• Identification of Alternatively-Activated Pathways between Primary Breast Cancer and Liver Metastatic Cancer Using Microarray Data 

  Wang, Limei; Li, Jin; Liu, Enze; Kinnebrew, Garrett; Zhang, Xiaoli; Stover, Daniel; Huo, Yang; Zeng, Zhi; Jiang, Wanli; Cheng, Lijun; Feng, Weixing; Li, Lang (MDPI, 2019-09-25)

  Alternatively-activated pathways have been observed in biological experiments in cancer studies, but the concept had not been fully explored in computational cancer system biology. Therefore, an alternatively-activated ...
• "Super Gene Set" Causal Relationship Discovery from Functional Genomics Data 

  Yue, Zongliang; Neylon, Michael T.; Nguyen, Thanh; Ratliff, Timothy; Chen, Jake Y. (IEEE, 2018-11)

  In this article, we present a computational framework to identify "causal relationships" among super gene sets. For "causal relationships," we refer to both stimulatory and inhibitory regulatory relationships, regardless ...
• Epitranscriptomic code and its alterations in human disease 

  Kadumuri, Rajashekar Varma; Janga, Sarath Chandra (Elsevier, 2018-10)

  Innovations in epitranscriptomics have resulted in the identification of more than 160 RNA modifications to date. These developments, together with the recent discovery of writers, readers, and erasers of modifications ...
• Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins 

  Porto, Felipe Wendt; Daulatabad, Swapna Vidhur; Janga, Sarath Chandra (MDPI, 2019-08-06)

  Recent developments in our understanding of the interactions between long non-coding RNAs (lncRNAs) and cellular components have improved treatment approaches for various human diseases including cancer, vascular diseases, ...
• The Longest Common Exemplar Subsequence Problem 

  Zhang, Shu; Wang, Ruizhi; Zhu, Daming; Jiang, Haitao; Feng, Haodi; Guo, Jiong; Liu, Xiaowen (IEEE, 2018-12)

  In this paper, we propose to find order conserved subsequences of genomes by finding longest common exemplar subsequences of the genomes. The longest common exemplar subsequence problem is given by two genomes, asks to ...
• Early transcriptome profile of goat peripheral blood mononuclear cells (PBMCs) infected with peste des petits ruminant's vaccine virus (Sungri/96) revealed induction of antiviral response in an interferon independent manner 

  Manjunath, Siddappa; Saxena, Shikha; Mishra, Bina; Santra, Lakshman; Sahu, Amit Ranjan; Wani, Sajad Ahmed; Tiwari, Ashok Kumar; Mishra, Bishnu Prasad; Singh, Raj Kumar; Janga, Sarath Chandra; Kumar, Gandham Ravi (Elsevier, 2019-06)

  Sungri/96 vaccine strain is considered the most potent vaccine providing long-term immunity against peste des petits ruminants (PPR) in India. Previous studies in our laboratory highlighted induction of robust antiviral ...
• Understanding older adults' medication decision making and behavior: A study on over-the-counter (OTC) anticholinergic medications 

  Holden, Richard J.; Srinivas, Preethi; Campbell, Noll L.; Clark, Daniel O.; Bodke, Kunal S.; Hong, Youngbok; Boustani, Malaz A.; Ferguson, Denisha; Callahan, Christopher M. (Elsevier, 2019-01)

  BACKGROUND: Older adults purchase and use over-the-counter (OTC) medications with potentially significant adverse effects. Some OTC medications, such as those with anticholinergic effects, are relatively contraindicated ...
• An Ontology For Formal Representation Of Medication Adherence-Related Knowledge: Case Study In Breast Cancer 

  Sawesi, Suhila; Jones, Josette F.; Duncan, William D. (2018-08)
• Studying the Impression of Saudi People towards Current Social Changes 

  Rabaan, Hawra; Chkraborty, Sunandan; Young, Alyson L. (ACM, 2018-11)

  In this work-in-progress paper, we examine how the campaign to end the guardianship law in Saudi Arabia is being discussed and debated on social media. Through a content analysis of tweets, we first identify those with ...
• Generalization of Machine Learning Approaches to Identify Notifiable Diseases Reported from a Statewide Health Information Exchange 

  Dexter, Gregory; Kasthurirathne, Suranga; Dixon, Brian E.; Grannis, Shaun (MEDINFO Conference proceedings, 2019-08-25)
• Evaluating Two Approaches for Parameterizing the Fellegi-Sunter Patient Matching Algorithm to Optimize Accuracy 

  Grannis, Shaun; Kasthurirathne, Suranga; Bo, Na; Huiping, Xu (Medinfo conference proceedings, 2019-08-25)
• HIV Vaccine Mystery and Viral Shell Disorder 

  Goh, Gerard Kian-Meng; Dunker, A. Keith; Foster, James A.; Uversky, Vladimir N. (MDPI, 2019-05)

  Hundreds of billions of dollars have been spent for over three decades in the search for an effective human immunodeficiency virus (HIV) vaccine with no success. There are also at least two other sexually transmitted ...
• Implementing Guided Inquiry Learning and Measuring Engagement Using an Electronic Health Record System in an Online Setting 

  Purkayastha, Saptarshi; Surapaneni, Asha Kiranmayee; Maity, Pallavi (Academic Conferences International Limited, 2018-11)

  In many courses, practical hands-on experience is critical for knowledge construction. In the traditional lab setting, this construction is easy to observe through student engagement. But in an online virtual lab, there ...
• Comparison of Open-Source Electronic Health Record Systems Based on Functional and User Performance Criteria 

  Purkayastha, Saptarshi; Allam, Roshini; Maity, Pallavi; Gichoya, Judy W. (The Korean Society of Medical Informatics, 2019-04)

  Objectives: Open-source Electronic Health Record (EHR) systems have gained importance. The main aim of our research is to guide organizational choice by comparing the features, functionality, and user-facing system ...
• Tissue-specific network-based genome wide study of amygdala imaging phenotypes to identify functional interaction modules 

  Yao, Xiaohui; Yan, Jingwen; Liu, Kefei; Kim, Sungeun; Nho, Kwangsik; Risacher, Shannon L.; Greene, Casey S.; Moore, Jason H.; Saykin, Andrew J.; Shen, Li; Alzheimer’s Disease Neuroimaging Initiative (Oxford University Press, 2017-10-15)

  Motivation: Network-based genome-wide association studies (GWAS) aim to identify functional modules from biological networks that are enriched by top GWAS findings. Although gene functions are relevant to tissue context, ...
• PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes 

  Singh, Deepak K.; Gholamalamdari, Omid; Jadaliha, Mahdieh; Li, Xiao Ling; Lin, Yo-Chuen; Zhang, Yang; Guang, Shuomeng; Hashemikhabir, Seyedsasan; Tiwari, Saumya; Zhu, Yuelin J.; Khan, Abid; Thomas, Anu; Chakraborty, Arindam; Macias, Virgilia; Balla, Andre K.; Bhargava, Rohit; Janga, Sarath Chandra; Ma, Jian; Prasanth, Supriya G.; Lal, Ashish; Prasanth, Kannanganattu V. (Oxford University Press, 2017-10-01)

  Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in BC initiation and progression. Here, we demonstrate the ...
• Deep Top-Down Proteomics Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Identification of 5700 Proteoforms from the Escherichia coli Proteome 

  McCool, Elijah N.; Lubeckyj, Rachele A.; Shen, Xiaojing; Chen, Daoyang; Kou, Qiang; Liu, Xiaowen; Sun, Liangliang (American Chemical Society, 2018-05-01)

  Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as a useful tool for top-down proteomics. However, its performance for deep top-down proteomics is still dramatically lower than ...
• Data Integration and Interoperability for Patient-Centered Remote Monitoring of Cardiovascular Implantable Electronic Devices 

  Daley, Carly; Toscos, Tammy; Mirro, Michael (MDPI, 2019-03-17)

  The prevalence of cardiovascular implantable electronic devices with remote monitoring capabilities continues to grow, resulting in increased volume and complexity of biomedical data. These data can provide diagnostic ...
• Erratum to: Providing Patients with Implantable Cardiac Device Data through a Personal Health Record: A Qualitative Study 

  Daley, Carly N.; Chen, Elizabeth M.; Roebuck, Amelia E.; Ghahari, Romisa Rohani; Sami, Areej F.; Skaggs, Cayla G.; Carpenter, Maria D.; Mirro, Michael J.; Toscos, Tammy R. (Thieme Medical Publishers, 2017-10)
• Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data 

  Yan, Jingwen; Risacher, Shannon L.; Shen, Li; Saykin, Andrew J. (Oxford University Press, 2018-11-27)

  In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of ...

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