Publications

Ramirez-Busby, S. M., Rodwell, T. C., Fink, L., Catanzaro, D., Jackson, R. L., Pettigrove, M., … Valafar, F. (2017). A Multinational Analysis of Mutations and Heterogeneity in PZase, RpsA, and PanD Associated with Pyrazinamide Resistance in M/XDR Mycobacterium tuberculosis. Scientific Reports, 7(1), 3790. (2017) http://doi.org/10.1038/s41598-017-03452-y

Elghraoui, Afif, Samuel J. Modlin, and Faramarz Valafar. “SMRT genome assembly corrects reference errors, resolving the genetic basis of virulence in Mycobacterium tuberculosis.” BMC genomics 18.1 (2017): 302. DOI: 10.1186/s12864-017-3687-5

Alotaibi, M., Reyes, B. D., Le, T., Luong, P., Valafar, F., Metzger, R. P., … & Hecht, D. (2017). Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. Journal of Molecular Graphics and Modelling, 71, 135-153. DOI:10.1016/j.jmgm.2016.10.011

Valafar, F. (2016). Pathogenesis of multi drug-resistant and extensively drug-resistant tuberculosis as a determinant of future treatment success. International journal of mycobacteriology, 5, S64. DOI:10.1016/j.ijmyco.2016.11.017

Catanzaro, A., Rodwell, T. C., Catanzaro, D. G., Garfein, R. S., Jackson, R. L., Seifert, M., Valafar, F., … & Crudu, V. (2015). Performance comparison of three rapid tests for the diagnosis of drug-resistant tuberculosis. PloS one, 10(8), e0136861. DOI:10.1371/journal.pone.0136861

Torres, J. N., Paul, L. V, Rodwell, T. C., Victor, T. C., Amallraja, A. M., Elghraoui, A., … Valafar, F. (2015). Novel katG mutations causing isoniazid resistance in clinical M. tuberculosis isolates. Emerging Microbes & Infections, 4(7), e42. DOI:10.1038/emi.2015.42

Ramirez-Busby, S. M., & Valafar, F. (2015). Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates. Antimicrobial agents and chemotherapy, 59(9), 5267-5277. DOI:10.1128/AAC.00204-15

Colman, R. E., Schupp, J. M., Hicks, N. D., Smith, D. E., Buchhagen, J. L., Valafar, F., … & Catanzaro, D. G. (2015). Detection of low-level mixed-population drug resistance in Mycobacterium tuberculosis using high fidelity amplicon sequencing. PloS one, 10(5), e0126626. DOI:10.1371/journal.pone.0126626

Hillery, N., Groessl, E. J., Trollip, A., Catanzaro, D., Jackson, L., Rodwell, T. C., Valafar, F., … & Park, D. (2014). The Global Consortium for Drug-resistant Tuberculosis Diagnostics (GCDD): design of a multi-site, head-to-head study of three rapid tests to detect extensively drug-resistant tuberculosis. Trials, 15(1), 434. DOI:10.1186/1745-6215-15-434

Rodwell, T. C., Valafar, F., Douglas, J., Qian, L., Garfein, R. S., Chawla, A., … & Catanzaro, D. (2014). Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations. Journal of clinical microbiology, 52(3), 781-789. DOI:10.1128/JCM.02701-13

Rudy, J., & Valafar, F. (2011). Empirical comparison of cross-platform normalization methods for gene expression data. BMC bioinformatics, 12(1), 467. DOI:10.1186/1471-2105-12-467

Bowman, B. N., McAdam, P. R., Vivona, S., Zhang, J. X., Luong, T., Belew, R. K., Valafar, F., … & Woelk, C. H. (2011). Improving reverse vaccinology with a machine learning approach. Vaccine, 29(45), 8156-8164. DOI:10.1016/j.vaccine.2011.07.142

Huss, J. W., Lindenbaum, P., Martone, M., Roberts, D., Pizarro, A., Valafar, F., … & Su, A. I. (2009). The Gene Wiki: community intelligence applied to human gene annotation. Nucleic acids research, gkp760. DOI:10.1093/nar/gkp760

Turner, J. L., Kelley, S. T., Otto, J. S., Valafar, F., & Bohonak, A. J. (2009). Parallelization and optimization of genetic analyses in isolation by distance web service. BMC genetics, 10(1), 28. DOI:10.1186/1471-2156-10-28

Huss III, J. W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T. J., Valafar, F., … & Su, A. I. (2008). A gene wiki for community annotation of gene function. PLoS Biol, 6(7), e175. DOI:10.1371/journal.pbio.0060175

Wegrzyn, J. L., Drudge, T. M., Valafar, F., & Hook, V. (2008). Bioinformatic analyses of mammalian 5′-UTR sequence properties of mRNAs predicts alternative translation initiation sites. BMC bioinformatics, 9(1), 232. DOI:10.1186/1471-2105-9-232

Hernandez, G., Valafar, F., & Stumph, W. E. (2007). Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity. Nucleic acids research, 35(1), 21-34. DOI:10.1093/nar/gkl982

Valafar, F. (2002). Pattern recognition techniques in microarray data analysis. Annals of the New York Academy of Sciences, 980(1), 41-64. PMID:12594081

Valafar, H., Prestegard, J. H., & Valafar, F. (2002). Datamining protein structure databanks for crystallization patterns of proteins. Annals of the New York Academy of Sciences, 980(1), 13-22. PMID:12594078