BI: Personalized Diagnostics, Virginia G. Piper Center for (PD)

Research Output

2020

A community-maintained standard library of population genetic models

Adrion, J. R., Cole, C. B., Dukler, N., Galloway, J. G., Gladstein, A. L., Gower, G., Kyriazis, C. C., Ragsdale, A. P., Tsambos, G., Baumdicker, F., Carlson, J., Cartwright, R. A., Durvasula, A., Gronau, I., Kim, B. Y., McKenzie, P., Messer, P. W., Noskova, E., Vecchyo, D. O. D., Racimo, F. & 9 others, Struck, T. J., Gravel, S., Gutenkunst, R. N., Lohmueller, K. E., Ralph, P. L., Schrider, D. R., Siepel, A., Kelleher, J. & Kern, A. D., Jun 2020, In : eLife. 9, p. 1-39 39 p., e54967.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

Orr, A. J., Padovan, A., Kainer, D., Külheim, C., Bromham, L., Bustos-Segura, C., Foley, W., Haff, T., Hsieh, J. F., Morales-Suarez, A., Cartwright, R. A. & Lanfear, R., Mar 11 2020, In : Proceedings of the Royal Society B: Biological Sciences. 287, 1922, 20192364.

Research output: Contribution to journalArticle

Open Access

Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening

Tang, Y., Saul, J., Nagaratnam, N., Martin-Garcia, J. M., Fromme, P., Qiu, J. & LaBaer, J., Dec 1 2020, In : Scientific reports. 10, 1, 13323.

Research output: Contribution to journalArticle

Open Access

Enhanced X-ray diffraction of in vivo-grown μNS crystals by viscous jets at XFELs

Nagaratnam, N., Tang, Y., Botha, S., Saul, J., Li, C., Hu, H., Zaare, S., Hunter, M., Lowry, D., Weierstall, U., Zatsepin, N., Spence, J. C. H., Qiu, J., LaBaer, J., Fromme, P. & Martin-Garcia, J. M., Jun 1 2020, In : Acta Crystallographica Section F:Structural Biology Communications. 76, p. 278-289 12 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Evaluation of oxidative stress in biological samples using the thiobarbituric acid reactive substances assay

Aguilar Diaz De Leon, J. & Borges, C. R., May 2020, In : Journal of Visualized Experiments. 2020, 159, e61122.

Research output: Contribution to journalArticle

Hyperthermia induced by transient receptor potential vanilloid-1 (TRPV1) antagonists in human clinical trials: Insights from mathematical modeling and meta-analysis

Garami, A., Shimansky, Y. P., Rumbus, Z., Vizin, R. C. L., Farkas, N., Hegyi, J., Szakacs, Z., Solymar, M., Csenkey, A., Chiche, D. A., Kapil, R., Kyle, D. J., Van Horn, W. D., Hegyi, P. & Romanovsky, A. A., Apr 2020, In : Pharmacology and Therapeutics. 208, 107474.

Research output: Contribution to journalReview article

Open Access
5 Scopus citations

Methanogens and Methanotrophs Show Nutrient-Dependent Community Assemblage Patterns Across Tropical Peatlands of the Pastaza-Marañón Basin, Peruvian Amazonia

Finn, D. R., Ziv-El, M., van Haren, J., Park, J. G., del Aguila-Pasquel, J., Urquiza–Muñoz, J. D. & Cadillo-Quiroz, H., Apr 24 2020, In : Frontiers in Microbiology. 11, 746.

Research output: Contribution to journalArticle

Open Access

PIRT the TRP channel regulating protein binds calmodulin and cholesterol-like ligands

Sisco, N. J., Luu, D. D., Kim, M. & Van Horn, W. D., Mar 2020, In : Biomolecules. 10, 3, 478.

Research output: Contribution to journalArticle

Open Access

Relationship Between Chronic Kidney Disease, Glucose Homeostasis, and Plasma Osteocalcin Carboxylation and Fragmentation

Kratz, M., Zelnick, L. R., Trenchevska, O., Jeffs, J. W., Borges, C. R., Tseng, H. H., Booth, S. L., Kestenbaum, B. R., Utzschneider, K. M. & de Boer, I. H., 2020, (Accepted/In press) In : Journal of Renal Nutrition.

Research output: Contribution to journalArticle

Structure-Based Design of Novel Biphenyl Amide Antagonists of Human Transient Receptor Potential Cation Channel Subfamily M Member 8 Channels with Potential Implications in the Treatment of Sensory Neuropathies

Journigan, V. B., Feng, Z., Rahman, S., Wang, Y., Amin, A. R. M. R., Heffner, C. E., Bachtel, N., Wang, S., Gonzalez-Rodriguez, S., Fernández-Carvajal, A., Fernández-Ballester, G., Hilton, J. K., Van Horn, W. D., Ferrer-Montiel, A., Xie, X. Q. & Rahman, T., Feb 5 2020, In : ACS chemical neuroscience. 11, 3, p. 268-290 23 p.

Research output: Contribution to journalArticle

2 Scopus citations

Transcriptome changes during the initiation and progression of Duchenne muscular dystrophy in Caenorhabditis elegans

Hrach, H. C., O'Brien, S., Steber, H. S., Newbern, J., Rawls, A. & Mangone, M., Jun 27 2020, In : Human Molecular Genetics. 29, 10, p. 1607-1623 17 p.

Research output: Contribution to journalArticle

Open Access

Tumor-derived exosomes (TDEs): How to avoid the sting in the tail

Wan, M. H., Ning, B., Spiegel, S., Lyon, C. J. & Hu, T. Y., Jan 1 2020, In : Medicinal Research Reviews. 40, 1, p. 385-412 28 p.

Research output: Contribution to journalReview article

Open Access
2 Scopus citations

Unique genomic and neoepitope landscapes across tumors: a study across time, tissues, and space within a single lynch syndrome patient

Phung, T. N., Lenkiewicz, E., Malasi, S., Sharma, A., Anderson, K. S., Wilson, M. A., Pockaj, B. A. & Barrett, M. T., Dec 1 2020, In : Scientific reports. 10, 1, 12190.

Research output: Contribution to journalArticle

Open Access
2019

A human organotypic microfluidic tumor model permits investigation of the interplay between patient-derived fibroblasts and breast cancer cells

Truong, D. D., Kratz, A., Park, J. G., Barrientos, E. S., Saini, H., Nguyen, T., Pockaj, B., Mouneimne, G., LaBaer, J. & Nikkhah, M., Jun 15 2019, In : Cancer Research. 79, 12, p. 3139-3151 13 p.

Research output: Contribution to journalArticle

12 Scopus citations

ALG-1 influences accurate mrna splicing patterns in the Caenorhabditis elegans intestine and body muscle tissues by modulating splicing factor activities

Kotagama, K., Schorr, A. L., Steber, H. S. & Mangone, M., Jul 2019, In : Genetics. 212, 3, p. 931-951 21 p.

Research output: Contribution to journalArticle

1 Scopus citations

A noninvasive blood-based combinatorial proteomic biomarker assay to detect breast cancer in women over age 50 with BI-RADS 3, 4, or 5 Assessment

Henderson, M. C., Silver, M., Tran, Q., Letsios, E. E., Mulpuri, R., Reese, D. E., Lourenco, A. P., LaBaer, J., Anderson, K., Alpers, J., Costantini, C., Rohatgi, N., Ali, H., Baker, K., Northfelt, D. W., Ghosh, K., Grobmyer, S. R., Polen, W. & Wolf, J. K., Jan 1 2019, In : Clinical Cancer Research. 25, 1, p. 142-149 8 p.

Research output: Contribution to journalArticle

Cathepsin B Dependent Cleavage Product of Serum Amyloid A1 Identifies Patients with Chemotherapy-Related Cardiotoxicity

Zhang, F., Lyon, C. J., Walls, R. J., Ning, B., Fan, J. & Hu, T. Y., May 21 2019, In : ACS Pharmacology and Translational Science. 2, 5, p. 333-341 9 p.

Research output: Contribution to journalArticle

1 Scopus citations
Open Access
1 Scopus citations

Competitive Interactions between PIRT, the Cold Sensing Ion Channel TRPM8, and PIP2 Suggest a Mechanism for Regulation

Sisco, N. J., Helsell, C. V. M. & Van Horn, W. D., Dec 1 2019, In : Scientific reports. 9, 1, 14128.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
Open Access

Delta-S-cys-albumin: A lab test that quantifies cumulative exposure of archived human blood plasma and serum samples to thawed conditions

Jeffs, J. W., Jehanathan, N., Thibert, S. M. F., Ferdosi, S., Pham, L., Wilson, Z. T., Breburda, C. & Borges, C. R., 2019, In : Molecular and Cellular Proteomics. 18, 10, p. 2121-2137 17 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Diagnostic and Prognostic Performance of Blood Plasma Glycan Features in the Women Epidemiology Lung Cancer (WELCA) Study

Hu, Y., Ferdosi, S., Kapuruge, E. P., Diaz De Leon, J. A., Stücker, I., Radoï, L., Guénel, P. & Borges, C. R., Jan 1 2019, (Accepted/In press) In : Journal of Proteome Research.

Research output: Contribution to journalArticle

Discovery of an autoantibody signature for the early diagnosis of knee osteoarthritis: Data from the Osteoarthritis Initiative

Camacho-Encina, M., Balboa-Barreiro, V., Rego-Perez, I., Picchi, F., Vanduin, J., Qiu, J., Fuentes, M., Oreiro, N., Labaer, J., Ruiz-Romero, C. & Blanco, F. J., Dec 1 2019, In : Annals of the Rheumatic Diseases. 78, 12, p. 1699-1705 7 p.

Research output: Contribution to journalArticle

3 Scopus citations

Extracellular vesicles as cancer liquid biopsies: From discovery, validation, to clinical application

Zhao, Z., Fan, J., Hsu, Y. M. S., Lyon, C. J., Ning, B. & Hu, Y., Apr 7 2019, In : Lab on a Chip. 19, 7, p. 1114-1140 27 p.

Research output: Contribution to journalReview article

18 Scopus citations

HPV: Immunology lessons from an ancient oncotarget

Krishna, S. & Anderson, K., Feb 1 2019, In : Oncotarget. 10, 13, p. 1269-1270 2 p.

Research output: Contribution to journalEditorial

Open Access

MALDI-TOF mass spectrometry-based quantification of C-peptide in diabetes patients

Wan, M. H., Wang, Y., Zhan, L., Fan, J. & Hu, T. Y., Jan 1 2019, (Accepted/In press) In : European Journal of Mass Spectrometry.

Research output: Contribution to journalArticle

miRNA profiling for early detection and treatment of duchenne muscular dystrophy

Hrach, H. C. & Mangone, M., Sep 2 2019, In : International journal of molecular sciences. 20, 18, 4638.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes

Ferdosi, S. R., Ewaisha, R., Moghadam, F., Krishna, S., Park, J., Ebrahimkhani, M. R., Kiani, S. & Anderson, K., Dec 1 2019, In : Nature communications. 10, 1, 1842.

Research output: Contribution to journalArticle

Open Access
20 Scopus citations

Multi-platform Approach for Microbial Biomarker Identification Using Borrelia burgdorferi as a Model

Pflughoeft, K. J., Mash, M., Hasenkampf, N. R., Jacobs, M. B., Tardo, A. C., Mitchell Magee, D., Song, L., LaBaer, J., Philipp, M. T., Embers, M. E. & AuCoin, D. P., 2019, In : Frontiers in Cellular and Infection Microbiology. 9, JUN, 179.

Research output: Contribution to journalArticle

Open Access

Nanotrap-enabled quantification of KRAS-induced peptide hydroxylation in blood for cancer early detection

Deng, Z., Zhao, Z., Ning, B., Basilio, J., Mann, K., Fu, J., Gu, Y., Ye, Y., Wu, X., Fan, J., Chiao, P. & Hu, Y., Jun 1 2019, In : Nano Research. 12, 6, p. 1445-1452 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Nickel affinity: A sensible approach for extracellular vesicles isolation?

Hu, T. Y., Jun 2019, In : EBioMedicine. 44, p. 14-15 2 p.

Research output: Contribution to journalComment/debate

Open Access

Parallel experimental evolution reveals a novel repressive control of GalP on xylose fermentation in Escherichia coli

Kurgan, G., Sievert, C., Flores, A., Schneider, A., Billings, T., Panyon, L., Morris, C., Taylor, E., Kurgan, L., Cartwright, R. & Wang, X., Aug 2019, In : Biotechnology and bioengineering. 116, 8, p. 2074-2086 13 p.

Research output: Contribution to journalArticle

3 Scopus citations

Personalized circulating tumor DNA analysis to detect residual disease after neoadjuvant therapy in breast cancer

McDonald, B. R., Contente-Cuomo, T., Sammut, S. J., Odenheimer-Bergman, A., Ernst, B., Perdigones, N., Chin, S. F., Farooq, M., Mejia, R., Cronin, P. A., Anderson, K. S., Kosiorek, H. E., Northfelt, D. W., McCullough, A. E., Patel, B. K., Weitzel, J. N., Slavin, T. P., Caldas, C., Pockaj, B. A. & Murtaza, M., Aug 7 2019, In : Science Translational Medicine. 11, 504, eaax7392.

Research output: Contribution to journalArticle

16 Scopus citations

Point-of-Care Tissue Analysis Using Miniature Mass Spectrometer

Zou, R., Cao, W., Chong, L., Hua, W., Xu, H., Mao, Y., Page, J., Shi, R., Xia, Y., Hu, Y., Zhang, W. & Ouyang, Z., Jan 2 2019, In : Analytical chemistry. 91, 1, p. 1157-1163 7 p.

Research output: Contribution to journalArticle

15 Scopus citations

Serving Individuals and Populations Within Integrated Health Systems: A Bridge Too Far?

Moses, H., Matheson, D. H. M. & Poste, G., Jan 1 2019, In : JAMA - Journal of the American Medical Association.

Research output: Contribution to journalComment/debate

Structural and Evolutionary Insights Point to Allosteric Regulation of TRP Ion Channels

Hilton, J. K., Kim, M. & Van Horn, W., Jun 18 2019, In : Accounts of chemical research. 52, 6, p. 1643-1652 10 p.

Research output: Contribution to journalArticle

7 Scopus citations

The burden of 14 hr-HPV genotypes in women attending routine cervical cancer screening in 20 states of Mexico: a cross-sectional study

Campos-Romero, A., Anderson, K. S., Longatto-Filho, A., Luna-Ruiz Esparza, M. A., Morán-Portela, D. J., Castro-Menéndez, J. A., Moreno-Camacho, J. L., Calva-Espinosa, D. Y., Acosta-Alfaro, M. A., Meynard-Mejía, F. A., Muñoz-Gaitán, M. & Alcántar-Fernández, J., Dec 1 2019, In : Scientific reports. 9, 1, 10094.

Research output: Contribution to journalArticle

Open Access

The C. elegans 3' UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3'-UTR biology, and miRNA targeting

Steber, H. S., Gallante, C., O'Brien, S., Chiu, P. L. & Mangone, M., 2019, In : Genome research. 29, 12, p. 2104-2116 13 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

The neoepitope landscape of breast cancer: Implications for immunotherapy

Narang, P., Chen, M., Sharma, A. A., Anderson, K. & Wilson, M. A., Mar 4 2019, In : BMC Cancer. 19, 1, 200.

Research output: Contribution to journalArticle

11 Scopus citations

Ultra-Sensitive Automated Profiling of EpCAM Expression on Tumor-Derived Extracellular Vesicles

Amrollahi, P., Rodrigues, M., Lyon, C. J., Goel, A., Han, H. & Hu, T. Y., Dec 17 2019, In : Frontiers in Genetics. 10, 1273.

Research output: Contribution to journalArticle

Open Access

Using Nanoplasmon-Enhanced Scattering and Low-Magnification Microscope Imaging to Quantify Tumor-Derived Exosomes

Wan, M., Amrollahi, P., Sun, D., Lyon, C. & Hu, T. Y., May 24 2019, In : Journal of visualized experiments : JoVE. 147

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Weakly immunogenic CRISPR therapies

Wilson, E. A. & Anderson, K. S., Oct 1 2019, In : Nature Biomedical Engineering. 3, 10, p. 761-762 2 p.

Research output: Contribution to journalComment/debate

2018

accuMUlate: a mutation caller designed for mutation accumulation experiments

Winter, D. J., Wu, S. H., Howell, A. A., Azevedo, R. B. R., Zufall, R. A. & Cartwright, R. A., Aug 1 2018, In : Bioinformatics (Oxford, England). 34, 15, p. 2659-2660 2 p.

Research output: Contribution to journalArticle

A compact, low-cost, quantitative and multiplexed fluorescence detection platform for point-of-care applications

Obahiagbon, U., Smith, J. T., Zhu, M., Katchman, B. A., Arafa, H., Anderson, K. & Blain Christen, J., Oct 15 2018, In : Biosensors and Bioelectronics. 117, p. 153-160 8 p.

Research output: Contribution to journalArticle

19 Scopus citations

Adaptive global innovative learning environment for glioblastoma: GBM AGILE

GBM AGILE Network, Feb 15 2018, In : Clinical Cancer Research. 24, 4, p. 737-743 7 p.

Research output: Contribution to journalReview article

35 Scopus citations

Advances in cell-free protein array methods

Yu, X., Petritis, B., Duan, H., Xu, D. & LaBaer, J., Jan 2 2018, In : Expert Review of Proteomics. 15, 1, p. 1-11 11 p.

Research output: Contribution to journalArticle

9 Scopus citations
7 Scopus citations

A low cost mobile phone dark-field microscope for nanoparticle-based quantitative studies

Sun, D. & Hu, Y., Jan 15 2018, In : Biosensors and Bioelectronics. 99, p. 513-518 6 p.

Research output: Contribution to journalArticle

7 Scopus citations

An Automated Microfluidic Assay for Photonic Crystal Enhanced Detection and Analysis of an Antiviral Antibody Cancer Biomarker in Serum

Race, C. M., Kwon, L. E., Foreman, M. T., Huang, Q., Inan, H., Kesiraju, S., Le, P., Lim, S. J., Smith, A. M., Zangar, R. C., Demirci, U., Anderson, K. & Cunningham, B. T., Feb 15 2018, In : IEEE Sensors Journal. 18, 4, p. 1464-1473 10 p., 8119803.

Research output: Contribution to journalArticle

2 Scopus citations

Antigen 85B peptidomic analysis allows species-specific mycobacterial identification

Zhang, W., Shu, Q., Zhao, Z., Fan, J., Lyon, C. J., Zelazny, A. M. & Hu, Y., Jan 8 2018, In : Clinical Proteomics. 15, 1, 1.

Research output: Contribution to journalArticle

3 Scopus citations