Research Scientist

Wellesley College

Biography

I am a microbiologist and immunologist teaching and researching at Wellesley College. I use computational methods to explore the relationships between the microbiome and childhood cognitive development and to understand complex microbial communities. I also teach about the immune system and infectious disease, as well as introductory programming for biology students.

I develop software tools in the julia programming language.

Interests

  • Computational Biology
  • The Human Microbiome
  • Microbial Communities
  • Immunology
  • Julia Programming Language

Education

  • PhD in Immunology, 2014

    Harvard University

  • BS in Biochemistry and Cell Biology, 2006

    University of California, San Diego

Skills

Git

cli, github, and gitlab

Data Science

EDA, stats, and modeling

Scientific Illustration

Figures and cartoons

Experience

 
 
 
 
 

Research Scientist

Wellesley College

Jan 2018 – Present Massachusetts

Klepac-Ceraj Lab

Research Topics:

  • Human microbiome
  • Child cognitive development
  • Computational biology education
  • Diversity in STEM
  • Open source development
 
 
 
 
 

Postdoctoral Fellow

Harvard TH Chan School of Public Health

May 2017 – Dec 2018 Boston

Huttenhower Lab

Research Topics:

  • Human microbiome
  • Inflammatory arthritis
  • Computational biology education
 
 
 
 
 

Postdoctoral Fellow

University of California, San Diego

May 2014 – Jun 2017 San Diego

Dutton Lab

Research Topics:

  • Horizontal Gene Transfer
  • Microbial communities
  • Modeling interspecies interactions
 
 
 
 
 

Curriculum Fellow

Harvard Medical School

May 2014 – Jun 2017 Boston

Masters in Immunology
2014-2016

Responsibilities:

  • Course design and instruction
  • Course: Methods in Basic and Clinical Immunology
  • Course: Understanding Immunology Research
  • Masters Program administration
  • Student Mentoring

Harvard Medical School Online Learning
2016-2017

Responsibilities:

  • Course design and instruction
  • Course: HMX Fundamentals - Biochemistry

Recent Posts

Sesshin of the Original Face

The 2019 summer sesshin of Boundless Way Zen just wrapped up yesterday. I had the honor to serve as Jiki (time keeper). The water must know If it is hot
Last updated on Sep 30, 2020 1 min read

Lake Arrowhead Microbial Genomics 2018 #LAMG2018

This was my first time at the Lake Arrowhead Microbial Genomics meeting, and it was excellent! There were tons of great talks, friendly people and a beautiful location. Plus the food was fantastic, and the beer and wine were free (Jeffery Miller was insistant that this was important).
Last updated on Sep 30, 2020 1 min read

Matching Publications to PubMed IDs

Earlier this week, I got an e-mail from Lucia Santamaria from the “ Gender Gap in Science” project from the International Council for Science. They are trying to systematically measure the gender gap in a number of ways, including looking at publication records.
Last updated on Sep 30, 2020 8 min read

Getting Back on the Horse - Part 2: Deploying a new Site

Yeah, so my last post was clearly a bit too optomistic. I’ve only just now set up this new website using the Hugo static site generator and Academic theme which is pretty nifty.
Last updated on Sep 30, 2020 5 min read

Getting Back on the Horse

Well, it’s been far too long since I wrote anything here. In the mean time I’ve: completed the HMX biochemistry course Got two papers accepted ( eLife paper on HGT is out, PLoS Comp Bio paper needs some final touches) started a postdoc in the Huttenhower lab and… that seems like enough Also finally updated the header image on this site to be one of mine rather than the default.
Last updated on Sep 30, 2020 1 min read
See all posts

Projects

Horizontal Gene Transfer

Microbes sharing (stealing?) genes with (from) one another.

Microbiome.jl

A julia package for working with microbiome and microbial community data.

Women in Computational Biology

An analysis of the forces that decrease the representation of women in computational biology, and efforts to overcome them.

Recent & Upcoming Talks

Recent Publications

Quickly discover relevant content by filtering publications.

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Inflammatory bowel diseases, which include Crohn’s disease and ulcerative colitis, affect several million individuals worldwide. …
Jason Lloyd-Price, Cesar Arze, Ashwin N. Ananthakrishnan, Melanie Schirmer, Julian Avila-Pacheco, Tiffany W. Poon, Elizabeth Andrews, Nadim J. Ajami, Kevin S. Bonham, Colin J. Brislawn, David Casero, Holly Courtney, Antonio Gonzalez, Thomas G. Graeber, A. Brantley Hall, Kathleen Lake, Carol J. Landers, Himel Mallick, Damian R. Plichta, Mahadev Prasad, Gholamali Rahnavard, Jenny Sauk, Dmitry Shungin, Yoshiki Vázquez-Baeza, Richard A. White III, IBDMDB Investigators, Jonathan Braun, Lee A. Denson, Janet K. Jansson, Rob Knight, Subra Kugathasan, Dermot P. B. McGovern, Joseph F. Petrosino, Thaddeus S. Stappenbeck, Harland S. Winter, Clary B. Clish, Eric A. Franzosa, Hera Vlamakis, Ramnik J. Xavier, Curtis Huttenhower
PDF Code Dataset

Women are underrepresented in computational biology publications: An analysis of the scholarly literature in biology, computer science and computational biology

While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender …
KS Bonham, MI Stefan
PDF Code Dataset Project

Extensive horizontal gene transfer in cheese-associated bacteria

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or …
KS Bonham, BE Wolfe, RJ Dutton
PDF Code Dataset Project

Innate immune pattern recognition: a cell biological perspective.

Receptors of the innate immune system detect conserved determinants of microbial and viral origin. Activation of these receptors …
SW Brubaker, KS Bonham, I Zanoni, JC Kagan
PDF

Biochemistry of Toll-Like Receptors

Recognition of potentially pathogenic organisms is a critical first step in an immune response. To prevent pathogen outgrowth, this …
KS Bonham, JC Kagan
PDF
See all publications

Popular Topics

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