Cubillos-Ruiz A, Morales J, Zambrano MM. Analysis of the genetic variation in Mycobacterium tuberculosis strains by multiple genome alignments. BMC Res Notes. 2008;1(1):110.
PubMed
PubMed Central
Google Scholar
Cole S, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon S, Eiglmeier K, Gas S, Barry Iii C. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393(6685):537.
CAS
PubMed
Google Scholar
Behr M, Wilson M, Gill W, Salamon H, Schoolnik G, Rane S, Small P. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science. 1999;284(5419):1520–3.
CAS
PubMed
Google Scholar
Camus J-C, Pryor MJ, Médigue C, Cole ST. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology. 2002;148(10):2967–73.
CAS
PubMed
Google Scholar
Advani J, Verma R, Chatterjee O, Pachouri PK, Upadhyay P, Singh R, Yadav J, Naaz F, Ravikumar R, Buggi S, et al. Whole genome sequencing of Mycobacterium tuberculosis clinical isolates from India reveals genetic heterogeneity and region-specific variations that might affect drug susceptibility. Front Microbiol. 2019;10:309.
PubMed
PubMed Central
Google Scholar
Brown AC, Bryant JM, Einer-Jensen K, Holdstock J, Houniet DT, Chan JZ, Depledge DP, Nikolayevskyy V, Broda A, Stone MJ, et al. Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples. J Clin Microbiol. 2015;53(7):2230–7.
CAS
PubMed
PubMed Central
Google Scholar
Kidenya BR, Mshana SE, Fitzgerald DW, Ocheretina O. Genotypic drug resistance using whole-genome sequencing of Mycobacterium tuberculosis clinical isolates from North-Western Tanzania. Tuberculosis (Edinb). 2018;109:97–101.
CAS
Google Scholar
Takiff HE, Feo O. Clinical value of whole-genome sequencing of Mycobacterium tuberculosis. Lancet Infect Dis. 2015;15(9):1077–90.
CAS
PubMed
Google Scholar
Roa MB, Tablizo FA, Morado EKD, Cunanan LF, Uy IDC, Ng KCS, Manalastas-Cantos KG, Reyes JM, Ganchua SKC, Ang CF, et al. Whole-genome sequencing and single nucleotide polymorphisms in multidrug-resistant clinical isolates of Mycobacterium tuberculosis from the Philippines. J Glob Antimicrob Resist. 2018;15:239–45.
PubMed
Google Scholar
Ford C, Yusim K, Ioerger T, Feng S, Chase M, Greene M, Korber B, Fortune S. Mycobacterium tuberculosis–heterogeneity revealed through whole genome sequencing. Tuberculosis (Edinb). 2012;92(3):194–201.
CAS
Google Scholar
Gagneux S, Small PM. Global phylogeography of Mycobacterium tuberculosis and implications for tuberculosis product development. Lancet Infect Dis. 2007;7(5):328–37.
PubMed
Google Scholar
Gao Q, Kripke KE, Saldanha AJ, Yan W, Holmes S, Small PM. Gene expression diversity among Mycobacterium tuberculosis clinical isolates. Microbiology. 2005;151(1):5–14.
CAS
PubMed
Google Scholar
Rehren G, Walters S, Fontan P, Smith I, Zárraga AM. Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis. Tuberculosis (Edinb). 2007;87(4):347–59.
CAS
Google Scholar
Sandgren A, Strong M, Muthukrishnan P, Weiner BK, Church GM, Murray MB. Tuberculosis drug resistance mutation database. PLoS Med. 2009;6(2):e1000002.
PubMed Central
Google Scholar
Zhang H, Li D, Zhao L, Fleming J, Lin N, Wang T, Liu Z, Li C, Galwey N, Deng J. Genome sequencing of 161 Mycobacterium tuberculosis isolates from China identifies genes and intergenic regions associated with drug resistance. Nat Genet. 2013;45(10):1255.
CAS
PubMed
Google Scholar
Sharma M, Bose M, Sharma L, Diwakar A, Kumar S, Gaur SN, Banavalikar JN. Intracellular survival of Mycobacterium tuberculosis in macrophages is modulated by phenotype of the pathogen and immune status of the host. Int J Mycobacteriol. 2012;1(2):65–74.
PubMed
Google Scholar
Tandon R, Ponnan P, Aggarwal N, Pathak R, Baghel AS, Gupta G, Arya A, Nath M, Parmar VS, Raj HG. Characterization of 7-amino-4-methylcoumarin as an effective antitubercular agent: structure–activity relationships. J Antimicrob Chemother. 2011;66(11):2543–55.
CAS
PubMed
Google Scholar
Chernyaeva EN, Shulgina MV, Rotkevich MS, Dobrynin PV, Simonov SA, Shitikov EA, Ischenko DS, Karpova IY, Kostryukova ES, Ilina EN, et al. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. BMC Genomics. 2014;15:308.
PubMed
PubMed Central
Google Scholar
Joshi KR, Dhiman H, Scaria V. tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. Database. 2014;2014:bat083.
McEvoy CR, Cloete R, Müller B, Schürch AC, Van Helden PD, Gagneux S, Warren RM, van Pittius NCG. Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints. PLoS One. 2012;7(4):e30593.
CAS
PubMed
PubMed Central
Google Scholar
Bhattacharyya K, Bandopadhyay U, Singh A, Prakash A, Nemaysh V, Jain S, Varma-Basil M, Lynn AM, Bose M, Luthra PM. Modulation of macrophage defense responses by Mycobacterial persistence protein MprA (Rv0981) in human THP-1 cells: effect of single amino acid variation on host-pathogen interactions. bioRxiv. 2020.04.27.063602.
Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protoc. 2013;8(8):1551.
PubMed
PubMed Central
Google Scholar
Joon M, Bhatia S, Pasricha R, Bose M, Brahmachari V. Functional analysis of an intergenic non-coding sequence within mce1 operon of M. tuberculosis. BMC Microbiol. 2010;10(1):128.
PubMed
PubMed Central
Google Scholar
Sharma K, Gupta M, Pathak M, Gupta N, Koul A, Sarangi S, Baweja R, Singh Y. Transcriptional control of the mycobacterial embCAB operon by PknH through a regulatory protein, EmbR, in vivo. J Bacteriol. 2006;188(8):2936–44.
CAS
PubMed
PubMed Central
Google Scholar
Cui Z, Li Y, Cheng S, Yang H, Lu J, Hu Z, Ge B. Mutations in the embC-embA region contribute to M. tuberculosis resistance to ethambutol. Antimicrob Agents Chemother. 2014;58(11):6837–43.
Rastogi N, Labrousse V, Goh KS. In vitro activities of fourteen antimicrobial agents against drug susceptible and resistant clinical isolates of Mycobacterium tuberculosis and comparative intracellular activities against the virulent H37Rv strain in human macrophages. Curr Microbiol. 1996;33(3):167–75.
CAS
PubMed
Google Scholar
Pang Y, Lu J, Wang Y, Song Y, Wang S, Zhao Y. Study of the rifampin monoresistance mechanism in Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2013;57(2):893–900.
CAS
PubMed
PubMed Central
Google Scholar
Comas I, Borrell S, Roetzer A, Rose G, Malla B, Kato-Maeda M, Galagan J, Niemann S, Gagneux S. Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat Genet. 2012;44(1):106.
CAS
Google Scholar
Q-j L, W-w J, Q-q Y, Xu F, Li J-Q, Sun L, Xiao J, Li Y-J, Mokrousov I, Huang H-R. Compensatory mutations of rifampin resistance are associated with transmission of multidrug-resistant Mycobacterium tuberculosis Beijing genotype strains in China. Antimicrob Agents Chemother. 2016;60(5):2807–12.
Google Scholar
Shrivastava K, Garima K, Narang A, Bhattacharyya K, Vishnoi E, Singh RK, Chaudhry A, Prasad R, Bose M, Varma-Basil M. Rv1458c: a new diagnostic marker for identification of Mycobacterium tuberculosis complex in a novel duplex PCR assay. J Med Microbiol. 2017;66(3):371–6.
CAS
PubMed
Google Scholar
Varma-Basil M, Garima K, Pathak R, Dwivedi SKD, Narang A, Bhatnagar A, Bose M. Development of a novel PCR restriction analysis of the hsp65 gene as a rapid method to screen for the Mycobacterium tuberculosis complex and nontuberculous mycobacteria in high-burden countries. J Clin Microbiol. 2013;51(4):1165–70.
CAS
PubMed
PubMed Central
Google Scholar
Singh A, Kashyap VK. Specific and rapid detection of Mycobacterium tuberculosis complex in clinical samples by polymerase chain reaction. Interdiscip Perspect Infect Dis. 2012;2012:654694.
Bose M, Chander A, Das R. A rapid and gentle method for the isolation of genomic DNA from mycobacteria. Nucleic Acids Res. 1993;21(10):2529.
CAS
PubMed
PubMed Central
Google Scholar
Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
CAS
PubMed
PubMed Central
Google Scholar
Li H, Ruan J, Durbin R. Maq: mapping and assembly with qualities. Version. 2008;06:3.
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows–wheeler transform. Bioinformatics. 2009;25(14):1754–60.
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9.
PubMed
PubMed Central
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J. From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43(1):11.10. 11–11.10. 33.
Google Scholar
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–76.
Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2009;26(1):127–9.
PubMed
PubMed Central
Google Scholar
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
PubMed
PubMed Central
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.
CAS
PubMed
Google Scholar
Zdobnov EM, Apweiler R. InterProScan–an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001;17(9):847–8.
CAS
PubMed
Google Scholar
Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812–4.
CAS
PubMed
PubMed Central
Google Scholar
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y. Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition. Mol Cell. 2017;66(2):169–79 e168.
CAS
PubMed
PubMed Central
Google Scholar
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785–91.
CAS
PubMed
PubMed Central
Google Scholar
Johansson MU, Zoete V, Michielin O, Guex N. Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics. 2012;13(1):173.
PubMed
PubMed Central
Google Scholar
Fuhrmann J, Rurainski A, Lenhof HP, Neumann D. A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem. 2010;31(9):1911–8.
CAS
PubMed
Google Scholar