Sofia Publications

National Human Genome Research Institute

National Institutes of Health
U.S. Department of Health and Human Services


Heidi J. Sofia, Ph.D., M.P.H.

Program Director, The Cancer Genome Atlas
Division of Genomic Medicine, NHGRI

Staron, A., Sofia, H.J., Dietrich, S., Ulrich, L.E., Liesegang, H., Mascher, T. The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Molecular Microbiology, 74: 557-581. 2009. [PubMed]

Oehmen, C.S., Sofia, H.J., Baxter, D., Szeto, E., Hugenholtz, P., Kyrpides, N., Markowitz, V., Straatsma, T.P. Bringing large-scale multiple genome analysis one step closer: ScalaBLAST and beyond. Lawrence Berkeley National Laboratory. LBNL Paper, LBNL-62882. 2009. [Full Text]

Chin, G., Jr., Chavarria, D.G., Nakamura, G.C., Sofia, H.J. BioGraphE: High-performance bionetwork analysis using the Biological Graph Environment. BMC Bioinformatics, 9:S6. 2008. [PubMed]

Chavarria-Miranda, D., Gracio, D., Marquez, A., Nieplocha, J., Scherrer, C., Sofia, H., Bader, D.A., Madduri, K., Berry, J., Hendrickson, B. Cray. XMT brings new energy to high-performance computing. SciDAC Review, 9: 36-41. 2008. [Full TextPDF file]

Wong, P.C., Foote, H., Mackey, P., Chin, G., Jr., Sofia, H., Thomas, J. A dynamic multiscale magnifying tool for exploring large sparse graphs. Information Visualization, 7: 105-117. 2008. [Full TextPDF file]

Campbell, E.A., Greenwell, R., Anthony, J.R., Wang, S., Lim, L., Sofia, H.J., Donohue, T.J., Darst, S.A. A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria. Molecular Cell, 27: 793-805. 2007. [PubMed]

Chin G, Jr., Stephan, E.G., Klicker, K.R., Corrigan, A.L., Sofia, H.J. Supporting computational visual theories in biology. Proceedings of the IEEE 2004 Symposium on Visual Languages and Human-Centric Computing (VLHCC'04), September 26-29, Rome, Italy, pp 69-71. 2004.

Korner, H., Sofia, H.J., and Zumft, W.G. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol, Rev.27: 559-592. 2003. [PubMed]

Sofia, H.J., Chen, G., Hetzler, B.G., Reyes-Spindola, J.F., and Miller, N.E. Radical SAM: A novel protein superfamily that links unresolved steps in familiar biosynthetic pathways with radical mechanisms: Discovery and functional characterization using new analysis and information visualization methods. Nucleic Acids Res, 29: 1097-1106. 2001. [PubMed]

Kajkowski, E.M., Lo, C.F., Ning, X., Walker, S., Sofia, H.J., Wang, W., Edris, W., Chandra, P., Wagner, E., Vile, S., Ryan, K., McHendry-Rinde, B., Smith, S.C., Wood, A., Rhodes, K.J., Kennedy, J.D., Bard, J., Jacobsen, J.S., and Ozenberger, B.A. Beta-amyloid peptide-induced apoptosis regulated by a novel protein containing a G protein activation module. J Biol Chem, 276: 18748-18756. 2001. [PubMed]

Rudd, K.E., Sofia, H.J., Koonin, E.V., Plunkett, G. III, Lazar, S., and Rouviere, P.E. A new family of peptidyl-prolyl isomerases. Trends Biochem Sci, 20: 12-14. 1995. [PubMed]

Sofia, H.J., Burland, V., Daniels, D.L., Plunkett, G., III, and Blattner, F.R. Analysis of the Escherichia coli genome V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res, 22: 2576-2586. 1994. [PubMed]

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Last Updated: October 1, 2012