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• Author = Cruz AL

1. Brankin A, Malone KM, Barilar I, Battaglia S, Borroni E, Brandao AP, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SJ, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Mandal A, Mansjo M, Matias D, Meintjes G, Mendes FF, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Siqueira de Oliveira R, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson E, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Kohl TA, Smith G, Solano W, Spitaleri A, Supply P, Steyn AJC, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Rie A, Vijay S, Walker TM, Walker AS, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B, Fowler PW, Iqbal Z
Brankin, A., Malone, K.M., Barilar, I., Battaglia, S., Borroni, E., Brandao, A.P., Cabibbe, A.M., Carter, J., Chetty, D., Cirillo, D.M., Claxton, P., Clifton, D.A., Cohen, T., Coronel, J., Crook, D.W., Dreyer, V., Earle, S.G., Escuyer, V., Ferrazoli, L., Gao, G.F., Gardy, J., Gharbia, S., Ghisi, K.T., Ghodousi, A., Gibertoni Cruz, A.L., Grandjean, L., Grazian, C., Groenheit, R., Guthrie, J.L., He, W., Hoffmann, H., Hoosdally, S.J., Hunt, M., Ismail, N.A., Jarrett, L., Joseph, L., Jou, R., Kambli, P., Khot, R., Knaggs, J., Koch, A., Kohlerschmidt, D., Kouchaki, S., Lachapelle, A.S., Lalvani, A., Lapierre, S.J., Laurenson, I.F., Letcher, B., Lin, W.H., Liu, C., Liu, D., Mandal, A., Mansjo, M., Matias, D., Meintjes, G., Mendes, F.d.F., Merker, M., Mihalic, M., Millard, J., Miotto, P., Mistry, N., Moore, D., Musser, K.A., Ngcamu, D., Nhung, H.N., Niemann, S., Nilgiriwala, K.S., Nimmo, C., O’Donnell, M., Okozi, N., Oliveira, R.S., Omar, S.V., Paton, N., Peto, T.E.A., Pinhata, J.M.W., Plesnik, S., Puyen, Z.M., Rabodoarivelo, M.S., Rakotosamimanana, N., Rancoita, P.M.V., Rathod, P., Robinson, E., Rodger, G., Rodrigues, C., Rodwell, T.C., Roohi, A., Santos-Lazaro, D., Shah, S., Kohl, T.A., Smith, G., Solano, W., Spitaleri, A., Supply, P., Steyn, A.J.C., Surve, U., Tahseen, S., Thuong, N.T.T., Thwaites, G., Todt, K., Trovato, A., Utpatel, C., Van Rie, A., Vijay, S., Walker, T.M., Walker, A.S., Warren, R., Werngren, J., Wijkander, M., Wilkinson, R.J.,Wilson, D.J., Wintringer, P., Xiao, Y.X., Yang, Y., Yanlin, Z., Yao, S.Y., Zhu, B., Fowler, P.W., Iqbal, Z.: A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics, PLoS Biology, 20 (2022), no. 8, e3001721.

2. Earle SG, Wilson DJ, Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SH, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjo M, Matias D, Meintjes G, Mendes FF, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung H, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Siqueira de Oliveira R, Omar SV, Paton PN, Peto TEA, Pinhata TMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson E, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Kohl TA, Smith G, Solano W, Spitaleri A, Supply P, Steyn AJC, Surve U, Tahseen S, Thuong NT, Thwaites G, Todt K, Trovato A, Utpatel C, Rie A, Vijay S, Walker TM, Walker AS, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B
Earle, S.G., Wilson, D.J, Barilar, I., Battaglia, S., Borroni, E., Brandao, A.P., Brankin, A., Cabibbe, A.M., Carter, J., Chetty, D., Cirillo, D.M., Claxton, P., Clifton, D.A., Cohen, T., Coronel, J., Crook, D.W., Dreyer, V., Escuyer, V., Ferrazoli, L., Fowler, P.W., Gao, G.F., Gardy, J., Gharbia, S., Ghisi, K.T., Ghodousi, A., Gibertoni Cruz, A.L., Grandjean, L., Grazian, C., Groenheit, R., Guthrie, J.L., He, W., Hoffmann, H., Hoosdally, S.H., Hunt, M., Iqbal, Z., Ismail, N.A., Jarrett, L., Joseph, L., Jou, R., Kambli, P., Khot, R., Knaggs, J., Koch, A., Kohlerschmidt, D., Kouchaki, S., Lachapelle, A.S., Lalvani, A., Lapierre, S.G., Laurenson, I.F., Letcher, B., Lin, W.H., Liu, C., Liu, D., Malone, K.M., Mandal, A., Mansjo, M., Matias, D., Meintjes, G., Mendes, FdF, Merker, M., Mihalic, M., Millard, J., Miotto, P., Mistry, N., Moore, D., Musser, K.A., Ngcamu, D., Ngoc Nhung, H., Niemann, S., Nilgiriwala, K.S., Nimmo, C., O’Donnell, M., Okozi, N., Oliveira, R.S., Omar, S.V., Paton, N., Peto, T.E.A., Pinhata, T.M.W., Plesnik, S., Puyen, Z.M., Rabodoarivelo, M.S., Rakotosamimanana, N., Rancoita, P.M.V., Rathod, P., Robinson, E., Rodger, G., Rodrigues, C., Rodwell, T.C., Roohi, A., Santos-Lazaro, D., Shah, S., Kohl, T.A., Smith, G., Solano, W., Spitaleri, A., Supply, P., Steyn, A.J.C., Surve, U., Tahseen, S., Thuong Thuong, N.T., Thwaites, G., Todt, K., Trovato, A., Utpatel, C., Van Rie, A., Vijay, S., Walker, T.M., Walker, A.S., Warren, R., Werngren, J., Wijkander, M., Wilkinson, R.J., Wintringer, P., Xiao, Y.X., Yang, Y., Yanlin, Z., Yao, S.Y., Zhu, B.: Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms, PLoS Biology, 20 (2022), no. 8, e3001755.

3. 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.

4. 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.

5. 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.