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1. Kouchaki S, Yang Y, Lachapelle A, Walker TM, Walker AS, Hoosdally SJ, Cruz AL, Carter J, Grazian C, Earle SG, Fowler PW, Iqbal Z, Hunt M, Knaggs J, Smith GE, Rathod P, Jarrett L, Matias D, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaler A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Merker M, Hoffmann H, Todt K, Plesnik S, Ismail N, Omar SV, Joseph L, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Liu C, Ma A, Zhu B, Laurenson I, Claxton P, Koch A, Wilkinson R, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Lin WH, Ferrazoli L, Oliveira R, Arandjelovic I, Chaiprasert A, Comas I, Roig CR, Drobniewski FA, Farhat MR, Gao Q, Hee ROT, Sintchenko V, Supply P, van Soolingen D, Peto TEA, Crook DW, Clifton D
Samaneh Kouchaki, Yang Yang, Alexander Lachapelle, Timothy M. Walker, A. Sarah Walker, CRyPTIC Consortium, Timothy E. A. Peto, Derrick W. Crook and David A. Clifton: Multi-Label Random Forest Model for Tuberculosis Drug Resistance Classification and Mutation Ranking, Frontiers in Microbiology, 11 (2021), 1.

2. Wilson D, Crook DW, Peto TEA, Walker AS, Hoosdally SJ, Cruz AL, Carter J, Grazian C, Earle SG, Kouchaki S, Lachapelle A, Yang Y, Clifton DA, Fowler PW, Iqbal Z, Hunt M, Knaggs J, Smith EG, Rathod P, Jarrett L, Matias D, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl TA, Merker M, Hoffmann H, Todt K, Plesnik S, Ismail N, Omar SV, Joseph L, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Walker TM, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Liu C, Ma A, Zhu B, Laurenson I, Claxton P, Koch A, Wilkinson R, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Lin WH, Ferrazoli L, Siqueira de Oliveira R, Arandjelovic I, Chaipresert A, Comas I, Roig CJ, Drobniewski FA, Farhat MR, Gao Q, Hee ROT, Sintchenko V, Supply P, van Soolingen D
Wilson, D., Crook, D.W., Peto, T.E.A., Walker, A.S., Hoosdally, S.J., Gibertoni Cruz, A.L., Carter, J., Grazian, C., Earle, S.G., Kouchaki, S., Lachapelle, A., Yang, Y., Clifton, D.A., Fowler, P.W., Iqbal, Z., Hunt, M., Knaggs, J., Smith, E.G., Rathod, P., Jarrett, L., Matias, D., Cirillo, D.M., Borroni, E., Battaglia, S., Ghodousi, A., Spitaleri, A., Cabibbe, A., Tahseen, S., Nilgiriwala, K., Shah, S., Rodrigues, C., Kambli, P., Surve, U., Khot, R., Niemann, S., Kohl, T.A., Merker, M., Hoffmann, H., Todt, K., Plesnik, S., Ismail, N., Omar, S.V., Joseph, L., Thwaites, G., Thuong, T.N.T., Ngoc, N.H., Srinivasan, V., Walker, T.M., Moore, D., Coronel, J., Solano, W., Gao, G.F., He, G., Zhao, Y., Liu, C., Ma, A., Zhu, B., Laurenson, I., Claxton, P., Koch, A., Wilkinson, R., Lalvani, A., Posey, J., Gardy, J., Werngren, J., Paton, N., Jou, R., Wu, M.H., Lin, W.H., Ferrazoli, L., Siqueira de Oliveira, R., Arandjelovic, I., Chaipresert, A., Comas, I., Roig, C.J., Drobniewski, F.A., Farhat, M.R., Gao, Q., Hee, R.O.T., Sintchenko, V., Supply, P., van Soolingen, D.: GenomegaMap: within-species genome-wide d_N/d_S estimation from over 10,000 genomes, Molecular Biology and Evolution, msaa069 (2020), na.

3. Kouchaki S, Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Clifton D, Hoosdally SJ, Gibertoni-Cruz AL, Carter J, Grazian C, Fowler PW, Iqbal Z, Hunt M, Smith GE, Rathod P, Jarrett L, Matias D, Cirillo DM, Borroni E, Battaglia E, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Molodtsov N, Plesnik S, Ismail N, Omar SV, Joseph L, Marubini E, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Ma A, Liu C, Zhu B, Laurenson I, Claxton P, Wilkinson RJ, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Lin WH, Ferrazoli L, Siqueira de Oliveira R, Arandjelovic I, Comas I, Drobniewski F, Gao Q, Sintchenko V, Supply P, SoolingenD
Kouchaki, S., Yang, Y., Walker, T. M., Walker, A. S., Wilson, D. J., Peto, T. E., Crook, D.W., Clifton, D. A., Hoosdally, S.J., Gibertoni-Cruz, A.L., Carter, J., Grazian, C., Fowler, P.W., Iqbal, Z., Hunt, M., Smith, G.E., Rathod, P., Jarrett, L., Matias, D., Cirillo, D.M., Borroni, E., Battaglia, E., Ghodousi, A., Spitaleri, A., Cabibbe, A. Tahseen, S., Nilgiriwala, K., Shah, S., Rodrigues, C., Kambli, P., Surve, Utkarsha, Khot, Rukshar, Niemann, S., Kohl, T., Merker, M., Hoffmann, H., Molodtsov, N., Plesnik, S., Ismail, N., Omar, S.V., Joseph, L., Marubini, E., Thwaites, G., Thuong, T.N.T., Ngoc, N.H., Srinivasan, V., Moore, D., Coronel, J., Solano, W., Gao, G.F., He, G., Zhao, Y., Ma, A., Liu, C., Zhu, B., Laurenson, I., Claxton, P., Wilkinson, R.J., Lalvani, A., Posey, J., Gardy, J., Werngren, J., Paton, N., Jou, R., Wu, M.H., Lin, W.H., Ferrazoli, L., de Oliveira, R.S., Arandjelovic, I., Comas, I., Drobniewski, F., Gao, Q., Sintchenko, V., Supply, P., van Soolingen, D.: Application of machine learning techniques to tuberculosis drug resistance analysis, Bioinformatics, 35 (2019), no. 13, 2276–2282.

4. Yang Y, Walker TM, Walker AS, Wilson DJ, Peto TEA, Crook DW, Shamout F, Arandjelovic I, Comas I, Farhat MR, Gao Q, Sintchenko V, Soolingen D, Hoosdally S, Cruz AL, Carter J, Grazian C, Earle S, Kouchaki S, Fowler PW, Iqbal Z, Hunt M, Smith EG, Rathod P, Jarrett L, Matias D, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Molodtsov N, Plesnik S, Ismail N, Omar SV, Joseph L, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Ma A, Liu C, Zhu B, Laurenson I, Claxton P, Koch A, Wilkinson R, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Lin WH, Ferrazoli L, Siqueira de Oliveira R, Zhu T, Clifton DA
Yang, Y., Walker, T.M., Walker, A.S., Wilson, D.J., Peto, T.E.A., Crook, D.W., Shamout, F., Arandjelovic, I., Comas, I., Farhat, M.R., Gao, Q., Sintchenko, V., van Soolingen, D., Hoosdally, S., Gibertoni Cruz, A.L., Carter, J., Grazian, C., Earle, S. G., Kouchaki, S., Fowler, P.W., Iqbal, Z., Hunt, M., Smith, E.G., Rathod, P., Jarrett, L., Matias, D., Cirillo, D.M., Borroni, E., Battaglia, S., Ghodousi, A., Spitaleri, A., Cabibbe, A., Tahseen, S., Nilgiriwala, K., Shah, S., Rodrigues, C., Kambli, P., Surve, U., Khot, R., Niemann, S., Kohl, T., Merker, M., Hoffmann, H., Molodtsov, N., Plesnik, S., Ismail, N., Omar, S.V., Joseph, L., Thwaites, G., Thuong, T.N.T., Ngoc, N.H., Srinivasan, V., Moore, D., Coronel, J., Solano, W., Gao, G.F., He, G., Zhao, Y., Ma, A., Liu, C., Zhu, B., Laurenson, I., Claxton, P., Koch, A., Wilkinson, R., Lalvani, A., Posey, J., Gardy, J., Werngren, J., Paton, N., Jou, R., Wu, M.H., Lin, W.H., Ferrazoli, L., de Oliveira, R.S., Zhu, T., Clifton, D.A.: DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis, Bioinformatics, 35 (2019), no. 18, 3240–3249.

5. Rancoita P, Cugnata F, Gibertoni Cruz AL, Borroni E, Hoosdally SJ, Walker TM, Grazian C, Davies TJ, Peto TEA, Crook DW, Fowler PW, Cirillo DM, Walker S, Wilson D, Clifton D, Iqbal Z, Hunt M, Smith EG, Rathod P, Jarrett L, Matias D, Battaglia S, Chiacchiaretta M, Filippo M, Cabibbe A, Tahseen S, Mistry N, Nilgiriwala K, Chitalia V, Ganesan N, Papewar A, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Lehmann S, Plesnik S, Ismail N, Omar SV, Joseph L, Marubini E, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, He G, Zhu B, Zhou Y, Ma A, Yu P, Schito M, Laurenson I, Claxton P
Rancoita, P., Cugnata, F., Gibertoni Cruz, A.L., Borroni, E., Hoosdally, S.J., Walker, T.M., Grazian, C., Davies, T.J., Peto, T.E.A., Crook, D.W., Fowler, P.W., Cirillo, D.M., Walker, S., Wilson, D., Clifton, D., Iqbal, z., Hunt, M., Smith, E.G., Rathod, P., Jarrett, L., Matias, D., Battaglia, S., Chiacchiaretta, M., De Filippo, M., Cabibbe, A., Tahseen, S., Mistry, N., Nilgiriwala, K., Chitalia, V., Ganesan, N., Papewar, A., Rodrigues, C., Kambli, P., Surve, U., Khot, R., Niemann, S., Kohl, T., Merker, M., Hoffmann, H., Lehmann, S., Plesnik, S., Ismail, N., Omar, S.V., Joseph, L., Marubini, E., Thwaites, G., Thuong, T.N.T., Ngoc, N.H., Srinivasan, V., Moore, D., Coronel, J., Solano, W., He, G., Zhu, B., Zhou, Y., Ma, A., Yu, P., Schito, M., Laurenson, I., Claxton, P.: Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis, Antimicrobial Agents and Chemotherapy, 62 (2018), no. 9, 1–15.