Staff Profile

Qualifications

PhD - Molecular cell biology of epithelial cells, membrane trafficking of the pIgR, University of Lausanne

BSc - Biochemistry, Zoology, Molecular Biology, University of Lausanne

Previous Positions

Senior Lecturer, Institute for Cell and Molecular Biosciences, Newcastle University, (2007-2013)

Senior Lecturer, School of Biology, Newcastle University, (2004-2007)

Senior Research Officer, Department of Zoology, The Natural History Museum, London, (2000-2004)

Honours and Awards

Wellcome Trust University Award, equivalent to a Senior Lecturer position, at the Department of Zoology, The Natural History Museum, London (2000-2005). Interrupted in May 2004 to move to Newcastle University

Wellcome Trust Research Fellow (Career Development Fellowship) at the Department of Zoology, The Natural History Museum, London (1996-2000)

Languages

French - mother tongue

German - basic conversation

Spanish - very basic conversation

Membership of learned societies

British Society of Parasitology (UK)

• Member of the BSP council (2018-22): Liaison with Learned Societies

Microbiology Society (UK)

• Member of the council (2021-23): Eukaryotic Division
• Member of the council (2024): Eukaryotic Division, Chair Elect

The Genetics Society (UK)

Society for Mucosal Immunology

Editorial Roles for Research Journals

Journal of Medical Microbiology (Microbiology Society, UK) - Editor (One Health – Emerging, Zoonotic and Environmental Diseases) (IF: 3.1)

Frontiers in Parasitology - Associate Editor (Molecular Cellular Parasitology) (IF: NA)

Frontiers in Cellular and Infection Microbiology - Review Editor (Parasite and Host) (IF: 4.3)

Systematic Biology (OUP) - Editorial Board Member (IF: 15.7)

Google Scholar and Web Of Science profiles

GS: https://scholar.google.com/citations?hl=en&user=gDZycOwAAAAJ

WOS: https://www.webofscience.com/wos/author/record/1060960

Research Interests

My lab uses microbial parasites as model systems to study eukaryote cell and genome evolution. This work also leads to new insights into the molecular basis of host-parasite and parasite-microbiota interactions. My research focus on the mucosal extracellular parasite Trichomonads and the intracellular parasites Microsporidia infecting human and/or animals. Topics include the role of lateral gene transfer and gene duplications in parasite genome evolution, surface and secreted proteins mediating host-parasite and parasite-microbiota interactions and mucosal microbiology. Studies of parasite-microbiota interactions at the digestive tract (gut and oral cavity), the urogenital tract and the respiratory tract also contribute at deciphering the molecular and cellular basis of parasite zoonotic infections.

Aims

• Provide a better understanding of eukaryote origins and diversification through comparative genomics and molecular phylogenetics

• Broaden comparative molecular and cellular studies of eukaryotes to provide a more comprehensive picture of their condition

• Contribute to deciphering the molecular and cellular basis of mucosal microbes interactions with their hosts, including the host microbiota, integrating both pathogens (microbial parasites) and mutualists (including bacteria)

Current Work

My research has the following research foci:

1) Comparative, Evolutionary and Functional Genomics

We are using comparative genomics and transcriptomics to investigate (i) the contrasting roles of vertical and horizontal inheritance, (ii) the role of gene duplications in shaping eukaryotic genomes and (iii) the functional importance of specific genes central to host-parasite and parasite-microbiota interactions. These investigations focuses on gene families acquired through horizontal gene transfer and those encoding proteins orchestrating (a) membrane trafficking and (b) host-parasite and parasite-microbiota interactions. These investigations also lead to new insights into human-microbiota interactions contributing to both health or disease.

2) Molecular and cellular basis of Trichomonas species pathobiology

We are investigating the molecular and cellular basis of Trichomonas-Bacteria and Trichomonas-Fungi interactions and their potential impact on their hosts. We employ comparative approaches across several species infecting different mucosal surfaces and hosts, including human and animal hosts. Models include Trichomonas vaginalis (the most common human cellular STI worldwide), Trichomonas tenax (a common obligate oral symbiont of humans and animals strongly associated with periodontitis) and Trichomonas gallinae (a common obligate symbiont of the upper digestive tracts of columbiformes, which can cause the disease canker). All three species can cause damaging inflammatory diseases in their hosts.

3) Microsporidia molecular and cellular pathobiology and genome / cellular reductive evolution

We are investigating the interplay between the strict obligate intracellular pathogens Microsporidia and the host cellular responses with a main focus on mammalian epithelial cells. We are interested in how Microsporidia-host cell interactions are modulated by host autophagy and bacterial secondary metabolites common in the human gut and key for gut epithelial cells energy and metabolism. We use the model system Encephalitozoon cuniculi and Trachipleistophora hominis.

We also investigate the highly divergent genes/proteins, cellular machines and organelles that characterise Microsporidia. The represent fascinating cases of functional divergence often challenging our understanding of eukaryotes molecular cell biology.

Postgraduate Supervision

Supervision of MSc, MSci and MRes students (up to two per year)

Supervision of PhD students:

- Lenshina Mpeyako (Commonwealth Scholarship Commission, Newcastle Uni, with Nick Jakubovics and Waldemar Vollmer) (2019-2024)

- Adam Hart (BBSRC-DTP, with Dave Bolam, Lis Lowe and Andrew Jackson Uni Liverpool) (2020-2024)

- Moudy Bin Saleh (PhD studentship-Saudi Government) (2022-2025)

- Israa Asker (PhD studentship-Egyptian Government) (2022-2025)

PhD studentship currently advertised at FindAPhD (BBSRC-DTP):

Trichomonas parasites CAZymes: roles in targeting host glycans and microbial biofilms?

https://www.findaphd.com/phds/project/trichomonas-parasites-cazymes-roles-in-targeting-host-glycans-and-microbial-biofilms/?p182763

Post-doc funding

Saatioiden post-doc funding to Dr Heli Monttinen: 'The potential impact of virus-mediated gene transfer in eukaryotic evolution' (104'760 euros) (2016-2018)

Oskari Huttunen foundation post-doc funding to Dr Heli Monttinen: 'Lateral Gene Transfers from Bacteriophages to Eukaryotes' (40'000 euros) (2018-2019).

Hosting of Research Fellows

MSCA Fellowship to Dr Johan Panek: MicroMAM, 'The mammalian intracellular response to Microsporidia infection', (195'455 euros) (2019-2022).

MSCA Fellowship to Dr Sergey Melnikov: MicroMISTRANS, 'Error-prone protein synthesis in fungal pathogens Microsporidia: its scope and potential therapeutic targeting', (224'934 euros) (2020-2022).

Overview

My teaching is led by my research on the comparative biology of microbial parasites and members of the mucosal microbiota and it aims at inspiring and stimulating students to participate in the process of fundamental research. It also illustrates how new biomedical knowledge can potentially be applied to reduce the impact of infectious diseases and chronic conditions involving host-microbe interactions. My teaching covers a broad range of topics around the molecular cell biology, genomics and evolution of microbial parasites and their bacteria and viral neighbours at mucosal surfaces. We also cover fundamentals of the host mucosal immune system required to protect us from pathogens and how members of the microbiota contribute to numerous aspects of mucosal homeostasis.

Undergraduate Teaching

FMS - School of Biomedical Sciences

Stage 1

- "Cell Biology" - Module CMB1004 (First three lectures)

- "Cell Biology Practical" - Module CMB1011 (Protist cell biology: Paramecium and Euglenids)

- "Microbiology and Immunology" - Module CMB1003 (One lecture: Microbial eukaryotes and parasites) 

- "Genetics" - Module BGM1004 (Four lectures on evolutionary genetics: Major transitions, origins of eukaryotes and modern humans)

Stage 2

- "Clinical Immunology and viral pathogens" - Module BMS2012 (Three lectures on mucosal immunology in relation to viral infections)

- "Health and disease at mucosal surfaces" - Module BMS2015 (Module leader)

- "Evolution" - Module BGM2058 (Four lectures on eukaryote origin and diversity)

- "Microbiology for Dentistry" - Module DEN2108 (one lecture on oral microbial parasites)

Stage 3

- "Evolution and genomics" - Module BGM3056 (Module leader)

- "Mucosal Microbiota and Pathogens" - Module MIC3046 (Module leader)

- "Research Project" - Module CMB3000/CMB3004 (supervision of 1-4 students)  

SAGE - School of Natural and Environmental Sciences (Stage 2 only)

- "Animal parasites" - Module ACE2031 (2 lectures on microbial parasites Trichomonads and Microsporidia)

Postgraduate Teaching

- MRes: "Mitochondrial Biology and Medicine" - Module MMB8034 (one lecture on Mitochondria evolution and diversity)

- MRes: "Human Health and the Impact of Microbial Genomics" - Module MMB8048 (three lectures on microbial pan-/meta-genomes and the human microbiota)

- Supervision of MRes/MSc/MSci students' research project (supervision of 1-2 students/year)

- Supervision of PhD students

Teaching outside Newcastle University

MSc course on Infection Diseases, University of Kent. "Advances in Parasitology" - Module BI855 (Contribute to one extended seminar)

MSc course on Comparative Genomics, ENS, Lyon, France. I have contributed since 2014 to this course. One extended lecture and a Q&A session: http://biologie.ens-lyon.fr/masterbiosciences/presentation-des-ue/les-ue-europe/ue-comparative-genomics

MeBoP: Middle Eastern Biology of Parasitism, University of Bern, Switzerland. I have contributed to this course in 2022 and 2023. International Course for participants from the Middle East, North and Sub-Saharan Africa. One extended lecture on our work on Trichomonads and Microsporidia: https://www.mebop.org/

• Articles

  • Ndeh DA, Nakjang S, Kwiatkowski KJ, Sawyers C, Koropatkin NM, Hirt RP, Bolam DN. A Bacteroides thetaiotaomicron genetic locus encodes activities consistent with mucin O-glycoprotein processing and N- acetylgalactosamine metabolism. Nature Communications 2025, 16, 3485.
  • Mpeyako LA, Hart AJ, Bailey NP, Carlton JM, Henrissat B, Sullivan SA, Hirt RP. Comparative genomics between Trichomonas tenax and Trichomonas vaginalis: CAZymes and candidate virulence factors. Frontiers in Microbiology 2024, 15, 1437572.
  • Schierholz L, Brown CR, Helena-Bueno K, Uversky VN, Hirt RP, Barandun J, Melnikov SV. A Conserved Ribosomal Protein Has Entirely Dissimilar Structures in Different Organisms. Molecular Biology and Evolution 2024, 41(1), msad254.
  • Bailey NP, Hirt RP. Revisiting faecal metatranscriptomics analyses of macaques with idiopathic chronic diarrhoea with a focus on trichomonad parasites. Parasitology 2023, 150(3), 248-261.
  • Barnett MJ, Pinheiro J, Keown JR, Biboy J, Gray J, Lucinescu I-W, Vollmer W, Hirt RP, Simoes-Barbosa A, Goldstone DC. NlpC/P60 peptidoglycan hydrolases of Trichomonas vaginalis have complementary activities that empower the protozoan to control host-protective lactobacilli. PLoS Pathogens 2023, 19(8), e1011563.
  • Al-Jourani O, Benedict ST, Ross J, Layton AJ, van der Peet P, Marando VM, Bailey NP, Heunis T, Manion J, Mensitieri F, Franklin A, Abellon-Ruiz J, Oram SL, Parsons L, Cartmell A, Wright GSA, Basle A, Trost M, Henrissat B, Munoz-Munoz J, Hirt RP, Kiessling LL, Lovering AL, Williams SJ, Lowe EC, Moynihan PJ. Identification of D-arabinan-degrading enzymes in mycobacteria. Nature communications 2023, 14(1), 2233-.
  • Bailey NP, Shao Y, Du S, Foster PG, Fettweis J, Hall N, Wang Z, Hirt RP. Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier. Frontiers in Microbiology 2023, 14, 1242275.
  • Margarita V, Bailey N, Rappelli P, Diaz N, Dessi D, Fettweis JM, Hirt RP, Fiori PL. Two different species of Mycoplasma endosymbionts can influence Trichomonas vaginalis pathophysiology. mBio 2022, 13(3).
  • Sendra KM, Watson AK, Kozhevnikova E, Moore AL, Embley TM, Hirt RP. Inhibition of mitosomal alternative oxidase causes lifecycle arrest of early-stage Trachipleistophora hominis meronts during intracellular infection of mammalian cells. PLoS Pathogens 2022, 18(12), e1011024.
  • Margarita V, Cao LC, Bailey NP, Ngoc THT, Ngo TMC, Nu PAT, Diaz N, Dessi D, Hirt RP, Fiori PL, Rappelli P. Effect of the Symbiosis with Mycoplasma hominis and Candidatus Mycoplasma girerdii on Trichomonas vaginalis Metronidazole Susceptibility. Antibiotics 2022, 11(6), 812.
  • Nicholson D, Salamina M, Panek J, Helena-Bueno K, Brown CR, Hirt RP, Ranson NA, Melnikov SV. Adaptation to genome decay in the structure of the smallest eukaryotic ribosome. Nature communications 2022, 13(1), 591.
  • Monttinen HAW, Bicep C, Williams TA, Hirt RP. The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large. Microbial Genomics 2021, 7(9), 000649.
  • Bailey NP, Velo-Rego E, Hirt RP. Sporadic isolation of Tetratrichomonas species from the cattle urogenital tract. Parasitology 2021, 148(11), 1339-1344.
  • Salloum T, Moussa R, Rahy R, Al Deek J, Khalifeh I, El Hajj R, Hall N, Hirt RP, Tokajian S. Expanded genome-wide comparisons give novel insights into population structure and genetic heterogeneity of Leishmania tropica complex. PLoS Neglected Tropical Diseases 2020, 14(9), e0008684.
  • Lewis WH, Lind AE, Sendra KM, Onsbring H, Williams TA, Esteban GF, Hirt RP, Ettema TJG, Embley TM. Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss. Molecular Biology and Evolution 2020, 37(2), 524-539.
  • Hirt RP. Mucosal microbial parasites/symbionts in health and disease: an integrative overview. Parasitology 2019, 146(9), 1109-1115.
  • Handrich MR, Garg SG, Sommerville EW, Hirt RP, Gould SB. Characterization of the BspA and Pmp protein family of trichomonads. Parasites and Vectors 2019, 12, 406.
  • Major P, Sendra K, Dean P, Williams TA, Watson AK, Thwaites DT, Embley TM, Hirt RP. A new family of cell surface located purine transporters in Microsporidia and related fungal endoparasites. eLife 2019, 8, e47037.
  • Dean P, Sendra KM, Williams TA, Watson AK, Major P, Nakjang S, Kozhevnikova E, Goldberg AV, Kunji ERS, Hirt RP, Embley TM. Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites. Nature Communications 2018, 9, 1709.
  • Pinheiro J, Biboy J, Vollmer W, Hirt RP, Keown JR, Artuyants A, Black MM, Goldstone DC, Simoes-Barbosa A. The Protozoan Trichomonas vaginalis Targets Bacteria with Laterally Acquired NlpC/P60 Peptidoglycan Hydrolases. mBio 2018, 9(6), e01784-18.
  • Freibert SA, Goldberg AV, Hacker C, Molik S, Dean P, Williams TA, Nakjang S, Long SJ, Sendra K, Bill E, Heinz E, Hirt RP, Lucocq JM, Embley TM, Lill R. Evolutionary conservation and in vitro reconstitution of microsporidian iron–sulfur cluster biosynthesis. Nature Communcations 2017, 8, 13932.
  • Margarita V, Rappelli P, Dessì D, Pintus G, Hirt RP, Fiori PL. Symbiotic Association with Mycoplasma hominis Can Influence Growth Rate, ATP Production, Cytolysis and Inflammatory Response of Trichomonas vaginalis. Frontiers in Microbiology 2016, 7, 953.
  • Williams TA, Nakjang S, Campbell SE, Freeman MA, Eydal M, Moore K, Hirt RP, Embley TM, Williams BA. A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian. Molecular Biology and Evolution 2016, 33(8), 2002-2015.
  • Watson AK, Williams TA, Williams BAP, Moore KA, Hirt RP, Embley TM. Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis. BMC Genomics 2015, 16, 983.
  • Dean P, Major P, Nakjang S, Hirt RP, Embley TM. Transport proteins of parasitic protists and their role in nutrient salvage. Frontiers in Plant Science 2014, 5, 153.
  • Heinz E, Hacker C, Dean P, Mifsud J, Goldberg AV, Williams TA, Nakjang S, Gregory A, Hirt RP, Lucocq JM, Kunji ER, Embley TM. Plasma Membrane-Located Purine Nucleotide Transport Proteins are Key Components for Host Exploitation by Microsporidian Intracellular Parasites. PLoS Pathogens 2014, 10(12), e1004547.
  • Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Embley T. Reduction and Expansion in Microsporidian Genome Evolution: New Insights from Comparative Genomics. Genome Biology and Evolution 2013, 5(12), 2285-2303.
  • Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology 2013, 14(2), R19.
  • Heinz E, Williams TA, Nakjnag S, Noël CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Bernhardt J, Dagan T, Hacker C, Lucocq JM, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM. The Genome of the Obligate Intracellular ParasiteTrachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution. PLoS Pathogens 2012, 8(10), e1002979.
  • Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A. Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud. Journal of Integrative Bioinformatics 2012, 9(2), 12.
  • Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR. Data mining the human gut microbiota for therapeutic targets. Briefings in Bioinformatics 2012, 13(6), 751-768.
  • Nakjang S, Ndeh DA, Wipat A, Bolam DN, Hirt RP. A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes. PLoS One 2012, 7(1), 1-18.
  • Kolluru B, Nakjang S, Hirt RP, Wipat A, Ananiadou S. Automatic extraction of microorganisms and their habitats from free text using text mining workflows. Journal of Integrative Bioinformatics 2011, 8(2), 184.
  • Hjort K, Goldberg AV, Tsaousis AD, Hirt RP, Embley TM. Diversity and reductive evolution of mitochondria among microbial eukaryotes. Philosophical Transactions of the Royal Society B: Biological Sciences 2010, 365(1541), 713-727.
  • Simoes-Barbosa A, Hirt RP, Johnson PJ. A metazoan/plant-like capping enzyme and cap modified nucleotides in the unicellular eukaryote Trichomonas vaginalis. PLoS Pathogens 2010, 6(7), e1000999.
  • Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori PL, Hirt RP. Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. BMC Genomics 2010, 11(1), 99.
  • Alsmark UC, Sicheritz-Ponten T, Foster PG, Hirt RP, Embley TM. Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. Methods in Molecular Biology 2009, 532, 489-500.
  • Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proceedings of the National Academy of Sciences 2008, 105(51), 20356-20361.
  • Smid O, Matuskova A, Harris SR, Kucera T, Novotny M, Horvathova L, Hrdy I, Kutejova E, Hirt RP, Embley TM, Janata J, Tachezy J. Reductive Evolution of the Mitochondrial Processing Peptidases of the Unicellular Parasites Trichomonas vaginalis and Giardia intestinalis. PLoS Pathogens 2008, 4(12), e1000243.
  • Goldberg AV, Molik S, Tsaousis AD, Neumann K, Kuhnke G, Delbac F, Vivares CP, Hirt RP, Lill R, Embley TM. Localization and functionality of microsporidian iron-sulphur cluster assembly proteins. Nature 2008, 452(7187), 624-628.
  • Tsaousis AD, Kunji ERS, Goldberg AV, Lucocq JM, Hirt RP, Embley TM. A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi. Nature 2008, 453(7194), 553-556.
  • Dacks B, Liapounova NA, Hampl V, Hirt RP, Embley TM, Gedamu L. Golgi-associated genes in the oxymonad Monocercomonoides sp suggest the presence of a cryptic organelle. Journal of Eukaryotic Microbiology 2007, 54(2), 38S-38S.
  • Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UCM, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van De Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Muller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu C-L, Osoegawa K, De Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik S-B, Logsdon Jr JM, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu C-H, Lee Y-S, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science 2007, 315(5809), 207-212.
  • Andersson JO, Sjogren AM, Horner DS, Murphy CA, Dyal PL, Svard SG, Logsdon Jr JM, Ragan MA, Hirt RP, Roger AJ. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics 2007, 8(51).
  • Andersson JO, Hirt RP, Foster PG, Roger AJ. Evolution of four gene families with patchy phylogenetic distributions: Influx of genes into protist genomes. BMC Evolutionary Biology 2006, 6(27), 18.
  • Lal K, Noel CJ, Field MC, Goulding D, Hirt RP. Dramatic reorganisation of Trichomonas endomembranes during amoebal transformation: A possible role for G-proteins. Molecular and Biochemical Parasitology 2006, 148(1), 99-102.
  • Loftus B, Anderson I, Davies R, Alsmark UCM, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri Jr WA, Clark CG, Embley TM, Barrell B, Fraser CM, Hall N. The genome of the protist parasite Entamoeba histolytica. Nature 2005, 433(7028), 865-868.
  • Lal K, Field MC, Carlton JM, Warwicker J, Hirt RP. Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis. Molecular and Biochemical Parasitology 2005, 143(2), 226-235.
  • Coombs GH, Westrop GD, Suchan P, Puzova G, Hirt RP, Embley TM, Mottram JC, Muller S. The amitochondriate eukaryote Trichomonas vaginalis contains a divergent thioredoxin-linked peroxiredoxin antioxidant system. Journal of Biological Chemistry 2004, 279(7), 5249-5256.
  • Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J, Embley TM. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 2004, 432(7017), 618-622.
  • Davidson CJ, Hirt RP, Lal K, Snell P, Elgar G, Tuddenham EG, McVey JH. Molecular evolution of the vertebrate blood coagulation network. Thrombosis and Haemostasis 2003, 89(3), 420-428.
  • Richards TA, Hirt RP, Williams BA, Embley TM. Horizontal gene transfer and the evolution of parasitic protozoa. Protist 2003, 154(1), 17-32.
  • Hirt RP, Lal K, Pinxteren J, Warwicker J, Healy B, Coombs GH, Field MC, Embley TM. Biochemical and genetic evidence for a family of heterotrimeric G-proteins in Trichomonas vaginalis. Molecular and Biochemical Parasitology 2003, 129(2), 179-189.
  • Baxter NJ, Hirt RP, Bodrossy L, Kovacs KL, Embley TM, Prosser JI, Murrell JC. The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath). Archives of Microbiology 2002, 177(4), 279-289.
  • Hirt RP, Muller S, Embley TM, Coombs GH. The diversity and evolution of thioredoxin reductase: new perspectives. Trends in Parasitology 2002, 18(7), 302-308.
  • Hirt RP, Harriman N, Kajava AV, Embley TM. A novel potential surface protein in Trichomonas vaginalis contains a leucine-rich repeat shared by micro-organisms from all three domains of life. Molecular Biochemistry and Parasitology 2002, 125(1-2), 195-199.
  • Hirt RP, Harriman N, Kajava AV, Embley TM. A novel potential surface protein in Trichomonas vaginalis contains a leucine-rich repeat shared by micro-organisms from all three domains of life. Molecular and Biochemical Parasitology 2002, 125(1-2), 195-199.
  • Williams BA, Hirt RP, Lucocq JM, Embley TM. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 2002, 418(6900), 865-869.
  • Kamynina E, Debonneville C, Hirt RP, Staub O. Liddle's syndrome: a novel mouse Nedd4 isoform regulates the activity of the epithelial Na⁺ channel. Kidney International 2001, 60(2), 466-471.
  • Hirt RP, Logsdon JM, Healy B, Dorey MW, Doolittle WF, Embley TM. Microsporidia are related to Fungi: Evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings Of the National Academy Of Sciences Of the United States Of America 1999, 96(2), 580-585.
  • Hirt RP, Logsdon Jr JM, Healy B, Dorey MW, Doolittle WF, Embley TM. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings of the National Academy of Sciences of the United States of America 1999, 96(2), 580-585.
  • Horner DS, Hirt RP, Embley TM. A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Molecular Biology and Evolution 1999, 16(9), 1280-1291.
  • Embley TM, Hirt RP. Early branching eukaryotes?. Current Opinion in Genetics & Development 1998, 8(6), 624-629.
  • van der Giezen M, Rechinger KB, Svendsen I, Durand R, Hirt RP, Fevre M, Embley TM, Prins RA. A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria. Molecular Microbiology 1997, 23(1), 11-21.
  • Hirt RP, Healy B, Vossbrinck CR, Canning EU, Embley TM. A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria. Current Biology 1997, 7(12), 995-998.
  • Horner DS, Hirt RP, Kilvington S, Lloyd D, Embley TM. Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proceedings of the Royal Society B: Biological Sciences 1996, 263(1373), 1053-1059.
  • Poulain-Godefroy O, Hirt RP, Fasel N, Kraehenbuhl JP. The polymeric immunoglobulin receptor: signals for polarized expression. Advances in Experimental Medicine and Biology 1995, 371A, 217-220.
  • Hirt RP, Dyal PL, Wilkinson M, Finlay BJ, Roberts DM, Embley TM. Phylogenetic relationships among karyorelictids and heterotrichs inferred from small subunit rRNA sequences: resolution at the base of the ciliate tree. Molecular Phylogenetics and Evolution 1995, 4(1), 77-87.
  • Embley TM, Finlay BJ, Dyal PL, Hirt RP, Wilkinson M, Williams AG. Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates. Proceedings of the Royal Society B: Biological Sciences 1995, 262(1363), 87-93.
  • Finlay BJ, Esteban G, Clarke KJ, Williams AG, Embley TM, Hirt RP. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiology Letters 1994, 117(2), 157-61.
  • Hirt RP, Fasel N, Kraehenbuhl JP. Inducible protein expression using a glucocorticoid-sensitive vector. Methods in Cell Biology 1994, 43, Pt. A, 247-262.
  • Embley TM, Hirt RP, Williams DM. Biodiversity at the molecular level: the domains, kingdoms and phyla of life. Philosophical Transactions of the Royal Society of London: Biological Sciences 1994, 345(1311), 21-33.
  • Hirt RP, Hughes GJ, Frutiger S, Michetti P, Perregaux C, Poulain-Godefroy O, Jeanguenat N, Neutra MR, Kraehenbuhl JP. Transcytosis of the polymeric Ig receptor requires phosphorylation of serine 664 in the absence but not the presence of dimeric IgA. Cell 1993, 74(2), 245-255.
  • Hirt RP, Poulain-Godefroy O, Billotte J, Kraehenbuhl JP, Fasel N. Highly inducible synthesis of heterologous proteins in epithelial cells carrying a glucocorticoid-responsive vector. Gene 1992, 111(2), 199-206.

• Book Chapters

  • Hirt RP, de Miguel N, Nakjang S, Dessi D, Liu YC, Diaz N, Rappelli P, Acosta-Serrano A, Fiori PL, Mottram JC. Trichomonas vaginalis Pathobiology: New Insights from the Genome Sequence. In: Rollinson, D., Hay, S.I, ed. Advances in Parasitology. London: Academic Press, 2011, pp.87-140.
  • Carlton JM, Malik SB, Sullivan SA, Sicheritz-Ponten T, Tang P, Hirt RP. Trichomonas vaginalis genome. In: Clark, CG; Johnson, PJ; Adam, RD, ed. Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. Portland, USA: Caister Academic Press, 2010, pp.45-80.
  • Williams BA, Hirt RP. RACE and RAGE cloning in parasitic microbial eukaryotes. In: Schatten, H, ed. Germ Cell Protocols: Volume 1: Sperm and Oocyte Analysis. New York, USA: Humana Press, 2004, pp.151-172.
  • Horner DS, Hirt RP. An overview on eukaryote origins and evolution: the beauty of the cell and the fabulous gene phylogenies. In: R. P. Hirt;D. S. Horner, ed. Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Boca Raton, USA: CRC Press, 2004, pp.1-23.
  • Horner DS, Hirt RP, Embley TM. Molecular phylogeny of Trichomonads and Naegleria: implication for the relative timing of the mitochondrion endosymbiosis. In: G.H. Coombs; K. Vickermann; M.A. Sleigh; A. Warren, ed. Evolutionary relationships among protozoa. London: Chapmann & Hall - Kluwer Academy Publisher, 1998, pp.133-148.
  • Hirt RP, Wilkinson M, Embley TM. Molecular and cellular evolution of ciliates: a phylogenetic perspective. In: G.H. Coombs; K. Vickermann; M.A. Sleigh; A. Warren, ed. Evolutionary relationships among protozoa. London: Chapmann & Hall - Kluwer Academy Publisher, 1998, pp.327-340.
  • Hughson EJ, Hirt RP. Assessment of cell polarity. In: A.J. Shaw, ed. Epithelial cell culture: a practical approach. Oxford: IRL Press-Oxford University Press, 1996, pp.37-66.
  • Kraehenbuhl JP, Michetti P, Hirt R, Perregaux C, Mekalanos J, Neutra MR. Role of transepithelial transport in triggering a mucosal immune response and in delivery of mucosal antibodies into secretions. In: P.J. Courtoy, ed. Endocytosis: from Cell Biology to Health, Disease and Therapy. Berlin, Heidelberg: Springer-Verlag, 1992, pp.363-366.
  • Michetti P, Hirt R, Weltzin R, Fasel N, Schaerer E, Neutra MR, Kraehenbuhl JP. Production and use of monoclonal IgA antibodies complexed with recombinant secretory component for passive mucosal protection. In: J. Mestecky et al, ed. Immunology of Milk and the Neonate. New York: Plenum Press, 1991, pp.183-185.

• Edited Book

  • Hirt RP, Horner DS, ed. Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. Boca Raton, Florida, USA: CRC Press, 2004.

• Letter

  • Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends in Ecology and Evolution 2007, 22(3), 114-115.

• Note

  • Simoes-Barbosa A, McRae KM, Waghorn TS, Dolezal P, Ralston KS, Bilic I, Hirt RP, Sullivan SA, Nozaki T. ICAP 2024: anaerobic protozoology in focus, a partnership with parasitology societies in the South Pacific. Trends in Parasitology 2024, 40(11), 935-941.

• Reviews

  • Salloum T, Tokajian S, Hirt RP. Advances in Understanding Leishmania Pathobiology: What does RNA-Seq Tell Us?. Frontiers in Cell and Developmental Biology 2021, 9, 702240.
  • Dean P, Hirt RP, Embley TM. Microsporidia: why make nucleotides if you can steal them?. PLoS Pathogens 2016, 12(11), e1005870.
  • Hirt RP, Sherrard J. Trichomonas vaginalis origins, molecular pathobiology and clinical considerations. Current Opinion in Infectious Diseases 2015, 28(1), 72-79.
  • Hirt RP, Alsmark C, Embley TM. Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites. Current Opinion in Microbiology 2015, 23(1), 155–162.
  • Maritz JM, Land KM, Carlton JM, Hirt RP. What is the importance of zoonotic trichomonads for human health?. Trends in Parasitology 2014, 30(7), 333-341.
  • Hirt RP. Trichomonas vaginalis virulence factors: an integrative overview. Sexually Transmitted Infections 2013, 89, 439-443.
  • Clark CG, Alsmark UCM, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noel CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillen N, Duchene M, Nozaki T, Hall N. Structure and Content of the Entamoeba histolytica Genome. Advances in Parasitology 2007, 65, 51-190.
  • Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J, Fiori P-L. Trichomonas vaginalis surface proteins: a view from the genome. Trends in Parasitology 2007, 23(11), 540-547.