Emily E. Ackerman

Emily E. Ackerman

She/her · Harvard Medical School

Hello!! I'm a postdoctoral researcher with the Lahav Lab in the systems biology department at Harvard Medical School. My focus lies in developing computational methods to understand the role of p53 protein dynamics in determining cell fate. Previous work includes network and mathematical modeling of immunoregulation during influenza and SARS-CoV-2 infection.




I joined Galit Lahav’s lab as a postdoctoral researcher in the systems biology department at Harvard Medical School in September 2021. My research uses computational methods to understand the connection between single cell p53 protein dynamics and transcriptomic profiles in cell fate decisions.

My PhD work at the University of Pittsburgh’s chemical and petroleum engineering program can be divided into two computational areas that address both influenza A virus and SARS-CoV-2 infection: antiviral drug target identification using network biology and dynamic modeling of the immune response to viral infection. This work at both the cellular and systems level aimed to better understand the mechanisms driving observed immunoregulatory behavior to improve drug development.

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 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

 
 
 
 
 

Postdoctoral Researcher

Lahav Lab, Harvard Medical School

Sep 2021 – Present Boston, MA
Exploring the connection between single cell p53 signalling dynamics and transcriptomics
 
 
 
 
 

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 – Aug 2021 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 Research Assistant

Swanson School of Engineering, University of Pittsburgh Apr 2021

Dr. James Coull Memorial Fellowship Award

Department of Chemical Engineering, University of Pittsburgh Feb 2021
Awarded annually to one senior Ph.D. student

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

Accessibility and The Crowded Sidewalk: Micromobility's Impact on Public Space

Over the past several years, micromobility devices—small-scale, networked vehicles used to travel short distances—have begun to pervade cities, bringing promises of sustainable transportation and decreased congestion. Drawing on interviews with disabled activists, government officials, and commercial representatives, we chart how devices and policies co-evolve to fulfill municipal sustainability goals, while creating obstacles for people with disabilities whose activism has long resisted inaccessible infrastructure. We reflect on efforts to redistribute space, institute tech governance, and offer accountability to those who involuntarily encounter interventions on the ground.
Cynthia Bennett, Emily E. Ackerman, Bonnie Fan, Jeffrey Bigham, Patrick Carrington, Sarah Fox
PDF

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
See all publications

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.

Writings and Interviews

(Photos are links)

Disability and Design

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

Redefining Accessibility in Design with Disabilities Advocate Emily Ackerman. Girlboss Radio.

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

On Living Disabled

Disability Visibility Project. Posted November 29, 2020. Podcast. Episode 91: Disabled Engineers

Disability Visibility Project. My Year of Nothing but Everything. Living in Pennsylvania During COVID-19. Emily Ackerman

Valuing Disabled Voices in STEM Workshop

In May 2021, I had the privilege of hosting a workshop to highlight the experiences and research of disabled academics. Talks included Dr. Cassandra McCall of Utah State University, Cynthia Bennett of CMU and Apple, and Ashley Shew of Virginia Tech as well as a disabled student panel.

A photo of Emily with the Ologies podcast logo.

Contact