Research Output 1978 2020

2020
Single-Cell Analysis
Tumor-Infiltrating Lymphocytes
Fluorescent Antibody Technique
Breast Neoplasms
Neoplasms
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
Dental Pulp
Acrylamide
Hydrogel
Blood Vessels
Microscopy
Artificial Pancreas
Accelerometry
Insulin
Insulin Resistance
Identification (control systems)
2 Citations (Scopus)

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

Insulin
Adaptive Learning
Tuning
Diabetes
Medical problems
7 Citations (Scopus)

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

Hereditary Angioedemas
Factor XII
Prekallikrein
Kallikreins
Chemical activation

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
Tracking System
Metadata
Controlled Vocabulary
Laboratory Personnel
Network protocols
1 Citation (Scopus)

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

Factor XI
Glycosaminoglycans
Blood Vessels
Prekallikrein
Heparin
3 Citations (Scopus)

Antithrombotic Strategies After Bioprosthetic Aortic Valve Replacement: A Systematic Review

Papak, J., Chiovaro, J., Noelck, N., Healy, L. D., Freeman, M., Quin, J. A., Paynter, R., Low, A., Kondo, K., McCarty, O. & Kansagara, D., Jan 1 2019, In : Annals of Thoracic Surgery.

Research output: Contribution to journalReview article

Aortic Valve
Aspirin
Warfarin
Hemorrhage
Mortality
Turkey
Fever
Climate
Emerging Communicable Diseases
Ticks

Artificial Intelligence in Radiation Oncology

Deig, C. R., Kanwar, A. & Thompson, R., Jan 1 2019, (Accepted/In press) In : Hematology/Oncology Clinics of North America.

Research output: Contribution to journalReview article

Radiation Oncology
Artificial Intelligence
Workflow
Quality of Health Care
Patient Safety
1 Citation (Scopus)

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

Fluorophores
Pancreatic Neoplasms
Adenocarcinoma
Tissue
Ducts

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. & Haley, K., Jan 1 2019, In : Platelets.

Research output: Contribution to journalArticle

Blood Platelets
Thrombin
Adenosine Diphosphate
Fetal Blood
PAR-1 Receptor
2 Citations (Scopus)

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
insulin-dependent diabetes mellitus
Medical problems
Type 1 Diabetes Mellitus
exercise
Hormones

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

Androgen Receptors
Castration
Prostatic Neoplasms
RNA Sequence Analysis
Neoplasms
2 Citations (Scopus)

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

Biomimetics
Platelets
Thrombosis
Alcohols
Blood Platelets
2 Citations (Scopus)

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
biological evolution
Ribonucleases
mutations
MicroRNAs
cancer
2 Citations (Scopus)

Computational Estimation of Microsecond to Second Atomistic Folding Times

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

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Viscosity
Proteins
Molecular dynamics
Uncertainty
3 Citations (Scopus)

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
Factor XI
Antibodies
Thrombosis
Hemostasis
Primates

Contact system sends defensins to the rescue

Healy, L. D. & McCarty, O., Jan 31 2019, In : Blood. 133, 5, p. 385-386 2 p.

Research output: Contribution to journalReview article

Defensins
Fibrin
Factor XIIa
Kallikreins
Fibrinolysis

Correlating thrombus constituents of surface-modified vascular graft materials to luminal volume using microct to better quantify clinical functionality

Anderson, D. E. J., Gupta, A. & Hinds, M., Jan 1 2019, Society for Biomaterials Annual Meeting and Exposition 2019: The Pinnacle of Biomaterials Innovation and Excellence - Transactions of the 42nd Annual Meeting. Society for Biomaterials, 1 p. (Transactions of the Annual Meeting of the Society for Biomaterials and the Annual International Biomaterials Symposium; vol. 40).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

X-Ray Microtomography
Biocompatible Materials
Platelets
Fibrin
Grafts

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., Rajhbeharrysingh, U., Hanks, C. & Jacobs, P., Sep 1 2019, In : Biosensors. 9, 3, 90.

Research output: Contribution to journalArticle

Open Access
Obstructive Sleep Apnea
Sleep Apnea Syndromes
Equipment and Supplies
Sleep
Polysomnography

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

Schaefer, J. M., Barth, C. W., Davis, S. C. & Gibbs, S., Feb 1 2019, In : Journal of biomedical optics. 24, 2, p. 1-9 9 p.

Research output: Contribution to journalArticle

staining
margins
Imaging techniques
Coloring Agents
Contrast Media
1 Citation (Scopus)

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
Fractals
Magnetic Resonance Imaging
Breast Neoplasms
Drug Therapy
Area Under Curve
1 Citation (Scopus)

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., Gailani, D., Gruber, A., Lupu, F. & McCarty, O., Jul 1 2019, In : Arteriosclerosis, thrombosis, and vascular biology. 39, 7, p. 1390-1401 12 p.

Research output: Contribution to journalArticle

Open Access
Factor XIa
Plasminogen Inactivators
Plasminogen Activator Inhibitor 1
Endothelial Cells
Kallikreins

Erratum: Correction: FGF2-FGFR1 signaling regulates release of leukemia-protective exosomes from bone marrow stromal cells (eLife (2019) 8 PII: e47174)

Javidi-Sharifi, N., Martinez, J., English, I., Joshi, S. K., Scopim-Ribeiro, R., Viola, S. K., Edwards, D. K., Agarwal, A., Lopez, C., Jorgens, D., Tyner, J., Druker, B. & Traer, E., Mar 29 2019, In : eLife. 8

Research output: Contribution to journalComment/debate

Open Access
Exosomes
Fibroblast Growth Factor 2
Mesenchymal Stromal Cells
Medicine
Bone

Erratum: Modeling subdiffusive light scattering by incorporating the tissue phase function and detector numerical aperture (Journal of Biomedical Optics (2017) 22:5 (050501) DOI: 10.1117/1.JBO.22.5.050501)

Post, A. L., Jacques, S., Sterenborg, H. J. C. M., Faber, D. J. & Van Leeuwen, T. G., Jun 30 2019, In : Journal of biomedical optics. 24, 6, 069801.

Research output: Contribution to journalComment/debate

Open Access
numerical aperture
Light scattering
light scattering
optics
Tissue

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

Mitochondria
Focused ion beams
Cells
Scanning electron microscopy
Electron microscopy
1 Citation (Scopus)

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
Exosomes
Fibroblast Growth Factor 2
Mesenchymal Stromal Cells
Protein-Tyrosine Kinases
Bone
1 Citation (Scopus)

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

Papio
Sepsis
Antithrombins
Escherichia coli
Factor Xa

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

Purinergic P2X7 Receptors
Lipoylation
Adenosine Triphosphate
Cryoelectron Microscopy
Guanosine

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
Galaxies
Annotation
Genome
Genes
Sequence Alignment
1 Citation (Scopus)

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

Breast Neoplasms
Cell Line
Small Interfering RNA
Growth
GRB7 Adaptor Protein

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
Thrombopoietin
Gene Silencing
Platelet Count
Breast Neoplasms
Liver

High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers

Banik, G., Betts, C. B., Liudahl, S. M., Sivagnanam, S., Kawashima, R., Cotechini, T., Larson, W., Goecks, J., Pai, S. I., Clayburgh, D., Tsujikawa, T. & Coussens, L. M., Jan 1 2019, Methods in Enzymology. Academic Press Inc., (Methods in Enzymology).

Research output: Chapter in Book/Report/Conference proceedingChapter

Tumors
Neoplasms
Tumor Microenvironment
Cells
Immunohistochemistry

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

Methylation
Platelets
Systems Analysis
Lysine
Identification (control systems)

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
Gene Expression Profiling
Glioblastoma
Cell Adhesion
Brain
Growth
3 Citations (Scopus)

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
Factor XI
Contact Inhibition
Papio
Sepsis
Disseminated Intravascular Coagulation
1 Citation (Scopus)

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
Atlases
p53 Genes
Tumors
Genes
Genome
1 Citation (Scopus)

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 1 2019, In : Bioengineering. 6, 1, 23.

Research output: Contribution to journalArticle

Open Access
Lanthanoid Series Elements
Rare earth elements
Antibodies
Nanoparticles
Proteins
1 Citation (Scopus)

Luminal plasma treatment for small diameter polyvinyl alcohol tubular scaffolds

Pohan, G., Chevallier, P., Anderson, D. E. J., Tse, J. W., Yao, Y., Hagen, M. W., Mantovani, D., Hinds, M. & Yim, E. K. F., Jan 1 2019, In : Frontiers in Bioengineering and Biotechnology. 7, MAY, 117.

Research output: Contribution to journalArticle

Polyvinyl Alcohol
Polyvinyl alcohols
Scaffolds
Grafts
Blood Vessels
3 Citations (Scopus)

Maintenance of MYC expression promotes de novo resistance to BET bromodomain inhibition in castration-resistant prostate cancer

Coleman, D. J., Gao, L., Schwartzman, J., Korkola, J., Sampson, D., Derrick, D. S., Urrutia, J., Balter, A., Burchard, J., King, C. J., Chiotti, K. E., Heiser, L. & Alumkal, J., Dec 1 2019, In : Scientific Reports. 9, 1, 3823.

Research output: Contribution to journalArticle

Open Access
Castration
Prostatic Neoplasms
Maintenance
Androgen Receptors
Cell Line
1 Citation (Scopus)

Mechanism of pharmacochaperoning in a mammalian KATP channel revealed by cryo-EM

Martin, G. M., Sung, M. W., Yang, Z., Innes, L. M., Kandasamy, B., David, L., Yoshioka, C. & Shyng, S-L., Jul 1 2019, In : eLife. 8, e46417.

Research output: Contribution to journalArticle

Open Access
Sulfonylurea Receptors
KATP Channels
repaglinide
Congenital Hyperinsulinism
ATP-Binding Cassette Transporters
1 Citation (Scopus)

Meiotic cellular rejuvenation is coupled to nuclear remodeling in budding yeast

King, G. A., Goodman, J. S., Schick, J. G., Chetlapalli, K., Jorgens, D., McDonald, K. L. & Ünal, E., Aug 9 2019, In : eLife. 8

Research output: Contribution to journalArticle

Open Access
Rejuvenation
Saccharomycetales
Meiosis
Germ Cells
Quality Control

Methodology for Detecting and Tracking Brain-Derived Neurotrophic Factor Complexes in Neurons Using Single Quantum Dots

Vermehren-Schmaedick, A., Jacob, T. & Vu, T. T., Jan 1 2019, Neuromethods. Humana Press Inc., p. 105-118 14 p. (Neuromethods; vol. 143).

Research output: Chapter in Book/Report/Conference proceedingChapter

Quantum Dots
Brain-Derived Neurotrophic Factor
Semiconductor quantum dots
Neurons
trkB Receptor

Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α

Spiriti, J., Subramanian, S. R., Palli, R., Wu, M. & Zuckerman, D., Apr 1 2019, In : PloS one. 14, 4, e0215694.

Research output: Contribution to journalArticle

Open Access
Estrogen Receptors
prediction
Proteins
proteins
Ligands

Modeling the effect of blood vessel bifurcation ratio on occlusive thrombus formation

Lakshmanan, H. H. S., Shatzel, J. J., Olson, S. R., McCarty, O. & Maddala, J., Jan 1 2019, In : Computer Methods in Biomechanics and Biomedical Engineering.

Research output: Contribution to journalArticle

Bifurcation (mathematics)
Blood vessels
Microfluidics
Shear deformation
Blood
5 Citations (Scopus)

Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting

Langer, E. M., Allen-Petersen, B. L., King, S. M., Kendsersky, N. D., Turnidge, M. A., Kuziel, G. M., Riggers, R., Samatham, R., Amery, T. S., Jacques, S., Sheppard, B., Korkola, J., Muschler, J., Thibault, G., Chang, Y. H., Gray, J., Presnell, S. C., Nguyen, D. G. & Sears, R., Jan 15 2019, In : Cell Reports. 26, 3, p. 608-623.e6

Research output: Contribution to journalArticle

Bioprinting
Tumors
Tissue
Phenotype
Scaffolds
3 Citations (Scopus)

Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients

Chu, Y., Elrod, N., Wang, C., Li, L., Chen, T., Routh, A., Xia, Z., Li, W., Wagner, E. J. & Ji, P., Jan 1 2019, In : Oncogene.

Research output: Contribution to journalArticle

Polyadenylation
Glioblastoma
3' Untranslated Regions
Glioma
Genes

Optical properties of living corals determined with diffuse reflectance spectroscopy

Jacques, S., Wangpraseurt, D. & Kühl, M., Jan 1 2019, In : Frontiers in Marine Science. 6, JUL, 472.

Research output: Contribution to journalArticle

Open Access
optical properties
optical property
corals
coral
reflectance

Patient Input for Design of a Decision Support Smartphone Application for Type 1 Diabetes

Wilson, L. M., Tyler, N., Jacobs, P., Gabo, V., Senf, B., Reddy, R. & Castle, J., Jan 1 2019, (Accepted/In press) In : Journal of Diabetes Science and Technology.

Research output: Contribution to journalArticle

Smartphones
Medical problems
Type 1 Diabetes Mellitus
Glucose
Application programs