Alex Valm

Alex Valm

Assistant Professor
Department of Biological Sciences
The RNA Institute

PhD, Brown University

Alex Valm

Valm Lab

Areas of Interest

  • Biophysics, cell and molecular biology
  • Structure-function relationships in the human microbiome
  • Microbial community assembly
  • Advanced imaging technologies
  • Computational analysis of complex community structure



My laboratory is interested in the relationship between structure and function in the human microbiome; especially how the physical structure of human associated-microbial communities influence health and disease. We use the human oral microbiome as a model system for studying microbial community structure and assembly because it is well-studied and accessible. We combine molecular and DNA sequencing approaches to understand what organisms, genes and potential functions are present in a community and we use advanced imaging technologies to map the spatial distribution of organisms within their environments. With our collaborators in the Biology department as well as outside the UAlbany community we study the systems level spatial structure of oral microbial biofilms in animal models and humans. We combine this discovery based research with hypothesis testing using in vitro culture systems. A second major focus of the lab is to further develop imaging technologies to expand the number of identifiable objects in a microbial sample as well as the development of computational tools for analysis of community structure.


  • A.M. Valm, S. Cohen, W. Legant, J. Melunis, U. Hershberg, E. Wait, A.R. Cohen, M. Davidson, E. Betzig, J. Lippincott-Schwartz. 2017.  Applying systems-level spectral imaging and analysis to reveal the organelle interactome. Nature 546:162-167.
  • R.J. Palmer, Jr., N. Shah, A. Valm, B. Paster, F. Dewhirst, T. Inue, J.O. Cisar. 2017.  Complementary molecular and phenotypic characterization of an oral bacterial biofilm community in two individuals. Applied Environ. Microbiol. 83:(11). pii:e00407-17.
  • A.M. Valm, R. Oldenbourg, G.G. Borisy. 2016. Multiplexed spectral imaging of 120 different fluorescent labels. PLoS One 11(7): e0158495. 
  • A.M. Valm, J.L. Mark Welch, R. Oldenbourg, and G.G. Borisy. 2011. CLASI-FISH: Principles of Combinatorial Labeling and Spectral Imaging for greatly expanding the number of distinguishable microbes in a single image.  Syst. Appl. Microbiol35(8):496-502. 
  • A.M. Valm, J. Mark Welch, C.W. Rieken, Y. Hasegawa, M.L. Sogin, R. Oldenbourg, F.E. Dewhirst, G.G. Borisy. 2011. From the Cover: Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging. Proc Natl Acad Sci USA 108(10):4152-7. 
  • Y. Hasegawa, J. Mark Welch, A.M. Valm, C.W. Rieken, M.L. Sogin, G.G. Borisy. 2010. Imaging marine bacteria with unique 16S rRNA V6 sequences by fluorescence in situ hybridization and spectral analysis. Geomicrobiology J. 27(3):251-260. 
  • Braun, K.M., T. Cornish, A. Valm, J. Cundiff, J.L. Pauly, and S. Fan. 1998. Immunotoxicology of cigarette smoke condensates: Suppression of macrophage responsiveness to interferon-gamma. Toxicol. Appl. Pharmacol149:136-43.