• Improving “Desktop medicine” efficiency using Guided Inquiry Learning in an Electronic Health Records System 

  Purkayastha, Saptarshi; Naliyatthaliyazchayil, Parvati Ravindranathan Menon; Surapaneni, Asha Kiranmayee; Kowkutla, Ashwini; Maity, Pallavi (2018-07-18)

  Recent studies have shown that more than 50% of physician time is spent on “desktop medicine” – the practice of medicine that requires the use of computers and other technology. Providers are trained in other medical ...
• Toward Timely Data for Cancer Research: Assessment and Reengineering of the Cancer Reporting Process 

  Jabour, Abdulrahman M; Dixon, Brian E; Jones, Josette F; Haggstrom, David A (JMIR Publications, 2018-03-01)

  Background Cancer registries systematically collect cancer-related data to support cancer surveillance activities. However, cancer data are often unavailable for months to years after diagnosis, limiting its utility. ...
• Mutational landscape of RNA-binding proteins in human cancers 

  Neelamraju, Yaseswini; Gonzalez-Perez, Abel; Bhat-Nakshatri, Poornima; Nakshatri, Harikrishna; Janga, Sarath Chandra (Taylor & Francis, 2018-01-02)

  RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is ...
• PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology 

  Yue, Zongliang; Zheng, Qi; Neylon, Michael T.; Yoo, Minjae; Shin, Jimin; Zhao, Zhiying; Tan, Aik Choon; Chen, Jake Y. (Oxford Academic, 2018-01-04)

  Integrative Gene-set, Network and Pathway Analysis (GNPA) is a powerful data analysis approach developed to help interpret high-throughput omics data. In PAGER 1.0, we demonstrated that researchers can gain unbiased and ...
• Macroergonomic factors in the patient work system: examining the context of patients with chronic illness 

  Holden, Richard J.; Valdez, Rupa S.; Schubert, Christiane C.; Thompson, Morgan J.; Hundt, Ann S. (Taylor & Francis, 2017-01)

  Human factors/ergonomics recognises work as embedded in and shaped by levels of social, physical and organisational context. This study investigates the contextual or macroergonomic factors present in the health-related ...
• Provider Use of a Novel EHR display in the Pediatric Intensive Care Unit. Large Customizable Interactive Monitor (LCIM) 

  Asan, Onur; Holden, Richard J.; Flynn, Kathryn E.; Yang, Yushi; Azam, Laila; Scanlon, Matthew C. (Schattauer, 2016-07-20)

  OBJECTIVES: The purpose of this study was to explore providers' perspectives on the use of a novel technology, "Large Customizable Interactive Monitor" (LCIM), a novel application of the electronic health record system ...
• Model Checking Temporal Logic Formulas Using Sticker Automata 

  Zhu, Weijun; Feng, Changwei; Wu, Huanmei (hindawi publishing corporation, 2017)

  As an important complex problem, the temporal logic model checking problem is still far from being fully resolved under the circumstance of DNA computing, especially Computation Tree Logic (CTL), Interval Temporal Logic ...
• TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization 

  Kou, Qiang; Xun, Likun; Liu, Xiaowen (Oxford University Press, 2016-11-15)

  Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of ...
• Systematic Study of Data Science and Analytics Programs 

  Wu, Huanmei (ASEE, 2017-06)

  Rapid advances in information technologies have led to the generation of massive data sets, especially in life science and biomedical informatics. These data sets are valuable assets and in great needs to be analyzed. ...
• RNA-binding proteins in eye development and disease: implication of conserved RNA granule components 

  Dash, Soma; Siddam, Archana D.; Barnum, Carrie E.; Janga, Sarath Chandra; Lachke, Salil A. (Wiley, 2016-07)

  The molecular biology of metazoan eye development is an area of intense investigation. These efforts have led to the surprising recognition that although insect and vertebrate eyes have dramatically different structures, ...
• Conversion of JPG Image into DICOM Image Format with One Click Tagging 

  Oladiran, Olakunle; Gichoya, Judy; Purkayastha, Saptarshi (Springer, 2017)

  DICOM images are the centerpiece of radiological imaging. They contain a lot of metadata information about the patient, procedure, sequence of images, device and location. To modify, annotate or simply anonymize images for ...
• An informatics approach to medication adherence assessment and improvement using clinical, billing, and patient-entered data 

  Dixon, Brian E.; Jabour, Abdulrahman M.; O’Kelly Phillips, Erin; Marrero, David G. (Oxford University Press, 2014-05)

  The aim of this study was to describe an integrated informatics approach to aggregating and displaying clinically relevant data that can identify problems with medication adherence and facilitate patient-provider communication ...
• Mobile-Application Based Cognitive Behavior Therapy (CBT) for Identifying and Managing Depression and Anxiety 

  Addepally, Siva Abhishek; Purkayastha, Saptarshi (Springer, 2017-07)

  Mobile technology is a cost effective and scalable platform for developing a therapeutic intervention. This paper discusses the development of a mobile application for people suffering with depression and anxiety. The ...
• Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations 

  Srivastava, Rajneesh; Budak, Gungor; Dash, Soma; Lachke, Salil A.; Janga, Sarath Chandra (Nature Publishing group, 2017-09-14)

  Lens development involves a complex and highly orchestrated regulatory program. Here, we investigate the transcriptomic alterations and splicing events during mouse lens formation using RNA-seq data from multiple developmental ...
• RNA Editing in Pathogenesis of Cancer 

  Baysal, Bora E.; Sharma, Shraddha; Hashemikhabir, Seyedsasan; Janga, Sarath Chandra (AACR, 2017-07)

  Several adenosine or cytidine deaminase enzymes deaminate transcript sequences in a cell type or environment-dependent manner by a programmed process called RNA editing. RNA editing enzymes catalyze A>I or C>U transcript ...
• Proteomic characterization reveals that MMP-3 correlates with bronchiolitis obliterans syndrome following allogeneic hematopoietic cell and lung transplantation 

  Liu, Xiaowen; Yue, Zongliang; Yu, Jeffrey; Daguindau, Etienne; Kushekhar, Kushi; Zhang, Qing; Ogata, Yuko; Gafken, Philip R.; Inamoto, Yoshihiro; Gracon, Adam; Wilkes, David S.; Hansen, John A.; Lee, Stephanie J.; Chen, Jake Y.; Paczesny, Sophie (Wiley, 2016-08)

  Improved diagnostic methods are needed for bronchiolitis obliterans syndrome (BOS), a serious complication after allogeneic hematopoietic cell transplantation (HCT) and lung transplantation. For proteins candidate discovery, ...
• Express: A database of transcriptome profiles encompassing known and novel transcripts across multiple development stages in eye tissues 

  Budak, Gungor; Dash, Soma; Srivastava, Rajneesh; Lachke, Salil A.; Janga, Sarath Chandra (Elsevier, 2018)

  Advances in sequencing have facilitated nucleotide-resolution genome-wide transcriptomic profiles across multiple mouse eye tissues. However, these RNA sequencing (RNA-seq) based eye developmental transcriptomes are not ...
• Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry 

  Kou, Qiang; Wu, Si; Liu, Xiaowen (Wiley, 2018)

  Complex proteoforms contain various primary structural alterations resulting from variations in genes, RNA, and proteins. Top-down mass spectrometry is commonly used for analyzing complex proteoforms because it provides ...
• Translational Biomedical Informatics and Pharmacometrics Approaches in the Drug Interactions Research 

  Zhang, Pengyue; Wu, Heng-Yi; Chiang, Chien-Wei; Binkheder, Samar; Wang, Xueying; Zeng, Donglin; Quinney, Sara K.; Li, Lang (Wiley, 2018)

  Drug interaction is a leading cause of adverse drug events and a major obstacle for current clinical practice. Pharmacovigilance data mining, pharmacokinetic modeling, and text mining are computation and informatic tools ...
• A Coherent Healthcare System with RDBMS, NoSQL and GIS Databases 

  Wu, Huanmei; Ambavane, Ashish; Mukherjee, Sunanda; Mao, Songan (2017)

  With new database system development and new data types emerging, many applications are no longer using a monolithic, simple client/server structure, but using more than one types of database systems to store heterogeneous ...

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