Emily R. Miraldi, PhD
Associate Professor

The Divisions of Immunobiology and Biomedical Informatics

Email: emily.miraldi@cchmc.org
Phone: 513-517-2063

Learn more about Emily via her bio page, including research interests, biography, education and training. 

View publications on Google Scholar.

Joe Wayman, PhD
Postdoctoral Research Fellow

Email: joseph.wayman@cchmc.org

Cellular behavior is determined by highly regulated control over gene expression, whose malfunction gives rise to many diseases. My research in the Miraldi Lab at Cincinnati Children’s Hospital focuses on building computational models of these so-called gene regulatory networks, helping us better understand and treat immune disease. We leverage state-of-the-art genomics datasets that provide snapshots of the inner workings of single cells, allowing us to investigate the biological programs that code cell function. Our current work focuses on age-related changes in T cell immunity as well as the factors driving autoimmune liver disease.

Anthony Bejjani
Molecular Developmental Biology PhD Candidate
Email: anthony.elbejjani@cchmc.org

I am a graduate student in the molecular and developmental biology (MDB) PhD program at the University of Cincinnati / Cincinnati Children’s Hospital Medical Center. My current project aims to understand and model patient-specific response of airway epithelial cells to influenza A viral infection using a combination of high-throughput genomics, bioinformatics, and machine learning. I am interested in the interplay between immune non-immune cells during autoimmunity, and the role of immune cells during sterile inflammation. Coming from a purely experimental background, joining the Miraldi lab has been challenging, but my research thus far and the support of everyone in the lab has exposed me to concepts in mathematics, genomics, and bioinformatics which have allowed me to evolve into a well-rounded computational biologist.

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Alexander Katko
Immunology PhD Candidate (MSTP)
Email: alexander.katko@cchmc.org

I am a MD / PhD student currently in the immunology PhD program at Cincinnati Children’s Hospital Medical Center and the University of Cincinnati. I am interested in combining the powers of computational and biological tools to study the etiology of autoimmune diseases. Juvenile idiopathic arthritis (JIA) is one such disease that has a large impact on the quality of life of both children and adults. I plan to use data directly from patients (gene expression, chromatin accessibility, chromosome conformation) in order to build transcription factor gene interaction models. These models can be used to produce novel, testable predictions about the genetic drivers of the disease.

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Phuc Nguyen, Undergraduate Researcher

Email: Phuc.Nguyen@cchmc.org

I am Phuc Nguyen, an undergraduate student at the University of Cincinnati majoring in Biomedical Engineering and Computer Science. I am interested in applying computational statistical and deep learning-based models to understand gene regulation from high-throughput sequencing data. My research project in the Miraldi lab involves improving maxATAC, a deep learning model for cell type-specific transcription factor binding predictions. I worked on creating a novel maxATAC transformer architecture, benchmarking maxATAC on new primary cell types, discovering TF binding motifs with gradient saliency methods, and integrating bulk, single-cell ATAC-seq, and nucleosome positioning for better binding predictions.

View publication on Google Scholar.

Seyifumni Owoeye
Student
Email: seyifumni.owoeye@cchmc.org

Faiz Rizvi
Systems Biology and Physiology PhD Program

Email: rizvifw@mail.uc.edu

I am a graduate student in the Systems Biology and Physiology PhD program at the University of Cincinnati. I am interested in using machine learning algorithms as well as deep learning techniques to develop a more genetically aware model (accounting for the fundamental diploid nature of human genetics) and predict context-specific epigenetic states. My research interests include mathematical & computational biology as well as bioinformatics and genomics.

Akshata Rudrapatna, Biomedical Informatics PhD Candidate (MSTP)
Email: rudrapan@mail.uc.edu

I am an MD/PhD student at the University of Cincinnati currently pursuing my PhD in Biomedical Informatics. My research interests include mathematical and computational modeling of biological systems, and I am particularly interested in the role of stochasticity in biological phenomena. My current research focuses on improving predictions of transcription factor (TF) binding sites using deep neural network models (i.e., via the maxATAC software, previously designed by the Miraldi Lab). Among other applications, this work will help us understand how mutations of DNMT3A and TET2 impact DNA methylation, TF binding and gene expression. DNMT3A and TET2 are two genes implicated in a disorder known as clonal hematopoiesis of indeterminate potential – so we can ultimately better understand this condition through this project.

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Zi Yang
Molecular Developmental Biology PhD Candidate
Email: zi.yang@cchmc.org

My research focuses on utilizing system biology principles to understand autoimmune liver disease, specifically I’m working on translational collaboration (co-advised by Dr. Alexander Miethke) involving genomics analysis of human patient liver biopsies and a mouse model of liver injury and fibrosis. Based on single cell genomics and population-level genomics data, we’ll cross-compare cellular gene expression patterns, decipher cell-cell communication networks and construct gene regulatory networks to understand mechanisms of autoimmune liver disease.

View publications on Google Scholar.

Nada Abdalla
Fulbright Scholar, Masters in Immunology

I am a Fulbright Scholar pursuing a masters in immunology. My thesis research focuses on innate lymphoid cells (ILC), their impact on other immune cells and the microenvironment. I’m currently building a human ILC transcriptional regulatory network model to identify how transcription factors control gene expression and key ILC functions.

Current position: Graduate student in the immunology PhD program at Washington University in St. Louis

Jordan Aron
Summer 2017 Student Intern

I am currently a senior at Carleton College and will graduate in the spring of 2018 with a degree in mathematics. During my time in the Miraldi lab, I worked to model single-cell RNA-seq data and build transcriptional regulatory networks. 

Current position: Biostatistics PhD Program at the University of Minnesota

Tareian Cazares
Immunology PhD Candidate

I am a graduate student in the Immunology PhD program at Cincinnati Children’s Hospital Medical Center and the University of Cincinnati. My research focuses on developing computational methods to study how genomic regulation contributes to cellular behavior in rare immune cell types. Currently, I am working with a team of interdisciplinary scientists on a project called maxATAC. MaxATAC is a computational method that utilizes state-of-the-art machine-learning methods to predict transcription factor binding across cell types using ATAC-seq data and DNA sequence. Our plans are to use maxATAC to predict transcription factor binding in rare cell populations, like those derived from patient biopsies, where experimental ChIP-seq is not feasible. My time in the Miraldi lab has challenged me to grow academically and exposed me to concepts in computational biology, machine learning, genomics, immunology-based systems biology, mathematics, and engineering.

Current Position: Postdoctoral Fellow at Eli Lilly

Peter DeWeirdt
Summer 2018 Student Intern

I graduated from  Hamilton College in 2018 with a degree in mathematics and a minor in computer science. As a summer intern in the Miraldi lab, I inferred transcriptional regulatory networks from multiple data sources by using a multitask machine learning algorithm. I am currently working at the Broad Institute to work on their genetic perturbation platform.

Current position: Computational Associate at the Broad Institute at MIT and Harvard

Tianyi (Ethan) Li
Summer Undergraduate Research Fellow and Medical Sciences Program

I am an undergraduate student attending the University of Cincinnati studying medical sciences. My research focused on inferring gene regulatory models that incorporate motif information from transcription factors that bind as dimers. Currently, I am working on modeling gene regulatory networks for epithelial response to influenza virus. My research interests include genomics and bioinformatics.

Diep H. Nguyen
Summer 2017 Student Intern

I graduated from Oberlin College with a major in Biology and minor in Computer Science. I am interested in systems biology, particularly in high-dimensional genomics data and mathematical / computational models of complex biological systems. In the Miraldi lab at Cincinnati Children’s Hospital, my research focused on development of methods for inference of  transcriptional regulatory networks from single-cell RNA-seq (scRNA-seq) data. Using T Helper 17 cells as a model system, I benchmarked different statistical methods to normalize scRNA-seq data matrices and transcriptional regulatory network frameworks, evaluating quality of network inference using gold-standard interactions from knock-out and ChIP-seq studies.

Current position: Computational and Systems Biology PhD Program at Massachusetts Institute of Technology

Ronald C. Taylor, PhD
The Divisions of Immunobiology and Biomedical Informatics

I served as a senior computational biologist and bioinformatician in the Miraldi lab, leaving in June 2018 for a position at the National Institutes of Health (NIH), where I work as a bioinformatics advisor in the High Performance Computing and Informatics Office, Center for Information Technology (CIT), on the main NIH campus in Bethesda, MD. I develop software, perform analysis and modeling, and provide general bioinformatics support for intramural NIH researchers.

Education

Ph.D., Bioinformatics, George Mason University; M.S., Biology, Case Western Reserve University (CWRU); M.S., Computer Engineering, CWRU; B.S., Physics, CWRU

Specialties

Computational biology, systems biology, large-scale analytics and HPC (e.g., Hadoop, Spark), next gen sequencing analysis (RNA-seq, de novo assembly), reconstruction of biological networks, algorithms for inference of regulatory networks, metabolic modeling, gene expression analysis, metatranscriptomics, automated reasoning and machine learning, database and data warehouse design.

Publications

Journal articles, conference papers and additional background information can be found at:

• NCBI / NIH Bibliography
• ORCiD
• ResearchGate
• LinkedIn
• Google Scholar

Current position: Supervisory Biologist (Bioinformatics, GS-15) at the National Cancer Institute