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William S. Barnes



Coordinator Molecular Biology/Biotechnology Program


BS Biology, Marietta College

PhD University of Massachusetts, Amherst


(W):  (814) 393-2559


Office:  RM 351 STC



Professional Associations


Pennsylvania Academy of Sciences

Courses Taught

BIOL 201 Genetics

BIOL 404 Genomics and Bioinformatics

Research Interests

In the past, my research interests have been in the area of Nutritional Carcinogenesis and the Molecular Biology of Pollen, but I am now refocusing on Computational Biology and Bioinformatics.

A current interest is the relationship between amino acid conservation over evolutionary time and importance to protein function. Presumably evolutionary conservation should be diagnostic for function, but like all other assays and tests, the sensitivity, specificity,  positive and negative predictivity must be determined. Proteins such as alpha and beta hemoglobin, lysozyme and the histones provide good validation models because their structure-function relationships have been well studied. Hemoglobin provides an especially interesting test case because it has been studied intensively at both the atomic level by Physical Chemists, and at the organismal level by Physicians. However there has been little effort to see that the results are consistent with each other, or with what is known of molecular function at the level of the cell. Preliminary indications are that amino acid conservation is not always a good negative or positive predictor of function, which is perhaps not surprising considering that not much effort has been made to reconcile these two research traditions. The failure of negative predictivity may be especially useful because it implies regions of functional importance at the cellular and organismal level, which have not received attention at the atomic level, but may inform the mechanism of cooperativity.

A current difficulty in the field of Genomics is that the technical capacity to sequence DNA has far outstripped the capacity to analyze it. As a result there are now many whole genomes which have been annotated by computer, but still need to be inspected by humans. For this reason the Joint Genome Institute of DOE has instituted a program in which undergraduate institutions "adopt" a genome which is then annotated by faculty and students. This is a project I intend to pursue in the coming year.

Recent Publications

Barnes, WS. (2009) Introduction to dot plots using Dotlet, a java application for pair-wise sequence alignments. Computational Science Education Reference Desk (CSERD). Submitted.

Barrnes WS.. (2009) Study guides for DNA tutorial and Hemoblobin tutorial in JMOL. Submitted

"Banjo O.  (2007  )Genetic analysis of environmental plasmids isolated from the Clarion River", M.S. thesis, Clarion University.

Barnes, W.S. and Murray J.,  (2006) A Hypertextbook of Computational Biology", Vermont Genetics Network, Burlington VT. 

Anderson, J.R., W.S. Barnes, and P. Bedinger (2002) The effect of 2,6-Dichlorobenzonitril, an inhibitor of cellulose biosynthesis, on the in vitro growth of petunia and lily pollen tubes, Journal of Plant Physiology 159: 62-67

Stratford, S., W. Barnes, D.L. Hohorst, J.G. Sagert, A. Golubiewski, A.M. Showalter, S. McCormick, R. Cotter and P. Bedinger (2001) A leucine-rich repeat region is conserved in pollen extensin-like (Pex) proteins in monocots and dicots. Plant Molecular Biology 46: 43-56

Bedinger, P., DL. Hohorst, S. Stratford, W. Barnes, J.G Sagert, R. Cotter, A. Golubiewski, J.R. Anderson and S. McCormick (2001) Extensin chimeras in the pollen extracellular matrix: possible role in cell-cell communication. In Cell Biology of Plant and Fungal Tip Growth, NATO Science Series, A. Geitmann, M. Cresti, I.B. Heath, eds., IOS press, pg 171-186

Barnes WS (1999) Response to David Miller, "Being an Absolute Skeptic", Letter to Sciences Compass, Science 285:200.