Deanne M. Taylor, PhD

faculty photo
Research Assistant Professor of Pediatrics
Director, Bioinformatics Group, Children's Hospital of Philadelphia, Department of Biomedical and Health Informatics, University of Pennsylvania
Department: Pediatrics

Contact information
Children's Hospital of Philadelphia
Biomedical and Health Informatics
3535 Market Street, Suite 1024
Philadelphia, PA 19104
Education:
AA (General Studies, Honors)
North Shore Community College, 1991.
BA (Physics, Astronomy)
Wellesley College, 1995.
MS (Biophysics)
University of Michigan, 1998.
PhD (Biophysics)
University of Michigan, 2001.
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Description of Research Expertise

Translational Computational Biology: Development of bioinformatics methods using mathematical and computational approaches to better understand the genetic contribution of biological variation to disease, coupling clinical information with high-dimensional biomedical data from next-gen sequencing, microarray, PCR, and proteomics experiments.

Computational Systems Biology: approaches to understanding the effects of genetic variation on developing biological systems through analysis of functional genomics studies and associated contributions to disease. Modeling of biological systems.

Bioinformatics: Machine-learning methods development and use. Next-generation sequence analysis. Microarray analysis. Database and knowledge management and data mining.

Genetics and genomics of development and reproduction.

Selected Publications

Francisco J. Enguita, Ana Lúcia Leitão, J. Tyson McDonald, Viktorija Zaksas, Saswati Das, Diego Galeano, Deanne Taylor, Eve Syrkin Wurtele, Amanda Saravia-Butler, Stephen B. Baylin, Robert Meller, D. Marshall Porterfield, Douglas C. Wallace, Jonathan C. Schisler, Christopher E. Mason, Afshin Beheshti: The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response. Theranostics Jul 2022 Notes: Role: Data analysis, writing, review. In press. doi:10.7150/thno.73268.

Tianyu Cai, Agnès Gouble, Kathryn L Black, Anna Skwarska, Ammar S Naqvi, Deanne Taylor, Ming Zhao, Qi Yuan, Mayumi Sugita, Qi Zhang, Roman Galetto, Stéphanie Filipe, Antonio Cavazos, Lina Han, Vinitha Kuruvilla, Helen Ma, Connie Weng, Chang-Gong Liu, Xiuping Liu, Sergej Konoplev, Jun Gu, Guilin Tang, Xiaoping Su, Gheath Al-Atrash, Stefan Ciurea, Sattva S Neelapu, Andrew A Lane, Hagop Kantarjian, Monica L Guzman, Naveen Pemmaraju, Julianne Smith, Andrei Thomas-Tikhonenko, Marina Konopleva: Targeting CD123 in blastic plasmacytoid dendritic cell neoplasm using allogeneic anti-CD123 CAR T cells. Nature Communications 13(1): 1-11, Apr 2022 Notes: Role: Senior bioinformatics analyst on the project. Oversight, methods development, and paper review.

Guy Karlebach, Bruce Aronow, Stephen B Baylin, Daniel Butler, Jonathan Foox, Shawn Levy, Cem Meydan, Christopher Mozsary, Amanda M Saravia-Butler, Deanne M Taylor, Eve Wurtele, Christopher E Mason, Afshin Beheshti, Peter N Robinson: Betacoronavirus-specific alternate splicing. Genomics 114(2): 110270, Mar 2022.

Alexa A Woodward, Deanne M Taylor, Elizabeth Goldmuntz, Laura E Mitchell, AJ Agopian, Jason H Moore, Ryan J Urbanowicz: Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. BioData Mining 15(1): 1-16, Feb 2022 Notes: Role: Bioinformatics analyst, generated all data and aided in analysis, paper review, conception of the project.

Nadir Yehya, Hossein Fazeliniah, Deanne M Taylor, Gladys Gray Lawrence, Lynn A Spruce, Jill M Thompson, Susan S Margulies, Steven H Seeholzer, G Scott Worthen: Differentiating septic children with and without acute respiratory distress syndrome using proteomics. American Journal of Physiology-Lung Cellular and Molecular Physiology 322: L365–L372, Jan 2022 Notes: Role: Senior bioinformatics analyst, generated all machine-learning, visualization and analysis code, produced all figures, and aided in analysis, paper writing, review, conception of the project.

J Tyson McDonald, Francisco Javier Enguita, Deanne Taylor, Robert J Griffin, Waldemar Priebe, Mark R Emmett, Mohammad M Sajadi, Anthony D Harris, Jean Clement, Joseph M Dybas, Nukhet Aykin-Burns, Joseph W Guarnieri, Larry N Singh, Peter Grabham, Stephen B Baylin, Aliza Yousey, Andrea N Pearson, Peter M Corry, Amanda Saravia-Butler, Thomas R Aunins, Sadhana Sharma, Prashant Nagpal, Cem Meydan, Jonathan Foox, Christopher Mozsary, Bianca Cerqueira, Viktorija Zaksas, Urminder Singh, Eve Syrkin Wurtele, Sylvain V Costes, Gustavo Gastão Davanzo, Diego Galeano, Alberto Paccanaro, Suzanne L Meinig, Robert S Hagan, Natalie M Bowman, Matthew C Wolfgang, Selin Altinok, Nicolae Sapoval, Todd J Treangen, Pedro M Moraes-Vieira, Charles Vanderburg, Douglas C Wallace, Jonathan Schisler, Christopher E Mason, Anushree Chatterjee, Robert Meller, Afshin Beheshti, UNC COVID-19 Pathobiology Consortium: Role of miR-2392 in Driving SARS-CoV-2 Infection. Cell Reports. Cell Press, Page: doi: 10.1101, Aug 2021 Notes: Role: Analysis, writing, review.

Fadi I Musfee, AJ Agopian, Elizabeth Goldmuntz, Hakon Hakonarson, Bernice E Morrow, Deanne M Taylor, Martin Tristani-Firouzi, W Scott Watkins, Mark Yandell, Laura E Mitchell: Common Variation in Cytoskeletal Genes is Associated with Conotruncal Heart Defects. Genes 12(5): 655, Jun 2021 Notes: Role: Senior bioinformatician, data management, analysis of array data. Paper review.

Florence T Bourgeois, Alba Gutiérrez-Sacristán, Mark S Keller, Molei Liu, Chuan Hong, Clara-Lea Bonzel, Amelia LM Tan, Bruce J Aronow, Martin Boeker, John Booth, Jaime Cruz Rojo, Batsal Devkota, Noelia García Barrio, Nils Gehlenborg, Alon Geva, David A Hanauer, Meghan R Hutch, Richard W Issitt, Jeffrey G Klann, Yuan Luo, Kenneth D Mandl, Chengsheng Mao, Bertrand Moal, Karyn L Moshal, Shawn N Murphy, Antoine Neuraz, Kee Yuan Ngiam, Gilbert S Omenn, Lav P Patel, Miguel Pedrera Jiménez, Neil J Sebire, Pablo Serrano Balazote, Arnaud Serret-Larmande, Andrew M South, Anastasia Spiridou, Deanne M Taylor, Patric Tippmann, Shyam Visweswaran, Griffin M Weber, Isaac S Kohane, Tianxi Cai, Paul Avillach, James R Aaron, Giuseppe Agapito, Adem Albayrak, Mario Alessiani, Danilo F Amendola, François Angoulvant, Li LLJ Anthony, Andrew Atz, James Balshi, Brett K Beaulieu-Jones, Douglas S Bell, Antonio Bellasi, Riccardo Bellazzi, Vincent Benoit, Michele Beraghi, José Luis Bernal Sobrino, Mélodie Bernaux, Romain Bey, Alvar Blanco Martínez, Silvano Bosari, Robert L Bradford, Gabriel A Brat, Stéphane Bréant, Nicholas W Brown, William A Bryant, Mauro Bucalo, Anita Burgun, Mario Cannataro, Aldo Carmona, Charlotte Caucheteux, Julien Champ, Krista Chen, Jin Chen, Luca Chiovato, Lorenzo Chiudinelli, James J Cimino, Tiago K Colicchio, Sylvie Cormont, Sébastien Cossin, Jean B Craig, Juan Luis Cruz Bermúdez, Arianna Dagliati, Mohamad Daniar, Christel Daniel, Anahita Davoudi, Julien Dubiel, Scott L DuVall, Loic Esteve, Shirley Fan, Robert W Follett, Paula SA Gaiolla, Thomas Ganslandt, Lana X Garmire, Tobias Gradinger, Alexandre Gramfort, Romain Griffier, Nicolas Griffon, Olivier Grisel, Christian Haverkamp, Bing He, Darren W Henderson, Martin Hilka, John H Holmes, Petar Horki, Kenneth M Huling, Anne Sophie Jannot, Vianney Jouhet, Ramakanth Kavuluru, Katie Kirchoff, Ian D Krantz, Detlef Kraska, Ashok K Krishnamurthy, Sehi L'Yi, Trang T Le, Judith Leblanc, Andressa RR Leite, Guillaume Lemaitre, Leslie Lenert, Damien Leprovost, Ne Hooi Will Loh, Kristine E Lynch, Sadiqa Mahmood, Sarah Maidlow, Alberto Malovini, Anupama Maram, Patricia Martel, Aaron J Masino, Michael E Matheny, Thomas Maulhardt, Maria Mazzitelli, Michael T McDuffie, Arthur Mensch, Marianna Milano, Marcos F Minicucci, Jason H Moore, Cinta Moraleda, Jeffrey S Morris, Michele Morris, Sajad Mousavi, Danielle L Mowery, Douglas A Murad, Thomas P Naughton, James B Norman, Jihad Obeid, Marina P Okoshi, Karen L Olson, Nina Orlova, Brian D Ostasiewski: International Analysis of Electronic Health Records of Children and Youth Hospitalized With COVID-19 Infection in 6 Countries. JAMA network open. American Medical Association, 4(6): e2112596-e2112596, Jun 2021 Notes: Role: Senior bioinformatician, leading analyses on medical record analyses and reviews for the CHOP component of the paper.

Omobola O Oluwafemi, Fadi I Musfee, Laura E Mitchell, Elizabeth Goldmuntz, Hongbo M Xie, Hakon Hakonarson, Bernice E Morrow, Tingwei Guo, Deanne M Taylor, Donna M McDonald-McGinn, Beverly S Emanuel, AJ Agopian: Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States. Genes 12(7): 1030, Jun 2021 Notes: Role: Senior bioinformatician. Analysis, mentoring, writing, reviews.

Eliah G Overbey, Amanda M Saravia-Butler, Zhe Zhang, Komal S Rathi, Homer Fogle, Willian A da Silveira, Richard J Barker, Joseph J Bass, Afshin Beheshti, Daniel C Berrios, Elizabeth A Blaber, Egle Cekanaviciute, Helio A Costa, Laurence B Davin, Kathleen M Fisch, Samrawit G Gebre, Matthew Geniza, Rachel Gilbert, Simon Gilroy, Gary Hardiman, Raul Herranz, Yared H Kidane, Colin PS Kruse, Michael D Lee, Ted Liefeld, Norman G Lewis, J Tyson McDonald, Robert Meller, Tejaswini Mishra, Imara Perera, Shayoni Ray, Sigrid Reinsch, Sara Brin Rosenthal, Michael Strong, Nathaniel J Szewczyk, Candice GT Tahimic, Deanne M Taylor, Joshua P Vandenbrink, Alicia Villacampa, Silvio Weging, Chris Wolverton, Sarah E Wyatt, Luis Zea, Sylvain V Costes, Jonathan M Galazka: NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data. iScience 24(4): 102361, March 2021 Notes: Role: Project involvement, discussion, writing, review.

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Last updated: 07/27/2022
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