Jonathan Livny, PhD


Senior Fellow – Biology

Advises academic, business, and governmental clients on how to analyze and resolve complex challenges rooted in microbiology, with a focus on the development and scaling of methods for generating and interpreting high-throughput sequencing data to better understand, diagnose, and treat infectious diseases.
Boston Health Insurance

About Jonathan:


A highly accomplished wet-lab and computational researcher, Jonathan brings together a notable breadth and depth of biology knowledge with a demonstrated savvy for team leadership to help his clients develop and implement high-throughput methodologies to detect and classify diverse microbes and characterize the key factors that influence the impact of microbial pathogens on human health.


Jonathan’s unique expertise stems from his deep foundational knowledge of microbial genetics and pathogenesis, his training and experience in bioinformatics, and his extensive work designing, optimizing, and scaling complex wet-bench and data analysis workflows. This diverse, inter-disciplinary background enables Jonathan to both understand the fundamental principles underlying key challenges in the fields of microbiology and infectious diseases and to devise and execute innovative, systematic approaches to overcome these challenges.


Jonathan’s research career has spanned over two decades, advancing efforts to combat numerous infectious diseases, including tuberculosis, cholera, Lyme disease, and COVID-19, and driving the development of a new generation of rapid diagnostics for microbial pathogens. He is a consummate collaborator, with a long track record of working within multidisciplinary teams of world-class scientists to tackle real-world problems with cutting-edge solutions. Moreover, as a pioneer and leader in the field of microbial transcriptomics, Jonathan has also provided expert advice and guidance on experimental design and data analysis to scientists around the world. He has an extensive and distinguished publication record, has received several NIH awards and subawards, has served on multiple NIH review panels, and is an oft-invited speaker at universities and academic conferences around the world.


When not helping Welltide clients, Jonathan serves as senior research scientist and senior group leader at the Broad Institute of MIT and Harvard, where he co-directs the Microbial Omics Core in the Infectious Disease and Microbiome Program and heads the Technology Core of the Broad Institute’s Genomic Center for Infectious Diseases. Other consulting clients include Gingko Bioworks and Biobot.



Cell, Molecular, and Microbiology

  • Culturing and characterizing diverse bacteria
  • Implementing a wide variety of techniques for genetic manipulation of microorganisms
  • Devising innovative molecular biology methods for next-generation sequencing applications



  • Comparative transcriptomics and gene discovery by RNA-Seq
  • Design of oligonucleotides for hybridization-based detection and/or amplification of target sequences
  • Development and deployment of data and sample tracking infrastructures


Lab Process and Optimization

  • Extraction of nucleic acids from a wide variety of sample types
  • Generation of whole genome, cDNA, and amplicon libraries for diverse next generation sequencing platforms
  • Targeted nucleic acid enrichment and depletion
  • Streamlining, parallelization, and automation of sequencing library construction and serology protocols


Public Health

  • Scaling sample processing and data generation workflows for genomic surveillance of malaria and COVID serology

Past Experiences:


The Broad Institute; Cambridge, MA

Senior Group Leader, Infectious Disease & Microbiome Program (current)


Brigham and Women’s Hospital / Harvard Medical School; Boston

Postdoctoral Research Fellow


Tufts University School of Medicine; Boston

Postdoctoral Research Fellow



University of Michigan, Ann Arbor

PhD, Cell and Molecular Biology


University of Wisconsin, Madison

Bachelor of Science, Molecular Biology