Emily E. Ackerman

Emily E. Ackerman

She/her · University of Pittsburgh

Hello! I'm a sixth year chemical engineering PhD student using network and mathematical modeling to study immunoregulation during influenza and SARS-CoV-2 infection. I'm looking for a computational postdoc position to start in Fall 2021.




I am a sixth year PhD student in the University of Pittsburgh’s chemical and petroleum engineering program. My thesis work can be divided into two areas:

  • Antiviral drug target identification using network biology
  • Dynamic modeling of the immune response to viral infection

Working at the cellular and systems level, my aim is to better understand the mechanisms driving observed immunoregulatory behavior to improve drug development. While initially using influenza A virus as the primary infection of study, I repeated network controllability studies to efficiently prioritize drug repositioning candidates for treating SARS-CoV-2 infection at the onset of the COVID-19 pandemic.

As a queer, disabled woman in STEM, I am passionate about the advancement of underrepresented populations in STEM. I have had the opportunity to perform diversity and equity work in academia with Future of Research, the TAE Consortium, and the Howard Hughes Medical Institute as a Gilliam Fellow. I am also an active advocate in the disability community for equitable access to education and technology. In my free time, I enjoy painting, union organizing with my fellow grad workers, and spending time with my cat, Poppy.

Skills

Mathematical Modeling

MCMC parameter fitting methods for ODE models of the immune response to viral infection

Network Biology

Virus-host protein networks to identify disease host factors and drug opportunities

Diversity and Equity Work

Advocacy for underrepresented populations in academia, particularly the disabled

Experience

 
 
 
 
 

Board of Directors

Future of Research

Aug 2020 – Present

Co-director of the Labor Task Force, investigating labor conditions of early career researchers

Responsibilities:

  • Perform large scale survey of workplace conditions for academic early career researchers (in progress)
  • Work with Board of Directors and Executive Board to empower junior researchers through equitable, grassroots action
 
 
 
 
 

Co-founder, Executive Board Member

TAE (Transforming Academic Ecosystems) Consortium

Jan 2020 – Present

An initiative based group of ECR’s aiming to redefine the conversation around mental health in academia, particularly by supporting the unique needs of underrepresented researchers.

Website and Social Media initiative lead

Responsibilities:

  • Hold weekly meetings to guide and act on initiatives.
  • Create and maintain website and social media
  • Organized mental health sessions at the Howard Hughes Medical Institute’s 2020 Gilliam Fellowship meeting
 
 
 
 
 

Ph.D. Candidate

Ph.D. in Chemical Engineering

Shoemaker Immunosystems Lab, University of Pittsburgh

Aug 2015 – Present Pittsburgh, PA

Experience:

  • Chemical Engineering and Systems Biology curriculum
  • President, Graduate Women in Engineering Network
  • Organizer, Graduate Student Unionization Campaign

Research accomplishments:

  • Identified host factors of influenza infection using virus-host protein network topology and controllability analyses
  • Prioritized drug repositioning candidates for SARS-CoV-2 infection using network controllability methods
  • Developed model of immune response to influenza infection and software to perform shared parameter fitting on multiple data sets.
 
 
 
 
 

Intern

Albany Molecular Research Inc. (AMRI)

Jun 2015 – Aug 2015 Rensselaer, NY

Computer-Aided Drug Discovery (CADD) department under Dr. Douglas Kitchen
Responsibilities:

  • Development of in-house docking/scoring methods for protein interactions
  • Optimization and automation of all methods for department-wide use
 
 
 
 
 

Undergraduate Researcher

Rensselaer Polytechnic Institute

May 2013 – May 2015 Troy, NY

Awarded funding to participate in the Undergraduate Research Program under Dr. Curt Breneman
Research accomplishments:

  • Identified ligands to inhibit HIV GP120-CD4 binding using high-throughput screening methods
  • Developed novel super-flexible docking/scoring method with binding site comparison in Autodock Vina and MOE
  • Assisted small team in writing an R21 NIH grant proposal
 
 
 
 
 

Undergraduate Student

B.S. in Chemical Engineering

Rensselaer Polytechnic Institute

Aug 2011 – May 2015 Troy, NY

Experience in:

  • Traditional chemical engineering curriculum
  • Process controls modeling in Simulink, Aspen Plus
  • Bioprocessing laboratory

Awards

Outstanding Ph.D. Paper, Summer 2019

Department of Chemical Engineering, University of Pittsburgh Dec 2019
A Dual Controllability Analysis of Influenza Virus-Host Protein-Protein Interaction Networks for Antiviral Drug Target Discovery

OXE Research Award, Best Oral Presentation, Chemical Engineering Department Research Day

Department of Chemical Engineering, University of Pittsburgh Feb 2019
Network Methods for Identifying Regulators of Influenza A Virus

Gilliam Fellow, Gilliam Fellowships for Advanced Studies

Howard Hughes Medical Institute Sep 2018
A graduate fellowship for underrepresented groups preparing to enter academic leadership roles to foster the development of a healthier, more inclusive academic scientific ecosystem

NSF Graduate Research Fellowship, Honorable Mention

National Science Foundation Mar 2017
A graduate fellowship which supports outstanding STEM graduate students based on broader impacts and intellectual merit

Recent & Upcoming Talks

The Accessibility and Tech Cycle

Sep 29, 2020 12:00 PM STEM and Society Lectures, Graduate Student Organizing Committee Virtual
Slides

Identifying Regulators of Infection in Virus-Host Networks

Jul 26, 2020 12:00 PM International Conference on Intelligent Systems for Molecular Biology Virtual
Video

The Accessibility Gap for Tech Users and Developers

Apr 2, 2020 1:00 PM CMU Accessibility Group Carnegie Mellon University
Slides

Network Methods for Identifying Regulators of Influenza A Virus Infection

Feb 14, 2019 10:05 AM Chemical Engineering Department Research Day University of Pittsburgh
Slides

Controllability of the Influenza Virus-Host Protein-Protein Interaction Network: Engineering Insights into Host-Virus Interactions

Feb 1, 2018 9:15 AM AICHE 2018 Pittsburgh, PA
Abstract

Publications

Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning

8 proteins are prioritized as possible drug repositioning targets for SARS-CoV-2 where two, PVR and SCARB1, are previously unexplored. Known compounds targeting these genes are suggested for viral inhibition study. Prioritized proteins in agreement with previous analysis and viral inhibition studies verify the ability of network controllability to predict biologically relevant candidates using small amounts of virus-specific data.
Emily E. Ackerman, Jason E. Shoemaker
PDF

A Dual Controllability Analysis of Influenza Virus-Host Protein-Protein Interaction Networks for Antiviral Drug Target Discovery

Identified 24 proteins as holding regulatory roles specific to the infected cell by measures of topology, controllability, and functional role. This research aims to increase the efficiency of antiviral drug target discovery using existing protein-protein interaction data and network analysis methods.
Emily E. Ackerman, John F. Alcorn, Takeshi Hase, Jason E. Shoemaker
PDF

Strain-Specific Immune Response to Influenza Virus Infection

Developed a mechanism-based mathematical model to compare the immune dynamics invoked by deadly H5N1 and moderately pathogenic H1N1 influenza viruses to aid in clinical understanding of infection severity. Results suggest that the kinetics of the immune response, specifically those related to the virus as well as those involved in interferon production, differ between H1N1 and H5N1 infections.
Emily E. Ackerman, Ericka Mochan, Jason E. Shoemaker
PDF

Network-Guided Discovery of Influenza Virus Replication Host Factors

Host factors of influenza infection are identified using a novel virus-host protein network. Interaction cascades between host proteins that directly interact with viral proteins and host factors that are important to influenza replication are enriched for signaling and immune processes. Novel host factors are validated with an siRNA screen, demonstrating that integrated virus-host networks are useful in the identification of antiviral drug target candidates.
Emily E. Ackerman, Eiryo Kawakami, Manami Katoh, Tokiko Watanabe, Shinji Watanabe, Yuriko Tomita, Tiago J. Lopes, Yukiko Matsuoka, Hiroaki Kitano", Jason E. Shoemaker
PDF

A systems and treatment perspective of models of influenza virus-induced host responses

A review of the current state of mathematical models of influenza-induced host responses. Analysis shows that the structure of current models does not allow for significant responses to increased interferon concentrations, suggesting that the current library of available published models of influenza infection does not adequately represent the complex interactions of the virus, interferon, and other aspects of the immune response.
Ericka Mochan, Emily E. Ackerman, Jason E. Shoemaker
PDF

Disability Advocacy

As a proud disabled person, I am passionate about equity for the disabled, both inside and outside of academia. I am committed to fighting the often overlooked ableism that is engrained into our institutions, particularly at the intersection of multiple marginalized identities.

A stick figure stands at the bottom of two steps to REPRESENTATION. The first is labeled 'equal access to tech for users' and the second is labeled 'Developer access to industries'
A cycle with four parts: 1. Better, more accessible tech, 2. Greater access to education, 3. More disabled people in STEM, and 4. More representation in industry

Driven by an experience with autonomous robots whose inaccessibility poses a tangible threat to the disability community, I am interested in exploring the inequity created by the inaccessibility of tech and education. I believe that representation in STEM and the design process is key, and that it must be addressed at two levels: making tech accessible for the disabled user to gain equitable access to education, and making the tech industry more accessible and supportive for disabled developers. I have given talks, written an op-ed for Bloomberg's Citylab, and been the featured story in the Financial Times (linked below).

Coming soon! Ologies and Disability Visibility Project podcast episodes

My Fight With a Sidewalk Robot. A life-threatening encounter with AI technology convinced me that the needs of people with disabilities need to be engineered into our autonomous future. An article for Citylab by Emily Ackerman

How to design AI that eliminates disability bias. An article for the Financial Times by Alicia Clegg

I am available for talks, podcasts, consulting, collaborations, and more, just ask!

Contact