Article

Hailu, Elena, Cantillon, Daire, Madrazo, Carlos, Rose, Graham, Wheeler, Paul R, Golby, Paul, Adnew, Bethlehem, Gagneux, Sebastien, Aseffa, Abraham, Gordon, Stephen V, Comas, Iñaki, Young, Douglas B, Waddell, Simon J, Larrouy-Maumus, Gerald and Berg, Stefan (2023) Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom, 9 (5). pp. 1-16. ISSN 2057-5858

Napier, Gary, Khan, Anwar Sheed, Jabbar, Abdul, Khan, Muhammad Tahir, Ali, Sajid, Qasim, Muhammad, Mohammad, Noor, Hasan, Rumina, Hasan, Zahra, Campino, Susana, Ahmad, Sajjad, Khattak, Baharullah, Waddell, Simon J, Khan, Taj Ali, Phelan, Jody E and Clark, Taane G (2022) Characterisation of drug-resistant Mycobacterium tuberculosis mutations and transmission in Pakistan. Scientific Reports, 12 (1). a7703 1-10. ISSN 2045-2322

Cantillon, Daire, Goff, Aaron, Taylor, Stuart, Salehi, Emad, Fidler, Katy, Stoneham, Simon and Waddell, Simon J (2022) Search for new therapeutic options for the uncommon pathogen Mycobacterium chimaera: an open drug discovery approach. Lancet Microbe. pp. 1-10. ISSN 2666-5247

Medley, Jamie, Goff, Aaron, Bettencourt, Paulo J G, Dare, Madelaine, Cole, Liam, Cantillon, Daire and Waddell, Simon J (2022) Dissecting the mycobacterium bovis BCG response to macrophage infection to help prioritize targets for anti-tuberculosis drug and vaccine discovery. Vaccines, 10 (1). a113 1-14. ISSN 2076-393X

Bacon, Joanna, Waddell, Simon J and Flores-Valdez, Mario Alberto (2022) Biofilms in tuberculosis: what have we learnt in the past decade and what is still unexplored? Tuberculosis, 132. a102153 1-3. ISSN 1472-9792

Mekonnen, Daniel, Derbie, Awoke, Mihret, Adane, Yimer, Solomon Abebe, Tønjum, Tone, Gelaw, Baye, Nibret, Endalkachew, Munshae, Abaineh, Waddell, Simon J and Aseffa, Abraham (2021) Lipid droplets and the transcriptome of Mycobacterium tuberculosis from direct sputa: a literature review. Lipids in Health and Disease, 20 (1). a129 1-13. ISSN 1476-511X

Houghton, Joanna, Rodgers, Angela, Rose, Graham, D’Halluin, Alexandre, Kipkorir, Terry, Barker, Declan, Waddell, Simon J and Arnvig, Kristine B (2021) The mycobacterium tuberculosis sRNA F6 modifies expression of essential chaperonins, GroEL2 and GroES. Microbiology Spectrum, 9 (2). a01095-21 1. ISSN 2165-0497

Price, James R, Yokoyama, Maho, Cole, Kevin, Sweetman, Jonathan, Behar, Laura, Stoneham, Simon, Cantillon, Daire, Waddell, Simon J, Hyde, Jonathan, Alam, Ruhina, Crook, Derrick, Paul, John and Llewelyn, Martin J (2021) Undetected carriage explains apparent Staphylococcus aureus acquisition in a non-outbreak healthcare setting. Journal of Infection, 83 (3). pp. 332-338. ISSN 0163-4453

Gerbino, Filippo, Tretola, Giovanni, Morgan, Robert, Atkins, Penny, Waddell, Simon, Pitt, Sarah and Vogiaztaki, Konstantina (2021) Evolving droplet dynamics during violent expiratory events at various ambient environments. Atomization and Sprays. ISSN 1044-5110

Lu, Lu, Wei, Ran-Lei, Bhakta, Sanjib, Waddell, Simon J and Boix, Ester (2021) Correction to: Lu et al. weighted gene co-expression network analysis identifies key modules and hub genes associated with mycobacterial infection of human macrophages. antibiotics 2021, 10, 97. Antibiotics, 10 (7). pp. 1-2. ISSN 2079-6382

Kenyon, Emma J, Kirkwood, Nerissa K, Kitcher, Sian R, Goodyear, Richard J, Derudas, Marco, Cantillon, Daire, Baxendale, Sarah, de la Vega de León, Antonio, Mahieu, Virginia N, Osgood, Richard T, Wilson, Charlotte Donald, Bull, James C, Waddell, Simon J, Whitfield, Tanya T, Ward, Simon E, Kros, Corne J and Richardson, Guy P (2021) Identification of a series of hair-cell MET channel blockers that protect against aminoglycoside-induced ototoxicity. JCI Insight, 6 (7). a145704 1-22. ISSN 2379-3708

Cantillon, Daire, Wroblewska, Justyna, Cooper, Ian, Newport, Melanie J and Waddell, Simon J (2021) Three-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance. npj Biofilms and Microbiomes, 7. a12 1-8. ISSN 2055-5008

Lu, Lu, Wei, RanLei, Bhakta, Sanjib, Waddell, Simon and Boix, Ester (2021) Weighted gene co-expression network analysis identifies key modules and hub genes associated with mycobacterial infection of human macrophages. Antibiotics, 10 (2). a97 1-16. ISSN 2079-6382

Pollo, Luiz A E, Martin, Erlon F, Machado, Vanessa R, Cantillon, Daire, Wildner, Leticia Muraro, Bazzo, Maria Luiza, Waddell, Simon J, Biavatti, Maique W and Sandjo, Louis P (2021) Search for antimicrobial activity among fifty-two natural and synthetic compounds identifies anthraquinone and polyacetylene classes that inhibit Mycobacterium tuberculosis. Frontiers in Microbiology, 11. a622629 1-11. ISSN 1664-302X

De Siena, Barbara, Campolattano, Nicoletta, D'Abrosca, Gianluca, Russo, Luigi, Cantillon, Daire, Morasco, Rosangela, Muscariello, Lidia, Waddell, Simon J and Sacco, Margherita (2020) Characterization of the mycobacterial MSMEG-3762/63 efflux pump in Mycobacterium smegmatis drug efflux. Frontiers in Microbiology, 11. a575828 1-11. ISSN 1664-302X

Maitra, Arundhati, Evangelopoulos, Dimitrios, Chrzastek, Alina, Martin, Liam T, Hanrath, Aidan, Chapman, Ellie, Hailes, Helen C, Lipman, Marc, McHugh, Timothy D, Waddell, Simon J and Bhakta, Sanjib (2020) Carprofen elicits pleiotropic mechanisms of bactericidal action with the potential to reverse antimicrobial drug resistance in tuberculosis. Journal of Antimicrobial Chemotherapy. pp. 1-8. ISSN 0305-7453

Goff, Aaron, Cantillon, Dairre, Murano Wildner, Leticia and Waddell, Simon J (2020) Multi-omics technologies applied to tuberculosis drug discovery. Applied Sciences, 10 (13). a4629 1-20. ISSN 2076-3417

Stoneham, Simon M, Cantillon, Daire M, Waddell, Simon J and Llewelyn, Martin J (2020) Spontaneously occurring small-colony variants of staphylococcus aureus show enhanced clearance by THP-1 macrophages. Frontiers in Microbiology, 11 (1300). pp. 1-8. ISSN 1664-302X

Bettencourt, Paulo, Muller, Julius, Nicastri, Annalisa, Cantillon, Daire, Madhaven, Meera, Charles, Philip D, Fotso, Carine B, Wittenburg, Rachel, Bull, Naomi, Pinpathomrat, Nawamin, Waddell, Simon J, Stylianou, Elena, Hill, Adrain V S, Ternette, Nicola and McShane, Helen (2020) Identification of antigens presented by MHC for vaccines against tuberculosis. npj Vaccines, 5 (a2). pp. 1-14. ISSN 2059-0105

Jabbar, Abdul, Phelan, Jody E, de Sessions, Paola Florez, Khan, Taj Ali, Rahman, Hazir, Khan, Sadiq Noor, Cantillon, Daire M, Muraro Wildner, Leticia, Ali, Sajid, Campino, Susana, Waddell, Simon J and Clark, Taane G (2019) Whole genome sequencing of drug resistant Mycobacterium tuberculosis isolates from a high burden tuberculosis region of North West Pakistan. Scientific Reports, 9. ISSN 2045-2322

Alqaseer, Kawther, Turapov, Obolbek, Barthe, Philippe, Jagatia, Heena, De Visch, Angélique, Roumestand, Christian, Wegrzyn, Malgorzata, Bartek, Iona L, Voskuil, Martin I, O’Hare, Helen M, Ajuh, Paul, Bottrill, Andrew R., Witney, Adam A, Cohen‐Gonsaud, Martin, Waddell, Simon and Mukamolova, Galina V (2019) Protein kinase B controls Mycobacterium tuberculosis growth via phosphorylation of the transcriptional regulator Lsr2 at threonine 112. Molecular Microbiology. ISSN 0950-382X

O'Reilly, Molly, Kirkwood, Nerissa K, Kenyon, Emma J, Huckvale, Rosemary, Cantillon, Daire M, Waddell, Simon J, Ward, Simon E, Richardson, Guy P, Kros, Corné J and Derudas, Marco (2019) Design, synthesis and biological evaluation of a new series of carvedilol derivatives that protect sensory hair cells from aminoglycoside-induced damage by blocking the mechanoelectrical transducer channel. Journal of Medicinal Chemistry, 62 (11). pp. 5312-5329. ISSN 0022-2623

Kenyon, Emma J, Kirkwood, Nerissa K, Kitcher, Siân R, O'Reilly, Molly, Derudas, Marco, Cantillon, Daire M, Goodyear, Richard J, Secker, Abigail, Baxendale, Sarah, Bulley, James C, Waddell, Simon J, Whitfield, Tanya T, Ward, Simon E, Kros, Corné J and Richardson, Guy P (2017) Identification of ion-channel modulators that protect against aminoglycoside-induced hair cell death. Journal of Clinical Investigation Insight, 2 (24). a96773 1-16. ISSN 2379-3708

Hemingway, Cheryl, Berk, Maurice, Anderson, Suzanne T, Wright, Victoria J, Hamilton, Shea, Eleftherohorinou, Hariklia, Kaforou, Myrsini, Goldgof, Greg M, Hickman, Katy, Kampmann, Beate, Schoeman, Johan, Eley, Brian, Beatty, David, Pienaar, Sandra, Nicol, Mark P, Griffiths, Michael J, Waddell, Simon J, Newton, Sandra M, Coin, Lachlan J, Relman, David A, Montana, Giovanni and Levin, Michael (2017) Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function. PLoS ONE, 12 (11). e0185973. ISSN 1932-6203

Perrone, Filomena, De Siena, Barbara, Muscariello, Lidia, Kendall, Sharon L, Waddell, Simon J and Sacco, Margherita (2017) A novel TetR-like transcriptional regulator is induced in acid-nitrosative stress and controls expression of an efflux pump in mycobacteria. Frontiers in Microbiology, 8 (2039). ISSN 1664-302X

Castañeda-García, A, Prieto, A I, Rodríguez-Beltrán, J, Alonso, N, Cantillon, D, Costas, C, Pérez-Lago, L, Zegeye, E D, Herranz, M, Plociński, P, Tonjum, T, García de Viedma, D, Paget, M, Waddell, S J, Rojas, A M, Doherty, A J and Blázquez, J (2017) A non-canonical mismatch repair pathway in prokaryotes. Nature Communications, 8. a14246. ISSN 2041-1723

Honeyborne, Isobella, McHugh, Timothy D, Kuittinen, Iitu, Cichonska, Anna, Evangelopoulos, Dimitrios, Ronacher, Katharina, van Helden, Paul D, Gillespie, Stephen H, Fernandez-Reyes, Delmiro, Walzl, Gerhard, Rousu, Juho, Butcher, Philip D and Waddell, Simon J (2016) Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy. BMC Medicine, 14 (1). a68. ISSN 1741-7015

Evangelopoulos, Dimitrios, Fonseca, Joana Diniz da and Waddell, Simon J (2015) Understanding anti-tuberculosis drug efficacy: rethinking bacterial populations and how we model them. International Journal of Infectious Diseases, 32. pp. 76-80. ISSN 1201-9712

Salina, Elena G, Waddell, Simon J, Hoffmann, Nadine, Rosenkrands, Ida, Butcher, Philip D and Kaprelyants, Arseny S (2014) Potassium availability triggers Mycobacterium tuberculosis transition to, and resuscitation from, non-culturable (dormant) states. The Open Biology Journal, 4 (10). ISSN 1874-1967

Turapov, Obolbek, Waddell, Simon J, Burke, Bernard, Glenn, Sarah, Sarybaeva, Asel A, Tudo, Griselda, Labesse, Gilles, Young, Danielle I, Young, Michael, Andrew, Peter W, Butcher, Philip D, Cohen-Gonsaud, Martin and Mukamolova, Galina V (2014) Oleoyl-coenzyme A regulates interaction of transcriptional regulator RaaS (Rv1219c) with DNA in mycobacteria. Journal of biological chemistry, 289 (36). pp. 25241-25249. ISSN 1083-351X

Turapov, Obolbek, Waddell, Simon J, Burke, Bernard, Glenn, Sarah, Sarybaeva, Asel A, Tudo, Griselda, Labesse, Gilles, Young, Danielle I, Young, Michael, Andrew, Peter W, Butcher, Philip D, Cohen-Gonsaud, Martin and Mukamolova, Galina V (2014) Antimicrobial treatment improves mycobacterial survival in nonpermissive growth conditions. Antimicrobial Agents and Chemotherapy, 58 (5). pp. 2798-2806. ISSN 1098-6596

Pathan, Nazima, Burmester, Margarita, Adamovic, Tanja, Berk, Maurice, Ng, Keng Wooi, Betts, Helen, Macrae, Duncan, Waddell, Simon, Paul-Clark, Mark, Nuamah, Rosamund, Mein, Charles, Levin, Michael, Montana, Giovanni and Mitchell, Jane A (2011) Intestinal injury and endotoxemia in children undergoing surgery for congenital heart disease. American Journal of Respiratory and Critical Care Medicine, 184 (11). pp. 1261-1269. ISSN 1073-449X

Minas, Christopher, Waddell, Simon J and Montana, Giovanni (2011) Distance-based differential analysis of gene curves. Bioinformatics, 27 (22). pp. 3135-3141. ISSN 1367-4803

Botella, Hélène, Peyron, Pascale, Levillain, Florence, Poincloux, Renaud, Poquet, Yannick, Brandli, Irène, Wang, Chuan, Tailleux, Ludovic, Tilleul, Sylvain, Charrière, Guillaume M, Waddell, Simon J, Foti, Maria, Lugo-Villarino, Geanncarlo, Gao, Qian, Maridonneau-Parini, Isabelle, Butcher, Philip D, Castagnoli, Paola Ricciardi, Gicquel, Brigitte, de Chastellier, Chantal and Neyrolles, Olivier (2011) Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages. Cell Host and Microbe, 10 (3). pp. 248-259. ISSN 1931-3128

Carroll, Paul, Waddell, Simon J, Butcher, Philip D and Parish, Tanya (2011) Methionine sulfoximine resistance in Mycobacterium tuberculosis is due to a single nucleotide deletion resulting in increased expression of the major glutamine synthetase, GlnA1. Microbial Drug Resistance, 17 (3). pp. 351-355. ISSN 1076-6294

Pathan, Nazima, Franklin, Joanne L, Eleftherohorinou, Hariklia, Wright, Victoria J, Hemingway, Cheryl A, Waddell, Simon J, Griffiths, Michael, Dennis, Jayne L, Relman, David A, Harding, Sian E and Levin, Michael (2011) Myocardial depressant effects of interleukin 6 in meningococcal sepsis are regulated by p38 mitogen-activated protein kinase. Critical Care Medicine, 39 (7). pp. 1692-1711. ISSN 0090-3493

Coleman, David, Waddell, Simon J and Mitchison, Denis A (2011) Effects of low incubation temperatures on the bactericidal activity of anti-tuberculosis drugs. Journal of Antimicrobial Chemotherapy, 66 (1). pp. 146-150. ISSN 0305-7453

Tudo, Griselda, Laing, Ken, Mitchison, Denis A, Butcher, Philip D and Waddell, Simon J (2010) Examining the basis of isoniazid tolerance in nonreplicating Mycobacterium tuberculosis using transcriptional profiling. Future Medicinal Chemistry, 2 (8). pp. 1371-1383. ISSN 1756-8919

Li, Alice H, Waddell, Simon J, Hinds, Jason, Malloff, Chad A, Bains, Manjeet, Hancock, Robert E, Lam, Wan L, Butcher, Philip D and Stokes, Richard W (2010) Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. PLoS ONE, 5 (6). e11066. ISSN 1932-6203

Waddell, Simon J, Popper, Stephen J, Rubins, Kathleen H, Griffiths, Michael J, Brown, Patrick O, Levin, Michael and Relman, David A (2010) Dissecting interferon-induced transcriptional programs in human peripheral blood cells. PLoS ONE, 5 (3). e9753. ISSN 1932-6203

Waddell, Simon J. (2010) Reprogramming the Mycobacterium tuberculosis transcriptome during pathogenesis. Drug Discovery Today: Disease Mechanisms, 7 (1). e67-e73. ISSN 17406765

Stokes, Richard W and Waddell, Simon J (2009) Adjusting to a new home: Mycobacterium tuberculosis gene expression in response to an intracellular lifestyle. Future Microbiology, 4 (10). pp. 1317-1335. ISSN 1746-0921

Makarov, Vadim, Manina, Giulia, Mikusova, Katarina, Möllmann, Ute, Ryabova, Olga, Saint-Joanis, Brigitte, Dhar, Neeraj, Pasca, Maria Rosalia, Buroni, Silvia, Lucarelli, Anna Paola, Milano, Anna, De Rossi, Edda, Belanova, Martina, Bobovska, Adela, Dianiskova, Petronela, Kordulakova, Jana, Sala, Claudia, Fullam, Elizabeth, Schneider, Patricia, McKinney, John D, Brodin, Priscille, Christophe, Thierry, Waddell, Simon, Butcher, Philip, Albrethsen, Jakob, Rosenkrands, Ida, Brosch, Roland, Nandi, Vrinda, Bharath, Sowmya, Gaonkar, Sheshagiri, Shandil, Radha K, Balasubramanian, Venkataraman, Balganesh, Tanjore, Tyagi, Sandeep, Grosset, Jacques, Riccardi, Giovanna and Cole, Stewart T (2009) Benzothiazinones kill Mycobacterium tuberculosis by blocking arabinan synthesis. Science, 324 (5928). pp. 801-804. ISSN 0036-8075

Waddell, Simon J, Laing, Ken, Senner, Claire and Butcher, Philip D (2008) Microarray analysis of defined Mycobacterium tuberculosis populations using RNA amplification strategies. BMC Genomics, 9. p. 94. ISSN 1471-2164

Waddell, Simon J, Tailleux, Ludovic, Pelizzola, Mattia, Mortellaro, Alessandra, Withers, Michael, Tanne, Antoine, Castagnoli, Paola Ricciardi, Gicquel, Brigitte, Stoker, Neil G, Butcher, Philip D, Foti, Maria and Neyrolles, Olivier (2008) Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS ONE, 3 (1). e1403. ISSN 1932-6203

Waddell, Simon, Garton, Natalie J, Sherratt, Anna L, Lee, Su-Min, Smith, Rebecca J, Senner, Claire, Hinds, Jason, Rajakumar, Kumar, Adegbola, Richard A, Besra, Gurdyal S, Butcher, Philip D and Barer, Michael R (2008) Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Medicine, 5 (4). pp. 634-645. ISSN 1549-1676

Sidders, Ben, Withers, Mike, Kendall, Sharon L, Bacon, Joanna, Waddell, Simon J, Hinds, Jason, Golby, Paul, Movahedzadeh, Farahnaz, Cox, Robert A, Frita, Rosangela, Ten Bokum, Annemieke M C, Wernisch, Lorenz and Stoker, Neil G (2007) Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biology, 8 (12). R265. ISSN 1465-6906

Waddell, Simon J, Butcher, Philip D and Stoker, Neil G (2007) RNA profiling in host-pathogen interactions. Current Opinion in Microbiology, 10 (3). pp. 297-302. ISSN 1369-5274

Waddell, S J and Butcher, P D (2007) Microarray analysis of whole genome expression of intracellular Mycobacterium tuberculosis. Current Molecular Medicine, 7 (3). pp. 287-296. ISSN 1566-5240

Kampmann, Beate, Hemingway, Cheryl, Stephens, Alick, Davidson, Robert, Goodsall, Anna, Anderson, Suzanne, Nicol, Mark, Schölvinck, Elisabeth, Relman, David, Waddell, Simon J, Langford, Paul, Sheehan, Brian, Semple, Lynn, Wilkinson, Katalin A, Wilkinson, Robert J, Ress, Stanley, Hibberd, Martin and Levin, Michael (2005) Acquired predisposition to mycobacterial disease due to autoantibodies to IFN-γ. Journal of Clinical Investigation, 115 (9). pp. 2480-2488. ISSN 0021-9738

Waddell, S J, Chung, G A, Gibson, K J C, Everett, M J, Minnikin, D E, Besra, G S and Butcher, P D (2005) Inactivation of polyketide synthase and related genes results in the loss of complex lipids in Mycobacterium tuberculosis H37Rv. Letters In Applied Microbiology, 40 (3). pp. 201-6.

Waddell, Simon J, Stabler, Richard A, Laing, Ken, Kremer, Laurent, Reynolds, Robert C and Besra, Gurdyal S (2004) The use of microarray analysis to determine the gene expression profiles of Mycobacterium tuberculosis in response to anti-bacterial compounds. Tuberculosis, 84 (3-4). pp. 263-274. ISSN 1472-9792

Li, Ming-Shi, Waddell, Simon, Monahan, Irene M, Mangan, Joseph A, Martin, Steve L, Everett, Martin J and Butcher, Philip D (2004) Increased transcription of a potential sigma factor regulatory gene Rv1364c in Mycobacterium bovis BCG while residing in macrophages indicates use of alternative promoters. FEMS Microbiology Letters, 233 (2). pp. 333-339. ISSN 0378-1097

Li, Ming-Shi, Monahan, Irene M, Waddell, Simon J., Mangan, Joseph A, Martin, Steve L, Everett, Martin J and Butcher, Philip D (2001) cDNA-RNA subtractive hybridization reveals increased expression of mycocerosic acid synthase in intracellular Mycobacterium bovis BCG. Microbiology, 147 (8). pp. 2293-2305. ISSN 1350-0872

Book Section

Wildner, Leticia Muraro, Gould, Katherine A and Waddell, Simon J (2018) Transcriptional profiling mycobacterium tuberculosis from patient sputa. In: Antibiotic Resistance Protocols. Methods in Molecular BIology, 1736 . Humana Press, pp. 117-128. ISBN 9781493976362

Evangelopoulos, Dimitrios and Waddell, Simon (2016) The use of transcriptomics to predict drug efficacy and treatment outcome in tuberculosis. In: Kurosu, Michio and Denny, William (eds.) Advances in Tuberculosis Medicinal Chemistry. Future Science Ltd, pp. 90-103. ISBN 9781910419144

Waddell, Simon J and Butcher, Philip D (2013) Transcriptomic approaches to mapping responses to drug therapy for tuberculosis. In: MuHugh, Timothy D (ed.) Tuberculosis: laboratory diagnosis and treatment strategies. Advances in molecular and cellular microbiology series (21). CAB International, Wallingford, pp. 173-183. ISBN 9781845938079

Waddell, Simon J, von Kamp, Axel, Klamt, Steffen and Neyrolles, Olivier (2012) Host-pathogen interactions. In: McFadden, Johnjoe, Beste, Dany J V and Kierzek, Andrzej M (eds.) Systems Biology of Tuberculosis. Springer, pp. 107-126. ISBN 9781461449669

Waddell, Simon J and Butcher, Philip D (2010) Use of DNA arrays to study transcriptional responses to antimycobacterial compounds. In: Methods molecular biology: antibiotic resistance protocols. Springer, pp. 75-91.

Waddell, Simon J and Butcher, Philip D (2009) Intracellular microbe whole-genome expression profiling: methodological considerations and biological inferences. In: Ulrich, E Schaible and Haas, Albert (eds.) Intracellular Niches of Microbes– A Pathogen's Guide through the Host Cell. Wiley-VCH Publishers. ISBN 9783527322077

Waddell, Simon J, Hinds, Jason and Butcher, Philip D (2008) Whole genome analysis using microarrays. In: Parish, Tanya and Brown, Amanda Claire (eds.) Mycobacteria Protocols : Second Edition. Methods in Molecular Biology, 465 . Springler, Totowa, NJ, pp. 1-12. ISBN 978-1-58829-889-8