Life Sciences Graduate Programs

Research Output

Filter
Article
2019

An ancillary genomics system to support the return of pharmacogenomic results

Rasmussen, L. V., Smith, M. E., Almaraz, F., Persell, S. D., Rasmussen-Torvik, L. J., Pacheco, J. A., Chisholm, R. L., Christensen, C., Herr, T. M., Wehbe, F. H. & Starren, J. B., Feb 19 2019, In : Journal of the American Medical Informatics Association. 26, 4, p. 306-310 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

Cancer classification and pathway discovery using non-negative matrix factorization

Zeng, Z., Vo, A. H., Mao, C., Clare, S. E., Khan, S. A. & Luo, Y., Aug 2019, In : Journal of Biomedical Informatics. 96, 103247.

Research output: Contribution to journalArticle

7 Scopus citations
Open Access
8 Scopus citations

Considerations for Improving the Portability of Electronic Health Record-Based Phenotype Algorithms

Rasmussen, L. V., Brandt, P. S., Jiang, G., Kiefer, R. C., Pacheco, J. A., Adekkanattu, P., Ancker, J. S., Wang, F., Xu, Z., Pathak, J. & Luo, Y., Jan 1 2019, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2019, p. 755-764 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Developing a portable natural language processing based phenotyping system

Sharma, H., Mao, C., Zhang, Y., Vatani, H., Yao, L., Zhong, Y., Rasmussen, L., Jiang, G., Pathak, J. & Luo, Y., Apr 4 2019, In : BMC Medical Informatics and Decision Making. 19, 78.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
6 Scopus citations

Evaluating the Portability of an NLP System for Processing Echocardiograms: A Retrospective, Multi-site Observational Study

Adekkanattu, P., Jiang, G., Luo, Y., Kingsbury, P. R., Xu, Z., Rasmussen, L. V., Pacheco, J. A., Kiefer, R. C., Stone, D. J., Brandt, P. S., Yao, L., Zhong, Y., Deng, Y., Wang, F., Ancker, J. S., Campion, T. R. & Pathak, J., Jan 1 2019, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2019, p. 190-199 10 p.

Research output: Contribution to journalArticle

IDH3α regulates one-carbon metabolism in glioblastoma

May, J. L., Kouri, F., Hurley, L. A., Liu, J., Tommasini-Ghelfi, S., Ji, Y., Gao, P., Calvert, A. E., Lee, A., Chandel, N., Davuluri, R. V., Horbinski, C. M., Locasale, J. W. & Stegh, A. H., Jan 1 2019, In : Science Advances. 5, 1, eaat0456.

Research output: Contribution to journalArticle

7 Scopus citations

Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization

Luo, Y., Mao, C., Yang, Y., Wang, F., Ahmad, F. S., Arnett, D., Irvin, M. R. & Shah, S. J., Jan 1 2019, In : Bioinformatics. 35, 8, p. 1395-1403 9 p.

Research output: Contribution to journalArticle

Is Cerebellar Ataxia, Neuropathy, and Vestibular Areflexia Syndrome (CANVAS) a Vestibular Ganglionopathy?

Yacovino, D. A., Zanotti, E. & Hain, T. C., Aug 1 2019, In : The journal of international advanced otology. 15, 2, p. 304-308 5 p.

Research output: Contribution to journalArticle

Open Access

Migraine associated vertigo

Hain, T. C. & Cherchi, M., Jan 1 2019, In : Advances in oto-rhino-laryngology. 82, p. 119-126 8 p.

Research output: Contribution to journalArticle

Pharmacogenomic clinical decision support design and multi-site process outcomes analysis in the eMERGE Network

Herr, T. M., Peterson, J. F., Rasmussen, L. V., Caraballo, P. J., Peissig, P. L. & Starren, J. B., Jan 1 2019, In : Journal of the American Medical Informatics Association. 26, 2, p. 143-148 6 p.

Research output: Contribution to journalArticle

3 Scopus citations

Platform-independent classification system for predicting high-grade serous ovarian carcinoma molecular subtypes

Shilpi, A., Kandpal, M., Ji, Y., Seagle, BL. & Davuluri, RV., Apr 3 2019, In : JCO Clinical Cancer Informatics. 3, 1, p. 1-9 9 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Predicting ICU readmission using grouped physiological and medication trends

Xue, Y., Klabjan, D. & Luo, Y., Apr 1 2019, In : Artificial Intelligence In Medicine. 95, p. 27-37 11 p.

Research output: Contribution to journalArticle

6 Scopus citations

Risk Adjusting Health Care Provider Collaboration Networks

Chandler, A. E., Mutharasan, R. K., Amelia, L., Carson, M. B., Scholtens, D. M. & Soulakis, N. D., Jan 1 2019, In : Methods of Information in Medicine. 58, 2-3, p. 71-78 8 p.

Research output: Contribution to journalArticle

2 Scopus citations
Open Access

Varying levels of X chromosome coalescence in female somatic cells alters the balance of X-linked dosage compensation and is implicated in female-dominant systemic lupus erythematosus

Laskowski, A. I., Neems, D. S., Laster, K., Strojny-Okyere, C., Rice, E. L., Konieczna, I. M., Voss, J. H., Mathew, J. M., Leventhal, J. R., Ramsey-Goldman, R., Smith, E. D. & Kosak, S. T., Dec 1 2019, In : Scientific reports. 9, 1, 8011.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations
2018
3 Scopus citations

BACE1 mediates HIV-associated and excitotoxic neuronal damage through an APP-dependent mechanism

Stern, A. L., Ghura, S., Gannon, P. J., Akay-Espinoza, C., Phan, J. M., Yee, A. C., Vassar, R., Gelman, B. B., Kolson, D. L. & Jordan-Sciutto, K. L., May 2 2018, In : Journal of Neuroscience. 38, 18, p. 4288-4300 13 p.

Research output: Contribution to journalArticle

13 Scopus citations

Characteristics of vestibular corrective saccades in patients with slow visual saccades, vestibular disorders and controls: A descriptive analysis

Yacovino, D. A., Martin, L. A., Akly, M. P. & Hain, T. C., May 2018, In : PloS one. 13, 5, e0197079.

Research output: Contribution to journalArticle

5 Scopus citations

Characterization of brain tumor initiating cells isolated from an animal model of CNS primitive neuroectodermal tumors

Malchenko, S., Sredni, S. T., Boyineni, J., Bi, Y., Margaryan, N. V., Guda, M. R., Kostenko, Y., Tomita, T., Davuluri, R. V., Velpula, K., Hendrix, M. J. C. & Soares, M. B., Jan 1 2018, In : Oncotarget. 9, 17, p. 13733-13747 15 p.

Research output: Contribution to journalArticle

3 Scopus citations

ER stress is not elevated in the 5XFAD mouse model of Alzheimer’s disease

Sadleir, K. R., Popovic, J. & Vassar, R., Jan 1 2018, In : Journal of Biological Chemistry. 293, 48, p. 18434-18443 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

Improving the Accuracy of Scores to Predict Gastrostomy after Intracerebral Hemorrhage with Machine Learning

Garg, R., Prabhakaran, S., Holl, J. L., Luo, Y., Faigle, R., Kording, K. & Naidech, A. M., Dec 2018, In : Journal of Stroke and Cerebrovascular Diseases. 27, 12, p. 3570-3574 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

Metastatic cancers promote cachexia through ZIP14 upregulation in skeletal muscle

Wang, G., Biswas, AK., Ma, W., Kandpal, M., Coker, C., Grandgenett, PM., Hollingsworth, MA., Jain, R., Tanji, K., Lomicronpez-Pintado, S., Borczuk, A., Hebert, D., Jenkitkasemwong, S., Hojyo, S., Davuluri, RV., Knutson, MD., Fukada, T. & Acharyya, S., Jun 8 2018, In : Nature Medicine. 24, 6, p. 770-781 12 p.

Research output: Contribution to journalArticle

28 Scopus citations

Radiomic MRI signature reveals three distinct subtypes of glioblastoma with different clinical and molecular characteristics, offering prognostic value beyond IDH1

Rathore, S., Akbari, H., Rozycki, M., Abdullah, K. G., Nasrallah, M. P., Binder, Z. A., Davuluri, R. V., Lustig, R. A., Dahmane, N., Bilello, M., O'Rourke, D. M. & Davatzikos, C., Dec 1 2018, In : Scientific reports. 8, 1, 5087.

Research output: Contribution to journalArticle

29 Scopus citations

Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes

Luo, Y., Cheng, Y., Uzuner, Ö., Szolovits, P. & Starren, J. B., Jan 1 2018, In : Journal of the American Medical Informatics Association. 25, 1, p. 93-98 6 p., ocx090.

Research output: Contribution to journalArticle

19 Scopus citations

The Gain-Time constant product quantifies total vestibular output in bilateral vestibular loss

Hain, T. C., Cherchi, M. & Perez-Fernandez, N., Jun 11 2018, In : Frontiers in Neurology. 9, JUN, 396.

Research output: Contribution to journalArticle

1 Scopus citations

Using natural language processing and machine learning to identify breast cancer local recurrence

Zeng, Z., Espino, S., Roy, A., Li, X., Khan, S. A., Clare, S. E., Jiang, X., Neapolitan, R. & Luo, Y., Dec 28 2018, In : BMC bioinformatics. 19, 498.

Research output: Contribution to journalArticle

7 Scopus citations
2017

A152T tau allele causes neurodegeneration that can be ameliorated in a zebrafish model by autophagy induction

Lopez, A., Lee, S. E., Wojta, K., Ramos, E. M., Klein, E., Chen, J., Boxer, A. L., Gorno-Tempini, M. L., Geschwind, D. H., Schlotawa, L., Ogryzko, N. V., Bigio, E. H., Rogalski, E., Weintraub, S., Mesulam, M. M., Fleming, A., Coppola, G., Miller, B. L., Rubinsztein, D. C., Agosta, F. & 31 others, Alberici, A., Babacan-Yildiz, G., Bennett, D. A., Bilguvar, K., Borroni, B., Caglayan, A. O., Combarros, O., Comi, G., Cortés, E. P., Ferrer, I., Genç, Ş., Gunel, M., Gylys, K. H., Indakoetxea, B., Karageorgiou, C. E., Karydas, A., Kilic, U., De Munain, A. L., Magnani, G., Mahley, R. W., Boneschi, F. M., Martinez, J., Mazzeo, S., Moreno, F., Padovani, A., Papatriantafyllou, J., Rogaeva, E., Sanchez-Juan, P., Santangelo, R., Small, G. W. & Tauopathy Genetics Consortium, Apr 1 2017, In : Brain. 140, 4, p. 1128-1146 19 p.

Research output: Contribution to journalArticle

33 Scopus citations

A Becn1 mutation mediates hyperactive autophagic sequestration of amyloid oligomers and improved cognition in Alzheimer's disease

Rocchi, A., Yamamoto, S., Ting, T., Fan, Y., Sadleir, K., Wang, Y., Zhang, W., Huang, S., Levine, B., Vassar, R. & He, C., Aug 2017, In : PLoS genetics. 13, 8, e1006962.

Research output: Contribution to journalArticle

28 Scopus citations

A mixed-methods study of veterans affairs providers’ experiences communicating with patients about the affordable care act

Martinez, R. N., Gordon, E. J., Tully, S., Silva, A., Tarlov, E., French, D. D., Huo, Z., Smith, B. M., Gordon, H. S. & Stroupe, K. T., May 2017, In : Military medicine. 182, 5, p. e1715-e1723

Research output: Contribution to journalArticle

1 Scopus citations

Association of plasma neurofilament light with neurodegeneration in patients with Alzheimer disease

Alzheimer's Disease Neuroimaging Initiative, May 2017, In : JAMA Neurology. 74, 5, p. 557-566 10 p.

Research output: Contribution to journalArticle

172 Scopus citations

Cancer-Associated IDH1 Promotes Growth and Resistance to Targeted Therapies in the Absence of Mutation

Calvert, A. E., Chalastanis, A., Wu, Y., Hurley, L. A., Kouri, F., Bi, Y., Kachman, M., May, J. L., Bartom, E. T., Hua, Y., Mishra, R. K., Schiltz, G. E., Dubrovskyi, O., Mazar, A. P., Peter, M. E., Zheng, H., James, C. D., Burant, C. F., Chandel, N., Davuluri, R. V. & 2 others, Horbinski, C. M. & Stegh, A. H., May 30 2017, In : Cell reports. 19, 9, p. 1858-1873 16 p.

Research output: Contribution to journalArticle

42 Scopus citations

Cerebrospinal fluid markers detect Alzheimer's disease in nonamnestic dementia

Oboudiyat, C., Gefen, T., Varelas, E., Weintraub, S., Rogalski, E., Bigio, E. H. & Mesulam, M. M., May 2017, In : Alzheimer's and Dementia. 13, 5, p. 598-601 4 p.

Research output: Contribution to journalArticle

4 Scopus citations

Combining anti-miR-155 with chemotherapy for the treatment of lung cancers

Van Roosbroeck, K., Fanini, F., Setoyama, T., Ivan, C., Rodriguez-Aguayo, C., Fuentes-Mattei, E., Xiao, L., Vannini, I., Redis, R. S., D'Abundo, L., Zhang, X., Nicoloso, M. S., Rossi, S., Gonzalez-Villasana, V., Rupaimoole, R., Ferracin, M., Morabito, F., Neri, A., Ruvolo, P. P., Ruvolo, V. R. & 20 others, Pecot, C. V., Amadori, D., Abruzzo, L., Calin, S., Wang, X., You, M. J., Ferrajoli, A., Orlowski, R., Plunkett, W., Lichtenberg, T. M., Davuluri, R. V., Berindan-Neagoe, I., Negrini, M., Wistuba, I. I., Kantarjian, H. M., Sood, A. K., Lopez-Berestein, G., Keating, M. J., Fabbri, M. & Calin, G. A., Jun 1 2017, In : Clinical Cancer Research. 23, 11, p. 2891-2904 14 p.

Research output: Contribution to journalArticle

55 Scopus citations

Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms

Dapas, M., Kandpal, M., Bi, Y. & Davuluri, R. V., Jan 1 2017, In : Briefings in Bioinformatics. 18, 2, p. 260-269 10 p.

Research output: Contribution to journalArticle

12 Scopus citations

Effect of a mobile web app on kidney transplant candidates' knowledge about increased risk donor kidneys: A randomized controlled trial

Gordon, E. J., Sohn, M. W., Chang, C. H., Mcnatt, G., Vera, K., Beauvais, N., Warren, E., Mannon, R. B. & Ison, M. G., Jan 1 2017, In : Transplantation. 101, 6, p. 1167-1176 10 p.

Research output: Contribution to journalArticle

12 Scopus citations

Evaluating and improving recruitment and retention in an mHealth clinical trial: An example of iterating methods during a trial

Pfammetter, AF., Mitsos, A., Wang, S., Hood, SH. & Spring, B., Nov 2017, In : mHealth. 3, 49, p. 1-10 10 p.

Research output: Contribution to journalArticle

Fluctuating vestibulo-ocular reflex in ménière's disease

Yacovino, D. A., Hain, T. C. & Musazzi, M., Jan 1 2017, In : Otology and Neurotology. 38, 2, p. 244-247 4 p.

Research output: Contribution to journalArticle

7 Scopus citations

Functional Connectivity is Reduced in Early-stage Primary Progressive Aphasia When Atrophy is not Prominent

Bonakdarpour, B., Rogalski, E. J., Wang, A., Sridhar, J., Mesulam, M. M. & Hurley, R. S., May 1 2017, In : Alzheimer Disease and Associated Disorders. 31, 2, p. 101-106 6 p.

Research output: Contribution to journalArticle

8 Scopus citations

HIV Protease Inhibitors Alter Amyloid Precursor Protein Processing via β-Site Amyloid Precursor Protein Cleaving Enzyme-1 Translational Up-Regulation

Gannon, P. J., Akay-Espinoza, C., Yee, A. C., Briand, L. A., Erickson, M. A., Gelman, B. B., Gao, Y., Haughey, N. J., Zink, M. C., Clements, J. E., Kim, N. S., Van De Walle, G., Jensen, B. K., Vassar, R., Pierce, R. C., Gill, A. J., Kolson, D. L., Diehl, J. A., Mankowski, J. L. & Jordan-Sciutto, K. L., Jan 1 2017, In : American Journal of Pathology. 187, 1, p. 91-109 19 p.

Research output: Contribution to journalArticle

13 Scopus citations

Identification of genetic and epigenetic variants associated with breast cancer prognosis by integrative bioinformatics analysis

Shilpi, A., Bi, Y., Jung, S., Patra, S. K. & Davuluri, R. V., Jan 9 2017, In : Cancer Informatics. 16

Research output: Contribution to journalArticle

7 Scopus citations

Identification of natural products with neuronal and metabolic benefits through autophagy induction

Fan, Y., Wang, N., Rocchi, A., Zhang, W., Vassar, R., Zhou, Y. & He, C., Jan 2 2017, In : Autophagy. 13, 1, p. 41-56 16 p.

Research output: Contribution to journalArticle

23 Scopus citations

Orthogonal ubiquitin transfer identifies ubiquitination substrates under differential control by the two ubiquitin activating enzymes

Liu, X., Zhao, B., Sun, L., Bhuripanyo, K., Wang, Y., Bi, Y., Davuluri, R. V., Duong, D. M., Nanavati, D., Yin, J. & Kiyokawa, H., Jan 30 2017, In : Nature communications. 8, 14286.

Research output: Contribution to journalArticle

18 Scopus citations

Psychological well-being in elderly adults with extraordinary episodic memory

Maher, A. C., Kielb, S., Loyer, E., Connelley, M., Rademaker, A., Mesulam, M. M., Weintraub, S., McAdams, D., Logan, R. & Rogalski, E., Oct 2017, In : PloS one. 12, 10, e0186413.

Research output: Contribution to journalArticle

10 Scopus citations

Quantitative Comparison of Dense-Core Amyloid Plaque Accumulation in Amyloid-β Protein Precursor Transgenic Mice

Liu, P., Reichl, J. H., Rao, E. R., McNellis, B. M., Huang, E. S., Hemmy, L. S., Forster, C. L., Kuskowski, M. A., Borchelt, D. R., Vassar, R., Ashe, K. H. & Zahs, K. R., Jan 1 2017, In : Journal of Alzheimer's Disease. 56, 2, p. 743-761 19 p.

Research output: Contribution to journalArticle

5 Scopus citations
5 Scopus citations

Stabilization of HIF-1α and HIF-2α, upregulation of MYCC and accumulation of stabilized p53 constitute hallmarks of CNS-PNET animal model

Malchenko, S., Sredni, S. T., Bi, Y., Margaryan, N. V., Boyineni, J., Mohanam, I., Tomita, T., Davuluri, R. V. & Soares, M. B., Mar 2017, In : PloS one. 12, 3, e0173106.

Research output: Contribution to journalArticle

1 Scopus citations