publications.md

Error in user YAML: Alias parsing is not enabled.

---
layout: article
titles:
  en      : &EN       Publications
  en-GB   : *EN
  en-US   : *EN
  en-CA   : *EN
  en-AU   : *EN
  zh-Hans : &ZH_HANS  关于
  zh      : *ZH_HANS
  zh-CN   : *ZH_HANS
  zh-SG   : *ZH_HANS
  zh-Hant : &ZH_HANT  關於
  zh-TW   : *ZH_HANT
  zh-HK   : *ZH_HANT
  ko      : &KO
  ko-KR   : *KO
key: page-publications
---

Full citations and indices can be found on my Google Scholar page

Current indices: H-index 29 2019

• GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions; MR Farhat, L Freschi, R Calderon, T Ioerger, M Snyder, CJ Meehan, ...; Nature communications; 10 (1), 2128; 2019
  
  
• Mycobacterium ulcerans population genomics to inform on the spread of Buruli ulcer across central Africa; K Vandelannoote, DM Phanzu, K Kibadi, M Eddyani, CJ Meehan, ...; mSphere; 4 (1), e00472-18; 2019
  
  
• A genome-based species taxonomy of the Lactobacillus Genus Complex; S Wittouck, S Wuyts, CJ Meehan, V van Noort, S Lebeer; bioRxiv; 537084; 2019
  
  
• Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues; CJ Meehan, GA Goig, TA Kohl, L Verboven, A Dippenaar, M Ezewudo, ...; Nature Reviews Microbiology; 1; 2019
  
  
• Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium; E Tortoli, CJ Meehan, A Grottola, GF Serpini, A Fabio, A Trovato, ...; Infection, Genetics and Evolution; 75, 103983; 2019
  
  
• Ethical Considerations for Movement Mapping to Identify Disease Transmission Hotspots.; BC de Jong, BM Gaye, J Luyten, B van Buitenen, E Andr√©, CJ Meehan, ...; Emerging infectious diseases; ; 2019
  
  
• Storage of Sputum in Cetylpyridinium Chloride, OMNIgene. SPUTUM, and Ethanol Is Compatible with Molecular Tuberculosis Diagnostic Testing; CND Sanoussi, BC de Jong, D Affolabi, CJ Meehan, M Odoun, L Rigouts; Journal of clinical microbiology; 57 (7), e00275-19; 2019
  
  
• Superimposing incident sexually transmitted infections on HIV phylogram to investigate possible misclassification of men who have sex with men as heterosexuals in a cohort in Antwerp, Belgium.; KK Osbak*, CJ Meehan*, S G Ribas, L Heyndrickx, KK Ari√´n, ...; International Journal of STD & AIDS; 9.56462E+14; 2019
  
  
• The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia; MI Gr√∂schel, CJ Meehan, I Barilar, M Diricks, A Gonzaga, M Steglich, ...; bioRxiv; 748954; 2019
  
  
• Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data; KCS Ng, JCS Ngabonziza, P Lempens, BC de Jong, F van Leth, ...; bioRxiv; 628099; 2019
  
  

2018

• Comparative genomics shows that Mycobacterium ulcerans migration and expansion preceded the rise of buruli ulcer in Southeastern Australia; AH Buultjens, K Vandelannoote, CJ Meehan, M Eddyani, BC de Jong, ...; Appl. Environ. Microbiol.; 84 (8), e02612-17; 2018
  
  
• The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology; CJ Meehan, P Moris, TA Kohl, J Peƒçerska, S Akter, M Merker, C Utpatel, ...; EBioMedicine; 37, 410-416; 2018
  
  
• Xpert Ultra can unambiguously identify specific rifampicin resistance-conferring mutations; KCS Ng, A van Deun, CJ Meehan, G Torrea, M Driesen, S Gabri√´ls, ...; Journal of clinical microbiology, JCM.; 00686-18; 2018
  
  
• Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high-confidence resistance-conferring mutations; P Lempens, CJ Meehan, K Vandelannoote, K Fissette, P de Rijk, ...; Scientific reports; 8 (1), 3246; 2018
  
  
• The repetitive element RLEP is a highly specific target for detection of Mycobacterium leprae; S Braet, K Vandelannoote, CJ Meehan, ANB Fontes, E Hasker, PS Rosa, ...; Journal of clinical microbiology; 56 (3), e01924-17; 2018
  
  
• Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches; ID Otchere, M Coscoll√°, L S√°nchez-Bus√≥, A Asante-Poku, D Brites, ...; Scientific reports; 8 (1), 11269; 2018
  
  
• Potential application of digitally linked tuberculosis diagnostics for real-time surveillance of drug-resistant tuberculosis transmission: validation and analysis of test results; KC Ng, CJ Meehan, G Torrea, L Goeminne, M Diels, L Rigouts, ...; JMIR medical informatics; 6 (1), e12; 2018
  
  
• Candidate Treponema pallidum biomarkers uncovered in urine from individuals with syphilis using mass spectrometry; KK Osbak, GA Van Raemdonck, M Dom, CE Cameron, CJ Meehan, ...; Future microbiology; 13 (13), 1497-1510; 2018
  
  
• Whole genome sequence of Mycobacterium kansasii isolates of the genotype 1 from Brazilian patients with pulmonary disease demonstrates considerable heterogeneity; E Machado, SEG Vasconcellos, C Cerdeira, LL Gomes, R Junqueira, ...; Mem Inst Oswaldo Cruz.; 113 (9); 2018
  
  

2017

• Genomic characterization of Nontuberculous Mycobacteria; T Fedrizzi*, CJ Meehan*, A Grottola, E Giacobazzi, GF Serpini, ...; Scientific Reports; 7; 2017
  
  
• Modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments and its impact on gene expression; F Dumetz, H Imamura, M Sanders, V Seblova, J Myskova, P Pescher, ...; mBio; 8 (3), e00599-17; 2017
  
  
• The new phylogeny of the genus Mycobacterium: the old and the news; E Tortoli*, T Fedrizzi*, CJ Meehan*, A Trovato, A Grottola, E Giacobazzi, ...; Infection, Genetics and Evolution; 56, 19-25; 2017
  
  
• Multiple Introductions and Recent Spread of the Emerging Human Pathogen Mycobacterium ulcerans across Africa; K Vandelannoote, CJ Meehan, M Eddyani, D Affolabi, DM Phanzu, ...; Genome biology and evolution; 9 (3), 414-426; 2017
  
  
• Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum; B Cuypers, F Van den Broeck, N Van Reet, CJ Meehan, J Cauchard, ...; Genome biology and evolution; 9 (8), 1990-1997; 2017
  
  
• The predominance of Ethiopian specific Mycobacterium tuberculosis families and minimal contribution of Mycobacterium bovis in tuberculous lymphadenitis patients in Southwest Ethiopia.; M Tadesse, G Abebe, A Bekele, M Bezabih, P de Rijk, CJ Meehan, ...; Infection, Genetics and Evolution; 55, 251-259; 2017
  
  
• Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum; B Ofori-Anyinam, G Dolganov, T Van, JL Davis, ND Walter, BJ Garcia, ...; Tuberculosis; 104, 58-64; 2017
  
  
• Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease; C Van Leuvenhaege, K Vandelannoote, D Affolabi, F Portaels, G Sopoh, ...; PloS one; 12 (7), e0181994; 2017
  
  
• Tuberculosis resistance-conferring mutations with fitness cost among HIV-positive individuals in Uganda; W Ssengooba, D Lukoye, CJ Meehan, DP Kateete, ML Joloba, ...; The International Journal of Tuberculosis and Lung Disease; 21 (5), 531-536; 2017
  
  

2016

• Unexpected high prevalence of resistance-associated Rv0678 variants in MDR-TB patients without documented prior use of clofazimine or bedaquiline; C Villellas, N Coeck, CJ Meehan, N Lounis, B de Jong, L Rigouts, ...; Journal of Antimicrobial Chemotherapy; 72 (3), 684-690; 2016
  
  
• Diagnosis of bacterial bloodstream infections: a 16S metagenomics approach; S Decuypere*, CJ Meehan*, S Van Puyvelde, T De Block, J Maltha, ...; PLoS Negl Trop Dis; 10 (2), e0004470; 2016
  
  
• Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda; W Ssengooba, CJ Meehan, D Lukoye, GW Kasule, K Musisi, ML Joloba, ...; Infection, Genetics and Evolution; 40, 8-16; 2016
  
  
• Characterizing the syphilis-causing Treponema pallidum ssp. pallidum proteome using complementary mass spectrometry; KK Osbak, S Houston, KV Lithgow, CJ Meehan, M Strouhal, D ≈†majs, ...; PLoS neglected tropical diseases; 10 (9), e0004988; 2016
  
  
• Apolipoprotein L1 variant associated with increased susceptibility to trypanosome infection; B Cuypers, L Lecordier, CJ Meehan, F Van den Broeck, H Imamura, ...; mBio; 7 (2), e02198-15; 2016
  
  
• Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients; W Ssengooba, BC de Jong, ML Joloba, FG Cobelens, CJ Meehan; BMC infectious diseases; 16 (1), 371; 2016
  
  
• Discovery of an expanded set of avian leukosis subgroup E proviruses in chickens using Vermillion, a novel sequence capture and analysis pipeline; K Rutherford, CJ Meehan, MGI Langille, SG Tyack, JC McKay, ...; Poultry science; 95 (10), 2250-2258; 2016
  
  

2015

• Specific gyrA gene mutations predict poor treatment outcome in MDR-TB; L Rigouts, N Coeck, M Gumusboga, WB de Rijk, KJM Aung, MA Hossain, ...; Journal of Antimicrobial Chemotherapy; 71 (2), 314-323; 2015
  
  
• Characterizing the diverse mutational pathways associated with R5-tropic maraviroc resistance: HIV-1 that uses the drug-bound CCR5 coreceptor; X Jiang, F Feyertag, CJ Meehan, GP McCormack, SA Travers, C Craig, ...; Journal of virology; 89 (22), 11457-11472; 2015
  
  
• Frailty and the Microbiome; CJ Meehan, MGI Langille, RG Beiko; Frailty in Aging; 41, 54-65; 2015
  
  
• A genomic approach to resolving relapse versus reinfection among four cases of Buruli ulcer; M Eddyani, K Vandelannoote, CJ Meehan, S Bhuju, JL Porter, J Aguiar, ...; PLoS neglected tropical diseases; 9 (11), e0004158; 2015
  
  

2014

• A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria; CJ Meehan, RG Beiko; Genome Biology and Evolution; 6 (3), 703-713; 2014
  
  
• Microbial shifts in the aging mouse gut; MGI Langille, CJ Meehan, JE Koenig, AS Dhanani, RA Rose, SE Howlett, ...; Microbiome; 2 (1), 50; 2014
  
  
• Interactions in the microbiome: communities of organisms and communities of genes; E Boon*, CJ Meehan*, C Whidden, DHJ Wong, MGI Langille, RG Beiko, ...; FEMS microbiology reviews; 38 (1), 90-118; 2014
  
  

2013

• Being Aquifex aeolicus: Untangling a Hyperthermophile‚Äôs Checkered Past; RJM Eveleigh, CJ Meehan, JM Archibald, RG Beiko; Genome biology and evolution; 5 (12), 2478-2497; 2013
  
  

2012

• The evolution of the class A scavenger receptors; FJ Whelan, CJ Meehan, GB Golding, BJ McConkey, DME Bowdish; BMC evolutionary biology; 12 (1), 227; 2012
  
  
• Lateral gene transfer of an ABC transporter complex between major constituents of the human gut microbiome; CJ Meehan, RG Beiko; BMC microbiology; 12 (1), 248; 2012
  
  
• Human microbiome: a genetic bazaar for microbes?; MGI Langille, CJ Meehan, RG Beiko; Current Biology; 22 (1), R20-R22; 2012
  
  

2010

• Emergence, dominance, and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection; CJ Meehan, JA Hedge, DL Robertson, GP McCormack, SAA Travers; Journal of medical virology; 82 (12), 2004-2012; 2010