and secretion

Ngo, A. T. P., Sheriff, J., Rocheleau, A. D., Bucher, M., Jones, K. R., Sepp, A. L. I., Malone, L. E., Zigomalas, A., Maloyan, A., Bahou, W. F., Bluestein, D., McCarty, O. J. T. & Haley, K. M., Jan 2 2020, In : Platelets. 31, 1, p. 68-78 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Deregulating MYC in a model of HER2+ breast cancer mimics human intertumoral heterogeneity

Risom, T., Wang, X., Liang, J., Zhang, X., Pelz, C., Campbell, L. G., Eng, J., Chin, K., Farrington, C., Narla, G., Langer, E. M., Sun, X. X., Su, Y., Daniel, C. J., Dai, M. S., Löhr, C. V. & Sears, R. C., Jan 2 2020, In : Journal of Clinical Investigation. 130, 1, p. 231-246 16 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

EmrE reminds us to expect the unexpected in membrane transport

Grabe, M., Zuckerman, D. M. & Rosenberg, J. M., Jan 6 2020, In : The Journal of general physiology. 152, 1

Research output: Contribution to journalArticle

Open Access

Evaluation of the Antihemostatic and Antithrombotic Effects of Lowering Coagulation Factor VII Levels in a Non-human Primate

Wallisch, M., Olson, S. R., Crosby, J., Johnson, J., Murray, S. F., Shatzel, J. J., Tucker, E. I., McCarty, O. J. T., Hinds, M. T., Monia, B. P. & Gruber, A., Jun 1 2020, In : Cellular and Molecular Bioengineering. 13, 3, p. 179-187 9 p.

Research output: Contribution to journalArticle

Fucoidan functionalization on poly(vinyl alcohol) hydrogels for improved endothelialization and hemocompatibility

Yao, Y., Zaw, A. M., Anderson, D. E. J., Hinds, M. T. & Yim, E. K. F., Aug 2020, In : Biomaterials. 249, 120011.

Research output: Contribution to journalArticle

One-Pot Covalent Grafting of Gelatin on Poly(Vinyl Alcohol) Hydrogel to Enhance Endothelialization and Hemocompatibility for Synthetic Vascular Graft Applications

Rizwan, M., Yao, Y., Gorbet, M. B., Tse, J. W., Anderson, D. E. J., Hinds, M. T. & Yim, E. K. F., Jan 21 2020, In : ACS Applied Bio Materials. 3, 1, p. 693-703 11 p.

Research output: Contribution to journalArticle

Open Access

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

Rodchenkov, I., Babur, O., Luna, A., Aksoy, B. A., Wong, J. V., Fong, D., Franz, M., Siper, M. C., Cheung, M., Wrana, M., Mistry, H., Mosier, L., Dlin, J., Wen, Q., O'Callaghan, C., Li, W., Elder, G., Smith, P. T., Dallago, C., Cerami, E. & 5 others, Gross, B., Dogrusoz, U., Demir, E., Bader, G. D. & Sander, C., Jan 8 2020, In : Nucleic acids research. 48, D1, p. D489-D497

Research output: Contribution to journalArticle

Open Access

Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin

Schau, G. F., Burlingame, E. A., Thibault, G., Anekpuritanang, T., Wang, Y., Gray, J. W., Corless, C. & Chang, Y. H., Jan 1 2020, In : Journal of Medical Imaging. 7, 1, 012706.

Research output: Contribution to journalArticle

Quantification of fluorophore distribution and therapeutic response in matched in vivo and ex vivo pancreatic cancer model systems

Solanki, A., King, D., Thibault, G., Wang, L. & Gibbs, S. L., Jan 1 2020, In : PloS one. 15, 2, e0229407.

Research output: Contribution to journalArticle

Open Access

RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging

Chang, Y. H., Chin, K., Thibault, G., Eng, J., Burlingame, E. & Gray, J. W., Dec 1 2020, In : Communications Biology. 3, 1, 111.

Research output: Contribution to journalArticle

Open Access

TGFβ signaling is critical for maintenance of the tendon cell fate

Tan, G. K., Pryce, B. A., Stabio, A., Brigande, J. V., Wang, C., Xia, Z., Tufa, S. F., Keene, D. R. & Schweitzer, R., Jan 2020, In : eLife. 9, e52695.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The Efficacy of Basal Rate and Carbohydrate Ratio Learning Algorithm for Closed-Loop Insulin Delivery (Artificial Pancreas) in Youth with Type 1 Diabetes in a Diabetes Camp

Palisaitis, E., El Fathi, A., Von Oettingen, J. E., Krishnamoorthy, P., Kearney, R., Jacobs, P., Rutkowski, J., Legault, L. & Haidar, A., Mar 2020, In : Diabetes Technology and Therapeutics. 22, 3, p. 185-194 10 p.

Research output: Contribution to journalArticle

The protein C activator AB002 rapidly interrupts thrombus development in baboons

Tucker, E. I., Verbout, N. G., Markway, B. D., Wallisch, M., Lorentz, C. U., Hinds, M. T., Shatzel, J. J., Pelc, L. A., Wood, D. C., McCarty, O. J. T., Di Cera, E. & Gruber, A., Feb 27 2020, In : Blood. 135, 9, p. 689-699 11 p.

Research output: Contribution to journalArticle

Open Access
2019

3D-Imaging of Whole Neuronal and Vascular Networks of the Human Dental Pulp via CLARITY and Light Sheet Microscopy

França, C. M., Riggers, R., Muschler, J., Widbiller, M., Lococo, P. M., Diogenes, A. & Bertassoni, L., Dec 1 2019, In : Scientific Reports. 9, 1, 10860.

Research output: Contribution to journalArticle

Open Access

Adaptive tuning of basal and bolus insulin to reduce postprandial hypoglycemia in a hybrid artificial pancreas

Resalat, N., El Youssef, J., Reddy, R., Castle, J. & Jacobs, P., Aug 1 2019, In : Journal of Process Control. 80, p. 247-254 8 p.

Research output: Contribution to journalArticle

3 Scopus citations

A mechanism for hereditary angioedema with normal C1 inhibitor: an inhibitory regulatory role for the factor XII heavy chain

Ivanov, I., Matafonov, A., Sun, M. F., Mohammed, B. M., Cheng, Q., Dickeson, S. K., Kundu, S., Verhamme, I. M., Gruber, A., McCrae, K. & Gailani, D., Mar 7 2019, In : Blood. 133, 10, p. 1152-1163 12 p.

Research output: Contribution to journalArticle

12 Scopus citations

Annot: A Django-based sample, reagent, and experiment metadata tracking system

Bucher, E., Claunch, C. J., Hee, D., Smith, R. L., Devlin, K., Thompson, W., Korkola, J. E. & Heiser, L. M., Nov 1 2019, In : BMC bioinformatics. 20, 1, 542.

Research output: Contribution to journalArticle

Open Access

A non-circulating pool of factor XI associated with glycosaminoglycans in mice

Mohammed, B. M., Cheng, Q., Matafonov, A., Verhamme, I. M., Emsley, J., McCrae, K. R., McCarty, O., Gruber, A. & Gailani, D., Jan 1 2019, In : Journal of Thrombosis and Haemostasis.

Research output: Contribution to journalArticle

4 Scopus citations

Assessment of human pancreas cancer tissue and precursor lesions via a fluorophore with inherent PDAC selectivity

Munhenzva, I. R., Barth, C. W., Sibrian-Vazquez, M., Wang, L. G., Escobedo, J. O., Gibbs, S. & Strongin, R. M., Jan 1 2019, In : Methods.

Research output: Contribution to journalArticle

2 Scopus citations

A statistical virtual patient population for the glucoregulatory system in type 1 diabetes with integrated exercise model

Resalat, N., El Youssef, J., Tyler, N., Castle, J. & Jacobs, P., Jan 1 2019, In : PloS one. 14, 7, e0217301.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer

Coleman, D. J., Gao, L., King, C. J., Schwartzman, J., Urrutia, J., Sehrawat, A., Tayou, J., Balter, A., Burchard, J., Chiotti, K. E., Derrick, D. S., Sun, D., Xia, Z., Heiser, L. & Alumkal, J., Jan 1 2019, In : Oncogene.

Research output: Contribution to journalArticle

4 Scopus citations

Biomimetic modification of poly(vinyl alcohol): Encouraging endothelialization and preventing thrombosis with antiplatelet monotherapy

Anderson, D. E. J., Truong, K. P., Hagen, M. W., Yim, E. K. F. & Hinds, M., Jan 1 2019, (Accepted/In press) In : Acta Biomaterialia.

Research output: Contribution to journalArticle

5 Scopus citations

Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis

Vedanayagam, J., Chatila, W. K., Aksoy, B. A., Majumdar, S., Skanderup, A. J., Demir, E., Schultz, N., Sander, C. & Lai, E. C., Dec 1 2019, In : Nature communications. 10, 1, 3682.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Circulating tumor DNA dynamics using patient-customized assays are associated with outcome in neoadjuvantly treated breast cancer

Butler, T. M., Boniface, C. T., Johnson-Camacho, K., Tabatabaei, S., Melendez, D., Kelley, T., Gray, J., Corless, C. L. & Spellman, P. T., Jan 1 2019, In : Cold Spring Harbor Molecular Case Studies. 5, 2, a003772.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation

Weng, T., Ko, J., Masamha, C. P., Xia, Z., Xiang, Y., Chen, N. Y., Molina, J. G., Collum, S., Mertens, T. C., Luo, F., Philip, K., Davies, J., Huang, J., Wilson, C., Thandavarayan, R. A., Bruckner, B. A., Jyothula, S. S. K., Volcik, K. A., Li, L., Han, L. & 5 others, Li, W., Assassi, S., Karmouty-Quintana, H., Wagner, E. J. & Blackburn, M. R., May 1 2019, In : Journal of Clinical Investigation. 129, 5, p. 1984-1999 16 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Computational Estimation of Microsecond to Second Atomistic Folding Times

Adhikari, U., Mostofian, B., Copperman, J., Subramanian, S. R., Petersen, A. A. & Zuckerman, D. M., Apr 24 2019, In : Journal of the American Chemical Society. 141, 16, p. 6519-6526 8 p.

Research output: Contribution to journalArticle

4 Scopus citations

Contact Activation Inhibitor and Factor XI Antibody, AB023, Produces Safe, Dose-Dependent Anticoagulation in a Phase 1 First-In-Human Trial

Lorentz, C. U., Verbout, N. G., Wallisch, M., Hagen, M. W., Shatzel, J. J., Olson, S. R., Puy, C., Hinds, M., McCarty, O., Gailani, D., Gruber, A. & Tucker, E., Apr 1 2019, In : Arteriosclerosis, thrombosis, and vascular biology. 39, 4, p. 799-809 11 p.

Research output: Contribution to journalArticle

Open Access

Design and evaluation of a non-contact bed-mounted sensing device for automated in-home detection of obstructive sleep apnea: A pilot study

Mosquera-Lopez, C., Leitschuh, J., Condon, J., Hagen, C. C., Rajhbeharrysingh, U., Hanks, C. & Jacobs, P. G., Sep 2019, In : Biosensors. 9, 3, 90.

Research output: Contribution to journalArticle

Open Access

Diagnostic performance of receptor-specific surgical specimen staining correlates with receptor expression level

Schaefer, J. M., Barth, C. W., Davis, S. C. & Gibbs, S. L., Feb 1 2019, In : Journal of biomedical optics. 24, 2, 026002.

Research output: Contribution to journalArticle

3 Scopus citations

DIRAS3 (ARHI) Blocks RAS/MAPK Signaling by Binding Directly to RAS and Disrupting RAS Clusters

Sutton, M. N., Lu, Z., Li, Y. C., Zhou, Y., Huang, T., Reger, A. S., Hurwitz, A. M., Palzkill, T., Logsdon, C., Liang, X., Gray, J. W., Nan, X., Hancock, J., Wahl, G. M. & Bast, R. C., Dec 10 2019, In : Cell Reports. 29, 11, p. 3448-3459.e6

Research output: Contribution to journalArticle

Open Access

Early Prediction of Breast Cancer Therapy Response using Multiresolution Fractal Analysis of DCE-MRI Parametric Maps

Machireddy, A., Thibault, G., Tudorica, L. A., Afzal, A., Mishal, M., Kemmer, K., Naik, A., Troxell, M., Goranson, E., Oh, K., Roy, N., Jafarian, N., Holtorf, M., Huang, W. & Song, X., Mar 1 2019, In : Tomography (Ann Arbor, Mich.). 5, 1, p. 90-98 9 p.

Research output: Contribution to journalArticle

Open Access

Endothelial PAI-1 (plasminogen activator inhibitor-1) blocks the intrinsic pathway of coagulation, inducing the clearance and degradation of FXIA (activated factor XI)

Puy, C., Ngo, A. T. P., Pang, J., Keshari, R. S., Hagen, M. W., Hinds, M. T., Gailani, D., Gruber, A., Lupu, F. & McCarty, O. J. T., Jan 1 2019, In : Arteriosclerosis, thrombosis, and vascular biology. 39, 7, p. 1390-1401 12 p.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data

Dietlmeier, J., McGuinness, K., Rugonyi, S., Wilson, T., Nuttall, A. & O'Connor, N. E., Dec 1 2019, In : Pattern Recognition Letters. 128, p. 521-528 8 p.

Research output: Contribution to journalArticle

FGF2-FGFR1 signaling regulates release of Leukemia-Protective exosomes from bone marrow stromal cells

Javidi-Sharifi, N., Martinez, J., English, I., Joshi, S. K., Scopim-Ribiero, R., Edwards, D. K., Agarwal, A., Lopez, C., Jorgens, D., Tyner, J., Druker, B. & Traer, E., Feb 5 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Fondaparinux pentasaccharide reduces sepsis coagulopathy and promotes survival in the baboon model of Escherichia coli sepsis

Keshari, R. S., Silasi, R., Popescu, N. I., Georgescu, C., Chaaban, H., Lupu, C., McCarty, O. J. T., Esmon, C. T. & Lupu, F., Jan 1 2019, (Accepted/In press) In : Journal of Thrombosis and Haemostasis.

Research output: Contribution to journalArticle

1 Scopus citations

Full-Length P2X7 Structures Reveal How Palmitoylation Prevents Channel Desensitization

McCarthy, A. E., Yoshioka, C. & Mansoor, S. E., Oct 17 2019, In : Cell. 179, 3, p. 659-670.e13

Research output: Contribution to journalArticle

6 Scopus citations

G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes

Liu, Y., Sargent, L., Leung, W., Elgin, S. C. R. & Goecks, J., Nov 1 2019, In : Bioinformatics. 35, 21, p. 4422-4423 2 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

GRB7 dependent proliferation of basal-like, HER-2 positive human breast cancer cell lines is mediated in part by HER-1 signaling

Luoh, S-W., Wagoner, W., Wang, X., Hu, Z., Lai, X., Chin, K-Y., Sears, R. & Ramsey, E., Jan 1 2019, In : Molecular Carcinogenesis.

Research output: Contribution to journalArticle

1 Scopus citations

Hepatic thrombopoietin gene silencing reduces platelet count and breast cancer progression in transgenic MMTV-PyMT mice

Shirai, T., Revenko, A. S., Tibbitts, J., Ngo, A. T. P., Mitrugno, A., Healy, L. D., Johnson, J., Tucker, E. I., Hinds, M. T., Coussens, L. M., McCarty, O. J. T., Monia, B. P. & Gruber, A., Oct 22 2019, In : Blood Advances. 3, 20, p. 3080-3091 12 p.

Research output: Contribution to journalArticle

Open Access

High-throughput single-particle tracking reveals 1 nested membrane domains that dictate krasg12d 2 diffusion and trafficking

Lee, Y., Phelps, C., Huang, T., Mostofian, B., Wu, L., Zhang, Y., Tao, K., Chang, Y. H., Stork, P. J. S., Gray, J. W., Zuckerman, D. M. & Nan, X., Nov 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Hyperspectral imaging in automated digital dermoscopy screening for melanoma

Hosking, A. M., Coakley, B. J., Chang, D., Talebi-Liasi, F., Lish, S., Lee, S. W., Zong, A. M., Moore, I., Browning, J., Jacques, S. L., Krueger, J. G., Kelly, K. M., Linden, K. G. & Gareau, D. S., Mar 2019, In : Lasers in Surgery and Medicine. 51, 3, p. 214-222 9 p.

Research output: Contribution to journalArticle

6 Scopus citations

Identification, Quantification, and System Analysis of Protein N-ε Lysine Methylation in Anucleate Blood Platelets

Rocheleau, A. D., Melrose, A. R., Cunliffe, J. M., Klimek, J., Babur, O., Tassi Yunga, S., Ngo, A. T. P., Pang, J., David, L., McCarty, O. & Aslan, J., Jan 1 2019, In : Proteomics. 1900001.

Research output: Contribution to journalArticle

Identification of SERPINE1 as a regulator of glioblastoma cell dispersal with transcriptome profiling

Seker, F., Cingoz, A., Sur-Erdem, İ., Erguder, N., Erkent, A., Uyulur, F., Selvan, M. E., Gümüş, Z. H., Gönen, M., Bayraktar, H., Wakimoto, H. & Bagci-Onder, T., Nov 2019, In : Cancers. 11, 11, 1651.

Research output: Contribution to journalArticle

Open Access

Inhibition of contact-mediated activation of factor XI protects baboons against S aureus-induced organ damage and death

Silasi, R., Keshari, R. S., Lupu, C., Van Rensburg, W. J., Chaaban, H., Regmi, G., Shamanaev, A., Shatzel, J. J., Puy, C., Lorentz, C. U., Tucker, E., Gailani, D., Gruber, A., McCarty, O. & Lupu, F., Feb 26 2019, In : Blood advances. 3, 4, p. 658-669 12 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas

The Cancer Genome Atlas Network, Jul 30 2019, In : Cell Reports. 28, 5, p. 1370-1384.e5

Research output: Contribution to journalArticle

Open Access
8 Scopus citations

Lanthanide-Loaded Nanoparticles as Potential Fluorescent and Mass Probes for High-Content Protein Analysis

Ngamcherdtrakul, W., Sangvanich, T., Goodyear, S., Reda, M., Gu, S., Castro, D. J., Punnakitikashem, P. & Yantasee, W., Mar 2019, In : Bioengineering. 6, 1, 23.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations