Translational bioinformatics in mental health: open access data sources and computational biomarker discovery

Tenenbaum JD, Bhuvaneshwar K, Gagliardi JP, Fultz Hollis K, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Rozenblit L. Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. Brief Bioinform. 2017 Nov 27. doi: 10.1093/bib/bbx157. [Epub ahead of print] PMID: 29186302

Mental illness is increasingly recognized as both a significant cost to society and a significant area of opportunity for biological breakthrough. As -omics and imaging technologies enable researchers to probemolecular and physiological underpinnings of multiple diseases, opportunities arise to explore the biological basis for behavioral health and disease. From individual investigators to large international consortia, researchers have generated rich data sets in the area of mental health, including genomic, transcriptomic,metabolomic, proteomic, clinical and imaging resources. General data repositories such as the Gene Expression Omnibus (GEO) and Database of Genotypes and Phenotypes (dbGaP) andmental health (MH)-specific initiatives, such as the Psychiatric Genomics Consortium, MH Research Network and PsychENCODE represent a wealth of information yet to be gleaned. At the same time, novel approaches to integrate and analyze data sets are enabling important discoveries in the area ofmental and behavioral health. This review will discuss and catalog into an organizing framework the increasingly diverse set of MH data resources available, using schizophrenia as a focus area, and will describe novel and integrative approaches tomolecular biomarker discovery thatmake use of mental health data.

Publication Year: 
2017
Publication Credits: 
Tenenbaum JD, Bhuvaneshwar K, Gagliardi JP, Fultz Hollis K, Jia P, Ma L, Nagarajan R, Rakesh G, Subbian V, Visweswaran S, Zhao Z, Rozenblit L.
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What Dental Educators Need to Understand About Emerging Technologies to Incorporate Them Effectively into the Educational Process

Stein CD, Eisenberg ES, O'Donnell JA, Spallek H. What dental educators need to understand about emerging technologies to incorporate them effectively into the educational process. J Dent Educ. 2014 Apr;78(4):520-9. PubMed PMID: 24706681

Many dental schools are currently struggling with the adoption of emerging technologies and the incorporation of these technologies into the educational process. Dental students exhibit an increasing degree of digital comfort when using social networking, mobile devices, search engines, or e-textbooks. Although the majority of students might consider themselves to be very skilled at using information technology, many faculty members would claim the opposite when evaluating their own knowledge and skills in the use of technology. As the use of technology, both formally and informally, continues to increase, dental educators are faced with many questions, such as: Does students’ digital comfort disguise a lack of information literacy? What is the appropriate path of implementing technology into teaching and learning, and how can institutions support such an implementation? This article surveys a series of myths that exist about the use of technology in education and raises questions about their validity and how dental educators can avoid being misled by them.

Publication Year: 
2014

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping

Rafael Ceschin, Ashok Panigrahy, Vanathi Gopalakrishnan. sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.  Cancer Informatics 2015:Suppl. 2 1-9

A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.

Publication Year: 
2015
Publication Credits: 
Ashok Panigrahy, Vanathi Gopalakrishnan

Building a gold standard to construct search filters: A case study with biomarkers for oral cancer.

John J. Frazier, Corey D. Stein, Eugene Tseytlin, Tanja Bekhuis. Building a gold standard to construct search filters: A case study with biomarkers for oral cancer. J Med Libr Assoc. 2015 Jan;103(1):22-30. doi: 10.3163/1536-5050.103.1.005.

OBJECTIVE: To support clinical researchers, librarians and informationists may need search filters for particular tasks. Development of filters typically depends on a "gold standard" dataset. This paper describes generalizable methods for creating a gold standard to support future filter development and evaluation using oral squamous cell carcinoma (OSCC) as a case study. OSCC is the most common malignancy affecting the oral cavity. Investigation of biomarkers with potential prognostic utility is an active area of research in OSCC. The methods discussed here should be useful for designing quality search filters in similar domains.

METHODS: The authors searched MEDLINE for prognostic studies of OSCC, developed annotation guidelines for screeners, ran three calibration trials before annotating the remaining body of citations, and measured inter-annotator agreement (IAA).

RESULTS: We retrieved 1,818 citations. After calibration, we screened the remaining citations (n = 1,767; 97.2%); IAA was substantial (kappa = 0.76). The dataset has 497 (27.3%) citations representing OSCC studies of potential prognostic biomarkers.

CONCLUSIONS: The gold standard dataset is likely to be high quality and useful for future development and evaluation of filters for OSCC studies of potential prognostic biomarkers.

IMPLICATIONS: The methodology we used is generalizable to other domains requiring a reference standard to evaluate the performance of search filters. A gold standard is essential because the labels regarding relevance enable computation of diagnostic metrics, such as sensitivity and specificity. Librarians and informationists with data analysis skills could contribute to developing gold standard datasets and subsequent filters tuned for their patrons' domains of interest.

Publication Year: 
2015
Publication Credits: 
John J. Frazier, Corey D. Stein, Eugene Tseytlin, Tanja Bekhuis

Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems

Borromeo CD, Schleyer TK, Becich MJ, Hochheiser H.  Finding Collaborators: Toward Interactive Discovery Tools for Research Network Systems. J Med Internet Res 2014;16(11):e244 DOI: 10.2196/jmir.3444 PMID: 25370463

Background: Research networking systems hold great promise for helping biomedical scientists identify collaborators with the expertise needed to build interdisciplinary teams. Although efforts to date have focused primarily on collecting and aggregating information, less attention has been paid to the design of end-user tools for using these collections to identify collaborators. To be effective, collaborator search tools must provide researchers with easy access to information relevant to their collaboration needs.

Objective: The aim was to study user requirements and preferences for research networking system collaborator search tools and to design and evaluate a functional prototype.

Methods: Paper prototypes exploring possible interface designs were presented to 18 participants in semistructured interviews aimed at eliciting collaborator search needs. Interview data were coded and analyzed to identify recurrent themes and related software requirements. Analysis results and elements from paper prototypes were used to design a Web-based prototype using the D3 JavaScript library and VIVO data. Preliminary usability studies asked 20 participants to use the tool and to provide feedback through semistructured interviews and completion of the System Usability Scale (SUS).

Results: Initial interviews identified consensus regarding several novel requirements for collaborator search tools, including chronological display of publication and research funding information, the need for conjunctive keyword searches, and tools for tracking candidate collaborators. Participant responses were positive (SUS score: mean 76.4%, SD 13.9). Opportunities for improving the interface design were identified.

Conclusions: Interactive, timeline-based displays that support comparison of researcher productivity in funding and publication have the potential to effectively support searching for collaborators. Further refinement and longitudinal studies may be needed to better understand the implications of collaborator search tools for researcher workflows.

Publication Year: 
2014
Faculty Author: 
Publication Credits: 
Borromeo CD, Schleyer TK, Becich MJ, Hochheiser H

Congratulations to Dr. Matt Stokes

Post Date: 
07/29/2014

Matt Stokes successfully defending his doctoral dissertation entitled “Novel extension of label propagation for biomarker discovery in genomic data” on Thursday, July 17, 2014. Congratulations to Dr. Stokes!

Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics

Dutta-Moscato J, Gopalakrishnan V, Lotze MT, Becich MJ. Creating a pipeline of talent for informatics: STEM initiative for high school students in computer science, biology, and biomedical informatics. J Pathol Inform 2014;5:12

http://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2014;volume=5;issue=1;spage=12;epage=12;aulast=Dutta-Moscato

This editorial provides insights into how informatics can attract highly trained students by involving them in science, technology, engineering, and math (STEM) training at the high school level and continuing to provide mentorship and research opportunities through the formative years of their education. Our central premise is that the trajectory necessary to be expert in the emergent fields in front of them requires acceleration at an early time point. Both pathology (and biomedical) informatics are new disciplines which would benefit from involvement by students at an early stage of their education. In 2009, Michael T Lotze MD, Kirsten Livesey (then a medical student, now a medical resident at University of Pittsburgh Medical Center (UPMC)), Richard Hersheberger, PhD (Currently, Dean at Roswell Park), and Megan Seippel, MS (the administrator) launched the University of Pittsburgh Cancer Institute (UPCI) Summer Academy to bring high school students for an 8 week summer academy focused on Cancer Biology. Initially, pathology and biomedical informatics were involved only in the classroom component of the UPCI Summer Academy. In 2011, due to popular interest, an informatics track called Computer Science, Biology and Biomedical Informatics (CoSBBI) was launched. CoSBBI currently acts as a feeder program for the undergraduate degree program in bioinformatics at the University of Pittsburgh, which is a joint degree offered by the Departments of Biology and Computer Science. We believe training in bioinformatics is the best foundation for students interested in future careers in pathology informatics or biomedical informatics. We describe our approach to the recruitment, training and research mentoring of high school students to create a pipeline of exceptionally well-trained applicants for both the disciplines of pathology informatics and biomedical informatics. We emphasize here how mentoring of high school students in pathology informatics and biomedical informatics will be critical to assuring their success as leaders in the era of big data and personalized medicine.

Publication Year: 
2014
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