The document is a CV for Thomas Peterson that outlines his education, skills, research experience, publications, and teaching experience. He received his Ph.D. in Biological Sciences from UMBC, specializing in bioinformatics and computational biology, and has extensive experience developing bioinformatics tools and analyzing genomic and biological data. He currently works as a lab manager and software developer at UMBC, where he also teaches undergraduate courses in bioinformatics.
Top downloaded article in academia 2020 - International Journal of Computatio...ijcsity
International Journal of Computational Science and Information Technology (IJCSITY) focuses on Complex systems, information and computation using mathematics and engineering techniques. This is an open access peer-reviewed journal will act as a major forum for the presentation of innovative ideas, approaches, developments, and research projects in the area of Computation theory and applications. It will also serve to facilitate the exchange of information between researchers and industry professionals to discuss the latest issues and advancement in the area of advanced Computation and its applications.
Open Access and Property Rights on a Collision Course with ScholarsKimberly Yang
This seminar talk focused on open access as a philosophy directly affecting scholars, academics, and consumers and its tension with property rights (intellectual property, copyright, proprietary databases). These impact our ability (or inability) to search, identify, retrieve, access, and use full-text publications or data relevant to research topics and investigations. It impacts our ability to use others' works (and our own work) in our research, writing, publishing and teaching.
Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK NeISSProject
Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK . Talk given by Richard Sinnott at Urban Research Infrastructure Network Workshops, Melbourne, Brisbane, Sydney, September 2010.
Top downloaded article in academia 2020 - International Journal of Computatio...ijcsity
International Journal of Computational Science and Information Technology (IJCSITY) focuses on Complex systems, information and computation using mathematics and engineering techniques. This is an open access peer-reviewed journal will act as a major forum for the presentation of innovative ideas, approaches, developments, and research projects in the area of Computation theory and applications. It will also serve to facilitate the exchange of information between researchers and industry professionals to discuss the latest issues and advancement in the area of advanced Computation and its applications.
Open Access and Property Rights on a Collision Course with ScholarsKimberly Yang
This seminar talk focused on open access as a philosophy directly affecting scholars, academics, and consumers and its tension with property rights (intellectual property, copyright, proprietary databases). These impact our ability (or inability) to search, identify, retrieve, access, and use full-text publications or data relevant to research topics and investigations. It impacts our ability to use others' works (and our own work) in our research, writing, publishing and teaching.
Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK NeISSProject
Infrastructures Supporting Inter-disciplinary Research - Exemplars from the UK . Talk given by Richard Sinnott at Urban Research Infrastructure Network Workshops, Melbourne, Brisbane, Sydney, September 2010.
Enhancing Onsite Experience of Attendees Using the W.E.D FrameworkGEVME
Running a memorable event is challenging? How can you leverage on technology to make your event memorable and delightful for your attendees? W.E.D. is a simple framework that event organizers can use to enhance the onsite experience at events. This presentation is full of tips and tools you can use.
Enhancing Onsite Experience of Attendees Using the W.E.D FrameworkGEVME
Running a memorable event is challenging? How can you leverage on technology to make your event memorable and delightful for your attendees? W.E.D. is a simple framework that event organizers can use to enhance the onsite experience at events. This presentation is full of tips and tools you can use.
Accessing and Sharing Electronic Personal Health Data.Maria Karampela
An increasing attention has been given to personal health data (PHD) research over the last years. The rise of researchers’ interest could be attributed to the increasing amount of PHD that are stored across various databases, as a result of individuals’ rapidly- evolving digital life. Accessing and sharing PHD is essential to create personalized health services and to involve patients in the design process of these services. This paper conducts a survey of literature to present an overview of literature about accessing and sharing of PHD. This study aims to identify limitations in research and propose future directions. Sixteen studies were selected from various bibliographic databases and were classified according to three criteria: research type, empirical type and contribution type. The results provide a preliminary review with respect to access and sharing of PHD, addressing a need for more research about PHD accessibility and for solution proposals for both topics.
Accessing and Sharing Electronic Personal Health DataSofia Ouhbi
Accessing and sharing PHD is essential to create personalized health services and to involve patients in the design process of these services. This paper conducts a survey of literature to present an overview of literature about accessing and sharing of PHD. This study aims to identify limitations in research and propose future directions.
Social Media Datasets for Analysis and Modeling Drug Usageijtsrd
This paper based on the research carried out in the area of data mining depends for managing bulk amount of data with mining in social media on using composite applications for performing more sophisticated analysis. Enhancement of social media may address this need. The objective of this paper is to introduce such type of tool which used in social network to characterised Medicine Usage. This paper outlined a structured approach to analyse social media in order to capture emerging trends in medicine abuse by applying powerful methods like Machine Learning. This paper describes how to fetch important data for analysis from social network. Then big data techniques to extract useful content for analysis are discussed. Sindhu S. B | Dr. B. N Veerappa "Social Media Datasets for Analysis and Modeling Drug Usage" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-3 | Issue-5 , August 2019, URL: https://www.ijtsrd.com/papers/ijtsrd25246.pdfPaper URL: https://www.ijtsrd.com/engineering/computer-engineering/25246/social-media-datasets-for-analysis-and-modeling-drug-usage/sindhu-s-b
PhD Thesis Defence: From Participation Factors to Co-Calibration of Patient- ...Vlad Manea
From Participation Factors to Co-Calibration of Patient- and Wearable-Reported Outcomes in Behavioural, Health, and Quality of Life Studies / PhD Thesis Defence • April 14th, 2021 • University of Copenhagen
Cite this work: From Participation Factors to Co-Calibration of Patient- and Wearable-Reported Outcomes in Behavioural, Health, and Quality of Life Studies. Vlad Manea. PhD thesis, Quality of Life Technologies Lab, Section of Human-Centered Computing, Department of Computer Science, Faculty of Science, University of Copenhagen, 2020. Copenhagen, Denmark
Abstract
Chronic diseases represent a significant share of the burden of disease globally. They are responsible for 86% of premature deaths in Europe. Unhealthy behaviours, such as physical inactivity, insufficient sleep, poor nutrition, and tobacco intake, explain up to 50% of chronic disease risk. However, the evidence is not precise enough to assess the risk for each disease. Human subject studies monitoring behaviours over long periods (longitudinally) during daily life (in situ) by leveraging unobtrusive (observational) technology can allow human behaviours to unfold. They can not only qualify, but also quantify the relationships between behaviours, health, and Quality of Life (QoL) outcomes from compliant participants.
This PhD thesis explores two research areas. In the first area, we research the motivation and facilitation of participation in human subject studies. We propose a presentational model using personalised stories to improve human studies’ participation. We design two unifying frameworks for conducting a wide range of human subject studies (mQoL mobile app, mQoL-Chat chatbot). They leverage two modules designed and developed by the author in mQoL-Lab, the lab platform of the Quality of Life Technologies lab.
In the second area, we research the relationships between behavioural, health, and QoL outcomes (co-calibration). We present the coQoL computational model for co-calibration. We demonstrate its feasibility in a study on N = 42 healthy older individuals (a population at risk, appropriate for disease prevention, and having benefitted from insufficient co-calibrations). They answered questionnaires on eight physical and psychological validated scales (physical activity: IPAQ, social support:
MSPSS, anxiety and depression: GADS, nutrition: PREDIMED and SelfMNA, memory: MFE, sleep: PSQI, and health-related QoL: EQ-5D-3L). They wore consumer wearables (Fitbit Charge 2) for up to two years. The wearables reported behavioural markers (physical activity, sleep, heart rate) in situ. We observed new relationships between these outcomes. We described the study’s human factors and data quality.
The scientific contributions in both research areas can inform the design of future studies leveraging consumer technology that monitors behaviours longitudinally in situ to assess and improve health and QoL.
As we are into the age of digital information, the problem of data overload emerges so worryingly ahead. Our ability to analyze and understand immense datasets wrap extreme behind our ability together and stores the data. But a new age group of computational techniques and tools is required to support the extraction of useful knowledge from the rapidly increasing volumes of data. These techniques and tools are the focus of emerging fields of Knowledge Discovery in Databases (KDD) and also called data mining. Data mining is highly noticeable in the fields like marketing, e-commerce or e-business or the fame of its use in KDD in other sectors or industries also. Among these sectors that are just discovering data mining are the fields of medicine and public health also. This research paper provides a survey of current technique of data mining/KDD for healthcare.
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
Usability analysis of sms alert system for immunization in the context of ban...eSAT Journals
Abstract Both the market and academia strongly encourage the development of usable systems, and they do so by relying on a number of standards, guide-lines, research and good practice streams. Unfortunately, in the health sector, whilst being the owner of standards under many purposes and topics, seems still falling and running behind as the conceptual issues and practical implications of usability are concerned. In this study, it was found that rapid growth of mobile applications through SMS increases in a significant way in developing countries particularly in Bangladesh. Public satisfaction was highly shown in mobile health services through SMS. In our paper, usability has been analytically investigated throughout a simulated health oriented action setting and against a prototype of SMS based health services in Bangladesh, and several provoking conclusions in terms of “rethinking usability” applied to academic actions and decision making have been derived. Various health institutes can be influenced by this study to challenge existing difficulties against usability potential. Keywords: ICT, mHealth, Mobile applications, SMS, Usability
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Improving Prediction Accuracy Results by Using Q-Statistic Algorithm in High ...rahulmonikasharma
Classification problems in high dimensional information with little sort of observations became furthercommon significantly in microarray information. The increasing amount of text data on internet sites affects the agglomerationanalysis. The text agglomeration could also be a positive analysis technique used for partitioning a huge amount of datainto clusters. Hence, the most necessary draw back that affects the text agglomeration technique is that the presenceuninformative and distributed choices in text documents. A broad class of boosting algorithms is known as actingcoordinate-wise gradient descent to attenuate some potential performs of the margins of a data set. This paperproposes a novel analysis live Q-statistic that comes with the soundness of the chosen feature set to boot to theprediction accuracy. Then we've a bent to propose the Booster of associate degree FS algorithm that enhances theworth of the Q-statistic of the algorithm applied.
This presentation was provided by Anne Stone of TBI Communications during the NISO Training Thursday event, Metrics Case Studies, held on December 14, 2017.
Stone Altmetrics Measuring Success of New Approaches
Thomas_Peterson_CV
1. tpeters1{at}umbc.edu
410-241-1702 Thomas A. Peterson, Ph.D.
1306 Scheeler Ave.
Baltimore, MD 21237
Linkedin.com/in/ThomasAndrewPeterson
______________________________________________________________________
EDUCATION
University of Maryland, Baltimore County (UMBC) GPA: 4.0/4.0
Ph.D. in Biological Sciences; Specialization in Bioinformatics & Computational Biology
Baltimore, MD
Spring 2016
B.S. in Information Systems with Web Development Certificate 2011
______________________________________________________________________
SKILLS
Languages: Perl, R, Matlab, Java, Python, HTML, CSS, PHP, Ruby on Rails, JavaScript, Ajax, JQuery, MySql,
PostgreSQL, C, C++, C#, creating programs for parallel computing environments
Bioinformatics Tools: BioPerl, BioPython, Bioconductor, Weka, Cytoscape, experience creating publication-
worthy figures and editing them in photoshop, experience with NLP / text-mining
Research Tools: Markdown, Snakemake, Latex, Bibtex, EndNote, experience with GitHub and version control
software (SVN, OpenCVS)
______________________________________________________________________
RESEARCH & COMPUTATIONAL EXPERIENCE
UMBC - Biological Sciences Department Baltimore, MD
Dr. Maricel Kann’s Bioinformatics Lab 2009-Present
Lab Manager: Helped in training, coordinating, and supervising research from
undergraduate and graduate students in the lab. Collaboration with other research teams
to organize research projects and contributing to grant proposals.
2012- Present
Software & Web Developer: Planning and creation of tools and research projects. 2008-Present
Grant Writer: Submitted an F31 grant (PA-11-111) as Principle Investigator (not
awarded)
2014
Systems Administrator: Management of the Unix systems in the lab. This includes
updating, repairing, and the installation of new software / tools on three red hat servers
and twelve dual booted windows/linux workstations.
2008-2012
Facilities Management Department of Information Technology 2006-2008
Information Technology Staff Manager: Management of all staff and students
responsible for the information technology support for over 50 personal computers and
3 Red Hat / Active Directory servers.
______________________________________________________________________
AWARDS & HONORS
Honors society: Selected to be a member of Phi Kappa Phi Honors Society for achieving a
perfect GPA at UMBC
2015
Best graduate poster award: from UMBC’s GABS Graduate Student Research Symposium 2013
Best pre-doctoral poster: award from UMB’s Second Annual Cancer Biology Research Retreat 2012
2. Thomas A. Peterson
2
SUBMITTED PUBLICATIONS
Peterson, T.A., Mort, M., Cooper, D., Radivojac, P., Kann, M.G., Mooney, S., Incorporation of genomic
regions identified by the ENCODE project increases predictive performance of functional regularity variants
(submitted to Human Mutation, 2016)
______________________________________________________________________
PEER REVIEWED PUBLICATIONS
Peterson, T.A., E. Doughty, and M.G. Kann, Towards Precision Medicine: Advances in Computational
Approaches for the Analysis of Human Variants. Journal of Molecular Biology, 2013. PMID: 23962656
Peterson, T.A., D. Park, and M.G. Kann, A protein domain-centric approach for the comparative analysis of
human and yeast phenotypically relevant mutations. BMC Genomics, 2013. 14(Suppl 3): p. S5. PMID:
23819456
Zhang, C., Q. Xie, R.G. Anderson, G. Ng, N.C. Seitz, T. A. Peterson, C.R. McClung, J.M. McDowell, D.
Kong, J.M. Kwak, and H. Lu, Crosstalk between the circadian clock and innate immunity in Arabidopsis. PLoS
Pathog, 2013. 9(6): p. e1003370. PMID: 23754942
Peterson, T.A., N.L. Nehrt, D. Park, and M.G. Kann, Incorporating molecular and functional context into the
analysis and prioritization of human variants associated with cancer. J Am Med Inform Assoc, 2012. 19(2): p.
275-83. PMID: 22319177
Nehrt, N.L§
., T.A. Peterson§
, D. Park, and M.G. Kann, Domain landscapes of somatic mutations in cancer.
BMC Genomics, 2012. 13 Suppl 4: p. S9. PMID: 22759657 §
These authors contributed equally to this work
Doughty, E., A. Kertesz-Farkas, O. Bodenreider, G. Thompson, A. Adadey, T. A. Peterson, and M.G. Kann,
Toward an automatic method for extracting cancer- and other disease-related point mutations from the
biomedical literature. Bioinformatics, 2011. 27(3): p. 408-15. PMID: 21138947
Peterson, T.A., A. Adadey, I. Santana-Cruz, Y. Sun, A. Winder, and M.G. Kann, DMDM: domain mapping of
disease mutations. Bioinformatics, 2010. 26(19): p. 2458-9. PMID: 206859561
______________________________________________________________________
CONFERENCE PROCEEDINGS
N.L. Nehrt, Peterson, T.A., M. G. Kann, Clustering Disease Connections Using DMDM: Domain Mapping of
Disease Mutations. Paper presented at ISMB/ECCB, Vienna, 2011 (Conference proceeding)
______________________________________________________________________
IN PROGRESS PAPERS
Peterson, T.A., Ivy, I., Park, D, and Kann, M.G., Oncodomains: A Protein Domain-Centric Framework for
Prioritizing Rare Variants in Tumor Samples (in progress)
Yesupriya, N., Peterson, T.A., Quasie-Woode, D., Kann, M.G., EMUS: Extractor of Mutations in Biomedical
Literature for Multiple Species (in progress)
Ivy, I. Peterson, T.A., Kann, M.G., Spouge, J., Park D., Zero-inflated Poisson local fdr for identifying
significantly enriched positions within protein domain positions for large-scale population studies. (in progress)
3. Thomas A. Peterson
3
ARTICLES PEER REVIEWED
Conferences
Translational Bioinformatics Conference (TBC) 2015
Pacific Symposium on Biocomputing (PSB) 2015 & 2013
Association for Computing Machinery Conference on Bioinformatics, Computational
Biology, and Biomedical Informatics (ACM / BCB)
2014 & 2013
International Society for Molecular Biology / European Conference for Computational
Biology (ISMB / ECCB)
2014
Journals
PLoS Computational Biology (PLoS-CB) 2015 & 2014
Bioinformatics 2013
Journal of the American Medical Informatics Association (JAMIA) 2013 & 2012
______________________________________________________________________
WEBSITES DESIGNED & DEVELOPED
DMDM: Domain Mapping of Disease Mutations ( http://bioinf.umbc.edu/dmdm/ )
Over 1,000 unique users per week
Externally linked by NCBI and UniProt for all human proteins with domain regions
Created in 2010
Updated in 2014
DS-Score ( http://bioinf.umbc.edu/ds-score/ )
Visualization tool for the results of our Domain Significance Score
Created in 2013
EMU: Extractor of Mutations ( http://bioinf.umbc.edu/emu/ )
Visualization tool for the results of our EMU text-mining tool
Created in 2010
Facilities Management Web Resource ( http://fm.umbc.edu/ )
Interface for submitting tickets to a work order system for plumbers, electricians, etc.
Created in 2009
______________________________________________________________________
SOCIETAL MEMBERSHIPS
Phi Kappa Phi Honors Society 2015-current
ISCB Student Council 2013-current
President and Founder: ISCB-Student Council Regional Student Group for DC 2014-current
Coordinating bi-monthy meetings between students and professors from UMBC,
University of Maryland, College Park, Johns Hopkins, Georgetown, and NIH
Planning yearly student symposia and quarterly workshops or tutorials
This community promises to be a lasting resource for local students to have a
chance to connect and share their research with peers who share similar research
interests at neighboring institutions
International Society for Computational Biology (ISCB) 2012-current
American Medical Informatics Association (AMIA) 2012-current
4. Thomas A. Peterson
4
TEACHING EXPERIENCE
UMBC - Biological Sciences Department
Graduate courses
Baltimore, MD
Seminar in Bioinformatics
Engaging students with Bioinformatics tools and programming
Leading a two hour long session in the computer lab every Friday
Design of two new lab projects and two guest lectures about bioinformatics &
computational biology for analyzing cancer datasets
2010-Present
Undergraduate courses
Introduction to Bioinformatics
Helping students from many different backgrounds familiarize themselves with
concepts in biology, computer science, and math.
2010-Present
Lead TA for Introduction to Wet Lab Techniques
Teaching common laboratory skills such as using pipettes, spectrophotometers,
microscopes, and other laboratory equipment while performing experiments.
2013-2014
______________________________________________________________________
SELECTED MEETINGS & CONFERENCES
Participant: HGVS meeting: Pathogenicity Interpretation in the Age of Precision Medicine October 2015
Oral presentation & Session Chair: ISCB-SC RSG-DC Student Research Symposium May 2015
Oral presentation: Machine Learning Session at the SLAS in Washington DC February 2015
Participant: AMIA Join Summit on Translational Science in Washington DC November 2014
Poster: GRC Human Single Nucleotide Polymorphisms & Disease in Boston August 2014
Participant: International RNA Informatics Summit at UCSC June 2014
Oral presentation: Sean Mooney's lab at The Buck Institute in San Francisco June 2014
Oral presentation: GABS Graduate Student Research Symposium at UMBC April 2014
Participant: Biomedical Informatics Symposium at Georgetown University October 2013
Participant: ACM / BCB in Washington DC September 2013
Poster: UMB's Third Annual Cancer Biology Research Retreat May 2013
Poster: A Look Ahead XVI at UMBC April 2013
(award) Poster: GABS Graduate Student Research Symposium March 2013
Oral presentation: MIRTHE Summer Workshop at UMBC August 2012
Participant: 20th Annual ISCB in Long Beach, CA July 2012
Data Integration in Life Sciences (DILS) at the University of Maryland June 2012
(award) Poster: UMB's Second Annual Cancer Biology Research Retreat May 2012
Poster: A Look Ahead XV at UMBC April 2012
Oral presentation: Sean Mooney's Stanford Retreat March 2012
Participant: AMIA Joint Summit on Translational Science in San Francisco March 2012
