Dr

Roy

Chaudhuri

All publications

Journal articles

• Bah SY, Khalid H, Jabang S, Chaudhuri RR, Tilley L, Green LR, Partridge D, de Silva TI & Turner CE (2026) Molecular analysis of Lancefield group C/G streptococci causing human infections in Sheffield, UK. Microbial Genomics, 12(5).
• Fisher H, de Lussy Kubisa L, Jakhmola A, Walker E, Kirk JA, Oatley P, Chaudhuri RR, Douce GR, Ormsby MJ & Fagan RP (2026) A set of genetic tools for use in Clostridioides difficile and related species. Microbiology, 172(2).
• Buddle JE, Thompson LM, Williams AS, Wright RCT, Durham WM, Turner CE, Chaudhuri RR, Brockhurst MA & Fagan RP (2024) Identification of pathways to high-level vancomycin resistance in Clostridioides difficile that incur high fitness costs in key pathogenicity traits. PLOS Biology, 22(8). View this article in WRRO
• Hall JN, Bah SY, Khalid H, Brailey A, Coleman S, Kirk T, Hussain N, Tovey M, Chaudhuri RR, Davies S , Tilley L et al (2024) Molecular characterization of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022–2023 UK upsurge. Microbial Genomics, 10(8). View this article in WRRO
• Hassan MU, Chaudhuri RR & Williamson MP (2023) DUF916 and DUF3324 in the WxL protein cluster bind to WxL and link bacterial and host surfaces. Protein Science, 32(11). View this article in WRRO
• Ormsby MJ, Vaz F, Kirk JA, Barwinska-Sendra A, Hallam JC, Lanzoni-Mangutchi P, Cole J, Chaudhuri RR, Salgado PS, Fagan RP & Douce GR (2023) An intact S-layer is advantageous to Clostridioides difficile within the host. PLOS Pathogens, 19(6). View this article in WRRO
• Bah S, Keeley A, Armitage E, Khalid H, Chaudhuri R, Senghore E, Manneh J, Tilley L, Marks M, Darboe S , Sesay A et al (2023) Genomic characterization of skin and soft tissue Streptococcus pyogenes isolates from a low-income and a high-income setting. mSphere, 8(1). View this article in WRRO
• Qiu S, Bradley JM, Zhang P, Chaudhuri R, Blaxter M, Butlin RK & Scholes JD (2022) Genome-enabled discovery of candidate virulence loci in Striga hermonthica, a devastating parasite of African cereal crops. New Phytologist, 236(2), 622-638. View this article in WRRO
• Court EK, Chaudhuri RR, Kapoore RV, Villa RX, Pandhal J, Biggs CA & Stafford GP (2021) Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site. Microbiology, 167(12). View this article in WRRO
• Bossé JT, Li Y, Leanse LG, Zhou L, Chaudhuri RR, Peters SE, Wang J, Maglennon GA, Holden MTG, Maskell DJ , Tucker AW et al (2021) Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS). Animal Diseases, 1(1).
• Nlebedim VU, Chaudhuri RR & Walters K (2021) Corrigendum to: Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries. Bioinformatics, 37(19), 3387-3387.
• Nlebedim VU, Chaudhuri RR & Walters K (2021) Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries. Bioinformatics, 37(23), 4343-4349. View this article in WRRO
• Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M , Adriaenssens EM et al (2021) Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ, 9.
• Janganan TK, Mullin N, Dafis-Sagarmendi A, Brunt J, Tzokov SB, Stringer S, Moir A, Chaudhuri RR, Fagan RP, Hobbs JK & Bullough PA (2020) Architecture and self-assembly of clostridium sporogenes and clostridium botulinum spore surfaces illustrate a general protective strategy across spore formers. mSphere, 5(4). View this article in WRRO
• Haldenby S, Bronowski C, Nelson C, Kenny J, Martinez-Rodriguez C, Chaudhuri R, Williams NJ, Forbes K, Strachan NJ, Pulman J , Winstanley IN et al (2020) Increasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom. PLoS ONE, 15(1).
• Bossé JT, Li Y, Fernandez Crespo R, Angen Ø, Holden MTG, Weinert LA, Maskell DJ, Tucker AW, Wren BW, Rycroft AN & Langford PR (2020) Draft Genome Sequences of the Type Strains of Actinobacillus indolicus (46K2C) and Actinobacillus porcinus (NM319), Two NAD-Dependent Bacterial Species Found in the Respiratory Tract of Pigs. Microbiology Resource Announcements, 9(1).
• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N , Harris D et al (2019) Publisher Correction: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 10(1).
• Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Baym M, Ibba M & Hinton JCD (2019) The fitness landscape of the African salmonella typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid. PLOS Pathogens, 15(9).
• Gray K, Green LR, Chaudhuri RR & Shaw JG (2019) Draft whole-genome sequences of 10 Aeromonas strains from clinical and environmental sources. Microbiology Resource Announcements, 8(30). View this article in WRRO
• Canals R, Chaudhuri RR, Steiner RE, Owen SV, Quinones-Olvera N, Gordon MA, Ibba M & Hinton JCD (2019) The fitness landscape of the AfricanSalmonellaTyphimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid.
• Pattrick CA, Webb JP, Green J, Chaudhuri RR, Collins MO & Kelly DJ (2019) Proteomic profiling, transcription factor modeling, and genomics of evolved tolerant strains elucidate mechanisms of vanillin toxicity in Escherichia coli.. mSystems, 4(4). View this article in WRRO
• de Lussy-Kubisa L, Chaudhuri R & Fagan R (2019) Applying transposon-directed insertion site sequencing to industrially important, solventogenic species Clostridium saccharoperbutylacetonicum. Access Microbiology, 1(1A).
• Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J , Monack DM et al (2019) Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580.. PLoS Biology, 17(1). View this article in WRRO
• Vohra P, Chaudhuri RR, Mayho M, Vrettou C, Chintoan-Uta C, Thomson NR, Hope JC, Hopkins J & Stevens MP (2019) Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle.. BMC Genomics, 20. View this article in WRRO
• Brockmeier SL, Loving CL, Nicholson TL, Wang J, Peters SE, Weinert L, Chaudhuri R, Seilly DJ, Langford PR, Rycroft A , Wren BW et al (2018) Use of Proteins Identified through a Functional Genomic Screen To Develop a Protein Subunit Vaccine That Provides Significant Protection against Virulent Streptococcus suis in Pigs. Infection and Immunity, 86(3). View this article in WRRO
• Howell KJ, Weinert LA, Peters SE, Wang J, Hernandez-Garcia J, Chaudhuri RR, Luan S-L, Angen O, Aragon V, Williamson SM , Langford PR et al (2017) "Pathotyping" Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence. Journal of Clinical Microbiology, 55(9), 2617-2628. View this article in WRRO
• Oshota O, Conway M, Fookes M, Schreiber F, Chaudhuri RR, Yu L, Morgan FJE, Clare S, Choudhary J, Thomson NR , Lio P et al (2017) Transcriptome and proteome analysis of Salmonella enterica serovar Typhimurium systemic infection of wild type and immune-deficient mice. PLoS ONE, 12(8). View this article in WRRO
• Dunne KA, Chaudhuri RR, Rossiter AE, Beriotto I, Browning DF, Squire D, Cunningham AF, Cole JA, Loman N & Henderson IR (2017) Sequencing a piece of history: complete genome sequence of the original Escherichia coli strain. Microbial Genomics, 3. View this article in WRRO
• Bossé JT, Li Y, Rogers J, Fernandez Crespo R, Li Y, Chaudhuri RR, Holden MTG, Maskell DJ, Tucker AW, Wren BW , Rycroft AN et al (2017) Whole Genome Sequencing for Surveillance of Antimicrobial Resistance in Actinobacillus pleuropneumoniae. Frontiers in Microbiology, 8. View this article in WRRO
• Stafford GP, Chaudhuri RR, Haraszthy V, Friedrich V, Schäffer C, Ruscitto A, Honma K & Sharma A (2016) Draft Genome Sequences of Three Clinical Isolates of Tannerella forsythia Isolated from Subgingival Plaque from Periodontitis Patients in the United States.. Genome Announcements, 4(6). View this article in WRRO
• Li Y, Bossé JT, Williamson SM, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR, Peters SE, Weinert LA , Wang JT et al (2016) Actinobacillus pleuropneumoniae serovar 8 predominatesin England and Wales. Veterinary Record, 179(11). View this article in WRRO
• Bossé JT, Li Y, Crespo RF, Chaudhuri RR, Rogers J, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN , Langford PR et al (2016) ICEApl1, an integrative conjugative element related to ICEHin1056, identified in the pig pathogen Actinobacillus pleuropneumoniae. Frontiers in Microbiology, 7:810.
• Chen GE, Hitchcock A, Jackson PJ, Chaudhuri RR, Dickman MJ, Hunter CN & Canniffe DP (2016) Two Unrelated 8-Vinyl Reductases Ensure Production of Mature Chlorophylls in Acaryochloris marina. JOURNAL OF BACTERIOLOGY, 198(9), 1393-1400. View this article in WRRO
• Wielgoss S, Didelot X, Chaudhuri RR, Liu X, Weedall GD, Velicer GJ & Vos M (2016) A barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus. The ISME Journal, 10, 2468-2477.
• Grant AJ, Oshota O, Chaudhuri RR, Mayho M, Peters SE, Clare S, Maskell DJ & Mastroeni P (2016) Genes Required for the Fitness of Salmonella enterica Serovar Typhimurium during Infection of Immunodeficient gp91 −/− phox Mice. Infection and Immunity, 84(4), 989-997.
• Bossé JT, Chaudhuri RR, Li Y, Leanse LG, Fernandez Crespo R, Coupland P, Holden MTG, Bazzolli DM, Maskell DJ, Tucker AW , Wren BW et al (2016) Complete Genome Sequence of MIDG2331, a Genetically Tractable Serovar 8 Clinical Isolate of Actinobacillus pleuropneumoniae. Genome Announcements, 4(1), e01667-15-e01667-15.
• García-Lara J, Weihs F, Ma X, Walker L, Chaudhuri RR, Kasturiarachchi J, Crossley H, Golestanian R & Foster SJ (2015) Supramolecular structure in the membrane of Staphylococcus aureus. Proceedings of the National Academy of Sciences, 112(51), 15725-15730.
• Howell KJ, Peters SE, Wang J, Hernandez-Garcia J, Weinert LA, Luan S-L, Chaudhuri RR, Angen Ø, Aragon V, Williamson SM , Parkhill J et al (2015) Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis. Journal of Clinical Microbiology, 53(12), 3812-3821.
• Baig A, Weinert LA, Peters SE, Howell KJ, Chaudhuri RR, Wang J, Holden MTG, Parkhill J, Langford PR, Rycroft AN , Wren BW et al (2015) Whole genome investigation of a divergent clade of the pathogen Streptococcus suis. Frontiers in Microbiology , 6. View this article in WRRO
• Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MTG, Maskell DJ , Tucker AW et al (2015) Corrigendum to ‘Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae’ [Veterinary Microbiology 178 (2015) 279–282]. Veterinary Microbiology, 179(3-4), 341-341.
• Bossé JT, Li Y, Atherton TG, Walker S, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Holden MTG, Maskell DJ , Tucker AW et al (2015) Characterisation of a mobilisable plasmid conferring florfenicol and chloramphenicol resistance in Actinobacillus pleuropneumoniae. Veterinary Microbiology, 178(3-4), 279-282.
• Bossé JT, Li Y, Walker S, Atherton T, Fernandez Crespo R, Williamson SM, Rogers J, Chaudhuri RR, Weinert LA, Oshota O , Holden MTG et al (2015) Identification of dfrA14 in two distinct plasmids conferring trimethoprim resistance in Actinobacillus pleuropneumoniae. Journal of Antimicrobial Chemotherapy, 70(8), 2217-2222.
• Smith G, Smith C, Kenny JG, Chaudhuri RR & Ritchie MG (2015) Genome-Wide DNA Methylation Patterns in Wild Samples of Two Morphotypes of Threespine Stickleback (Gasterosteus aculeatus). Molecular Biology and Evolution, 32(4), 888-895.
• Moura AE, Kenny JG, Chaudhuri RR, Hughes MA, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N & Hoelzel AR (2015) Phylogenomics of the killer whale indicates ecotype divergence in sympatry. Heredity, 114(1), 48-55.
• Howell KJ, Weinert LA, Chaudhuri RR, Luan S-L, Peters SE, Corander J, Harris D, Angen O, Aragon V, Bensaid A , Williamson SM et al (2014) The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis. BMC Genomics, 15. View this article in WRRO
• Moura AE, Kenny JG, Chaudhuri R, Hughes MA, J. Welch A, Reisinger RR, de Bruyn PJN, Dahlheim ME, Hall N & Hoelzel AR (2014) Population genomics of the killer whale indicates ecotype evolution in sympatry involving both selection and drift. Molecular Ecology, 23(21), 5179-5192.
• Bosse JT, Li Y, Angen O, Weinert LA, Chaudhuri RR, Holden MT, Williamson SM, Maskell DJ, Tucker AW, Wren BW , Rycroft AN et al (2014) Multiplex PCR Assay for Unequivocal Differentiation of Actinobacillus pleuropneumoniae Serovars 1 to 3, 5 to 8, 10, and 12. Journal of Clinical Microbiology, 52(7), 2380-2385.
• Wilson R, Bourne C, Chaudhuri RR, Gregory R, Kenny J & Cossins A (2014) Single-Step Selection of Bivalent Aptamers Validated by Comparison with SELEX Using High-Throughput Sequencing. PLoS ONE, 9(6). View this article in WRRO
• Christiansen MT, Kaas RS, Chaudhuri RR, Holmes MA, Hasman H & Aarestrup FM (2014) Genome-Wide High-Throughput Screening to Investigate Essential Genes Involved in Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Survival. PLoS ONE, 9(2). View this article in WRRO
• Maglennon GA, Cook BS, Deeney AS, Bossé JT, Peters SE, Langford PR, Maskell DJ, Tucker AW, Wren BW & Rycroft AN (2013) Transposon mutagenesis in Mycoplasma hyopneumoniae using a novel mariner-based system for generating random mutations. Veterinary Research, 44(1).
• Capeness MJ, Lambert C, Lovering AL, Till R, Uchida K, Chaudhuri R, Alderwick LJ, Lee DJ, Swarbreck D, Liddell S , Aizawa S-I et al (2013) Activity of Bdellovibrio Hit Locus Proteins, Bd0108 and Bd0109, Links Type IVa Pilus Extrusion/Retraction Status to Prey-Independent Growth Signalling. PLOS ONE, 8(11).
• Maglennon GA, Cook BS, Matthews D, Deeney AS, Bossé JT, Langford PR, Maskell DJ, Tucker AW, Wren BW & Rycroft AN (2013) Development of a self-replicating plasmid system for Mycoplasma hyopneumoniae. Veterinary Research, 44(1).
• Luan S-L, Chaudhuri RR, Peters SE, Mayho M, Weinert LA, Crowther SA, Wang J, Langford PR, Rycroft A, Wren BW , Tucker AW et al (2013) Generation of a Tn5 transposon library in Haemophilus parasuis and analysis by transposon-directed insertion-site sequencing (TraDIS).. Vet Microbiol, 166(3-4), 558-566.
• Howell KJ, Weinert LA, Luan S-L, Peters SE, Chaudhuri RR, Harris D, Angen O, Aragon V, Parkhill J, Langford PR , Rycroft AN et al (2013) Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis.. J Bacteriol, 195(18), 4264-4273.
• Chaudhuri RR, Morgan E, Peters SE, Pleasance SJ, Hudson DL, Davies HM, Wang J, van Diemen PM, Buckley AM, Bowen AJ , Pullinger GD et al (2013) Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals.. PLoS Genet, 9(4), e1003456.
• Dziva F, Hauser H, Connor TR, van Diemen PM, Prescott G, Langridge GC, Eckert S, Chaudhuri RR, Ewers C, Mellata M , Mukhopadhyay S et al (2013) Sequencing and functional annotation of avian pathogenic escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms. Infection and Immunity, 81(3), 838-849.
• Chaudhuri RR & Henderson IR (2012) The evolution of the Escherichia coli phylogeny.. Infect Genet Evol, 12(2), 214-226.
• Chaudhuri RR, Yu L, Kanji A, Perkins TT, Gardner PP, Choudhary J, Maskell DJ & Grant AJ (2011) Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome.. Microbiology (Reading), 157(Pt 10), 2922-2932.
• Clarke DJ, Chaudhuri RR, Martin HM, Campbell BJ, Rhodes JM, Constantinidou C, Pallen MJ, Loman NJ, Cunningham AF, Browning DF & Henderson IR (2011) Complete genome sequence of the crohn's disease-associated adherent-invasive Escherichia coli strain HM605. Journal of Bacteriology, 193(17), 4540-4540.
• Eckert SE, Dziva F, Chaudhuri RR, Langridge GC, Turner DJ, Pickard DJ, Maskell DJ, Thomson NR & Stevens MP (2011) Retrospective application of transposon-directed insertion site sequencing to a library of signature-tagged mini-Tn5Km2 mutants of Escherichia coli O157:H7 screened in cattle. Journal of Bacteriology, 193(7), 1771-1776.
• Knowles TJ, Browning DF, Jeeves M, Maderbocus R, Rajesh S, Sridhar P, Manoli E, Emery D, Sommer U, Spencer A , Leyton DL et al (2011) Structure and function of BamE within the outer membrane and the β-barrel assembly machine.. EMBO Rep, 12(2), 123-128.
• Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL , Savarino SJ et al (2010) A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.. J Bacteriol, 192(21), 5822-5831.
• Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM , Frankel G et al (2010) Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042.. PLoS One, 5(1), e8801.
• Wang J, Chaudhuri RR & Ellar DJ (2010) Characterization of ISBth4, a functional new IS231 variant from Bacillus thuringiensis MEX312.. Plasmid, 63(1), 46-52.
• Chaudhuri RR (2009) MycoDB: an online database for comparative genomics of the mycobacteria and related organisms.. Methods Mol Biol, 465, 419-431.
• Chaudhuri RR, Peters SE, Pleasance SJ, Northen H, Willers C, Paterson GK, Cone DB, Allen AG, Owen PJ, Shalom G , Stekel DJ et al (2009) Comprehensive identification of Salmonella enterica serovar typhimurium genes required for infection of BALB/c mice. Plos Pathogens, 5(7).
• Chaudhuri RR, Allen AG, Owen PJ, Shalom G, Stone K, Harrison M, Burgis TA, Lockyer M, Garcia-Lara J, Foster SJ , Pleasance SJ et al (2009) Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).. BMC Genomics, 10, 291.
• Rasko DA, Rosovitz MJ, Myers GSA, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R , Henderson IR et al (2008) The pangenome structure of Escherichia coli: Comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology, 190(20), 6881-6893.
• Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ & Pallen MJ (2008) xBASE2: a comprehensive resource for comparative bacterial genomics.. Nucleic Acids Res, 36(Database issue), D543-D546.
• Chaudhuri RR, Ren C-P, Desmond L, Vincent GA, Silman NJ, Brehm JK, Elmore MJ, Hudson MJ, Forsman M, Isherwood KE , Gurycová D et al (2007) Genome sequencing shows that European isolates of Francisella tularensis subspecies tularensis are almost identical to US laboratory strain Schu S4.. PLoS One, 2(4), e352.
• Turner SM, Chaudhuri RR, Jiang Z-D, DuPont H, Gyles C, Penn CW, Pallen MJ & Henderson IR (2006) Phylogenetic comparisons reveal multiple acquisitions of the toxin genes by enterotoxigenic Escherichia coli strains of different evolutionary lineages.. J Clin Microbiol, 44(12), 4528-4536.
• Nagy G, Danino V, Dobrindt U, Pallen M, Chaudhuri R, Emödy L, Hinton JC & Hacker J (2006) Down-regulation of key virulence factors makes the Salmonella enterica serovar typhimurium rfaH mutant a promising live-attenuated vaccine candidate. Infection and Immunity, 74(10), 5914-5925.
• Ou HY, Chen LL, Lonnen J, Chaudhuri RR, Thani AB, Smith R, Garton NJ, Hinton J, Pallen M, Barer MR & Rajakumar K (2006) A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria. Nucleic Acids Research, 34(1), e3.
• Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T , Mori H et al (2006) Escherichia coli K-12: A cooperatively developed annotation snapshot - 2005. Nucleic Acids Research, 34(1), 1-9.
• Chaudhuri RR & Pallen MJ (2006) xBASE, a collection of online databases for bacterial comparative genomics.. Nucleic Acids Res, 34(Database issue), D335-D337.
• Ideses D, Gophna U, Paitan Y, Chaudhuri RR, Pallen MJ & Ron EZ (2005) A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis. Journal of Bacteriology, 187(23), 8164-8171.
• Desvaux M, Khan A, Scott-Tucker A, Chaudhuri RR, Pallen MJ & Henderson IR (2005) Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC 824.. Biochim Biophys Acta, 1745(2), 223-253.
• Parham NJ, Pollard SJ, Chaudhuri RR, Beatson SA, Desvaux M, Russell MA, Ruiz J, Fivian A, Vila J & Henderson IR (2005) Prevalence of pathogenicity island IICFT073 genes among extraintestinal clinical isolates of Escherichia coli.. J Clin Microbiol, 43(5), 2425-2434.
• Ou HY, Smith R, Lucchini S, Hinton J, Chaudhuri RR, Pallen M, Barer MR & Rajakumar K (2005) ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes. NUCLEIC ACIDS RESEARCH, 33(1).
• Pallen MJ, Penn CW & Chaudhuri RR (2005) Bacterial flagellar diversity in the post-genomic era.. Trends Microbiol, 13(4), 143-149.
• Zhang L, Chaudhuri RR, Constantinidou C, Hobman JL, Patel MD, Jones AC, Sarti D, Roe AJ, Vlisidou I, Shaw RK , Falciani F et al (2004) Regulators encoded in the Escherichia coli type III secretion system 2 gene cluster influence expression of genes within the locus for enterocyte effacement in enterohemorrhagic E. coli O157:H7.. Infect Immun, 72(12), 7282-7293.
• Ren C-P, Chaudhuri RR, Fivian A, Bailey CM, Antonio M, Barnes WM & Pallen MJ (2004) The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition.. J Bacteriol, 186(11), 3547-3560.
• Chaudhuri RR, Khan AM & Pallen MJ (2004) coliBASE: An online database for Escherichia coli, Shigella and Salmonella comparative genomics. Nucleic Acids Research, 32(DATABASE ISS.), D296-D299.
• Betts HJ, Chaudhuri RR & Pallen MJ (2004) An analysis of type-III secretion gene clusters in Chromobacterium violaceum.. Trends Microbiol, 12(11), 476-482.
• Chaudhuri RR, Khan AM & Pallen MJ (2004) coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics.. Nucleic Acids Res, 32(Database issue), D296-D299.
• Pallen MJ, Chaudhuri RR & Henderson IR (2003) Genomic analysis of secretion systems.. Curr Opin Microbiol, 6(5), 519-527.
• Pallen M, Chaudhuri R & Khan A (2002) Bacterial FHA domains: neglected players in the phospho-threonine signalling game?. Trends Microbiol, 10(12), 556-563.
• Sharp PM, Bailes E, Chaudhuri RR, Rodenburg CM, Santiago MO & Hahn BH (2001) The origins of acquired immune deficiency syndrome viruses: Where and when?. Philosophical Transactions of the Royal Society B Biological Sciences, 356(1410), 867-876.
• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Valimaki N , Harris D et al () Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 6. View this article in WRRO
• Weinert LA, Chaudhuri RR, Wang J, Peters SE, Corander J, Jombart T, Baig A, Howell KJ, Vehkala M, Välimäki N , Harris D et al () Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, 6(1).

Book chapters

• Bailes E, Chaudhuri RR, Santiago ML, Bibollet-Ruche F, Hahn BH & Sharp PM (2002) The Evolution of Primate Lentiviruses and the Origins of AIDS, The Molecular Epidemiology of Human Viruses (pp. 65-96). Springer US
• Chaudhuri RR & Thomas GH () Understanding the Model and the Menace: a Postgenomic View ofEscherichia Coli, Bacterial Pathogenomics (pp. 21-48). ASM Press

Conference proceedings

• Stopic V, Jost S, Haupt J, Brandt G, vander Linden C, Petry-Schmelzer JN, Dembek T, Fink G, Batzu L, Rizos A , Chaudhuri R et al (2024) Validation Study of the Parkinson's disease (PD) Stigma Questionnaire (PDStigmaQuest). MOVEMENT DISORDERS, Vol. 39 (pp S239-S239)
• Campese N, Calio B, Leys F, Kaltenbach L, Goebel G, Wanschitz J, Schlager A, Zamarian L, Bannister K, Chaudhuri R , Schrag A et al (2023) Pain in People with Multiple System Atrophy. MOVEMENT DISORDERS, Vol. 38 (pp S65-S66)
• Rascol O, Poewe W, Stocchi F, Chaudhuri R, Kassube J, Manzanares LL, Leta V, Zhang I, Bowling A, Wu S & Pappert E (2022) Safety and tolerability of apomorphine sublingual film and subcutaneous apomorphine for the treatment of OFF episodes in Parkinson's disease. MOVEMENT DISORDERS, Vol. 37 (pp S348-S348)
• Stocchi F, Rascol O, Poewe W, Chaudhuri R, Kassubek J, Manzanares LL, Leta V, Zhang I, Bowling A, Wu S & Pappert E (2022) Efficacy of apomorphine sublingual film versus subcutaneous apomorphine for the treatment of OFF episodes in Parkinson's Disease. MOVEMENT DISORDERS, Vol. 37 (pp S356-S356)
• Gonzalez-Robles C, Bartlett M, Burnell M, Chapman R, Chaudhuri R, Clarke C, Ellis-Doyle R, Hu M, Huxford B, Jha A , Lawton M et al (2022) Challenges in Outcome Measure Selection in Multi-Arm Multi-Stage Clinical Trials in Parkinson Disease. MOVEMENT DISORDERS, Vol. 37 (pp S329-S329)
• Ben-Joseph A, Haque T, Gallagher D, Budu C, Chaudhuri R, Simonet C & Noyce A (2020) Type 2 diabetes mellitus may worsen severity of motor symptoms in people with Parkinson's disease. MOVEMENT DISORDERS, Vol. 35 (pp S153-S153)

Preprints

• Bah SY, Khalid H, Jabang S, Chaudhuri R, Tilley L, Green LR, Patridge D, de Silva TI & Turner CE (2026) Molecular analysis of Lancefield group C/G streptococci causing human infections in Sheffield, UK, openRxiv.
• Hall JN, Bah SY, Khalid H, Brailey A, Coleman S, Kirk T, Hussain N, Tovey M, Chaudhuri RR, Davies S , Tilley L et al (2024) Molecular characterisation ofStreptococcus pyogenes(StrepA) non-invasive isolates during the 2022-23 UK upsurge, Cold Spring Harbor Laboratory.
• Bah SY, Keeley AJ, Armitage EP, Khalid H, Chaudhuri RR, Senghore E, Manneh J, Tilley L, Marks M, Darboe S , Sesay AK et al (2021) Comparative genomic analysis of skin and soft tissue Streptococcus pyogenes isolates from low- and high-income settings, Cold Spring Harbor Laboratory.
• Gilroy R, Ravi A, Getino M, Pursley I, Horton D, Alikhan N-F, Baker D, Gharbi K, Hall N, Watson M , Adriaenssens EM et al (2020) A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture, Springer Science and Business Media LLC.
• Gilroy R, Ravi A, Getino M, Pursley I, Horton D, Alikhan N-F, Baker D, Gharbi K, Hall N, Watson M , Adriaenssens EM et al (2020) A Genomic Census of the Chicken Gut Microbiome using Metagenomics and Culture, Springer Science and Business Media LLC.
• Gilroy R, Ravi A, Getino M, Pursley I, Horton D, Alikhan N-F, Baker D, Gharbi K, Hall N, Watson M , Adriaenssens EM et al (2020) A Genomic Blueprint of the Chicken Gut Microbiome, Springer Science and Business Media LLC.
• Janganan TK, Mullin N, Dafis-Sagarmendi A, Brunt J, Tzokov SB, Stringer S, Moir A, Chaudhuri R, Fagan RP, Hobbs JK & Bullough PA (2020) Architecture and self-assembly of theClostridium sporogenes/botulinumspore surface illustrate a general protective strategy across spore formers, Cold Spring Harbor Laboratory.
• Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J , Monack DM et al (2018) Adding function to the genome of AfricanSalmonellaST313, Cold Spring Harbor Laboratory.
• Bossé JT, Li Y, Leanse LG, Zhou L, Chaudhuri RR, Peters SE, Wang J, Maglennon GA, Holden MTG, Maskell DJ , Tucker AW et al (2018) Rationally designedmarinervectors to allow functional genomic analysis ofActinobacillus pleuropneumoniaeand other bacteria by transposon-directed insertion-site sequencing (TraDIS), Cold Spring Harbor Laboratory.