Life Sciences Graduate Programs

Research Output

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

Characterizing Design Patterns of EHR-Driven Phenotype Extraction Algorithms

Zhong, Y., Rasmussen, L., Deng, Y., Pacheco, J., Smith, M. E., Starren, J. B., Wei, W. Q., Speltz, P., Denny, J., Walton, N., Hripcsak, G., Chute, C. G. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1143-1146 4 p. 8621240. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

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

Deep Generative Classifiers for Thoracic Disease Diagnosis with Chest X-ray Images

Mao, C., Yao, L., Pan, Y., Luo, Y. & Zeng, Z., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1209-1214 6 p. 8621107. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

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

Early Prediction of Acute Kidney Injury in Critical Care Setting Using Clinical Notes

Li, Y., Yao, L., Mao, C., Srivastava, A., Jiang, X. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 683-686 4 p. 8621574. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

2 Scopus citations

Early prediction of acute kidney injury in critical care setting using clinical notes and structured multivariate physiological measurements

Sun, M., Baron, J., Dighe, A., Szolovits, P., Wunderink, R. G., Isakova, T. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 368-372 5 p. (Studies in Health Technology and Informatics; vol. 264).

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

1 Scopus citations

Erratum: Integrating hypertension phenotype and genotype with hybrid non-negative matrix factorization (Bioinformatics (2018) DOI: 10.1093/bioinformatics/bty804)

Luo, Y., Mao, C., Yang, Y., Wang, F., Ahmad, F. S., Arnett, D., Irvin, M. R. & Shah, S. J., Aug 15 2019, In : Bioinformatics. 35, 16, 1 p.

Research output: Contribution to journalComment/debate

Open Access

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

Implementing a Portable Clinical NLP System with a Common Data Model - A Lisp Perspective

Luo, Y. & Szolovits, P., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 461-466 6 p. 8621521. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

1 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

Migraine-Associated Vertigo

Hain, T. C. & Cherchi, M., Jan 1 2019, Dizziness and Vertigo Across the Lifespan. Elsevier Inc, p. 135-141 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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

Rich text formatted EHR narratives: A hidden and ignored trove

Zeng, Z., Zhao, Y., Sun, M., Vo, A. H., Starren, J. B. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 472-476 5 p. (Studies in Health Technology and Informatics; vol. 264).

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

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

Stratified mortality prediction of patients with acute kidney injury in critical care

Xu, Z., Luo, Y., Adekkanattu, P., Ancker, J. S., Jiang, G., Kiefer, R. C., Pacheco, J. A., Rasmussen, L. V., Pathak, J. & Wang, F., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 462-466 5 p. (Studies in Health Technology and Informatics; vol. 264).

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

Supervised Nonnegative Matrix Factorization to Predict ICU Mortality Risk

Chao, G., Mao, C., Wang, F., Zhao, Y. & Luo, Y., Jan 21 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 1189-1194 6 p. 8621403. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

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

1 Scopus citations
Open Access

Using machine learning to integrate socio-behavioral factors in predicting cardiovascular-related mortality risk

Wang, H., Li, Y., Ning, H., Wilkins, J. T., Lloyd-Jones, D. M. & Luo, Y., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 433-437 5 p. (Studies in Health Technology and Informatics; vol. 264).

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

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

Big Data and Data Science in Critical Care

Sanchez-Pinto, L. N., Luo, Y. & Churpek, M. M., Nov 2018, In : CHEST. 154, 5, p. 1239-1248 10 p.

Research output: Contribution to journalReview article

31 Scopus citations

Bilateral vestibular weakness

Hain, T. C., Cherchi, M. & Yacovino, D. A., May 31 2018, In : Frontiers in Neurology. 9, MAY, 344.

Research output: Contribution to journalReview article

2 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

Erratum: Publisher Correction: Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs (Nature communications (2017) 8 1 (1801))

Vannini, I., Wise, P. M., Challagundla, K. B., Plousiou, M., Raffini, M., Bandini, E., Fanini, F., Paliaga, G., Crawford, M., Ferracin, M., Ivan, C., Fabris, L., Davuluri, R. V., Guo, Z., Cortez, M. A., Zhang, X., Chen, L., Zhang, S., Fernandez-Cymering, C., Han, L. & 14 others, Carloni, S., Salvi, S., Ling, H., Murtadha, M., Neviani, P., Gitlitz, B. J., Laird-Offringa, I. A., Nana-Sinkam, P., Negrini, M., Liang, H., Amadori, D., Cimmino, A., Calin, G. A. & Fabbri, M., Jan 8 2018, In : Nature communications. 9, 1, 1 p.

Research output: Contribution to journalComment/debate

Open Access

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

APP mouse models for Alzheimer's disease preclinical studies

Sasaguri, H., Nilsson, P., Hashimoto, S., Nagata, K., Saito, T., De Strooper, B., Hardy, J., Vassar, R., Winblad, B. & Saido, T. C., Sep 1 2017, In : EMBO Journal. 36, 17, p. 2473-2487 15 p.

Research output: Contribution to journalReview article

153 Scopus citations

Approach to the patient with dizziness and vertigo

Hain, T. C. & Cherchi, M., Jan 6 2017, Practical Neurology: Fifth Edition. Wolters Kluwer Health Pharma Solutions (Europe) Ltd, p. 207-226 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

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