33 years at UW-Madison

Blog series

This June 2019 marked my 33 years at UW-Madison when I joined Prof. Paul Kaesberg‘s lab as a PostDoc to learn the then new methods of “cloning and sequencing” (i.e. Sanger sequencing.)

In this blog I will share memories and stories, images and perhaps (probably useless) software code… as often people ask me “how” or “why” I do what I do… and how I changed from being a Bench Scientist to a biologist using computing.

These will not necessarily be in chronological order.


Shortly after I joined the “Biophysics” Institute, Prof. Paul Kaesberg was instrumental in converting this institute as a founding member to create the Institute for Molecular Virology (IMV.)

For 28 years I was in whole or in part staff of this Institute first under Paul Kaesberg, and then with Prof. Roland Rueckert and Prof. Ann Palmenberg as mentors. In 1996 my position was split with the UW-Biotechnology Center and in 2014 the IMV portion transferred to the Biochemistry Department.

While I originally came to Madison as a bench scientist, my interest for computers and computing was already anchored in my interests while I was still a student at the Grenoble outstation of the European Molecular Laboratory (EMBL.) There I already used the “Genetics Computer Group” (GCG) software for sequence analysis on a digital company VAX computer and dabbed with BASIC programming.

My Ph.D. thesis was primarily an analysis of RNA-Protein interactions within the Brome Mosaic Virus (BMV) and that was a key element that brought me to Madison as this simple 3-genes plant virus was thoroughly studied in Paul Kaesberg’s lab at Biohysics. Paul Kaesberg, Ranjit Dasgupta and Paul Ahlquist were my heroes as they had already published a few papers detailing the RNA sequence of the BMV genome.

Prior to the “revolution” of RNA/DNA Sanger sequencing, Joseph Paul Moosic,  a Ph.D. student with Paul Kaesberg had painstakingly sequenced the BMV coat protein at the protein level with Edman methods. His thesis was published in 1978 The primary structure of brome mosaic virus coat protein which Prof Kaesberg had kindly mailed to me in France.

My other heroes “in America” were the structural biologists Michael Rossmann and Steve Harrison. In other posts I’ll share some work derived from interactions with Jack Johnson and Michael Rossmann via the Purdue/Wisconsin annual joint meetings. One of these, a software from Michael Rossmann, was a key ingredient to my later development of my now “famous” virus particle visualizations that later lead to the creation of Virusworld.

But that will require more posts!

JYS – Aug 27, 2019


“Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication.”
Ahlquist P.G., Dasgupta R., Kaesberg P.
J. Mol. Biol. 1984:369-383(1984) [PubMed] [Europe PMC] [Abstract]


“Primary structure of brome mosaic virus coat protein.”

Virology. 1983 Sep;129(2):517-20.