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)

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