Biomedical Informatics (BMI)

Research Output 1992 2019

2019
2 Citations (Scopus)

Adverse Drug Events Detection in Clinical Notes by Jointly Modeling Entities and Relations Using Neural Networks

Dandala, B., Joopudi, V. & Devarakonda, M., Jan 1 2019, (Accepted/In press) In : Drug Safety.

Research output: Contribution to journalArticle

Drug-Related Side Effects and Adverse Reactions
Neural networks
Pharmaceutical Preparations
Joints
Long-Term Memory

An interprofessional education pilot program on screening, brief intervention, and referral to treatment (SBIRT) improves student knowledge, skills, and attitudes

van Eeghen, C., Hitt, J., King, J. G., Atieno Okech, J. E., Rouleau, B., Melekis, K., Kessler, R. & Pinckney, R., Jan 1 2019, In : International Journal of Higher Education. 8, 1, p. 119-132 14 p.

Research output: Contribution to journalArticle

graduate
ability
education
student
medicine

Bi-directional Recurrent Neural Network Models for Geographic Location Extraction in Biomedical Literature

Magge, A., Weissenbacher, D., Sarker, A., Scotch, M. & Gonzalez-Hernandez, G., Jan 1 2019, In : Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 24, p. 100-111 12 p.

Research output: Contribution to journalArticle

Geographic Locations
Neural Networks (Computer)
Natural Language Processing
Phylogeography
Nucleic Acid Databases
2 Citations (Scopus)

Biological relevance of computationally predicted pathogenicity of noncoding variants

Liu, L., Sanderford, M. D., Patel, R., Chandrashekar, P., Gibson, G. & Kumar, S., Dec 1 2019, In : Nature communications. 10, 1, 330.

Research output: Contribution to journalArticle

Open Access
Virulence
Nucleotides
Alleles
predictions
Research
3 Citations (Scopus)

Breast cancer detection using targeted plasma metabolomics

Jasbi, P., Wang, D., Cheng, S. L., Fei, Q., Cui, J. Y., Liu, L., Wei, Y., Raftery, D. & Gu, H., Jan 15 2019, In : Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences. 1105, p. 26-37 12 p.

Research output: Contribution to journalArticle

Metabolomics
Metabolism
Discriminant analysis
Bioinformatics
Breast Neoplasms

Coccidioidomycosis Detection Using Targeted Plasma and Urine Metabolic Profiling

Jasbi, P., Mitchell, N. M., Shi, X., Grys, T. E., Wei, Y., Liu, L., Lake, D. & Gu, H., Jan 1 2019, In : Journal of Proteome Research.

Research output: Contribution to journalArticle

Coccidioidomycosis
Metabolites
Urine
Plasmas
Biomarkers
1 Citation (Scopus)

Evaluating the Quality of Health Information in a Changing Digital Ecosystem

Keselman, A., Arnott Smith, C., Murcko, A. C. & Kaufman, D., Feb 8 2019, In : Journal of medical Internet research. 21, 2, p. e11129

Research output: Contribution to journalArticle

Open Access
Ecosystem
Dietary Supplements
Health
Consumer Health Information
Anecdotes

Exome Sequencing of Two Siblings with Sporadic Autism Spectrum Disorder and Severe Speech Sound Disorder Suggests Pleiotropic and Complex Effects

Peter, B., Dinu, V., Liu, L., Huentelman, M., Naymik, M., Lancaster, H., Vose, C. & Schrauwen, I., Jan 1 2019, In : Behavior Genetics.

Research output: Contribution to journalArticle

Exome
Siblings
Apraxias
childhood
gene

Genome-wide analysis indicates association between heterozygote advantage and healthy aging in humans

Xu, K., Kosoy, R., Shameer, K., Kumar, S., Liu, L., Readhead, B., Belbin, G. M., Lee, H. C., Chen, R. & Dudley, J. T., Jul 2 2019, In : BMC Genetics. 20, 1, 52.

Research output: Contribution to journalArticle

Open Access
Genome-Wide Association Study
Heterozygote
Survival
Electronic Health Records
Age Factors

Identifying and visualizing part-to-part variation with spatially dense optical dimensional metrology data

Shi, Z., Apley, D. W. & Runger, G., Jan 1 2019, In : Journal of Quality Technology. 51, 1, p. 3-20 18 p.

Research output: Contribution to journalArticle

Quality control
Surface measurement
Specifications
Wealth
Dimensionality

Interpretable regularized class association rules algorithm for classification in a categorical data space

Azmi, M., Runger, G. & Berrado, A., May 1 2019, In : Information Sciences. 483, p. 313-331 19 p.

Research output: Contribution to journalArticle

Nominal or categorical data
Association rules
Association Rules
Lasso
Classifiers

Measuring the integration of primary care and behavioral health services

Mullin, D. J., Hargreaves, L., Auxier, A., Brennhofer, S. A., Hitt, J. R., Kessler, R., Littenberg, B., Macchi, C., Martin, M., Rose, G., Trembath, F. & van Eeghen, C., Jan 1 2019, In : Health Services Research.

Research output: Contribution to journalArticle

Health Services
Primary Health Care
Statistical Factor Analysis
Health Resources
Information Storage and Retrieval

Neutralizing the polarization effect of diamond diode detectors using periodic forward bias pulses

Holmes, J. M., Dutta, M., Koeck, F. A., Benipal, M. K., Hathwar, R., Brown, J., Fox, B., Johnson, H., Zaniewski, A., Alarcon, R., Chowdhury, S., Goodnick, S. & Nemanich, R., Apr 1 2019, In : Diamond and Related Materials. 94, p. 162-165 4 p.

Research output: Contribution to journalArticle

Diamond
Diamonds
Diodes
Polarization
Detectors

Overlaying multiple sources of data to identify bottlenecks in clinical workflow

Vankipuram, A., Patel, V., Traub, S. & Shortliffe, E. H., Mar 1 2019, In : Journal of Biomedical Informatics: X. 1, 100004.

Research output: Contribution to journalArticle

Open Access
Workflow
Information Storage and Retrieval
Health
Electronic Health Records
Sensors

Patient Perception and Satisfaction With Insulin Pump System: Pilot User Experience Survey

Grando, M., Bayuk, M., Karway, G., Corrette, K., Groat, D., Cook, C. B. & Thompson, B., Jan 1 2019, In : Journal of Diabetes Science and Technology.

Research output: Contribution to journalComment/debate

Insulin
Patient Satisfaction
Pumps
Type 1 Diabetes Mellitus
Blood Glucose

Projection-free kernel principal component analysis for denoising

Bui, A. T., Im, J. K., Apley, D. W. & Runger, G., Sep 10 2019, In : Neurocomputing. 357, p. 163-176 14 p.

Research output: Contribution to journalArticle

Principal Component Analysis
Principal component analysis
Observation

Smartphone-based meditation for myeloproliferative neoplasm patients: Feasibility study to inform future trials

Huberty, J., Eckert, R., Larkey, L., Kurka, J., De Jesús, S. A. R., Yoo, W. & Mesa, R., Apr 1 2019, In : Journal of medical Internet research. 21, 4, e12662.

Research output: Contribution to journalArticle

Open Access
Meditation
Feasibility Studies
Neoplasms
Sleep
Anxiety
2018
8 Citations (Scopus)

A 4.5 μm PIN diamond diode for detecting slow neutrons

Holmes, J., Dutta, M., Koeck, F. A., Benipal, M., Brown, J., Fox, B., Hathwar, R., Johnson, H., Malakoutian, M., Saremi, M., Zaniewski, A., Alarcon, R., Chowdhury, S., Goodnick, S. & Nemanich, R., Sep 21 2018, In : Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment. 903, p. 297-301 5 p.

Research output: Contribution to journalArticle

thermal neutrons
Diamonds
Neutrons
Diodes
diamonds
1 Citation (Scopus)

A convolutional route to abbreviation disambiguation in clinical text

Joopudi, V., Dandala, B. & Devarakonda, M., Oct 1 2018, In : Journal of Biomedical Informatics. 86, p. 71-78 8 p.

Research output: Contribution to journalArticle

Neural networks
Neural Networks (Computer)
Support vector machines
Learning systems
Datasets

A data science approach for the classification of low-grade and high-grade ovarian serous carcinomas

Lin, S., Wang, C., Zarei, S., Bell, D. A., Kerr, S. E., Runger, G. & Kocher, J. P. A., Nov 27 2018, In : BMC Genomics. 19, 1, 841.

Research output: Contribution to journalArticle

Open Access
Carcinoma
Neoplasms
Dermatoglyphics
Aneuploidy
Genomics
2 Citations (Scopus)
Apolipoproteins E
Alzheimer Disease
Alleles
Genotype
Age of Onset
2 Citations (Scopus)

A Lattice-Matched GaNP/Si Three-Terminal Tandem Solar Cell

Zou, Y., Zhang, C., Honsberg, C., Vasileska, D., King, R. & Goodnick, S., Nov 26 2018, 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion, WCPEC 2018 - A Joint Conference of 45th IEEE PVSC, 28th PVSEC and 34th EU PVSEC. Institute of Electrical and Electronics Engineers Inc., p. 279-282 4 p. 8548033

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

Solar cells
Sun
Absorption spectra
Lighting
Simulators
3 Citations (Scopus)

A method for the analysis and visualization of clinical workflow in dynamic environments

Vankipuram, A., Traub, S. & Patel, V., Mar 1 2018, In : Journal of Biomedical Informatics. 79, p. 20-31 12 p.

Research output: Contribution to journalArticle

Workflow
Visualization
Hospital Emergency Service
Cultural Anthropology
Electronic Health Records

A Multiscale Model to Study Transport in Silicon Heterojunction Solar Cells

Muralidharan, P., Bowden, S., Goodnick, S. & Vasileska, D., Nov 26 2018, 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion, WCPEC 2018 - A Joint Conference of 45th IEEE PVSC, 28th PVSEC and 34th EU PVSEC. Institute of Electrical and Electronics Engineers Inc., p. 3200-3203 4 p. 8547337

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

Silicon
Heterojunctions
Solar cells
Physics
Hot carriers

An ensemble of convolutional neural networks for the use in video endoscopy

Aksenov, S. V., Kostin, K. A., Ivanova, A. V., Liang, J. & Zamyatin, A. V., Jan 1 2018, In : Sovremennye Tehnologii v Medicine. 10, 2, p. 7-17 11 p.

Research output: Contribution to journalArticle

Endoscopy
Neural networks
Classifiers
Neural Networks (Computer)
Colonoscopy
Public Health Informatics
Information Storage and Retrieval
Zoonoses
Public health
Decision support systems
3 Citations (Scopus)

A Unified Model of Behavioral Health Integration in Primary Care

McGovern, M., Dent, K. & Kessler, R., Apr 1 2018, In : Academic Psychiatry. 42, 2, p. 265-268 4 p.

Research output: Contribution to journalArticle

Primary Health Care
Health
health

Avian influenza virus ecology and evolution through a climatic lens

Morin, C. W., Stoner-Duncan, B., Winker, K., Scotch, M., Hess, J. J., Meschke, J. S., Ebi, K. L. & Rabinowitz, P. M., Oct 1 2018, In : Environment International. 119, p. 241-249 9 p.

Research output: Contribution to journalReview article

avian influenza
virus
ecology
water temperature
persistence

Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes

Adam, D. C., Scotch, M. & MacIntyre, C. R., Nov 1 2018, In : Molecular Biology and Evolution. 35, 11, p. 2607-2617 11 p.

Research output: Contribution to journalArticle

smallpox
Modifier Genes
Phylogeography
Smallpox
modifiers (genes)
1 Citation (Scopus)

Behavioral and mental health risk factor profiles among diverse primary care patients

For The MOHR Study Group, Jun 1 2018, In : Preventive Medicine. 111, p. 21-27 7 p.

Research output: Contribution to journalArticle

Primary Health Care
Mental Health
Hispanic Americans
African Americans
Patient Acceptance of Health Care
3 Citations (Scopus)

Chronic care coordination by integrating care through a team-based, population-driven approach: A case study

Van Eeghen, C. O., Littenberg, B. & Kessler, R., May 23 2018, In : Translational Behavioral Medicine. 8, 3, p. 468-480 13 p.

Research output: Contribution to journalArticle

Population
Workflow
Documentation
Primary Health Care
Community Health Nurses
7 Citations (Scopus)

Clinical decision support models and frameworks: Seeking to address research issues underlying implementation successes and failures

Greenes, R., Bates, D. W., Kawamoto, K., Middleton, B., Osheroff, J. & Shahar, Y., Jan 1 2018, (Accepted/In press) In : Journal of Biomedical Informatics.

Research output: Contribution to journalArticle

Clinical Decision Support Systems
Decision Support Techniques
Research
Interoperability
Workflow

Correction: Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform(PLoS ONE (2018) 13:4 (e0196556) DOI: 10.1371/journal.pone.0196556)

Morris, S. M., Subramanian, J., Gel, E., Runger, G., Thompson, E. J., Mallery, D. W. & Weiss, G. J., Jun 1 2018, In : PLoS One. 13, 6, e0200224.

Research output: Contribution to journalComment/debate

Names
Tumors
Gels
gels
neoplasms
3 Citations (Scopus)

CRAFTER: a Tree-ensemble Clustering Algorithm for Static Datasets with Mixed Attributes and High Dimensionality

Lin, S., Azarnoush, B. & Runger, G., Feb 16 2018, (Accepted/In press) In : IEEE Transactions on Knowledge and Data Engineering.

Research output: Contribution to journalArticle

Clustering algorithms
Data mining
Costs
Experiments

Deep neural networks and distant supervision for geographic location mention extraction

Magge, A., Weissenbacher, D., Sarker, A., Scotch, M. & Gonzalez-Hernandez, G., Jul 1 2018, In : Bioinformatics. 34, 13, p. i565-i573

Research output: Contribution to journalArticle

Geographic Locations
Nucleic Acid Databases
Viruses
Virus
Neural Networks
3 Citations (Scopus)

Design and Testing of a Smartphone Application for Real-Time Self-Tracking Diabetes Self-Management Behaviors

Groat, D., Soni, H., Grando, M., Thompson, B., Kaufman, D. & Cook, C. B., Apr 1 2018, In : Applied Clinical Informatics. 9, 2, p. 440-449 10 p.

Research output: Contribution to journalArticle

Smartphones
Self Care
Medical problems
Testing
Alcohols
1 Citation (Scopus)

Determination of Minority Carrier Lifetime of Holes in Diamond PIN Diodes Using Reverse Recovery Method

Dutta, M., Mandal, S., Hathwar, R., Fischer, A. M., Koeck, F. A. M., Nemanich, R., Goodnick, S. & Chowdhury, S., Feb 9 2018, (Accepted/In press) In : IEEE Electron Device Letters.

Research output: Contribution to journalArticle

Diamond
Carrier lifetime
Diamonds
Time delay
Diodes

Development of a high-band gap high temperature III-nitride solar cell for integration with concentrated solar power technology

Williams, J. J., McFavilen, H., Fischer, A. M., Ding, D., Young, S. R., Vadiee, E., Ponce, F., Arena, C., Honsberg, C. & Goodnick, S., May 25 2018, 2017 IEEE 44th Photovoltaic Specialist Conference, PVSC 2017. Institute of Electrical and Electronics Engineers Inc., p. 1-3 3 p.

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

Nitrides
Solar energy
Solar cells
Energy gap
Volatile organic compounds
1 Citation (Scopus)

Emergency Physicians' Perceived Influence of EHR Use on Clinical Workflow and Performance Metrics

Denton, C. A., Soni, H. C., Kannampallil, T. G., Serrichio, A., Shapiro, J. S., Traub, S. J. & Patel, V., Jul 12 2018, In : Applied Clinical Informatics. 9, 3, p. 725-733 9 p.

Research output: Contribution to journalArticle

Workflow
Electronic Health Records
Emergencies
Health
Physicians

Focus on electronics, photonics and renewable energy

Goodnick, S., Nemnich, R. & Korkin, A., Jan 1 2018, In : Nanotechnology. 29, 36, 360201.

Research output: Contribution to journalEditorial

Photonics
Electronic equipment
1 Citation (Scopus)

GeoBoost: Accelerating research involving the geospatial metadata of virus GenBank records

Tahsin, T., Weissenbacher, D., O'Connor, K., Magge, A., Scotch, M. & Gonzalez-Hernandez, G., May 1 2018, In : Bioinformatics. 34, 9, p. 1606-1608 3 p.

Research output: Contribution to journalArticle

Nucleic Acid Databases
Metadata
Viruses
Virus
Software

Identifying nonlinear variation patterns with deep autoencoders

Howard, P., Apley, D. W. & Runger, G., Dec 2 2018, In : IISE Transactions. 50, 12, p. 1089-1103 15 p.

Research output: Contribution to journalArticle

Quality control

InGaN based solar cells with GaN tunnel junction contacts

Vadiee, E., Clinton, E. A., McFavilen, H., Engel, Z., Matthews, C., Arena, C., Honsberg, C., Goodnick, S. & Doolittle, W. A., Nov 26 2018, 2018 IEEE 7th World Conference on Photovoltaic Energy Conversion, WCPEC 2018 - A Joint Conference of 45th IEEE PVSC, 28th PVSEC and 34th EU PVSEC. Institute of Electrical and Electronics Engineers Inc., p. 965-968 4 p. 8547327

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

Tunnel junctions
Solar cells
Current density
Organic Chemicals
Organic chemicals

In Search of Vital Signs: A Comparative Study of EHR Documentation

Duncan, B. J., Zheng, L., Furniss, S. K., Solomon, A. J., Doebbeling, B., Grando, G., Burton, M., Poterack, K. A., Miksch, T. A., Helmers, R. A. & Kaufman, D., Jan 1 2018, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2018, p. 1233-1242 10 p.

Research output: Contribution to journalArticle

Workflow
Vital Signs
Documentation
Patient Safety
Nursing Assessment

Integrating Active Learning and Transfer Learning for Carotid Intima-Media Thickness Video Interpretation

Zhou, Z., Shin, J., Feng, R., Hurst, R. T., Kendall, C. B. & Liang, J., Jan 1 2018, (Accepted/In press) In : Journal of Digital Imaging.

Research output: Contribution to journalArticle

Carotid Intima-Media Thickness
Problem-Based Learning
Tuning
Neural networks
Ultrasonography

Know-GRRF: Domain-Knowledge Informed Biomarker Discovery with Random Forests

Guan, X. & Liu, L., Jan 1 2018, Bioinformatics and Biomedical Engineering - 6th International Work-Conference, IWBBIO 2018, Proceedings. Springer Verlag, p. 3-14 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10814 LNBI).

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

Random Forest
Biomarkers
Domain Knowledge
Feature extraction
Tuning
9 Citations (Scopus)
Programming Languages
Electronic Health Records
Artificial Intelligence
Machine Learning
MicroRNAs
Hepatocellular Carcinoma
Gene expression
Cell death
RNA

Modeling of a gallium phosphide/silicon heterojunction solar cells

Luppina, P., Bowden, S., Lugli, P. & Goodnick, S., May 25 2018, 2017 IEEE 44th Photovoltaic Specialist Conference, PVSC 2017. Institute of Electrical and Electronics Engineers Inc., p. 1-6 6 p.

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

Gallium phosphide
Silicon
Heterojunctions
Solar cells
Open circuit voltage

Multi-Method Study of Electronic Health Records Workflows

Grando, M., Manataki, A., Furniss, S. K., Duncan, B., Solomon, A., Kaufman, D., Hirn, S., Sunday, R., Bouchereau, J., Doebbeling, B., Burton, M., Poterack, K. A., Miksch, T. & Helmers, R. A., Jan 1 2018, In : AMIA ... Annual Symposium proceedings. AMIA Symposium. 2018, p. 498-507 10 p.

Research output: Contribution to journalArticle

Workflow
Electronic Health Records
Social Support
Quality of Health Care
Tertiary Care Centers