Welcome to our blog! Here you can find Interesting Things including code, opinions, tutorials, links to journal articles and other good stuff.

The Center for Communicable Disease Dynamics (CCDD) is housed in the Harvard T. H. Chan School of Public Health in Boston, MA. CCDD is focused on improving methods for mathematical modeling and statistical inference on infectious disease data, engagement with policy makers to use the results of transmission dynamic studies to improve decisions, and outreach to multiple constituencies to provide education about communicable disease dynamics, tools for their analysis, and opportunities for interaction with scientists in the field.

A common theme in our research is evolution and population dynamics of viral and bacterial pathogens, with special emphasis on vaccine preventable diseases, emerging pathogens, and antibiotic resistance. In addition, we seek to address fundamental questions about host-pathogen interactions and pathogen population genetics.

A significant portion of our research involves the pneumococcus (Streptococcus pneumoniae); however, we try not to show favoritism and lab members also work on pathogens including malaria, Staphylococcus aureus, Gonococci, influenza, cholera, and others. Almost all our work involves genomic data in some form or another, which may be used for anything from empirical observations of which lineages cause disease, to parameterizing theoretical models of transmission and evolution. If you are interested in pathogen evolution, epidemiology, population genetics or genomics, we hope you find something here to interest you.


Bill Hanage

whanage@hsph.harvard.edu - @BillHanage

I’m Bill, the PI. I am a recovering British Person who has been at the Chan School since 2010. I am an Associate Professor of Epidemiology. My PhD is from Imperial College London, where I was a Reader before I moved to Boston. I am interested in a lot of things, some of which are featured in this blog.

Lauren A. Cowley

lcowley@hsph.harvard.edu - @LaurenCowley4

I’m Lauren, I am a postdoc. I am a still barely functioning British Person who fled Brexit to only find myself in Trump lead America in 2016. My PhD is from the University of Edinburgh but was based at Public Health England for 4 years. I am interested in using genomics and machine learning to look at recombination and genomewide association in the pangenome of the pneumococcus.

Taj Azarian

tazarian@hsph.harvard.edu - @EpiDemos82 - Scholar

I am Taj, a postdoctoral research fellow working in the labs of Drs. Marc Lipsitch and Bill Hanage. In 2015, I received my PhD in Epidemiology from the University of Florida, where I studied the genomic epidemiology of methicillin-resistant Staphylococcus aureus in the neonatal intensive care unit. I am largely interested in antibiotic resistant bacteria and using genomic methods to understand their transmission, evolution, and host-pathogen interactions. I am currently studying the population genomics of Streptococcus pneumoniae and the impact of the pneumococcal conjugate vaccine. As an epidemiologist who became interested in genomics and phylogenetics, I understand the challenges in becoming proficient in bioinformatic tools necessary to bridge these two fields of study. Hopefully my contributions will help others that are on this journey.

Karel Břinda

kbrinda@hsph.harvard.edu - @karelbrinda - Github - Scholar

I am Karel, a postdoctoral researcher working with Bill Hanage. In 2016, I received my PhD in computer science from University of Paris-Est in France, where I worked on efficient algorithms and data structures for Next-Generation Sequencing data, with emphasis on read mapping and metagenomic classification. In general, I am interested in bioinformatics, computer science and antibiotic resistance. I am currently working on a Bill & Melinda Gates Foundation funded project to develop a system for surveillance of antibiotic resistance that interrogates a continuously updated database of sequence elements, to determine the risk a clinical specimen contains a resistant pathogen.

Michael Martin


I’m Mike, a second year Infectious Disease Epidemiology Master of Science student at the Chan School. I studied Biophysics as an undergrad at Johns Hopkins, but developed an interest in public health while working as an analyst at IMS Health. I am just begining to learn bioinformatics and am interested in the use of Next-Generation Sequencing data, along with traditional epidemiology, to better understand the transmission of pathogens, particularly Tuberculosis.