Patricia Francis-Lyon

Patricia A. Francis-Lyon

Assistant Professor

Full-Time Faculty

(415) 422-2810 Cowell Hall 203

Biography

Patricia teaches bioinformatics, clinical decision support and other courses in the health informatics program and the computer science department. She’s primarily interested in working with students to apply data analytics to the health domain, with the goal of producing software tools that perform analyses for clinicians, researchers, and the public.

Collaborating with her students is a big priority for Patricia; a number of them are co-authors of her peer-reviewed articles, and their work has been presented at conferences and published as web and mobile apps. Cooperative projects range from machine learning analyses of large EHR datasets for disease risk assessments (Influence Health, Healthgrades), to development of a database web tool to aid researchers in their work with GALNS gene disorders (BioMarin, Buck Institute), to development of a tablet app to identify Kenyan children in need of cognitive therapy (KEMRI). She and her team have also collaborated with the FBI to help identify child predators.

Patricia and her students are currently working with Friends of the Congo to identify an actionable genomic factor influencing racial disparity in cancer outcomes. Her other research areas include computational biology, precision medicine, and applications of genomics and proteomics to human health.

Appointments
Faculty Advisor for HIPSA (Health Informatics Professional Student Association)
Education
PhD, Computer Science with emphasis on Computational Biology, University of California at Davis
Experience
Assistant Professor of Health Informatics, USF, 2014–present
Assistant Professor of Computer Science, USF, 2011–14
Adjunct Professor of Computer Science, USF, 2010–11
Graduate Student Researcher at UC Davis, 2005–10
Graduate Student Research Assistant, Lawrence Berkeley National Laboratory, 2003
Java Developer/Database Programmer (Consultant), Ebates.com, San Francisco, CA, 2002–03
Software Engineer, Ebates.com, San Francisco, CA, 2000–02
Research
Application of Computational Biology
Algorithms and Mathematical models to problems and predictions involving protein structure and genomics
Selected Publications

Attiga A, Chen S, LaGue J, Ovalle O, Stott N, Brander T, Khaled A, Tyagi G, Francis-Lyon P, “Applying Deep Learning to Public Health: Using Unbalanced Demographic Data to Predict Thyroid Disorder”, IEEE Information Technology, Electronics & Mobile Communication Conference Proceedings, November 2018. Also presented as a talk at IEEE IEMCON 2018.

Francis-Lyon P, Abubakar A, Attiga Y, Manjunath R, Ramasubramanian U, Chaudhuri V, Nguyen T, Xu X, Zeng S, “ Tablet App for Child Cognitive Assessment in Low and Middle Income Countries”, IEEE Global Humanitarian Technology Conference 2017 Proceedings. Also presented as a talk at GHTC 2017

Francis-Lyon P, Koehl P,  “Protein side-chain modeling with a protein-dependent optimized rotamer library”, Proteins: Structure, Function and Bioinformatics Vol 82, Issue 9, 2014 

Morrone A, Caciotti 1 A, Atwood R, Davidson K, Du C, Francis-Lyon P, Harmatz P, Mealiffe M, Mooney S, Oron T, Ryles A, Zawadzki K, Miller N, "Morquio A Syndrome-Associated Mutations: A Review of Alterations in the GALNS gene and a New Locus-Specific Database", Human Mutation 2014 Nov;35(11):1271-9

Mack SJ, Yamaguchi KD, Salamon H, Pena AG, Horton RM, Francis-Lyon P, Maiers M, Hollenbach JA, “TIDES and BIGDAWG: An integrated HLA and KIR data management and analysis pipeline”, Human Immunology 75(6):481, 2014.

Ryles, A. B., Du, C., Oron, T., Atwood, R., Mooney, S. D., & Francis-Lyon, P, “Morquio syndrome type A locus-specific database: a framework for a curated database to identify and characterize pathogenic variants in the GALNS gene”. Molecular Genetics and Metabolism, 111(2), S92, 2014

Research Interests

Application of computational biology, algorithms and mathematical models to biological problems and predictions, with focus on protein structure and genomics .

Application of machine learning and data mining in bioinformatics.

Publications

Work in submission : Francis -Lyon P, Koehl P, “Improved protein side -chain modeling with a protein -dependent optimized rotamer library ”.

Francis -Lyon P , Belvadi S, Cheng F, “Detection and characterization of interactions of genetic risk factors in disease”, Proceedings of the 12 th Python in Science Conference , June 2013, p 34 -39

Also presented as a talk at SciPy 2013 July 2013 in Austin, TX

Francis -Lyon P, Gu S, Haas J, Amenta A, Koehl P “Sampling the conformation of protein surface residue s for flexible protein docking ”, BMC Bioinformatics 2010, 11:575 (23 November 2010)

Francis -Lyon P, Cristianini N, Holbrook S, “Terminator Detection by Support Vector Machine Utilizing a Stochastic Context -Free Gramm ar”, Computational Intelligence in Bioin formatics and Computational Biology , June 2007 p 170 -177.

Also presented as poster at CIBCB '07. IEEE Symposium April 2007 in Honolulu, HI

Abstracts and Presentations

Ryles A, Du, C, Oron T, Atwood R, Mooney S, Francis -Lyon P, “Morquio A Locus-Specific Database:A Framework for a Curated Database to Identify and Characterize Pathogenic Variants in the GALNS Gene”, submitted for Poster presentation at Lysosomal Disease Network 10 th Annual World Symposium

Mack S, Yamaguchi K, Salamon H, Pena A, Ho rton R, Francis -Lyon P, Maiers M, Hollenbach J,

" Tides and BIGDAWG: an integrated HLA and KIR data management and analysis pipeline", 2013, Accepted for Poster presentation at American Society of Histocompatibility and Immunogenetics

“Artificial Intellige nce in Computer Science”, invited talk, Lead America 2012 at UC Berkeley

Yang Y , Feng J, Hsieh L, Bor G, Bayarsaikhan N, Zhang Y , and Francis -Lyon P (presenter), “Use of Machine Learning to Detect and Characterize Gene Interactions in Disease”, May 2011, Poster presentation at Great Lakes Bioinformatics Conference, Athens, OH

Francis -Lyon P, Koehl P, “Application of Self Consistent Mean Field to Refinement in Protein Docking ”, June 2007 . Poster presentation at UC Davis Ge nome Center Review of Research

Francis-Lyon P, “Visualization of the Predictive Function of a Neural Network for Detecting RNA Genes”, 2002, Oral presentation at California State University Statewide Research competition.

Francis-Lyon P, “Investigation of TCGA in search of therapy target for Triple Negative Breast Cancer”, Poster presented at Molecular Medicine Tri-Conference 2018.

Francis-Lyon P, Lanka S, Navin Arbatti L, Tyagi G, Do H, “Predicting Phenotype from Genotype with Machine Learning”, Talk presented at 16th Scientific Computing with Python Conference, July 2017

Berger T, Francis-Lyon P, Parker J, Friedman P, Sengar P, Owens J, Moghaddasi A,  “Analysis of Patient-Reported Symptoms With Respect to TCS Usage: A Self-Identified Cohort of Patients With RSS/TSA/TSW”, poster and talk, American Academy of Dermatology, 75th Annual Meeting, 2017

Erin Dishington, Hai Nguyen, Michael Totagrande, Shih-Yin Chen, Meriam Vejiga, Patricia Francis-Lyon and Christina Tzagarakis-Foster, “Orphan nuclear receptor, DAX-1, expression during progressive stages of invasive ductal carcinoma”, Poster presentation at American Association for Cancer Research Annual Meeting, March 2017

Young V, Tu C, Sneha K, Francis-Lyon P and Spencer J, “Detection and Exploration of HCMV in Healthy Blood Donors”, 2016, Poster presentation at Pacific Symposium on Biocomputing

Service

Member of Board of Advisors for the Professional Science Master’s (PSM) in Biotechnology 2012 -present Faculty advisor for USF Women in Computer Science 2012 -2013

Set up collaboration between USF and Silicon Valley Internet Crimes Against Children Task Force , 2011-2013 : Set up talk by Sgt. Randy Schriefer and Detective Dave Johnson on role of the internet in child exploitation

Set up lunch meeting with Associate Dean Chris Brooks, Director of Social Justice & Community Action Enrique Bazan and others. The officers outlined areas where they would like USF assistance .

Organized a tour of the FBI computer forensics lab in Mountain View attended by 15 USF staff/students . These meetings led directly to projects f or ICAC developed by EJ Jung’s and my students.

Gave an invited talk on human trafficking at Zonta, International, Berkeley branch in 2012

Invited by Alameda County DA to attend and get the word out on Human Exploitation and Trafficking 2012 Coordinated and spoke at a Communi ty meeting on human trafficking in Berkeley Sep 2012

Volunteer for California Against Slavery 2012: towards passage of proposition 35 Ban on Human Trafficking . Freedom Summits 2011 and 2013: Bay Area resp onse to human trafficking .

Fair Trade Coordinator at UC Davis 2007 -2009 : our campus coffee house switch ed to Fair Trade beverages. Justice Task Force, First Presbyterian Church, Berkeley :

Organized a community meeting attend ed by 100+ people on child sexual exploitation in Oakland.

Set up speaking venues on human trafficking by Congolese nurse ( Global Strategies for HIV Prevention ) Organized a 6 session class on human trafficking attended by 30 people , taught 2 of the classes.

Regular contributor to Cry Justice! newsletter on justice issues.

University Ministries: co -led a small group of UC Berkeley students for First Presbyterian University Pastor

Professional Affiliations

Institute of Electrical and Electronics Engineers (IEEE) Association for Computing Machinery (ACM) International Society for Computational Biology (ISCB) Life Sciences Society (LSS)