Publications

• Samuel J. Modlin, Mikael Mansjö, Jim Werngren, Chidera M. Ejike, Sven E. Hoffner, Faramarz Valafar, Pyrazinamide-resistant Tuberculosis Obscured From Common Targeted Molecular Diagnostics, Drug Resistance Updates, Volume 68,(2023),100959,ISSN 1368-7646, https://doi.org/10.1016/j.drup.2023.100959
• Swenson, K.M., Elghraoui, A., Valafar, F., Mirarab, S. and Weller, M. Quantifying Hierarchical Conflicts in Homology Statements. In Comparative Genomics: 19th International Conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20–21, (2022), Proceedings (pp. 146-167). Cham: Springer International Publishing.  https://doi.org/10.1007/978-3-031-06220-9_9
• Thiede, Joshua M., Nicholas A. Dillon, Michael D. Howe, Ranee Aflakpui, Samuel J. Modlin, Sven E. Hoffner, Faramarz Valafar, Yusuke Minato, and Anthony D. Baughn. “Pyrazinamide susceptibility is driven by activation of the SigE-dependent cell envelope stress response in Mycobacterium tuberculosis.” Mbio 13, no. 1 (2022) https://doi.org/10.1128/mbio.00439-21
• Conkle-Gutierrez, D., Kim, C., Ramirez-Busby, S.M., Modlin, S.J., Mansjö, M., Werngren, J., Rigouts, L., Hoffner, S.E. and Valafar, F., Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrobial Agents and Chemotherapy, 66(6) (2022) https://doi.org/10.1128/aac.02075-21
• Modlin SJ * , Gunasekaran D * , Zlotnicki AM * , Elghraoui A * , Dillon N, Kuo N * , Chan CK * , Baughn A, Valafar F. Structure-aware M. tuberculosis annotation uncloaks resistance, effector, and metabolic genes. mSystems. (2021) https://doi.org/10.1128/mSystems.00673-21
• Modlin SJ * , Marbach T * , Werngren J, Mansjö M, Hoffner SE * , Valafar F. Atypical Genetic Basis of Pyrazinamide Resistance in Mono-resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother AAC.01916-20. (2021) https://doi.org/10.1128/AAC.01916-20. PMID: 33722890
• Modlin SJ * , Robinhold C * , Morrissey C * , Mitchell SN * , Ramirez-Busby SM * , Shmaya T * , Valafar F. Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases. Microb Genom.(2021)https://doi.org/10.1099/mgen.0.000465. PMID: 33502304.
• Modlin SJ * , Conkle-Gutierrez D * , Kim C * , Mitchell SN * , Morrissey C * , Weinrick BC, Jacobs WR, Ramirez-Busby SM * , Hoffner SE * , Valafar F. Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife ;9:e58542 (2020)DOI:10.7554/eLife.58542
• Alyamani EJ, Marcus SA, Ramirez-Busby SM * , Hansen C, Rashid J, El-kholy A, Spalink D, Valafar F, Almehdar HA, Fatani AJ, Khiyami MA, and Talaat AM. Genomic analysis of the emergence of drug-resistant strains of Mycobacterium tuberculosis in the Middle East. Nature Scientific Report, 9(1):4474. (2019) https://doi.org/10.1038/s41598-019-55790-8
• 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