Lukeš Julius

Prof., Ph.D.
Born May 14, 1963 in České Budějovice

• Member of Learned Society since 2004 

Professional Experience

• 1991–present: Research Scientist, Institute of Parasitology, České Budějovice
• 1992–2012: Member of the Scientific Board of the Institute of Parasitology
• 1993: Postdoctoral Fellow, E.C.Slater Institute, University of Amsterdam, The Netherlands
• 1995–2022: Head of the Laboratory of Molecular Parasitology, Institute of Parasitology
• 1994–1997: Assistant, Faculty of Biology, University of South Bohemia, České Budějovice
• 1997–1998: Postdoctoral Fellow, Department of Biology, University of California, Riverside
• 1998–1999: Visiting Scientist, Molecular Biology Institute, University of California, Los Angeles 
• 2003–2012: Chair of the Department of Molecular Biology, University of South Bohemia
• 2006–present: Professor, Faculty of Sciences, University of South Bohemia
• 2007–2012: Member of the Scientific Board of the Faculty of Sciences 
• 2008–2013: Member of the Scientific Board of the Faculty of Agriculture
• 2008–2012: Head of the Scientific Board of the Institute of Parasitology  
• 2012–2022: Director of the Institute of Parasitology 
• 2012–2018: Committee member of the International Society of Protistologists
• 2021–present: Vice–head of the principal Scientific Board of the Czech Academy of Sciences

Honors and Awards

• 1993: EMBO Fellowship
• 1995: Fulbright Travel Grant
• 1997: Young Scientist Award of the President of the Czech Academy of Sciences
• 2000–2005: European Councillor of the International Society for Evolutionary Protistology
• 2006–2008: President of the International Society for Evolutionary Protistology
• 2002: Prize of the Czech Academy of Sciences for outstanding young researchers
• 2003–2009: President of the Czech Society of Protozoology
• 2004–present: Member of the Learned Society of the Czech Republic
• 2007: Prize of the Czech Academy of Sciences
• 2007–2009: Vice–president of the International Society of Protistologists
• 2009–2011: Associate of the Canadian Institute for Advanced Research
• 2011: Prize of the Minister of Education for Excellence in Research
• 2012–2017: Senior Fellow of the Canadian Institute for Advanced Research
• 2013–present: Member of the Faculty of 1000
• 2013: Medal from the mayor for merits in research and education
• 2014–present: Fellow of the American Academy for Microbiology
• 2015–present: Fellow of the European Academy of Microbiology
• 2016–present: Member of the Comenius Academic Club
• 2018–present: Fellow of the American Association for the Advancement of Science (AAAS)
• 2020: Prize of the President of the Czech Academy of Sciences for research excellence 
• 2020–present: Member of the scientific board of the Neuron Endowment Fund
• 2023: Member - American Society for Biochemistry and Molecular Biology
• 2023-present: EMBO member
• 2023: J. G. Mendel medal for Achievements in Natural Sciences
• 2023: Prize of the Minister of Education for Excellence in Research
• 2024-present: Member of the U.S. National Academy of Sciences

Invited Lectures

• University of Hannover, Germany, 1991
• University of Amsterdam, The Netherlands, 1993, 1994, 2003
• University of Arizona, Tucson, USA, 1995
• State University of New York, Stony Brook, USA, 1995
• National Institutes of Health, Bethesda, USA, 1995
• Wesleyan University, Middletown, USA, 1997
• Johns Hopkins University, Baltimore, USA, 1997, 2000
• University of California, Los Angeles, USA, 1998, 1999, 2002 
• Charles University, Prague, Czech Republic, 1999, 2006, 2007, 2010 
• School of Hygiene and Tropical Medicine, London, UK, 2000
• Institute of Cytology, St. Petersburg, Russia, 2001
• De Duve Institute of Pathology, Brussels, Belgium, 2002, 2006
• Max–Planck–Institute for Molecular Physiology, Dortmund, Germany, 2002 
• Comenius University, Bratislava, Slovakia, 2003, 2008
• CIRAD, Montpellier, France, 2003
• Sun Yat–Sen University, Guangzhou, China, 2004, 2006, 2007, 2012, 2014
• Humboldt University, Berlin, Germany, 2004
• University of Wroclaw, Wroclaw, Poland, 2004 
• Oregon Health & Science University, Portland, USA, 2004
• New York University, New York, USA, 2004 
• University of Oxford, Oxford, UK, 2004
• University of Melbourne, Melbourne, Australia, 2005
• Canadian Institute for Advanced Research, Vancouver, Canada, 2005, 2006
• Foundation Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil, 2005
• University of Rio de Janeiro, Rio de Janeiro, Brazil, 2005
• Seattle Biomedical Research Institute, Seattle, USA, 2006, 2010
• Université de Montréal, Montréal, Canada, 2006
• South Medical University, Guangzhou, China, 2006 
• Kuvin Centre, Hebrew University, Jerusalem, Israel, 2006
• Technion–Institute of Technology, Haifa, Israel, 2006
• University of California, Riverside, USA, 2007
• Philipps University, Marburg, Germany, 2008
• University of Glasgow, Glasgow, U.K., 2008
• Newcastle University, U.K., 2008
• Canadian Institute for Advanced Research, Quebec, Canada, 2008
• University of Cambridge, U.K., 2008
• Dalhousie University, Halifax, Canada, 2008
• Trinity College, Dublin, Ireland, 2008
• University of Bern, Switzerland, 2008
• University of California, Irvine, USA, 2009
• Ohio State University, Columbus, USA, 2009
• University of Cardiff, Cardiff, U.K., 2010
• University of Brasilia, Brasilia, Brazil, 2010
• Tokyo University, Tokyo, Japan, 2010 
• Seattle Biomed, Seattle, USA, 2010, 2012
• Ohio State University, Columbus, USA, 2011, 2013
• King Abdulah University, Thuwal, Saudi Arabia, 2011
• Molecular Biology Laboratory, Cambridge, U.K., 2011
• University of Heidelberg, Heidelberg, Germany, 2011
• European Molecular Biology Laboratory, Heidelberg, Germany, 2011, 2012
• University of Queensland, Brisbane, Australia, 2011
• Biodiversity Institute, University of British Columbia, Vancouver, Canada, 2012
• University of Strathclyde, Glasgow, U.K., 2012
• University of California, Riverside, USA, 2012
• Philipps University, Marburg, Germany, 2012
• National Institutes of Alergy and Infectious Diseases, Bethesda, USA, 2012
• University of Pennsylvania, Philadelphia, USA, 2012
• University of Exeter, Exeter, U.K., 2012
• Chinese Agricultural University, Beijing, China, 2012
• Ecole Normale Superieure, Lyon, France, 2013 
• Robert Koch Institute, Berlin, Germany, 2013
• Clemson University, Clemson, USA, 2013
• University of South Carolina, Columbia, USA, 2013
• Institut Pasteur, Paris, France, 2013
• University of St. Andrews, St. Andrews, U.K., 2014
• Institute of Tropical Medicine, Havana, Cuba, 2014
• East China University of Science and Technology, Shanghai, China, 2014
• Beckman Centre, University of California, Irvine, USA, 2015
• University of Arizona, Tucson, USA, 2015
• Instituto Oswaldo Cruz, Rio de Janeiro, Brazil, 2015
• University of Cambridge, Cambridge, U.K., 2015
• Kavli Institute for Theoretical Physics, Santa Barbara, USA, 2015 
• Institut Pasteur, Paris, France, 2015
• Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia, 2016
• University of Kent, Canterbury, U.K., 2016
• University of Kaiserslautern, Kaiserslautern, Germany, 2016
• University of Wurzburg, Wurzburg, Germany, 2016
• Duke University, Durham, USA, 2017
• Ohio State University, Columbus, USA, 2017
• State University of New York, Buffalo, USA, 2017
• Université de la Reunion, St. Denis, France, 2017
• Gdansk University, Gdansk, Poland, 2017 
• London School of Hygiene and Tropical Medicine, London, U.K., 2017
• École Normal Superieure, Lyon, France, 2017
• Ahmed Ben Bella University, Oran, Algeria, 2017
• Canadian Institute for Advanced Research, Toronto, Canada, 2018
• Wageningen University & Research, Wageningen, The Netherlands, 2019
• École nationale vétérinaire d’Alfort, Paris, France, 2019
• Balaton Limnological Institute, Tihany, Hungary, 2020
• University of Glasgow, Glasgow, Scotland, 2020 (e–way)
• University of Cincinnati, Cincinnati, USA, 2020 (e–way)
• New York University, New York, USA, 2022 (e–way)
• University Medical Center, Amsterdam, The Netherlands, 2022
• National Chung Hsing University, Taichung, Taiwan, 2023
• Washington University School of Medicine, St Louis, USA, 2023
• EMBL, Heidelberg, Germany, 2023
• National Institute of Allergy and Infectious Diseases, Bethesda, USA, 2024
• University of Antioquia, Medellin, Colombia, 2024
• University of Edinburgh, Edinburgh, Scotland, 2024
• Comillas Pontifical University, Madrid, Spain, 2024

Editorial Board

• 2004–2006: Protistology 
• 2005–2011: Journal of Eukaryotic Microbiology 
• 2004–2008: Kinetoplastid Biology and Diseases
• 2009–present: The Open Parasitology Journal
• 2010–2012: International Journal for Parasitology
• 2011–2012: Folia Parasitologica (Associate Editor)
• 2015–present: PeerJ 
• 2017–present: Protist (Associate Editor)
• 2018–present: PLoS Pathogens (ad hoc Associate Editor)
• 2019–present: Frontiers in Cellular and Infection Microbiology (Associate Editor)
• 2020–present: µLife

Principal organizer of conferences

• XIII. biannual conference (International Society for Evolutionary Protistology) – August 2000 (120 participants)
• Trypanosomiasis and Leishmaniasis seminar (British Society of Parasitology) – August 2004 (140 participants)
• Euroleish Meeting (EU consortium) – September 2004 (30 participants)
• Mitochondrion of trypanosomes enters the postproteomic era – September 2009 (70 participants)
• Integrated Microbial Biodiversity workshop (Canadian Institute for Advanced Research) – June 2014 (75 participants)
• Trypanosomiasis and Leishmaniasis seminar (British Society of Parasitology) – September 2016 participants)
• Comparative genomics of unicellular eukaryotes: Interactions and symbioses (EMBO conference in St. Feliu de Guixols) – October 2022 (130 participants)

List of publications

References > 18,000; Hirsch index = 64)

• Aguado M., Carvalho S., Valdés-Tresanco M., Lin D., Padilla-Mejía N.E., Corpas-Lopez V., Tesařová M., Lukeš J., Gray D., Gonzáles-Bacerio J., Wyllie S. & Field M. (2024) Identification and validation of compounds targeting Leishmania major leucyl-aminopeptidase M17. ACS Infect. Dis. (accepted)
• Grybchuk D., Galan A., Klocek D., Macedo D.H., Wolf Y.I., Votýpka J., Butenko A., Lukeš J., Neri U., Záhonová K., Kostygov A.Y., Koonin E.V. & Yurchenko V. (2024) Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol. (in press)
• Chmelová L., Kraeva N., Saura A., Krayzel A., Vieira C.S., Neves Ferreira T., Soares R.P., Bučková B., Galan A., Horáková E., Ganyukova A.I., Malysheva M.N., Butenko A., Prokopchuk G., Frolov A.O., Lukeš J., Horváth A., Škodová-Sveráková I., Feder D., Kostygov A.Y. & Yurchenko V. (2024) Intricate balance of dually-localized catalase in Leptomonas seymouri (Kinetoplastea: Trypanosomatidae) modulates infectivity. Int. J. Parasitol. (in press)
• Afonin D.A., Gerasimov E.S., Škodová-Sveráková I., Záhonová K., Gahura O., Albanaz A.T.S., Myšková E., Bykova A., Paris Z., Lukeš J., Opperdoes F.R., Horváth A., Zimmer S. & Yurchenko V. (2024) Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucl. Acids Res. 52, 3870-3885.
• Votýpka J., Zeman Š., Stříbrná E., Pajer P., Bartoš O., Kment P., Lukeš J. IV & Lukeš J. III (2024) Multiple trypanosomatid co-infections of insects: The Cuban case study. Parasitology (in press)
• Cadena L.R., Edgcomb V.P. & Lukeš J. (2024) Gazing into the abyss: A glimpse into the diversity, distribution, and behavior of heterotrophic protists from the deep-sea floor. Environ. Microbiol. 26, e16598.
• Opperdoes F.R., Chmelová L., Škodová-Sveráková I., Záhonová K., Lukeš J. & Yurchenko V. (2024) In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics 25, 184.
• Bartošová-Sojková P., Butenko A., Richtová J., Fiala I., Oborník M. & Lukeš J. (2024) Inside the host: Understanding the evolutionary trajectories of intracellular parasitism. Annu. Rev. Microbiol. (in press)
• Butenko A., Lukeš J., Speijer D. & Weideman J.G. (2024) Mitochondrial genomes revisited: Why do different lineages retain different genes? BMC Biol. 22, 15.
• Kostygov A.Y., Albanaz A.T.S., Butenko A., Gerasimov E.S., Lukeš J. & Yurchenko V. (2024) Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends Parasitol. 40, 96-99.
• del Campo J., Carlos-Oliveira M., Čepička I., Hehenberger E., Horák A., Karnkowska A., Kolísko M., Lara E., Lukeš J., Pánek T., Piwosz K., Richter D., Škaloud P., Sutak R., Tachezy J. & Hampl V. (2024) The protist cultural renaissance. Trends Microbiol. 32, 128-131.
• Lukeš J., Čepička I. & Kolísko M. (2024) No end in sight for novel incredible (heterotrophic) protists. Curr. Biol. 34, R55-R58.
• Zhang P., Liu J., Yin X.-M., Zhou J.-Y., Lukeš J., Lun Z.-R. & Lai D.-H. (2023) Towards disentangling the classification of freshwater fish trypanosomes. Marine Life Sci. Technol. 5, 551-563.
• Lukeš J., Speijer D., Zíková A., Alfonzo J.D., Hashimi H. & Field M.C. (2023) Trypanosomes as a magnifying glass for cell and molecular biology. Trends Parasitol. 39, 902-912.
• Tashyreva D., Týč J., Horák A. & Lukeš J. (2023) Ultrastructure and 3D reconstruction of a diplonemid protist and its novel membranous organelle. mBio 14, e01921-23. 
• Macedo D.H., Grybchuk D., Režnarová J., Votýpka J., Klocek D., Yurchenko T., Ševčík J., Magri A., Urda Dolinská M., Záhonová K., Lukeš J., Servienė E., Jászayová A., Serva S., Malysheva M.N., Frolov A.O., Yurchenko V. & Kostygov A.Y. (2023) Diversity of RNA viruses in the cosmopolitan monoxenous trypanosomatid Leptomonas pyrrhocoris. BMC Biol. 21, 191.
• Albanaz A.T.S., Carrington M., Frolov A.O., Ganyukova A.I., Gerasimov E.S., Kostygov A.Y., Lukeš J., Malysheva M.N., Volf P., Votýpka J., Zakharova A., Záhonová K., Zimmer S.L., Yurchenko V. & Butenko A. (2023) Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics 24, 471.
• Pyrih J., Hammond M., Alves A., Dean S., Sunter J., Wheeler R., Gull K. & Lukeš J. (2023) Comprehensive sub-mitochondrial protein map of the parasitic protist Trypanosoma brucei unveils novel aspects of organellar biology. Cell Reports 42, 113083.
• Záhonová K., Valach M., Tripathi P., Benz C., Opperdoes F.R., Barath P., Lukáčová V., Danchenko M., Faktorová D., Horváth A., Burger G., Lukeš J. & Škodová-Sveráková I. (2023) Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates. Biochim. Biophys. Acta – Gen Subj. 1867, 130419.
• Sheikh S., Pánek T., Gahura O., Týč J., Záhonová K., Lukeš J., Eliáš M. & Hashimi H. (2023) A novel group of dynamin-related proteins shared by eukaryotes and giant viruses is able to remodel mitochondria from within the matrix. Mol. Biol. Evol. 40, msad134.
• Flegontova O., Lukeš J. & Horák A. (2023) Intra-genomic diversity of the V9 hypervariable region of the 18S rRNA gene in eukaryotes and its impact on metabarcoding. iScience 26, 107291.
• Valach M., Benz C., Aguilar L.C., Gahura O., Faktorová D., Zíková A., Oeffinger M., Burger G., Gray M.W. & Lukeš J. (2023) Miniature RNAs are embedded in an exceptionally protein-rich mitoribosomes via an elaborate assembly pathway. Nucleic Acids Res. 51, 6443-6460.
• Prokopchuk G., Butenko A., Dacks J.B., Speijer D., Field M.C. & Lukeš J. (2023) Lessons from the deep: Mechanisms behind the diversification of eukaryotic protein complexes. Biol. Reviews 98, 1910-1927.
• Zakharova A., Tashyreva D., Butenko A., Morales J., Saura A., Svobodová M., Poschmann G., Nandipati S., Zakharova A., Noyvert D., Gahura O., Týč J., Stühler K., Kostygov A.Y., Nowack E.C.M., Lukeš J. & Yurchenko V. (2023) A neo-functionalized homolog of a host transmembrane protein controls localization of bacterial endosymbionts in the trypanosomatid Novymonas esmeraldas. Curr. Biol. 33, 2690-2701.e5.
• Veselá-Strejcová J., Scalco E., Zingone A., Colin S., Caputi L., Sarno D., Nebesářová J., Bowler C. & Lukeš J. (2023) Diverse eukaryotic phytoplankton from around the Marquesas Islands documented by combined microscopy an molecular techniques. Protist 174, 125965.
• Faktorová D., Záhonová K., Benz C., Dacks J.B., Field M.C. & Lukeš J. (2023) Functional differentiation of Sec13 paralog in the euglenozoan protists. Open Biol. 13, 220364.
• Valášek L.S., Lukeš J. & Paris Z. (2023) Stops making sense – for the people? Clin. Transl. Med. 13, e1270.
• George E.E., Barcyte D., Lax G., Livingston S., Tashyreva D., Husnik F., Lukeš J., Eliáš M. & Keeling P.J. (2023) A single cryptomonad cell harbours a complex community of organelles, bacteria, a phage and selfish elements. Curr. Biol. 10, 1982-1996.e4.
• Bruce Krejčí A., Votýpková K., Lukeš J. & Votýpka J. (2023) Varroa destructor. Trends Parasitol. 39, 487-488.
• Valach M., Moreira S., Petitjean C., Benz C., Butenko A., Flegontova O., Nenarokova A., Prokopchuk G., Batstone T., Lapébie P., Lemogo L., Sarrasin M., Stretenowich P., Tripathi P., Yazaki E., Nara T., Henrissat B., Lang B.F., Gray M.W., Williams T.A., Lukeš J. & Burger G. (2023) Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes. BMC Biol. 21, 99.
• Muñoz-Gómez S.A., Cadena L.R., Léger M.M., Gardiner A.T., Sheikh S., Connell L., Bílý T., Beatty T., Kopejtka K., Koblížek M., Roger A.J., Slamovits C.H., Lukeš J. & Hashimi H. (2023) The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing protein Mic60. Curr. Biol. 33, 1099-1111.e6 
• Flegontova O., Flegontov P., Jachníková N., Lukeš J. & Horák A. (2023) Water masses shape pico-nano eukaryotic communities of the Weddell Sea. Commun. Biol. 6, 64.
• Pilátová J., Tashyreva D., Týč J., Vancová M., Bokhari S.N.H., Skoupý R., Klementová M., Küpper H., Mojzeš P. & Lukeš J. (2023) Massive accumulation of strontium and barium in diplonemid protists. mBio 14, e03279-22. 
• Kachale A., Pavlíková Z., Nenarokova A., Roithová A., Durante I.M., Miletínová P., Záhonová K., Nenarokov S., Votýpka J., Horáková E., Ross R.L., Yurchenko V., Beznosková P., Paris Z., Valášek L.S. & Lukeš J. (2023) Short tRNA anticodon stem with mutant eRF1 allow stop codon reassignment. Nature 613, 751-758.
• Gerasimov E.S., Afonin D.A., Korzhavina O.A., Lukeš J., Low R., Hall N., Tyler K., Yurchenko V. & Zimmer S.L. (2022) Mitochondrial RNA editing in Trypanoplasma borreli: new tools, new revelations. Comp. Struct. Biotech. J. 20, 6388-6402.
• Benz C., Müller N., Kaltenbrunner S., Váchová H., Vancová M., Lukeš J., Varga V. & Hashimi H. (2022) Kinetoplatid–specific X2–family kinesins interact with a kinesin–like plecstrin homology domain protein that localizes to the trypanosomal microtubule quartet. Mol. Microbiol. 118, 155–174.
• Lukeš J., Kachale A., Votýpka J., Butenko A. & Field M.C. (2022) African trypanosome strategies for conquering new hosts and territories: The end of monophyly? Trends Parasitol. 38, 724–736.
• Zhang P., Chen K., Svobodová M., Yang T.-B., Lukeš J. Zhang J., Lun Z.-R. & Lai D.-H. (2022) Does the fish infecting Trypanosoma micropteri belong to Trypanosoma carassii? Folia Parasitol. 69, 024.
• Zakharova A., Albanaz A.T.S., Opperdoes F.R., Škodová–Sveráková I., Zagirova D., Saura A., Chmelová L., Gerasimov E.S., Leštinová T., Bečvář T., Sádlová J., Volf P., Lukeš J., Horváth A., Butenko A. & Yurchenko V. (2022) Leishmania guyanensis M4147 as a new LRV1–bearing model parasite: phosphatidate phosphatase 2–like protein controls cell cycle progression and intracellular lipid content. PLoS Negl. Trop. Dis. 16, e0010510.
• Štefka J., Votýpka J., Lukeš J. & Balvín O. (2022) Parasite of the month: Cimex lectularius and Cimex hemipterus (Bed bugs). Trends Parasitol. 38, 919–920. 
• George E.E., Tashyreva D., Kwong W.K., Okamoto N., Horák A., Husnik F., Lukeš J. & Keeling P.J. (2022) Gene transfer agents in bacterial endosymbionts of microbial eukaryotes. Genome Biol. Evol. 14, 7.
• Horáková E., Lecordier L., Cunha P., Sobotka R., Changmai P., Langedijk C.J.M., Van den Abbeele J., Vanhollebeke B. & Lukeš J. (2022) Heme–deficient metabolism and impaired cellular differentiation as an evolutionary trade–off for human infectivity in Trypanosoma brucei gambiense. Nat. Commun. 13, 7075.
• Hammond M., Dorrell R.G., Speijer D. & Lukeš J. (2022) Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. BioEssays 44, 2100258.
• Tashyreva D., Simpson A., Prokopchuk G., Škodová–Sveráková I., Butenko A., Hammond M., George E.E., Flegontova O., Záhonová K., Faktorová D., Yabuki A., Horák A., Keeling P.J. & Lukeš J. (2022) Diplonemids–a review on „new“ flagellates on–the–oceanic–block. Protist 173, 125868.
• Prokopchuk G., Korytář T., Juricová V., Majstorovic J., Horák A., Šimek K. & Lukeš J. (2022) Trophic flexibility of marine diplonemids–switching from osmotrophy to bacterivory. ISME J. 16, 1409–1419.
• Votýpka J., Stříbrná E., Modrý D., Bryja J., Bryjová A. & Lukeš J. (2022) Unexpectedly high diversity of trypanosomes in small sub–Saharan mammals. Int. J. Parasitol. 52, 647-658.
• Jorge F., Brealey J.C., Brindley P.J., Cantacessi C., Duron O., Fitzpatrick C.R., Hahn M., Hervé V., Knoll L.J., Kohl K.D., Lalle M., Lukeš J., Martínez Martínez J., Perkins S.L., Poulin R., Rosario K., Schneider A.C., Schriml L.M., Thompson L.R. & Dheilly N.M. (2022) MIxS–SA: a MIxS extension defining the minimum information standard for sequence data from symbiotic organisms. ISME Commun. 1, 9.
• Kořený L., Oborník M., Horáková E., Waller R.S. & Lukeš J. (2022) The convoluted history of heme biosynthesis. Biol. Reviews 97, 141–162.
• Škodová–Sveráková I., Záhonová K., Juricová V., Danchenko M., Moos M., Baráth P., Prokopchuk G., Butenko A., Lukáčová V., Kohútová L., Bučková B., Horák A., Faktorová D., Horváth A., Šimek P. & Lukeš J. (2021) Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum. BMC Biol. 19, 251.
• Tortorelli G., Pettolino F., Lai D.-H., Tomčala A., Bacić A., Oborník M., Lukeš J. & McFadden G.I. (2021) The cell wall polysaccharides of a photosynthetic relative of apicomplexans, Chromera velia. J. Phycol. 57, 1805–1809.
• Hammond M., Zoltner M., Garrigan J., Butterfield E., Varga V., Lukeš J. & Field M.C. (2021) The distinctive flagellar proteome of Euglena gracilis illuminates the complexities of protistan flagella adaption. New Phytol. 232, 1323–1336.
• Zakharova A., Saura A., Butenko A., Podešvová L., Warmusová S., Kostygov A.Y., Nenarokova A., Lukeš J., Opperdoes F.R. & Yurchenko V. (2021) A new model trypanosomatid Novymonas esmeraldas: genomic perception of its “Candidatus Pandoraea novymonadis“ endosymbiont. mBio 12, e01606–21.
• Smilansky V., Jirků M., Milner D.S., Ibáñez R., Gratwicke B., Nicholls A., Lukeš J., Chambouvet A. & Richards T.A. (2021) Expanded host and geographic range of tadpole associations with the Severe Perkinsea Infection group. Biol. Letters 17, 20210166.
• Skalický T., Alves J.M.P., Morais A.C., Režnarová J., Butenko A., Lukeš J., Serrano M., Buck G.A., Teixeira M.G.M., Camargo E.P., Sanders M., Cotton J.A., Yurchenko V. & Kostygov A.Y. (2021) Endosymbiont capture, a repeated process of endosymbiont transfer with replacement in the trypanosomatid Angomonas spp. Pathogens 10, 702.
• Paris Z., Svobodová M., Kachale A., Horáková E., Nenarokova A. & Lukeš J. (2021) A mitochondrial cytidine deaminase is responsible for C to U editing of tRNATrp to decode the UGA codon in Trypanosoma brucei. RNA Biol. 18, 278–286.
• Husnik F., Tashyreva D., Boscaro V., George E.E., Lukeš J. & Keeling P.J. (2021) Bacterial and archaeal symbioses with protists. Curr. Biol. 31, R862–R877.
• Lopes A.L.K., Kriegová E., Lukeš J., Krieger M.A. & Ludwig A. (2021) Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists. PLoS One 16, e251133. 
• Záhonová K., Lax G., Sinha S.D., Richards T.A., Lukeš J. & Wideman J.G. (2021) Single–cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biol. 19, 103.
• Votýpka J., Petrželková K.J., Brzoňová J., Jirků M., Modrý D. & Lukeš J. (2021) How monoxenous trypanosomatids revealed hidden feeding habits of their tsetse fly hosts. Folia Parasitol. 68, 019.
• Albanaz A.T.S., Gerasimov E.S., Shaw J.J., Sádlová J., Lukeš J., Volf P., Opperdoes F.R., KostygovA.Y., Butenko A. & Yurchenko V. (2021) Genome analysis of Endotrypanum and Porcisia spp., closest phylogenetic relatives of Leishmania, highlights the role of amastins in shaping pathogenicity. Genes 12, 444.
• Padilla–Mejía N., Kořený L., Holden J., Vancová M., Lukeš J., Zoltner M. & Field M. (2021) A hub–and–spoke nuclear lamina architecture in trypanosomes. J. Cell Sci. 134, jcs251264.
• Feng J., Zhu H., Lukeš J., Korábečná M., Fohlerová Z., Mei T., Chang H. & Neužil P. (2021) Nano–watt simple microcalorimetry for dynamically monitoring the defense mechanism of Paramecium caudatum. Sensors & Actuators A. Physical 323, 112643.
• Poláková E., Záhonová K., Albanaz A.T.S., Butenko A., Lukeš J. & Yurchenko V. (2021) Diverse telomeres in trypanosomatids. Parasitology 148, 1254–1270.
• Bílý T., Sheikh S., Mallet A., Bastin P., Pérez–Morga D., Lukeš J. & Hashimi H. (2021) Ultrastructural changes of the mitochondrion during the life cycle of Trypanosoma brucei. J. Eukaryot. Microbiol. 68, e12846.
• Pyrih J., Pánek T., Durante I.M., Rašková V., Cimrhanzlová K., Kriegová E., Tsaousis A.D., Eliáš M. & Lukeš J. (2021) Vestiges of the bacterial signal recognition particle–based protein targeting in mitochondria. Mol. Biol. Evol. 38, 3170–3187.
• Gerasimov E.S., Gasparyan A.A., Afonin D.A., Zimmer S.L., Kraeva N., Lukeš J., Yurchenko V. & Kolesnikov A. (2021) Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non–canonical mitochondrial RNA editing events. Nucleic Acids Res. 49, 3354–3370.
• Kostygov A.Y., Karnkowska A., Votýpka J., Tashyreva D., Maciszewski K., Yurchenko V. & Lukeš J. (2021) Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses. Open Biol. 11, 200407.
• Lukeš J., Tesařová M., Yurchenko V. & Votýpka J. (2021) Characterization of a new cosmopolitan genus of trypanosomatid parasites, Obscuromonas gen. nov. (Blastocrithidiinae subfam. nov.). Europ. J. Protistol. 79, 125778.
• Opperdoes F.R., Butenko A., Zakharova A., Gerasimov E.S., Zimmer S.L., Lukeš J. & Yurchenko V. (2021) The remarkable metabolism of Vickermania ingenoplastis: genomic predictions. Pathogens 10, 68.
• Lukeš J., Kaur B. & Speijer D. (2021) RNA editing in mitochondria and plastids–weird and widespread. Trends Genet. 37, 99–102.
• Butenko A., Hammond M., Field M.C., Ginger M.L., Yurchenko V. & Lukeš J. (2021) Reductionist pathways for parasitism in Euglenozoans? Expanded datasets provide new insights. Trends Parasitol. 37, 100–116.
• Kostygov A.Y., Frolov A.O., Malysheva M.N., Ganyukova A.I., Chistyakova L.V., Tashyreva D., Tesařová M., Spodareva V.V., Režnarová J., Macedo D., Butenko A., d’Avila–Levy C.M., Lukeš J. & Yurchenko V. (2020) Vickermania, gen. nov., trypanosomatids that use two joined flagella to resist midgut peristaltic flow within the fly host. BMC Biol. 18, 187.
• Durante I.M., Butenko A., Rašková V., Charyyeva A., Svobodová M., Yurchenko V., Hashimi H. & Lukeš J. (2020) Large–scale phylogenetic analysis of trypanosomatid adenylate cyclases reveals associations with extracellular lifestyle and host–pathogen interplay. Genome Biol. Evol. 12, 2403–2416.
• Votýpka J., Kment P., Yurchenko V. & Lukeš J. (2020) Endangered monoxenous trypanosomatid parasites: a lesson from island biogeography. Biodiv. Conserv. 29, 3635–3667.
• Flegontova O., Flegontov P., Castañeda Londoño P.A., Walczowski W., Śantić D., Edgcomb V.P., Lukeš J. & Horák A. (2020) Environmental determinants of the distribution of planktonic diplonemids and kinetoplastids in the oceans. Environ. Microbiol. 22, 4014–4031.
• Li S.-J., Zhang X., Lukeš J., Li B.-Q., Wang J.-F., Qu L.-H., Hide G., Lun Z.-R. & Lai D.-H. (2020) Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi. Nucleic Acids Res. 48, 9747–9761.
• Kolísko M., Flegontova O., Karnkowska A., Lax G., Maritz J.M., Pánek T., Táborský P., Carlton J.M., Čepička I., Horák A., Lukeš J., Simpson A.G.B. & Tai V. (2020) EukRef–Excavates: Seven curated SSU ribosomal RNA gene databases. Database 2020, baaa080.
• Faktorová D., Kaur B., Valach M., Graf L., Benz C., Burger G. & Lukeš J. (2020) Targeted integration by homologous recombination enables in–situ tagging and replacement in the marine microeukaryote Diplonema papillatum. Environ. Microbiol. 22, 3660–3670.
• Pyrih J., Rašková V., Škodová–Sveráková I., Pánek T. & Lukeš J. (2020) ZapE/Afg1 interacts with Oxa1 and its depletion causes a multifaceted phenotype. PLoS One 15, e0234918.
• Speijer D., Hammond M. & Lukeš J. (2020) Comparing early eukaryotic integration of mitochondria and chloroplasts in the light of internal ROS challenges: Timing is of the essence. mBio 11, e00955–20.
• Škodová–Sveráková I., Záhonová K., Bučková B., Fussy Z., Yurchenko V. & Lukeš J. (2020) Catalase and ascorbate peroxidase in Euglenozoan protists. Pathogens 9, 317.
• Mehta V., Moshiri H., Srikanth A., Kala S., Lukeš J. & Salavati R. (2020) Sulfonated inhibitors of the RNA editing ligases validate the essential role of the MRP1/2 proteins in kinetoplastid RNA editing. RNA 26, 827–835. 
• Hammond M.J., Nenarokova A., Butenko A., Zoltner M., Lacová Dobáková E., Field M.C. & Lukeš J. (2020) A uniquely complex mitochondrial proteome from Euglena gracilis. Mol. Biol. Evol. 37, 2173–2191.
• Pánek T., Eliáš M., Vancová M., Lukeš J. & Hashimi H. (2020) Returning to the fold for lessons in mitochondrial cristae diversity and evolution. Curr. Biol. 30, R575–R588.
• Škodová–Sveráková I., Prokopchuk G., Peña–Diaz P., Záhonová K., Moos M., Horváth A., Šimek P. & Lukeš J. (2020) Unique dynamics of paramylon storage in the marine euglenozoan Diplonema papillatum. Protist 171, 125717.
• Faktorová D., Nisbet R.E.R., Fernandéz Robledo J.A., Casacuberta E., Sudek L., Allen A.E., Ares M. Jr., Aresté C., Balestreri C., Barbrook A.C., Beardslee P., Bender S., Booth D.S., Bouget F.-Y., Bowler C., Breglia S.A., Brownlee C., Burger G., Cerutti H., Cesaroni R., Chiurillo M.A., Clemente T., Coles D.B., Collier J.L., Cooney E.C., Coyne K., Docampo R., Dupont C.L., Edgcomb V., Einarsson E., Elustondo P.A., Federici F., Freire–Beneitez V., Freuria N.J., Fukuda K., García P.A., Girguis P.R., Gomaa F., Gornik S.G., Guo J., Hampl V., Hanawa Y., Haro–Contreras E.R., Hehenberger E., Highfield A., Hirakawa Y., Hopes A., Howe C.J., Hu I., Ibañez J., Irwin N.A.T., Ishii Y., Janowicz N.E., Jones A.C., Kachale A., Fujimura–Kamada K., Kaur B., Kaye J.Z., Kazana E., Keeling P.J., King N., Klobutcher L.A., Lander N., Lassadi I., Li Z., Lin S., Lozano J.-C., Luan F., Maruyama S., Matute T., Miceli C., Minagawa J., Moosburner M., Najle S.R., Nanjappa M., Nimmo I.C., Noble L., Novák Vanclová A.M.G., Nowacki M., Nuñez I., Pain A., Piersanti A., Pucciarelli S., Pyrih J., Rest J.S., Rius M., Robertson D., Ruaud A., Ruiz–Trillo I., Sigg M.A., Silver P.A., Slamovits C.H., Smith G.J., Sprecher B.N., Stern R., Swart E., Tsaousis A., Tsypin L., Turkewitz A., Turnšek J., Valach M., Vergé V., von Dassow P., von der Haar T., Waller R.F., Wang L., Wen X., Wheeler G., Woods A., Zhang H., Mock T., Worden A.Z. & Lukeš J. (2020) Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. Nature Methods 17, 481–494.
• Butenko A., Opperdoes F.R., Flegontova O., Horák A., Hampl V., Keeling P.J., Gawryluk R.M.R., Tikhonenkov D., Flegontov P. & Lukeš J. (2020) Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids and euglenids. BMC Biol. 18, 23.
• Podešvová L., Leštinová T., Horáková E., Lukeš J., Volf P. & Yurchenko V. (2020) Suicidal Leishmania: a new old approach for vaccination. Pathogens 9, 79.
• Aphasizheva I., Alfonzo J., Carnes J., Cestari I., Cruz–Reyes J., Göringer H.U., Hajduk S., Lukeš J., Madison–Antenucci S., Maslov D.A., McDermott S.M., Ochsenreiter T., Read L.K., Salavati R., Schnaufer A., Schneider A., Simpson L., Stuart K., Yurchenko V., Zhou H., Zíková A., Zhang L., Zimmer S. & Aphasizhev R. (2020) Lexis and grammar of mitochondrial RNA processing in trypanosomes. Trends Parasitol. 36, 337–355. 
• Kaur B., Záhonová K., Valach M., Faktorová D., Prokopchuk G., Burger G. & Lukeš J. (2020) Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. Nucleic Acids Res. 48, 2694–2708.
• George E.E., Husnik F., Tashyreva D., Prokopchuk G., Horák A., Kwong W.K., Lukeš J. & Keeling P.J. (2020) Highly reduced genomes of protist endosymbionts show evolutionary convergence. Curr. Biol. 30, 925–933.e3.
• Chambouvet A., Smilansky V., Jirků M., Isidoro–Ayza M., Itoiz S., Derrelle E., Monier A., Gower D., Wilkinson M., Yabsley M., Lukeš J. & Richards T. (2020) Diverse alveolate infections of tadpoles, a new threat to frogs. PLoS Pathogens 16: e1008107. 
• Horáková E., Faktorová D., Kraeva N., Kaur B., van den Abbeele J., Yurchenko V. & Lukeš J. (2020) Catalase compromises the development of the insect and mammalian stages of Trypanosoma brucei. FEBS J. 287, 964–977.
• Dixit S., Alfonzo J.D. & Lukeš J. (2020) RNA–binding proteins and their targets in Trypanosoma brucei: single nucleotide resolution using iCLIP and iCLAP. In: Michels P.A.M., Ginger M., & Zilberstein D. (eds.) Trypanosomatids. Methods in Molecular Biology (Elsevier) 2116, 303–323. 
• Lukeš J. & Votýpka J. (2020) Field isolation and cultivation of trypanosomatids from insects. In: Michels P.A.M., Ginger M., & Zilberstein D. (eds.) Trypanosomatids. Methods in Molecular Biology (Elsevier) 2116, 3–21. 
• Novák Vanclová A.M.G., Zoltner M., Kelly S., Soukal P., Záhonová K., Fussy Z., Ebenezer T.E., Lacová Dobáková E., Eliáš M., Lukeš J., Field M.C. & Hampl V. (2020) Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid. New Phytol. 225, 1578–1592.
• Kraeva N., Ishemgulova A., Butenko A., Majerová K., Vaselek S., Bespyatykh J., Charyyeva A., Spitzová T., Leštinová T., Kostygov A., Lukeš J., Volf P., Votýpka J. & Yurchenko V. (2019) LmxM.22.0250–encoded dual specificity protein/lipid phosphatase impairs Leishmania mexicana virulence in macrophages. Pathogens 8, 241.
• Králová J., Grybchuk–Ieremenko A., Votýpka J., Novotný V., Kment P., Lukeš J., Yurchenko V. & Kostygov A.Y. (2019) Insect trypanosomatids in Papua New Guinea: high endemism and diversity. Int. J. Parasitol. 49, 1075–1086.
• Butenko A., Kostygov A.Y., Sádlová J., Kleschenko Y., Bečvář T., Podešvová L., Macedo D.H., Žihala D., Lukeš J., Bates P.A., Volf P., Opperdoes F.O. & Yurchenko V. (2019) Comparative genomics of Leishmania (Mundinia). BMC Genomics 20, 726. 
• Eichenberger C., Oeljeklaus S., Bruggisser J., Mani J., Haenni B., Kaurov I., Niemann M., Zuber B., Lukeš J., Hashimi H., Warscheid B., Schimanski B. & Schneider A. (2019) The highly diverged trypanosomal MICOS complex is organized in a nonessential integral membrane and an essential peripheral module. Mol. Microbiol. 12, 1731–1743.
• Dheilly N.M., Martínez–Martínez J., Rosario K., Brindley P.J., Fichorova R.N., Kaye J.Z., Kohl K., Knoll L.J., Lukeš J., Perkins S.L., Poulin R., Schriml L. & Thompson L.R. (2019) Parasite Microbiome Project: Grand challenges. PLoS Pathogens 15, e1008028. 
• Bianchi C., Kostygov A.Y., Kraeva N., Záhonová K., Horáková E., Sobotka R., Lukeš J. & Yurchenko V. (2019) An enigmatic catalase of Blastocrithidia. Mol. Biochem. Parasitol. 232, 111199.
• Nenarokova A., Záhonová K., Krasilnikova M., Gahura O., McCulloch R., Zíková A., Yurchenko V. & Lukeš J. (2019) Causes and effects of loss of classical non–homologous end joining pathway in parasitic eukaryotes. mBio 10, 01541–19.
• Sobotková K., Parker W., Levá J., Růžková J., Lukeš J. & Jirků Pomajbíková K. (2019) Knowns and unknowns of helminth therapy, from the parasite perspective. Trends Parasitol. 35, 501–515. 
• Prokopchuk G., Tashyreva D., Yabuki A., Horák A., Masařová P. & Lukeš J. (2019) Morphological, ultrastructural, motility and evolutionary characterization of two new Hemistasiidae species. Protist 170, 259–282.
• Lukeš J. & Hyliš M. (2019) In love with microsporidia for 60+ years: Jiří Vávra passed away. J. Euk. Microbiol. 66, 533–534.
• Lukeš J. (2019) Questions and answers. Curr. Biol. 29, R142–R144.
• Lukeš J. (2019) Bridging the worlds of science and religion by creating unique positions in both domains. In: Bermejo, D. (ed.) Passion for Life–Pasión por la Vida. Alianza Editorial, Madrid (in press)
• Votýpka J., Kment P., Kriegová E., Vermeij M.J.A., Keeling P.J., Yurchenko V. & Lukeš J. (2019) High prevalence and endemism of trypanosomatids on a small Caribbean island. J. Euk. Microbiol. 66, 600–607. 
• Okamoto N., Gawryluk R.M.R., del Campo J., Strassert J.F.H., Lukeš J., Richards T.A., Worden A.Z., Santoro A.E. & Keeling P.J. (2019) A revised taxonomy of diplonemids including the Eupelagonemidae n. fam. and a type species, Eupelagonema oceanica n. gen. & sp. J. Euk. Microbiol. 66, 519–524.
• Ebenezer T., Zoltner M., Burrel A., Nenarokova A., Vanclová A., Prasad B., Soukal P., Santana–Molina C., O’Neill E., Nankissoor N., Vadakedath N., Daiker V., Obado S., Pereira S.S., Jackson A., Devos D., Lukeš J., Lebert M., Vaughn S., Hampl V., Carrington M., Ginger M., Kelly S., Dacks J. & Field M. (2019) Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol. 17, 11.
• Caputi L., Carradec Q., Eveillard D., Kirilovsky A., Pelletier E., Karlusich P.J.J., Vieira F.R.J., Villar E., Chaffron S., Malviya S., Scalco E., Acinas S.G., Alberti A., Aury J.-M., Benoiston A.-S., Bertrand A., Biard T., Bittner L., Boccara M., Brum J.R., Brunet C., Busseni G., Carratala A., Claustre H., Coeelho L.P., Colin S., D’Aniello S., Da Silva C., Del Core M., Doré H., Gasparini S., Kokoszka F., Jamet J.-L., Lejeusne C., Lepoivre C., Lescot M., Lima–Mendez G., Lombard F., Lukeš J., Maillet N., Madoui M.-A., Martinez E., Mazzocchi M.G., Néou M.B., Paz–Yepes J., Poulain J., Ramondenc S., Romagnan J.-B., Roux S., Salvagio Manta D., Sanges R., Speich S., Sprovieri M., Sunagawa S., Taillander V., Tanaka A., Tirichine L., Trottier C., Uitz J., Veluchamy A., Veselá J., Vincent F., Yau S., Kandels–Lewis S., Searson S., Dimier C., Picheral M., Bork P., Boss E., de Vargas C., Follows M.J., Grimsley N., Guidi L., Hingamp P., Karsenti E., Sordino P., Stemmann L., Sullivan M.B., Not F., Ribera d‘Alcala M., Wincker P., Bowler C. & Iudicone D. (2019) Community–level responses to iron availability in open ocean planktonic ecosystems. Global Biogeochem. Cycles 33, 391–419. 
• Adl S.M., Bass D., Lane C.E., Lukeš J., Schoch C.L., Smirnov A., Agatha S., Berney C., Brown M.W., Burki F., Cárdenas P., Čepička I., Chistyakova L., del Campo J., Dunthorn M., Edvardsen B., Eglit Y., Guillou L., Hampl V., Heiss A.A., Hoppenrath M., James T.Y., Karpov S., Kim E., Kolísko M., Kudryavtsev A., Lahr D.J.G., Lara E., Le Gall L., Lynn D.H., Mann D.G., Massana i Molera R., Mitchell E.A.D., Morrow C., Park J.S., Pawlowski J.W., Powell M.J., Richter D.J., Rueckert S., Shadwick L., Shimano S., Spiegel F.W., Torruella G., Youssef N., Zlatogursky V. & Zhang Q. (2019) Revision to the classification, nomenclature and diversity of eukaryotes. J. Euk. Microbiol. 66, 4–119.
• Maslov D.A., Opperdoes F.R., Kostygov A.Y., Hashimi H., Lukeš J. & Yurchenko V. (2019) Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 146, 1–27.
• Tonini M.L., Peña Diaz P., Haindrich A.C., Basu S., Kriegová E., Pierik A.J., Lill R., MacNeill S.A., Smith T.K. & Lukeš J. (2019) Branched late–steps of the cytosolic iron–sulfur cluster assembly machinery of Trypanosoma brucei. PLoS Pathogens 14, e1007326.
• Faktorová D., Bär A., Hashimi H., McKinney K., Horák A., Schnaufer A., Rubio M.A.T., Alfonzo J.D. & Lukeš J. (2018) TbUTP10, a protein involved in early stages of pre–18S rRNA processing in Trypanosoma brucei. Mol. Biochem. Parasitol. 225, 84–93.
• Grybchuk D., Kostygov A.Y., Macedo D.H., Votýpka J., Lukeš J. & Yurchenko V. (2018) RNA viruses in Blechomonas (Trypanosomatidae) and evolution of Leishmaniavirus. mBio 9, e01932–18.
• Kaurov I., Vancová M., Schimanski B., Cadena L.R., Heller J., Bílý T., Potěšil D., Eichenberger C., Bruce H., Oeljeklaus S., Warscheid B., Zdráhal Z., Schneider A., Lukeš J. & Hashimi H. (2018) The diverged trypanosome MICOS complex as a hub for mitochondrial cristae shaping and protein import. Curr. Biol. 28, 3393–3407.
• S. & Lukeš J. (2018) Combinatorial interplay of RNA–binding proteins tunes levels of mitochondrial mRNA in trypanosomes. RNA 24, 1594–1606.
• Moya A. et al. (+ 60 co–authors) (2018) Harrasment charges: unjustice done? Science 361, 655–656. 
• Spodareva V., Grybchuk–Ieremenko A., Losev A., Votýpka J., Lukeš J., Yurchenko V. & Kostygov A (2018) The diversity and evolution of anuran trypanosomes. Parasites & Vectors 11, 447.
• Yurchenko V. & Lukeš J. (2018) Parasites and their (endo)symbiotic microbes. Parasitology 145, 1261–1264.
• Lukeš J., Wheeler R., Jirsová D., David V. & Archibald J.M. (2018) Massive mitochondrial DNA content in diplonemid and kinetoplast protists. IUBMB Life 70, 1267–1274.
• Lukeš J. & Husník F. (2018) Microsporidia: A single horizontal gene transfer drives a great leap forward. Curr. Biol. 28, R712–R715.
• Peña Diaz P., Mach J., Kriegová E., Poliak P., Tachezy J. & Lukeš J. (2018) Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase. PLoS One 13, e0196474.
• Harmer J., Yurchenko V., Nenarokova A., Lukeš J. & Ginger M.L. (2018) Farming, slaving and enslavement: histories of endosymbioses during kinetoplastid evolution. Parasitology 145, 1311–1323.
• Peña Diaz P. & Lukeš J. (2018) Fe–S cluster assembly in the supergroup Excavata. J. Biol. Inorg. Chem. 23, 521–541.
• Votýpka J., Lukeš J. & Horák P. (2018) Paraziti jako naši spojenci. In: O parazitech a lidech (eds. Votýpka a kol), Triton, Praha; pp. 206–237.
• Lukeš J., Butenko A., Hashimi H., Maslov D.A., Votýpka J. & Yurchenko V. (2018) Trypanosomatids are much more than just trypanosomes: clues from the expanded family tree. Trends Parasitol. 34, 466–480.
• Silva F.M., Kostygov A.Y., Spodareva V.V., Butenko A., Tossou R., Lukeš J., Yurchenko V. & Alves J.M.P. (2018) The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the heme synthesis pathway. Parasitology 145, 1287–1293.
• Ishemgulova A., Hlaváčová J., Majerová K., Butenko A., Lukeš J., Votýpka J., Volf P. & Yurchenko V. (2018) CRISPR/Cas9 in Leishmania mexicana: a curious case of LmxM.22.0010–encoded BTN1. PLoS One 13, e0192723.
• Tashyreva D., Prokopchuk G., Votýpka J., Yabuki A., Horák A. & Lukeš J. (2018) Life cycle, ultrastructure and phylogeny of new diplonemids and their endosymbiotic bacteria. mBio 9, e02447–17.
• Flegontova O., Flegontov P., Malviya S., Poulain J., de Vargas C., Bowler C., Lukeš J. & Horák A. (2018) Neobodonids are dominant kinetoplastids in the global ocean. Environ. Microbiol. 20, 878–889.
• Kaur B., Valach M., Peña Diaz P., Moreira S., Keeling P.J., Burger G., Lukeš J. & Faktorová D. (2018) Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine micro–eukaryotes Diplonemida (Euglenozoa). Environ. Microbiol. 20, 1030–1040.
• Tashyreva D., Prokopchuk G., Yabuki A., Kaur B., Faktorová D., Votýpka J., Kusaka C., Fujikura K., Shiratori, T., Ishida K.-I., Horák A. & Lukeš J. (2018) Phylogeny and morphology of new diplonemids from Japan. Protist 169, 158–179.
• Faktorová D., Valach M., Kaur B., Burger G. & Lukeš J. (2018) Mitochondrial RNA editing and processing in diplonemid protists. In: M.W. Gray and J. Cruz–Reyes (Eds.), RNA Metabolism in Mitochondria. Springer, Cham, pp 145–176.
• Butenko A., da Silva Vieira T., Frolov A.O., Opperdoes F.R., Soares R.P., Kostygov A.Y., Lukeš J. & Yurchenko V. (2018) Leptomonas pyrrhocoris: genomic insight into parasite’s physiology. Curr. Genomics 19, 150–156.
• Schoenian G., Lukeš J., Stark O. & Cotton J. (2018) Molecular evolution and phylogeny of Leishmania. In: Drug resistance in Leishmania parasites, consequences, molecular mechanisms, and possible treatments (Ed: A. Ponte–Sucre), Springer (in press).
• Gerasimov E.S., Gasparyan A.A., Kaurov I., Tichý B., Logacheva M.D., Kolesnikov A.A., Lukeš J., Yurchenko V., Zimmer S.L. & Flegontov P. (2018) Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. Nucleic Acids Res. 46, 765–781.
• Schwelm A., Badstöber J., Bulman S., Desoignies N., Etemadi M., Falloon R.E., Gachon C.M.M., Legreve A., Lukeš J., Merz U., Nenarokova A., Strittmatter M., Sullivan B.K. & Neuhauser S. (2018) Not in your usual Top 10: protists that infect plants and algae. Mol. Plant Pathol. 19, 1029–1044. 
• Grybchuk D., Akopyants N.S., Kostygov A.Y., Konovalovas A., Lye L.-F., Dobson D.E., Zangger H., Fasel N., Butenko A., Frolov A.O., Votýpka J., d’Avila–Levy C.M., Kulich P., Moravcová J., Plevka P., Rogozin I.B., Serva S., Lukeš J., Beverley S.M. & Yurchenko V. (2018) Viral discovery and diversity in trypanosomatids with a focus on relatives of the human parasite Leishmania. Proc. Natl. Acad. Sci. USA 115, E506–E515. 
• Zíková A., Verner Z., Nenarokova A., Michels P.A.M. & Lukeš J. (2017) A paradigm shift: the mitoproteomes of procyclic and bloodstream Trypanosoma brucei are comparably complex. PLoS Pathogens 13, e1006679.
• Skalický T., Dobáková E., Wheeler R.J., Tesařová M., Flegontov P., Jirsová D., Votýpka J., Yurchenko V., Ayala F.J., Lukeš J. (2017) Extensive flagellar remodeling during the complex life cycle of Paratrypanosoma, an early–branching trypanosomatid. Proc. Natl. Acad. Sci. USA 114, 11757–11762. 
• Tanifuji G., Cenci U., Moog D., Dean S., Nakayama T., David V., Fiala I., Curtis B.A., Sibbald S., Onodera N.T., Colp M., Flegontov P., Johnson–MacKinnon J., McPhee M., Inagaki Y., Hashimoto T., Kelly S., Gull K., Lukeš J. & Archibald J.M. (2017) Genome sequencing reveals metabolic and cellular interdependence in an amoeba–kinetoplastid symbiosis. Sci. Reports 7, 11688.
• Kostygov A., Butenko A., Nenarokova A., Tashyreva D., Flegontov P, Lukeš J. & Yurchenko V. (2017) Genome of Ca. Pandoraea novymonadis, an endosymbiotic bacterium of the trypanosomatid Novymonas esmeraldas. Front. Microbiol. 8: 1940. 
• Ishemgulova A., Kraeva N., Hlaváčová J., Zimmer S.L., Butenko A., Podešvová L., Leštinová T., Lukeš J., Kostygov A., Votýpka J., Volf P. & Yurchenko V. (2017) A putative ATP/GTP binding protein affects Leishmania mexicana growth in insect vectors and vertebrate hosts. PLoS Negl. Trop. Dis. 11: e0005782.
• Benz C., Stříbrná E., Hashimi H. & Lukeš J. (2017) Dynamin–like proteins in Trypanosoma brucei: A division of labour between two paralogs? PLoS One 12: e0177200.
• Haindrich A.C., Boudová M., Vancová M., Peña Diaz P., Horáková E. & Lukeš J. (2017) The intermembrane space protein Erv1 of Trypanosoma brucei is essential for mitochondrial Fe–S cluster assembly and operates alone. Mol. Biochem. Parasitol. 214, 47–51.
• Peña Diaz P., Vancová M., Resl C., Field M.C. & Lukeš J. (2017) A leucine aminopeptidase is involved in kinetoplast DNA segregation in Trypanosoma brucei. PLoS Pathogens 13, e1006310.
• Ishemgulova A., Butenko A., Kortišová L., Boucinha C., Grybchuk–Ieremenko A., Morelli K.A., Tesařová M., Kraeva N., Grybchuk D., Pánek T., Flegontov P., Lukeš J., Votýpka J., Opperdoes F.R., Spodareva V., d’Avila–Levy C.M., Kostygov A. & Yurchenko V. (2017) Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila. PLoS One 12, e0174165.
• Horáková E., Changmai P., Vancová M., Sobotka R., Van Den Abbeele J., Vanhollebeke B. & Lukeš J. (2017) The Trypanosoma brucei TbHrg protein is a heme transporter involved in regulation of stage–specific morphological transitions. J. Biol. Chem. 292, 6998–7010.
• Votýpka J., Modrý D., Oborník M., Šlapeta J. & Lukeš J. (2017) Apicomplexa. In: J.M. Archibald et al. (eds.) Handbook of the Protists, Springer, pp. 1–65.
• Kraeva N., Horáková E., Kostygov A.Y., Kořený L., Butenko A., Yurchenko V. & Lukeš J. (2017) Catalase in Leishmaniinae: with me or against me? Infect., Genet. & Evol. 50, 121–127.
• Dixit S., Müller–McNicoll M., David V., Zarnack K., Ule J., Hashimi H. & Lukeš J. (2017) Differential binding of mitochondrial transcripts by MRB8170 and MRB4160 regulates distinct RNA processing fates in trypanosomes. mBio 8, e02288–16.
• Týč J., Novotná L., Peña Diaz P., Maslov D.A. & Lukeš J. (2017) RSM22, mtYsxC and PNKD–like proteins are required for mitochondrial translation in Trypanosoma brucei. Mitochondrion 34, 67–74.
• Akhoundi M., Downing T., Votýpka J., Kuhls K., Lukeš J., Cannet A., Ravel C., Marty P., Delaunay P., Kasbari M., Granouillac B., Gradoni L. & Sereno D. (2017) Leishmania infections: molecular targets and diagnostics. Mol. Asp. Med. 57, 1–29.
• Seward E.A., Votýpka J., Kment P., Lukeš J. & Kelly S. (2017) Description of Phytomonas oxycareni n.sp. obtained from the salivary glands of Oxycarenus lavaterae. Protist 168, 71–79.
• Valach M., Moreira S., Faktorová D., Lukeš J. & Burger G. (2016) Post–transcriptional remodeling of genes: a look under the hood of mitochondrial gene expression in diplonemids. RNA Biol. 13, 1204–1211. 
• Flegontova O., Flegontov P., Malviya S., Audic S., Wincker P., de Vargas C., Bowler C., Lukeš J. & Horák A. (2016) Unexpected diversity and abundance of planktonic diplonemids in the world ocean. Curr. Biol. 26, 3060–3065.
• Pyrih J., Pyrihová E., Kolísko M., Stojanovová D., Basu S., Harant K., Haindrich A., Doležal P., Lukeš J., Roger A. & Tachezy J. (2016) Minimal cytosolic iron–sulfur cluster assembly machinery in Giardia intestinalis is partially associated with mitosomes. Mol. Microbiol. 102, 701–714.
• Gawryluk R.M.R., del Campo J., Okamoto N., Strassert J.F.H., Lukeš J., Richards T.A., Worden A.Z., Santoro A.E. & Keeling P.J. (2016) Morphological identification and single–cell genomics of marine diplonemids. Curr. Biol. 26, 3053–3059. 
• Akopyants N.S., Lye L.-F., Dobson D.E., Lukeš J. & Beverley S.M. (2016) A Narnavirus in the trypanosomatid protozoan plant pathogen Phytomonas serpens. Genome Announc. 4, e00711–16. 
• Akopyants N.S., Lye L.-F., Dobson D.E., Lukeš J. & Beverley S.M. (2016) A novel bunyavirus–like virus of protozoan parasites. Genome Announc. 4, e00715–16.
• Drini S., Criscuolo A., Lechat P., Imamura H., Skalický T., Cotton J., Rachidi N., Lukeš J., Dujardin J.-C. & Späth G.F. (2016) Species–and strain–specific adaptation of the Hsp70 super family in early–branching trypanosomatid pathogens are driven by copy number variation and divergent evolution. Genome Biol. Evol. 8, 1980–1995.
• Ishemgulova A., Kraeva N., Faktorová D., Podešvová L., Lukeš J. & Yurchenko V. (2016) T7 polymerase–driven transcription is downregulated in metacyclic promastigote and amastigote Leishmania mexicana. Folia Parasitol. 63: 016.
• Benz C., Kovářová J., Králová–Hromadová I., Pierik A.J. & Lukeš J. (2016) Roles of the Nfu Fe–S targeting factors in the trypanosome mitochondrion. Int. J. Parasitol. 46, 641–651.
• Opperdoes F., Butenko A., Flegontov P., Yurchenko V. & Lukeš J. (2016) Comparative metabolism of free–living Bodo saltans and parasitic trypanosomatids. J. Euk. Microbiol. 63, 657–678.
• Lukeš J., López–García P., Boekhout T. & Louis E. (2016) Minutes from EMBO: 10 years of comparative genomics of eukaryotic microorganisms. Protist 167, 217–221.
• Faktorová D., Dobáková E., Peña Diaz P. & Lukeš J. (2016) From simple to supercomplex: mitochondrial genomes of euglenozoan protists. F1000 Research 5; 392.
• Flegontov P., Butenko A., Firsov S., Kraeva N., Eliáš M., Field M.C., Filatov D., Flegontova O.,  Gerasimov E.S., Hlaváčová J., Ishemgulova A., Jackson A.P., Kelly S., Kostygov A., Logacheva M.D., Maslov D.A., Opperdoes F., O´Reilly A., Sádlová J., Ševčíková T.,  Venkatesh D., Vlček Č., Volf P., Votýpka J., Záhonová K., Yurchenko V. & Lukeš J.  (2016) Genome of Leptomonas pyrrhocoris: a high–quality reference for monoxenous  trypanosomatids and new insights into evolution of Leishmania. Sci. Reports 6, 23704.
• Cenci U., Moog D., Curtis B.A., Tanifuji G., Eme L., Lukeš J. & Archibald J.M. (2016) Heme  pathway evolution in kinetoplastid protists. BMC Evol. Biol. 16, 109.
• Zíková A., Hampl V., Paris Z., Týč J. & Lukeš J. (2016) Aerobic mitochondria of parasitic protists:  diverse genomes and complex functions. Mol. Biochem. Parasitol. 209, 46–57.
• Hashimi H., Kaltenbrunner S., Zíková A. & Lukeš J. (2016) Trypanosome mitochondrial translation  and tetracycline: no sweat about tet. PLoS Pathogens 12, e1005492.
• Kostygov A., Dobáková E., Grybchuk–Ieremenko A., Váhala D., Maslov D.A., Votýpka J., Lukeš J. &  Yurchenko V. (2016) Novel trypanosomatid–bacterium association: evolution of  endosymbiosis in action. mBio 7, e01985–15.
• Read L.K., Lukeš J. & Hashimi H. (2016) Trypanosome RNA editing: the complexity of getting U in and taking U out. WIREs RNA 7, 33–51.
• Yurchenko V., Kostygov A., Havlová J., Grybchuk–Ieremenko A., Ševčíková T., Lukeš J., Ševčík J. & Votýpka J. (2016) Diversity of trypanosomatids in cockroaches. J. Euk. Microbiol. 63, 198–209.
• Basu S., Horáková E. & Lukeš J. (2016) Iron–associated biology of Trypanosoma brucei. Biochim. Biophys. Acta–Gen. Subj. 1860, 363–370.
• Lin R.-H., Lai D.-H., Zheng L.-L., Wu J., Lukeš J., Hide G. & Lun Z.-R. (2015) Analysis of the mitochondrial maxicircle of Trypanosoma lewisi, a neglected human pathogen. Parasites & Vectors 8, 665.
• Dobáková E., Flegontov P., Skalický T. & Lukeš J. (2015) Unexpectedly streamlined mitochondrial genome of the euglenozoan Euglena gracilis. Genome Biol. Evol. 7, 3358–3367.
• David V., Flegontov P., Gerasimov E., Tanifuji G., Hashimi H., Logacheva M.D., Maruyama S., Onodera N.T., Gray M.W., Archibald J.M. & Lukeš J. (2015) Gene loss and error–prone RNA editing in the mitochondrion of Perkinsela, an endosymbiotic kinetoplastid. mBio 6, e01498–15.
• d’Avila–Levy C.M., Boucinha C., Kostygov A., Santos H.L.C., Morelli K.A., Grybchuk–Ieremenko A., Duval L., Votýpka J., Yurchenko V., Grellier P. & Lukeš J. (2015) Exploring environmental diversity of kinetoplastid flagellates in the high–throughput DNA sequencing era. Mem. Inst. Osw. Cruz 110, 956–965.
• Huang Z., Faktorová D., Křížová A., Kafková L., Read L.K., Lukeš J. & Hashimi H. (2015) Integrity of the core mitochondrial RNA binding complex 1 is vital for trypanosome RNA editing. RNA 21, 2088–2102.
• Kumar D.S., Bartošová–Sojková P., Lukeš J. & Soldati–Favre D. (2015) Phylogeny, morphology, and metabolic and invasive capabilities of epicellular fish coccidium Goussia janae. Protist 166, 659–676.
• Kozminsky E., Kraeva N., Ishemgulova A., Dobáková E., Lukeš J., Kment P., Yurchenko V., Votýpka J., Maslov D.A. (2015) Host–specificity of monoxenous trypanosomatids: statistical analysisof the distribution and transmission patterns of the parasites from Neotropical Heteroptera.Protist 166, 551–568.
• Hamilton P.T., Votýpka J., Dostálová A., Yurchenko V., Bird N.H., Lukeš J., Lemaitre B. & Perlman S.J. (2015) Infection dynamics and immune response in a newly described Drosophila–trypanosomatid association. mBio 6, e01356–15 
• Kraeva N., Butenko A., Hlaváčová J., Kostygov A., Myšková J., Grybchuk D., Leštinová T., Votýpka J., Volf P., Opperdoes F., Flegontov P., Lukeš J. & Yurchenko V. (2015) Leptomonas seymouri: Adaptations to the dixenous life cycle analyzed by genome sequencing, transcriptome profiling and co–infection with Leishmania donovani. PLoS Pathogens 11, 1005127
• Horáková E., Changmai P., Paris Z., Salmon D. & Lukeš J. (2015) Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe–S cluster assembly but not heme import into mitochondrion of Trypanosoma brucei. FEBS J. 282, 4157–4175.
• Bartošová–Sojková P., Oppenheim R., Soldati–Favre D. & Lukeš J. (2015) Epicellular apicomplexans:  parasites „on–the–way–in“. PLoS Pathogens 11, e1005080.
• Sunter J.D., Benz C., Andre J., Whipple S., McKean P.G., Gull K., Ginger M.L. & Lukeš J. (2015) Modulation of flagellum attachment zone protein FLAM3 and regulation of the cell shape in T. brucei life cycle transitions. J. Cell Sci. 128, 3117–3130.
• Votýpka J., Rádrová J., Skalický T., Jirků M., Jirsová D., Mihalca A.D., D‘Amico G., Petrželková K. J., Modrý D. & Lukeš J. (2015) A tsetse and tabanid fly survey of African great apes habitat reveals the presence of a novel trypanosome lineage but the absence of T. brucei. Int. J. Parasitol. 45, 741–748.
• Lukeš J., Stensvold C.R., Jirků–Pomajbíková K. & Wegener Parfrey L. (2015) Are human intestinal eukaryotes beneficial or commensals? PLoS Pathogens 11, e1005039
• Woo Y.H., Ansari H., Otto T.D., Klinger C., Kolísko M., Michálek J., Saxena A., Shanmugam D., Tayyrov A., Veluchamy A., Ali S., Bernal A., del Campo C., Cihlář J., Flegontov P., Gornik S.G., Hajdušková E., Horák A., Janouškovec J., Katris N.J., Mast F., Miranda– Saavedra D., Mourier T., Naeem R., Nair M., Panigrahi A.K., Rawlings N., Regelado E.P., Ramaprasad A., Samad N., Tomčala A., Wilkes J., Neafsey D., Doerig C., Bowler C., Keeling P.J., Roos D.S., Dacks J., Templeton TJ., Waller R.F., Lukeš J., Oborník M. & Pain A. (2015) Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. eLife 4, e06974
• Votýpka J., d’Avila–Levy C.M., Grellier P., Maslov D.A., Lukeš J. & Yurchenko V. (2015) New approaches to systematics of Trypanosomatidae: criteria for taxonomic (re)description. Trends Parasitol. 31, 460–469.
• Jirků M., Votýpka J., Petrželková K.J., Jirků–Pomajbíková K., Kriegová E., Vodička R., Lankaster F., Leendertz S.A.J., Wittig R.M., Boesch C., Modrý D., Ayala F.J., Leendertz F.H. & Lukeš J. (2015) Wild chimpanzees are infected by Trypanosoma brucei. Int. J. Parasitol. Parasit. Wildl. 4, 277–282.
• Lukeš J., Flegontova O. & Horák A. (2015) Diplonemids. Curr. Biol. 25, R702–R704.
• Doležalová J., Vallo P., Petrželková K.J., Foitová I., Nurcahyo W., Mudakikwa A., Hashimoto C., Jirků M., Lukeš J., Scholz T. & Modrý D. (2015) Potentially zoonotic anoplocephalid tapeworms (Cestoda: Cyclophyllidea) in humans and primates: molecular phylogeny versus egg morphology. Parasitology 142, 1278–1289.
• Oborník M. & Lukeš J. (2015) The organellar genomes of Chromera and Vitrella, the phototrophic  relatives of apicomplexan parasites. Annu. Rev. Microbiol. 69, 129–144.
• Sample P., Kořený L., Paris Z., Gaston K.W., Rubio M.A., Fleming I.M., Hinger S., Horáková E.,  Limbach P.A., Lukeš J. & Alfonzo J.D. (2015) A common tRNA modification at an  unusual location: The discovery of wyosine biosynthesis in mitochondria. Nucl. Acids  Res. 43, 4262–4273.
• Speijer D., Lukeš J. & Eliáš M. (2015) Sex is ubiquitous, ancient, and inherent attribute of eukaryotic  life. Proc. Natl. Acad. Sci. USA 112, 8827–8834.
• de Vargas C., Audic S., Henry N., Decelle J., Mahé F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J.-M., Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horák A., Jaillon O., Lima Mendez G., Lukeš J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels–Lewis S., Acinas S.G., Bork P., Bowler C., Gaill F., Gorsky G., Grimsley N., Hingcamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P., Karsenti E., Boss E., Follows M., Karp–Boss L., Krzic U., Reynaud E.G., Sardet C., Sullivan M.B. & Velayoudon D. (2015) Eukaryotic plankton diversity in the sunlit global ocean. Science 348, 1261605.
• Flegontov P., Michálek J., Janouškovec J., Lai D.-H., Jirků M., Hajdušková E., Tomčala A., Otto T.D., Keeling P.J., Pain A., Oborník M. & Lukeš J. (2015) Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites. Mol. Biol. Evol. 32, 1115–1131.
• Zíková A., Oborník M. & Lukeš J. (2015) Fancy a gene? A surprisingly complex evolutionary history of peroxiredoxins. Microb. Cell 2, 33–37. 
• Gnipová A., Šubrtová K., Panicucci B., Horváth A., Lukeš J. & Zíková A. (2015) The ADP/ATP carrier and its relationship to OXPHOS in an ancestral protist, Trypanosoma brucei. Eukaryot. Cell 14, 297–310.
• Mapua M.I., Qablan M.A., Pomajbíková K., Petrželková K.J., Rádrová J., Votýpka J., Todd A., Jirků M., Leendertz F.H., Lukeš J., Neel C. & Modrý D. (2015) Ecology of malaria infections in western lowland gorillas inhabiting Dzanga Sangha Protected Areas, Central African Republic. Parasitology 142, 890–900.
• Škodová–Sveráková I., Verner Z., Skalický T., Votýpka J., Horváth A. & Lukeš J. (2015) Lineage– specific activities of a multipotent mitochondrion of trypanosomatid flagellates. Mol. Microbiol. 96, 55–67.
• Týč J., Klingbeil M.M., Lukeš J. (2015) Mitochondrial heat–shock protein machinery Hsp70/Hsp40 is indispensable for proper mitochondrial DNA maintenance and replication. mBio, e02425. 
• Losev A., Grybchuk–Yeremenko A., Kostygov A.Y., Lukeš J. & Yurchenko V. (2015) Host specificity, pathogenicity and mixed infections of trypanoplasms from freshwater fishes. Parasitol. Res. 114, 1071–1078.
• Carnes J., Anupama A., Balmer O., Jackson A., Lewis M., Brown R., Cestari I., Desquesnes M., Gendrin C., Gibson W., Hertz–Fowler C., Imamura H., Ivens A., Jansen A., Kořený L., Lai D.-H., MacLeod A., Martin D., McDermott S.M., Merritt C., Monnerat S., Moon W., Myler P., Phan I., Ramasamy G., Sivam D., Lun Z.-R., Lukeš J., Stuart K. & Schnaufer A. (2015) Genome and phylogenetic analyses of Trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty. PLoS Negl. Trop. Dis. 9, e3404.
• Verner Z., Basu S., Benz C., Dixit S., Dobáková E., Faktorová D., Hashimi H., Horáková E., Huang Z., Paris Z., Pena–Diaz P., Ridlon L., Týč J., Wildridge D., Zíková A. & Lukeš J. (2015) Malleable mitochondrion of Trypanosoma brucei. Int. Rev. Cell. Mol. Biol. 315, 73–151.
• Lukeš J. & Basu S. (2015) Fe/S protein biogenesis in trypanosomes–a review. Biochim. Biophys. Acta–Mol. Cell. Res. 1853, 1481–1492.
• Kraeva N., Ishemgulova A., Lukeš J. & Yurchenko V. (2014) Tet–inducible gene expression system in Leishmania mexicana. Mol. Biochem. Parasitol. 198, 11–13.
• Votýpka J., Kostygov A.Y., Kraeva N., Grybchuk–Ieremenko, A., Tesařová M., Grybchuk D., Lukeš J. & Yurchenko V. (2014) Kentomonas gen. n., a new genus of endosymbiont–containing trypanosomatids of Strigomonadinae subfam. n. Protist 165, 825–838.
• Huang Z., Kaltenbrunner S., Šimková E., Staněk D., Lukeš J. & Hashimi, H. (2014) The dynamics of mitochondrial RNA–binding protein complex in Trypanosoma brucei and its petite mutant under optimized immobilization conditions. Eukaryot. Cell 13, 1232–1240.
• Basu S., Netz D.J., Haindrich A.C., Herleth N., Lagny T.J., Pierik A.J., Lill R. & Lukeš J. (2014) Cytosolic iron–sulfur protein assembly is functionally conserved and essential in procyclic and bloodstream Trypanosoma brucei. Mol. Microbiol. 93, 897–910.
• Grybchuk–Ieremenko A., Losev A., Kostygov A.Y., Lukeš J. & Yurchenko V. (2014) Prevalence of mixed trypanosome infections of freshwater fishes. Folia Parasitol. 61, 495–504.
• Lukeš J., Kuchta R., Scholz T. & Pomajbíková K. (2014) (Self–) infections with parasites: re–interpretation for the present. Trends Parasitol. 30, 377–385.
• Lukeš J., Skalický T., Týč J., Votýpka J. & Yurchenko V. (2014) Evolution of parasitism in kinetoplastid flagellates. Mol. Biochem. Parasitol. 195, 115–122.
• Verner Z., Čermáková P., Škodová I., Kováčová B., Lukeš J. & Horváth A. (2014) Comparative analysis of respiratory chain and oxidative phosphorylation in Leishmania tarentolae, Crithidia fasciculata, Phytomonas serpens and procyclic stage of Trypanosoma brucei. Mol. Biochem. Parasitol. 193, 55–65.
• Smejkalová P., Votýpka J., Lukeš J. & Čepička I. (2014) The first report on the presence of trichomonads in true bugs. Folia Parasitol. 61, 189–194.
• Lukeš J. (2014) Mitochondrial genomes of Excavata. In: Bell E (ed) Molecular Life Sciences: An Encyclopedic Reference. Springer New York, pp 1–7.
• Lai D.-H., Poropat E., Pravia C., Landoni M., Couto A.S., Pérez Rojo, F.G., Fuchs A.G., Dubin M., Elingold I., Rodríguez J.B., Ferella M., Esteva M.I., Bontempi E.J. & Lukeš J. (2014) Solanesyl diphosphate synthase, an enzyme of the ubiquinone synthetic pathway, is required throughout the life cycle of Trypanosoma brucei. Eukaryot. Cell 13, 320–328.
• Pokluda P., Čížek L., Drag L., Stříbrná E., Lukeš J. & Novotný V. (2014) A goodbye letter to alcohol: an alternative method for field preservation of arthropod specimens and DNA suitable for mass collecting methods. Europ. J. Entomol. 111, 175–179.
• Kovářová J., Horáková E., Changmai P., Vancová M. & Lukeš J. (2014) Mitochondrial and nucleolar localization of cysteine desulfurase Nfs and the scaffold protein Isu in Trypanosoma brucei. Eukaryot. Cell 13, 353–361.
• Yurchenko V., Votýpka J., Tesařová M., Klepetková H., Kraeva N., Jirků M. & Lukeš J. (2014) Ultrastructure and molecular phylogeny of four new species of monoxenous trypanosomatids from flies (Diptera: Brachycera) with redefinition of the genus Wallaceina. Folia Parasitol. 61, 97–112.
• Heger T.J., Edgcomb V.P., Kim E., Lukeš J., Leander B.S. & Yubuki N. (2014) A resurgence in field research is essential to better understand the diversity, ecology and evolution of microbial eukaryotes. J. Euk. Microbiol. 61, 214–223. 
• Porcel B.M., Denoeud F., Opperdoes F., Noel B., Madoui M.-A., Hammarton T.C., Field M.C., Da Silva C., Couloux A., Poulain J., Katinka M., Jabbari K., Aury J.-M., Campbell D.A., Cintron R., Dickens N.J., Docampo R., Sturm N.R., Koumandou V.L., Fabre S., Flegontov P., Lukeš J., Michaeli S., Mottram J.C., Szoor B., Zilberstein D., Bringaud F., Wincker P. & Dollet M. (2014) The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants. PLoS Genet. 10, e1004007. 
• Škodová I., Verner Z., Bringaud F., Fabian P., Lukeš J. & Horváth A. (2013) Characterization of two mitochondrial FAD–dependent glycerol–3–phosphate dehydrogenases in Trypanosoma brucei. Eukaryot. Cell 12, 1664–1673.
• Ridlon L., Škodová I., Pan S., Lukeš J. & Maslov D.A. (2013) The importance of the 45S ribosomal small subunit–related complex for mitochondrial translation in Trypanosoma brucei. J. Biol. Chem. 288, 32963–32978. 
• Ammerman M.L., Tomasello D.L., Faktorová D., Kafková L., Hashimi H., Lukeš J. & Read L.K. (2013) A core MRB1 complex component is indispensable for RNA editing in insect and human infective stages of Trypanosoma brucei. PLoS One 8, e78015.
• Cristodero M., Mani J., Oeljeklaus S., Aeberhard L., Hashimi H., Ramrath D.J.F., Lukeš J., Warscheid B. & Schneider (2013) Mitochondrial translation factors of Trypanosoma brucei: Elongation factor–Tu has a unique subdomain that is essentials for its function. Mol. Microbiol. 90, 744–755.
• Janouškovec J., Sobotka R., Lai D.-H., Flegontov P., Koník P., Komenda J., Ali S., Prášil O., Pain A., Oborník M., Lukeš J. & Keeling P.J. (2013) Split photosystem protein, linear–mapping topology and growth of structural complexity in the plastid genome of Chromera velia. Mol. Biol. Evol. 30, 2447–2462.
• Votýpka J., Suková E., Kraeva N., Ishemgulova A., Duží I., Lukeš J. & Yurchenko V. (2013)Diversity of trypanosomatids (Kinetoplastea: Trypanosomatidae) parasitizing fleas (Insecta: Siphonaptera) and description of a new genus Blechomonas gen. n. Protist 164, 763–781.
• Hashimi H., McDonald L., Stříbrná E. & Lukeš J. (2013) Trypanosome Letm1 protein is essential for mitochondrial potassium homeostasis. J. Biol. Chem. 288, 26914–26925.
• Flegontov P., Votýpka J., Skalický T., Logacheva M.D., Penin A.A., Tanifuji G., Onodera N.T., Kondrashov A.S., Volf P., Archibald J.M. & Lukeš J. (2013) Paratrypanosoma is a novel early–branching trypanosomatid. Curr. Biol. 23, 1787–1793.
• Týč J., Votýpka J., Klepetková H., Šuláková H., Jirků M. & Lukeš J. (2013) Growing diversity of trypanosomatid parasites of flies (Diptera: Brachycera): frequent cosmopolitism and moderate host specificity. Mol. Phyl. Evol. 69, 255–264.
• Changmai P., Horáková E., Long S., Černotíková–Stříbrná E., McDonald L.M., Bontempi E.J. & Lukeš J. (2013) Both human ferredoxins equally efficiently rescue ferredoxin deficiency in Trypanosoma brucei. Mol. Microbiol. 89, 135–151.
• Mach J., Poliak P., Matušková A., Žárský V., Janata J., Lukeš J. & Tachezy J. (2013) An advanced system of the mitochondrial processing peptidase and core protein family in Trypanosoma brucei and multiple origins of the core I subunit in eukaryotes. Genome Biol. Evol. 5, 860–875.
• Qablan M.A., Oborník M., Petrželková K.J., Sloboda M., Shudiefat M.F., Hořín P., Lukeš J. & ModrýD. (2013) Infections by Babesia caballi and Theileria equi in Jordanian equids: epidemiology and genetic diversity. Parasitology 140, 1096–1103.
• Paris Z., Horáková E., Rubio M.A.T., Sample P., Fleming I.M.C., Armocida S., Lukeš J. & Alfonzo J.D. (2013) The T. brucei TRM5 methyltransferase plays an essential role in mitochondrial protein synthesis and function. RNA 19, 649–658.
• Oborník M. & Lukeš J. (2013) Cell biology of chromerids, the autotrophic relatives to apicomplexan parasites. Int. Rev. Cell. Mol. Biol. 306, 333–369.
• Basu S., Leonard J.C., Desai N., Mavridou D.A.I., Tang K.H., Goddard A.D., Ginger M.L., Lukeš J. & Allen J.W.A. (2013) Divergence of Erv1–associated mitochondrial import and export pathways in trypanosomes and anaerobic protists. Eukaryot. Cell 12, 343–355.
• Hashimi H., Zimmer S.L., Ammerman M.L., Read L.K. & Lukeš J. (2013) Dual core processing: MRB1 is an emerging kinetoplast RNA editing complex. Trends Parasitol. 29, 91–99.
• Maslov D.A., Votýpka J., Yurchenko V. & Lukeš J. (2013) Diversity and phylogeny of insect trypanosomatids: all that is hidden shall be revealed. Trends Parasitol. 29, 43–52.
• Vávra J., Lukeš J. (2013) Microsporidia and „the art of living together”. Adv. Parasitol. 82, 253–319.
• Kořený L., Oborník M. & Lukeš J. (2013) Make it, take it or leave it: Heme metabolism of parasites. PLoS Pathogens 9, e1003088.
• Verner Z., Škodová I., Poláková S., Ďurišová–Benkovičová V., Horváth A. & Lukeš J. (2013) Alternative NADH dehydrogenace (NDH2): intermembrane–space–facing counterpart of mitochondrial complex I in the procyclic Trypanosoma brucei. Parasitology 140, 328–337.
• Pawlowski J., Audic S., Adl S., Bass D., Belbahri L, Berney C., Bowser S.S., Čepička I., Decelle J., Dunthorn M., Fiore–Donno A.-M., Gile H.G., Holzmann M., Jahn R., Jirků M., Keeling P.J., Kostka M., Kudryavtsev A., Lara E., Lukeš J., Mann G.D., Mitchell A.D.E., Nitsche F., Romeralo M., Saunders W.G., Simpson A.G.B., Smirnov V.A., Spouge J., Stern F.R., Stoeck T., Zimmermann J., Schindel D. & de Vargas C. (2012) CBOL Protist Working Group: Barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms. PLoS Biology 10, e1001419. 
• Kafková L., Ammerman M.L., Faktorová D., Fisk J.C., Zimmer S.L., Sobotka R., Read L.K., Lukeš J. & Hashimi H. (2012) Functional characterization of two paralogs that are novel RNA binding proteins influencing mitochondrial transcripts of Trypanosoma brucei. RNA 18, 1846–1861.
• Adl S.M., Simpson A.G., Lane C.E., Lukeš J., Bass D., Bowser S.S., Brown M., Burki F., Dunthorn M., Hampl V., Heiss A., Hoppenrath M., Lara E., LeGall L., Lynn D.H., McManus H., Mitchell E.A.D., Mozley–Stanridge S.E., Wegener Parfrey L., Pawlowski J., Rueckert S., Shadwick L., Schoch C., Smirnov A. & Spiegel F.W. (2012) The revised classification of eukaryotes. J. Euk. Microbiol. 59, 429–493.    
• Tsaousis A.D., Ollagnier de Choudens S., Gentekaki E., Long S., Gaston D., Stechmann A., Vinella D., Py B., Fontecave M., Barras F., Lukeš J. & Roger A.J. (2012) The evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis. Proc. Natl. Acad. Sci. USA 109, 10426–10431.
• Burki F., Flegontov P., Oborník M., Cihlář J., Pain A., Lukeš J. & Keeling P.J. (2012) Reevaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin. Genome Biol. Evol. 4, 738–747.
• Gnipová A., Panicucci B., Paris Z., Verner Z., Horváth A., Lukeš J. & Zíková A. (2012) Disparatephenotypic effects from the knockdown of various Trypanosoma brucei cytochrome c oxidace subunits. Mol. Biochem. Parasitol. 184, 90–98.
• Jirků M., Yurchenko V.Y., Lukeš J. & Maslov D.A. (2012) New species of insect trypanosomatids from Costa Rica and the proposal for a new subfamily within the Trypanosomatidae. J. Euk. Microbiol. 59, 537–547.
• Flegontov P. & Lukeš J. (2012) Mitochondrial genomes of photosynthetic euglenids and alveolates. Adv. Botan. Res. 63, 127–153.
• Votýpka J., Klepetková H., Jirků M., Kment P. & Lukeš J. (2012) Phylogenetic relationships of trypanosomatids parasitizing true bugs (Insecta: Heteroptera) in sub–Saharan Africa. Int. J. Parasitol. 42, 489–500.
• Flegontova O., Lukeš J. & Flegontov P. (2012) Lack of evidence for integration of Trypanosoma cruzi minicircle DNA in South American human genomes. Int. J. Parasitol. 42, 437–441.    (Factor 6.0; must read)
• Lai D.-H., Bontempi E. & Lukeš J. (2012) Trypanosoma brucei solanesyl–diphosphate synthase localizes to the mitochondrion. Mol. Biochem. Parasitol. 183, 189–192.
• Ammerman M.L., Downey K.M., Hashimi H., Fisk J.C., Tomasello D.L., Faktorová D., Kafková L., King T., Lukeš J. & Read L.R. (2012) Architecture of the trypanosome RNA editing accessory  complex, MRB1. Nucl. Acids Res. 40, 5637–5650.
• Kořený L., Sobotka R., Kovářová J., Gnipová A., Flegontov P., Horváth A., Oborník M., Ayala F.J. & Lukeš J. (2012) Aerobic kinetoplastid flagellate Phytomonas does not require heme for viability. Proc. Natl. Acad. Sci. USA 109, 3808–3813.
• Montagnes D., Roberts E., Lukeš J. & Lowe C. (2012) The rise of model protozoa. Trends Microbiol. 20, 184–191.
• Jirků M., Pomajbíková K., Petrželková K.J., Hůzová Z., Modrý D. & Lukeš J. (2012) Detection of Plasmodium in human feces. Emerg. Infect. Dis. 18, 634–636.
• Votýpka J., Klepetková H., Yurchenko V.Y., Horák A., Lukeš J. & Maslov D.A. (2012) Cosmopolitan distribution of a trypanosomatid Leptomonas pyrrhocoris. Protist 163, 616–631.
• Qablan M.A., Sloboda M., Jirků M., Oborník M., Dwairi S., Amr Z.S., Hořín P., Lukeš J. & Modrý D. (2012) Quest for the piroplasms in camels: identification of Theileria equi and Babesia caballi in Jordanian dromedaries. Vet. Parasitol. 186, 456–460. 
• Docampo R. & Lukeš J. (2012) The solution of fifty years–calcium mystery and the promises of trypanosome mitochondria. Trends Parasitol. 28, 31–36.
• Oborník M., Modrý D., Lukeš M., Černotíková–Stříbrná E., Cihlář J., Tesařová M., Kotabová E., Vancová M., Prášil O. & Lukeš J. (2012) Morphology, ultrastructure and life cycle of Vitrella brassicaformis n. sp., n. gen., a novel chromerid from the Great Barrier Reef. Protist 163, 306–323.
• Long S., Changmai P., Tsaousis A.D., Skalický T., Verner Z., Wen Y.-Z., Roger A.J. & Lukeš J. (2011) Stage–specific requirement for Isa1 and Isa2 proteins in the mitochondrion of Trypanosoma brucei and heterologous rescue by human and Blastocystis orthologues. Mol. Microbiol. 81, 1403–1418.
• Tanifuji G., Kim E., Onodera N.T., Gibeault R., Dlutek M., Cawthorn R.J., Fiala I., Lukeš J., Greenwood S.J. & Archibald J.M. (2011) Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont. Eukaryot. Cell 10, 1143–1146.
• Flegontov P., Gray M.W., Burger G. & Lukeš J. (2011) Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa? Curr. Genet. 57, 225–232.
• Lukeš J., Archibald J.M., Keeling P.J., Doolittle W.F. & Gray M.W. (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63, 528–537.
• Doolittle W.F., Lukeš J., Archibald J.M., Keeling P.J. & Gray M.W. (2011) Does constructive neutral evolution play an important role in the origin of cellular complexity? BioEssays 33, 427–429.
• Szabová J., Růžička P., Verner Z., Hampl V. & Lukeš J. (2011) Experimental examination of EFL and MATX eukaryotic horizontal gene transfers: co–existence of mutually exclusive transcripts predates functional rescue. Mol. Biol. Evol. 28, 2371–2378.
• Ammerman M.L., Hashimi H., Novotná L., Čičová Z., McEvoy S.M., Lukeš J. & Read L.K. (2011) MRB3010 is a core component of the MRB1 complex that facilitates an early step of the kinetoplastid RNA editing process. RNA 17, 865–877.
• Alfonzo J.D. & Lukeš J. (2011) Assembling Fe/S–clusters and modifying tRNAs: ancient co–factors meet ancient adaptors. Trends Parasitol. 27, 235–238.
• Sloboda M., Jirků M., Lukešová D., Qablan M., Batsukh Z., Fiala I., Hořín P., Modrý D. & Lukeš J. (2011) A survey for piroplasmids in horses and Bactrian camels in north–eastern Mongolia. Vet. Parasitol. 179, 246–249.
• Vlček Č., Marande W., Teijeiro S., Lukeš J. & Burger G. (2011) Gene fragments scattered across amulti–partite mitochondrial genome. Nucl. Acids Res. 39, 979–988.
• Paris Z., Hashimi H., Lun S., Alfonzo J.D. & Lukeš J. (2011) Futile import of tRNAs and proteins into the mitochondrion of Trypanosoma brucei evansi. Mol. Biochem. Parasitol. 176, 116–120.
• Verner Z., Čermáková P., Škodová I., Kriegová E., Horváth A. & Lukeš J. (2011) Complex I (NADH:ubiquinone oxidoreductase) is active in but non–essential for procyclic Trypanosoma brucei. Mol. Biochem. Parasitol. 175, 196–200.
• Richterová L., Vávrová Z. & Lukeš J. (2011) DEAD–box RNA helicase is dispensable for mitochondrial translation in Trypanosoma brucei. Exp. Parasitol. 127, 300–303.
• Oborník M., Vancová M., Lai D.-H., Janouškovec J., Keeling P.J. & Lukeš J. (2011) Morphology and ultrastructure of multiple life cycle stages of the photosynthetic relative of Apicomplexa, Chromera velia. Protist 162, 115–130.
• Gray M.W., Lukeš J., Archibald J.M., Keeling P.J. & Doolittle W.F. (2010) Irremediable complexity? Science 330, 920–921.
• Lukeš J., Hashimi H., Verner Z. & Čičová Z. (2010) The remarkable mitochondrion of trypanosomes and related flagellates. In: Structures and organelles in pathogenic protists (ed. De Souza W.). Springer–Verlag Berlin, Heidelberg; pp. 228–252.
• Lukeš J., Raper J. (2010) Prophylactic antiparasitic transgenosis for human parasitic disease? Mol. Therapy 18, 1745–1747. 
• Lun Z.-R., Lai D.-H., Li F.-J., Lukeš J. & Ayala F.J. (2010) Trypanosoma brucei: two steps to spread out from Africa. Trends Parasitol. 26, 434–437.
• Gazdag M., Cirstea I., Breitling R., Lukeš J., Blankenfeldt W. & Alexandrov K. (2010) Purificationand crystallization of human Cu/Zn superoxide dismutase recombinantly produced in the protozoan Leishmania tarentolae. Acta Crystalograph. F66, 871–877.
• Týč J., Long S., Jirků M. & Lukeš J. (2010) YCF45 protein, usually associated with plastids, is targeted into the mitochondrion of Trypanosoma brucei. Mol. Biochem. Parasitol. 173, 43–47.
• Paris Z., Changmai P., Rubio M.A.T., Zíková A., Stuart K.D., Alfonzo J.D. & Lukeš J. (2010) The Fe/S cluster assembly protein Isd11 is essential for tRNA thiolation in Trypanosoma brucei. J. Biol. Chem. 285, 22394–22402.
• Janouškovec J., Horák A., Oborník M., Lukeš J. & Keeling P.J. (2010) A common red algal origin of the apicomplexan, dinoflagellate and heterokont plastids. Proc. Natl. Acad. Sci. USA 107, 10949–10954. 
• Keeling P.J., Leander B.S. & Lukeš J.(2010) Does complexity necessarily arise from selective advantage? Reply. Proc. Natl. Acad. Sci. USA 107, E26.
• Verner Z., Paris Z. & Lukeš J.(2010) Mitochondrial membrane potential–based genome–wide RNAi screen of Trypanosoma brucei. Parasitol. Res. 106, 1241–1244.
• Kořený L., Lukeš J. & Oborník M. (2010) Evolution of the heme synthetic pathway in kinetoplastid flagellates: An essential pathway that is not essential after all? Int. J. Parasitol. 40, 149–156.
• Maslov D.A., Yurchenko V.Y., Jirků M. & Lukeš J. (2010) Two new species of trypanosomatid parasites isolated from Heteroptera in Costa Rica. J. Euk. Microbiol. 57, 177–188.
• Poliak P., Van Hoewyk D., Oborník M., Zíková A., Stuart K.D., Tachezy J., Pilon M. & Lukeš J. (2010) Functions and cellular localization of cysteine desulfurase and selenocysteine lyase in Trypanosoma brucei. FEBS J. 277, 383–393.
• Votýpka J., Maslov D.A., Yurchenko V., Jirků M., Kment P., Lun Z.-R. & Lukeš J. (2010) Probing into the diversity of trypanosomatid flagellates parasitizing insect hosts in South–West China reveals both endemism and global distribution. Mol. Phyl. Evol. 54, 243–253.
• Simpson L., Aphasizhev R., Lukeš J. & Cruz–Reyes J. (2010) Guide to the nomenclature of kinetoplastid editing: A proposal. Protist 161, 2–6.
• Týč J., Faktorová D., Kriegová E., Jirků M., Vávrová Z., Maslov D.A. & Lukeš J. (2010) Probing forprimary functions of prohibitin in Trypanosoma brucei. Int. J. Parasitol. 40, 73–83.
• Hashimi H., Benkovičová V., Čermáková P., Lai D.-H., Horváth L. & Lukeš J. (2010) The assembly of F1FO ATP synthase disrupted upon the interference of RNA editing in Trypanosoma brucei. Int. J. Parasitol. 40, 45–54.
• Wohlgamuth–Benedum J.M., Rubio M.A.T., Paris Z., Long S., Poliak P., Lukeš J. & Alfonzo J.D. (2009) Thiolation controls cytoplasmic tRNA stability and acts as a negative determinant for tRNA editing in mitochondria. J. Biol. Chem. 284, 23947–23953.
• Paris Z., Rubio, M.A.T., Lukeš J. & Alfonzo J.D. (2009) Mitochondrial tRNA import in Trypanosoma brucei is independent of thiolation and the Rieske protein. RNA 15, 1398–1406.
• Lukeš J., Leander B.S. & Keeling P.J. (2009) Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc. Natl. Acad. Sci. USA 106, 9963–9970.  (Factor 6.0; must read)
• Gile G.H., Faktorová D., Castlejohn C.A., Burger G., Lang B.F., Farmer M.A., Lukeš J. & Keeling P.J. (2009) Distribution and phylogeny of EFL and EF–1a in Euglenozoa suggest ancestral co–occurrence followed by differential loss. PLoS One 4, e5162.
• Hashimi H., Čičová Z., Novotná L., Wen Y.-Z. & Lukeš J. (2009) Kinetoplastid guide RNAbiogenesis is dependent on subunits of the mitochondrial RNA binding complex 1 and mitochondrial RNA polymerase. RNA 15, 588–599.
• Foldynová–Trantírková S., Matulová J., Dötsch V., Löhr F., Cirstea I., Alexandrov K., Breitling R., Lukeš J. & Trantírek L. (2009) A cost–effective amino–acid–type selective isotope labeling of proteins expressed in Leishmania tarentolae. J. Biomolec. Struct. Dynam. 26, 755–763.  
• Lai D.-H., Wang Q.-P., Li Z., Lukeš J. & Lun Z.-R. (2009) Evolution of the serum resistence–associated SRA gene in African trypanosomes. Chin. Sci. Bull. 54, 1275–1278. 
• Yurchenko V., Lukeš J., Jirků M. & Maslov D.A. (2009) Selective recovery of the cultivation–prone components from mixed trypanosomatid infections: a case of several new species isolated from Neotropical Heteroptera. Int. J. Syst. Evol. Microbiol. 59, 893–909.
• Jirků M., Jirků M., Lukeš J., Oborník M., Petrželková K. & Modrý D. (2009) A model for taxonomic work on homoxenous coccidia: redescription, host specificity, and molecular phylogeny of Eimeria ranae Dobell, 1909, with critical review of Eimeria spp. parasitizing anuran hosts. J. Euk. Microbiol.. 56, 39–51.
• Jirků M., Jirků M., Oborník M., Lukeš J. & Modrý D. (2009) Goussia Abbé, 1896 (Apicomplexa, Eimeriorina) in Amphibia: diversity, biology, molecular phylogeny and comments on the status of the genus. Protist 160, 123–136.
• Oborník M., Janouškovec J., Chrudimský T. & Lukeš J. (2009) Evolution of the apicoplast and itshosts: from heterotrophy to autotrophy and back again. Int. J. Parasitol. 39, 1–12.
• Long S., Jirků M., Ayala F.J., Lukeš J. (2008) Mitochondrial localization but not processing of human frataxin is essential for a rescue of frataxin deficiency in the excavate flagellate Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 105, 13468–13473.
• Long S., Vávrová Z. & Lukeš J. (2008) The import and function of diatom and plant frataxins in themitochondrion of Trypanosoma brucei. Mol. Biochem. Parasitol. 162, 100–104.
• Long S., Jirků M., Mach J., Ginger M.L., Sutak R., Richardson D., Tachezy J. & Lukeš J. (2008) Ancestral roles of eukaryotic frataxin: mitochondrial frataxin function and heterologous expression of hydrogenosomal Trichomonas homologs in trypanosomes. Mol. Microbiol. 69, 94–109. 
• Hashimi H., Zíková A., Panigrahi A.K., Stuart K.D. & Lukeš J. (2008) TbRGG1, a component of a novel multiprotein complex involved in kinetoplastid RNA editing. RNA 14, 970–980.
• Lai D.-H., Hashimi H., Lun Z.-R., Ayala F.J. & Lukeš J. (2008) Adaptation of Trypanosoma brucei to gradual loss of kinetoplast DNA: T. equiperdum and T. evansi are petite mutants of T. brucei. Proc. Natl. Acad. Sci. USA 105, 1999–2004.  (Factor 10.0; exceptional)
• Zíková A., Kopečná J., Schumacher M.A., Stuart K.D., Trantírek L. & Lukeš J. (2008) Structure and function of the native and recombinant mitochondrial MRP1/MRP2 complex from Trypanosoma brucei. Int. J. Parasitol. 38, 901–912.
• Guler J., Kriegová E., Smith T.K., Lukeš J. & Englund P.T. (2008) Mitochondrial fatty acid synthesis is required for normal mitochondrial morphology and function in Trypanosoma brucei. Mol. Microbiol. 67, 1125–1142.
• Chocholová E, Jirků M. & Lukeš J. (2008) A diagnostic assay based on variable intergenic region distinguishes between Leishmania donovani and Leishmania infantum. Folia Parasitol. 55, 75–78.
• Yurchenko V.A., Lukeš J., Tesařová M., Jirků M. & Maslov D.A. (2008) Morphological discordance of the new trypanosomatid species phylogenetically associated with the genus Crithidia. Protist 159, 99–114.
• Čepička I., Lukeš J. & Vávra J. (2007) Protozoologie. In: Paraziti a jejich biologie (eds. Volf P., Horák P.), Triton, Praha; pp. 50–63. 
• Zamudio J.R., Mittra B., Foldynová–Trantírková S., Zeiner G.M., Lukeš J., Bujnicky J.M., Sturm N.R. & Campbell D.A. (2007) The 2’–O–ribose methyltransferase for cap 1 of spliced leader RNA and U1 small nuclear RNA in Trypanosoma brucei. Mol. Cell. Biol. 27, 6084–6092.
• Herder S., Votýpka J., Jirků M., Rádrová J., Janzen C.J. & Lukeš J. (2007) Trypanosoma brucei 29–13 strain is inducible in but not permissive for the tsetse fly vector. Exp. Parasitol. 117, 111–114.
• Lukeš J., Mauricio I.L., Schönian G., Dujardin J.-C., Soteriadou K., Dedet J.-P., Kuhls K.,Quispe Tintaya W., Jirků M., Chocholová E., Haralambous C., Pratlong F., Oborník M., Horák A., Ayala F.J. & Miles M.A. (2007) Evolutionary and geographical history of theLeishmania donovani complex with a revision of current taxonomy. Proc. Natl. Acad. Sci. USA 104, 9375–9380.  (Factor 6.0; must read)
• Čermáková P., Verner Z., Man P., Lukeš J. & Horváth A. (2007) Characterization of the NADH: ubiquinone oxidoreductase (complex I) in the trypanosomatid Phytomonas serpens (Kinetoplastida). FEBS J. 274, 3150–3158.
• Roy J., Faktorová D., Lukeš J. & Burger G. (2007) Unusual mitochondrial genome structure throughout Euglenozoa. Protist 158, 385–396.
• Sturm N.R., Dollet M., Lukeš J. & Campbell D.A. (2007) Meaningful sub–division of plant trypanosomes (Phytomonas spp.) based on minicircle conserved region analysis. Infect., Genet. & Evol. 7, 570–576. 
• Svobodová M., Zídková L., Čepička I., Oborník M., Lukeš J. & Votýpka J. (2007) Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida): a new parasite of the biting midges (Ceratopogonidae, Diptera). Int. J. Syst. Evol. Microbiol. 57, 423–432.
• Roy J., Faktorová D., Benada O., Lukeš J. & Burger G. (2007) Description of Rhynchopus euleeides n. sp. (Diplonemea), a free–living, marine euglenozoan. J. Euk. Microbiol. 54, 137–145. 
• Zemanová E., Jirků M., Mauricio I.L., Horák A., Miles M.A. & Lukeš J. (2007) The Leishmania donovani complex: Genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH, FH), new targets for multilocus sequence typing. Int. J. Parasitol. 37, 149–160. 
• Vávra J., Horák A., Modrý D., Lukeš J. & Koudela B. (2006) Trachipleistophora extenrec, n. sp., a new microsporidian (Fungi: Microsporidia) infecting mammals. J. Euk. Microbiol. 53, 464–476 
• Yurchenko V.A., Lukeš J., Jirků M., Zeledón R. & Maslov D.A. (2006) Leptomonas costaricensis sp.n. (Kinetoplastea: Trypanosomatidae), a member of the novel phylogenetic group of insect trypanosomatids closely related to the genus Leishmania. Parasitology 133, 537–546
• Smíd O., Horáková E., Vilímová V., Hrdý I., Cammack R., Horváth A., Lukeš J. & Tachezy J. (2006) Knock–downs of mitochondrial iron–sulfur cluster assembly proteins IscS and IscU down–regulate the active mitochondrion of procyclic Trypanosoma brucei. J. Biol. Chem. 281, 28679–28686 
• Schumacher M.A., Karamooz E., Zíková A., Trantírek L. & Lukeš J. (2006) Crystal structures of Trypanosoma brucei MRP1/MRP2 guide–RNA–binding complex reveals RNA matchmaking mechanism. Cell 126, 701–711 
• Zíková A., Horáková E., Jirků M., Dunajčíková P. & Lukeš J. (2006) The effect of down–regulation of mitochondrial RNA–binding proteins MRP1 and MRP2 on respiratory complexes in procyclic Trypanosoma brucei. Mol. Biochem. Parasitol. 149, 65–73 
• Wijová M., Moravec F., Horák A. & Lukeš J. (2006) Evolutionary relationships of Spirurina (Nematoda: Chromadorea: Rhabditida) with special emphasis on dracunculoid nematodes inferred from SSU rRNA gene sequences. Int. J. Parasitol. 36, 1067–1075 
• Lukeš J., Paris Z., Regmi S., Breitling R., Mureev S., Kushnir S., Pyatkov K., Jirků M. & Alexandrov K.A. (2006) Translational initiation in Leishmania tarentolae and Phytomonas serpens (Kinetoplastida) is strongly influenced by pre–ATG triplet and its 5‘ sequence context. Mol. Biochem. Parasitol. 148, 125–132 
• Mauricio I.L., Yeo M., Baghaei M., Doto D., Silk R., Pratlong F., Zemanová E., Dedet J.-P., Lukeš J. & Miles M.A. (2006) Towards multi locus sequence typing in the Leishmania donovani complex: resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GP1, NH1, NH2, PGD). Int. J. Parasitol. 36, 757–769 
• Simpson A.G.B., Stevens J.R. & Lukeš J. (2006) The evolution and diversity of kinetoplastid flagellates. Trends Parasitol. 22, 168–174 
• Jirků M., Zemanová E., Al–Jawabreh A., Schönian G. & Lukeš J. (2006) Development of a direct species–specific PCR assay for differential diagnosis of Leishmania tropica. Diagn.Microbiol. Infect. Dis. 55, 75–79
• Kopečná J., Jirků M., Oborník M., Tokarev Z.S., Lukeš J. & Modrý D. (2006) Phylogenetic analysis of coccidian parasites from invertebrates: Search for missing links. Protist 157, 173–183.
• Li F.-J., Lai D.-H., Lukeš J., Chen X.-G. & Lun Z.-R. (2006) Doubts about Trypanosoma equiperdum strains classed as Trypanosoma brucei or Trypanosoma evansi. Trends Parasitol. 22, 55–56.
• Yurchenko V., Lukeš J., Xu X. & Maslov D.A. (2006) An integrated morphological and molecular approach to a new species description in the Trypanosomatidae: the case of Leptomonas podlipaevi n.sp., a parasite of Boisea rubrolineata (Hemiptera: Rhopalidae). J. Euk. Microbiol. 53, 103–111. 
• Lukeš J., Hashimi H. & Zíková A. (2005) Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates. Curr. Genet. 48, 277–299. 
• Horváth A., Horáková E., Dunajčíková P., Verner Z., Pravdová E., Šlapetová I., Cuninková L. & Lukeš J. (2005) Down–regulation of the nuclear–encoded subunits of the complexes III and IV disrupts their respective complexes but not complex I in procyclic Trypanosoma brucei. Mol. Microbiol. 58, 116–130.
• Marande W., Lukeš J. & Burger G. (2005) Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids. Eukaryot. Cell 4, 1137–1146.  (Factor 6.0; must read)
• Lukeš J., Horák A. & Scholz T. (2005) Helminth genome projects: all or nothing. Trends Parasitol. 21, 265–266.
• Foldynová–Trantírková S., Paris Z., Sturm N.R., Campbell D.A. & Lukeš J. (2005) The Trypanosoma brucei La protein is a candidate poly(U) shield protein that impacts spliced leader RNA maturation and tRNA intron removal. Int. J. Parasitol. 35, 359–366. 
• Wijová M., Moravec F., Horák A., Modrý D. & Lukeš J. (2005) Phylogenetic position of Dracunculus medinensis and some related nematodes inferred from 18S rRNA. Parasitol. Res. 96, 133–135.
• Vondrušková E., van den Burg J., Zíková A., Ernst N.L., Stuart K., Benne R. & Lukeš J. (2005)
• RNA interference analyses suggest a transcript–specific regulatory role for MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J. Biol. Chem. 280, 2429–2438.
• Votýpka J., Lukeš J. & Oborník M. (2004) Phylogenetic relationship of Trypanosoma corvi and other Old World avian trypanosomes. Acta Protozool. 43, 225–231. 
• Zemanová E., Jirků M., Mauricio I.L., Miles M.A. & Lukeš J. (2004) Genetic polymorphism within the Leishmania donovani complex: correlation with geographical origin. Am. J. Trop. Med. Hyg. 70, 613–617.
• Podlipaev S.A., Sturm N.R., Fiala I., Fernandes O., Westenberger S.J., Dollet M., Campbell D.A. & Lukeš J. (2004) Diversity of insect trypanosomatids assessed from the spliced leader RNA and 5S rRNA genes and intergenic regions. J. Euk. Microbiol. 51, 283–290.
• Avliyakulov N.K., Lukeš J. & Ray D.S. (2004). Mitochondrial histone–like DNA–binding proteins are essential for normal cell growth and mitochondrial function in Crithidia fasciculata. Eukaryot. Cell 3, 518–526.
• Podlipaev S.A., Votýpka J., Jirků M., Svobodová M. & Lukeš J. (2004). Herpetomonas ztiplika n.sp. (Kinetoplastida: Trypanosomatidae)–parasite of the blood–sucking biting midge Culicoides kibunensis Tokunaga, 1937 (Diptera: Ceratopogonidae). J. Parasitol. 90, 342–347. 
• Zeiner G., Foldynová S., Sturm N.R., Lukeš J. & Campbell D.A. (2004). SmD1 is required for spliced leader RNA biogenesis. Eukaryot. Cell 3, 241–244.
• Dávila A.M.R. & Lukeš J. (2003) Towards a framework for the evolutionary genomics of Kinetoplastids: what kind of data and how much? Kinet. Biol. & Dis. 2, 16–19. 
• Zíková A., Vancová M., Jirků M. & Lukeš J. (2003). Cruzella marina (Bodonina, Kinetoplastida): non–catenated structure of poly–kinetoplast DNA. Exp. Parasitol. 104: 159–161.
• Gažiová I. & Lukeš J. (2003). Mitochondrial and nuclear localization of topoisomerase II in the flagellate Bodo saltans (Kinetoplastida), a species with non–catenated kinetoplast DNA. J. Biol. Chem. 278: 10900–10907.
• Dyková I., Fiala I., Lom J. & Lukeš J. (2003). Perkinsiella amoebae–like endosymbionts of Neoparamoeba spp., relatives of the kinetoplastid Ichthyobodo. Europ. J. Protistol. 39: 37–52.
• Šlapeta J.R., Modrý D., Votýpka J., Jirků M., Lukeš J. & Koudela B. (2003). Evolutionary relationships among cyst–forming coccidia Sarcocystis spp. (Alveolata: Apicomplexa: Coccidea) in endemic African tree vipers and perspective for evolution of heteroxenous life cycle. Mol. Phyl. Evol. 27: 464–475.
• Jirků M., Modrý D., Šlapeta J.R., Koudela B. & Lukeš J. (2002). The phylogeny of Goussia and Choleoeimeria (Apicomplexa; Eimeriorina) and the evolution of excystation structures in coccidia. Protist 153: 380–389.
• Maslov D.A., Zíková A., Kyselová I. & Lukeš J. (2002). A novel nuclear–encoded putative subunit of the cytochrome c oxidase complex in trypanosomatids. Mol. Biochem. Parasitol. 125: 113–125. 
• Lukeš J., Guilbride D.L., Votýpka J., Zíková A., Benne R. & Englund P.T. (2002). The kinetoplast DNA network: Evolution of an improbable structure. Eukaryot. Cell 1: 495–502.
• Modrý D., Šlapeta J.R., Kyselová I., Hořejš R., Lukeš J., Koudela B. (2002) Dog shedding oocysts of Neospora caninum: diagnostic and phylogenetic approach to the taxonomy of related organisms. Vet. Parasitol. 109: 157–167. 
• Simpson A.G.B., Lukeš J., Roger A.J. (2002). The evolutionary history of kinetoplastids and their kinetoplast. Mol. Biol. Evol. 19: 2071–2083.
• Votýpka J., Oborník M., Volf P., Svobodová M. & Lukeš J. (2002) Trypanosoma avium of raptors (Falconiformes): Phylogeny and identification of vectors. Parasitology 125: 253–263. 
• Šlapeta J.R., Kyselová I., Richardson A.O., Modrý D., Lukeš J. (2002). Phylogeny and sequence variability of the Sarcocystis singaporensis Zaman and Colley (1975) 1976 ssrDNA. Parasitol. Res. 88: 810–815.
• Šlapeta J. R., Koudela B., Votýpka J., Modrý D., Hořejš R. & Lukeš J. (2002). Coprodiagnosis of Hammondia heydorni in dogs by PCR based on ITS 1 rRNA: Differentiation from morphologically indistinguishable oocysts of Neospora caninum. Vet. J. 163: 147–154.
• Horváth A., Neboháčová M., Lukeš J. & Maslov D.A. (2002). Unusual polypeptide synthesis in the kinetoplast–mitochondria from Leishmania tarentolae. Identification of individual de novo translation products. J. Biol. Chem. 277: 7222–7230.
• Oborník M., Van de Peer Y., Hypša V., Frickey T., Šlapeta J.R., Meyer A. & Lukeš J. (2002) Phylogenetic analyses suggest a possible lateral gene transfer from the mitochondrion to the apicoplast. Gene 285: 109–118. 
• Oborník M., Jirků M., Šlapeta J.R., Modrý D., Koudela B. & Lukeš J. (2002). Notes on coccidian phylogeny based on the apicoplast small subunit ribosomal RNA. Parasitol. Res. 88: 360–363.
• Santana D.M., Lukeš, J., Sturm N.R. & Campbell D.A. (2001). Two sequence classes of kinetoplastid 5S ribosomal RNA gene revealed among bodonid spliced leader RNA gene arrays. FEMS Lett. 204: 33–237. 
• Votýpka J., Ray D.S. & Lukeš J. (2001). Crithidia fasciculata: a test for genetic exchange. Exp. Parasitol. 99: 104–107.
• Lukeš J., Hines J.C., Evans C.J., Avliyakulov N.K., Prabhu V.P., Chen J. & Ray D.S. (2001). Disruption of the Crithidia fasciculata KAP1 gene results in extensive structural rearrangement of the kinetoplast disc. Mol. Biochem. Parasitol. 117:179–186.
• Dyková I., Kyselová I., Pecková H., Oborník M. & Lukeš J. (2001). Identity of Naegleria strains isolated from organs of freshwater fishes. Dis. aquat. Org. 46:115–121. 
• Modrý D., Šlapeta J. R., Jirků M., Oborník M., Lukeš J. & Koudela B. (2001) Phylogentic position of a renal coccidium of the European green frog, Isospora lieberkuehni Labbe, 1894 (Apicomplexa: Sarcocystidae: Toxoplasmatinae) and the taxonomic implications. Int. J. Syst. Evol. Microbiol. 51:767–772.
• Šlapeta J. R., Modrý D., Votýpka J., Jirků M., Oborník M., Lukeš J. & Koudela B. (2001) Eimeria telekii n. sp. (Apicomplexa: Coccidia) from Lemniscomys striatus (Rodentia: Muridae): morphology, pathology and phylogeny. Parasitology 122: 133–145.
• Maslov D.A., Podlipaev S.A. & Lukeš J. (2001). Phylogeny of the Kinetoplastida: Taxonomic problems and insights into the evolution of parasitism. Mem. Inst. Osw. Cruz 96: 397–402.
• Štolba P., Jirků M. & Lukeš J. (2001) Polykinetoplast DNA structure in Dimastigella trypaniformis and Dimastigella mimosa (Kinetoplastida). Mol. Biochem. Parasitol. 113: 323–326.
• Šlapeta J.R., Modrý D., Votýpka J., Jirků M., Koudela B. & Lukeš J. (2001). Multiple origin of the dihomoxenous life cycle in sarcosporidia. Int. J. Parasitol. 31: 413–417.
• Lukeš J. & Votýpka J. (2000). Trypanosoma avium: Novel features of the kinetoplast structure. Exp. Parasitol. 96: 178–181.
• Kodedová I., Doležel D., Broučková M., Jirků M., Hypša V., Lukeš J. & Scholz T. (2000). On the phylogenetic position of the Caryophyllidea, Pseudophyllidea and Proteocephalidea (Eucestoda) inferred from 18S rRNA. Int. J. Parasitol. 30: 1109–1113.
• Doležel D., Jirků M., Maslov D.A. & Lukeš J. (2000) Phylogeny of the bodonid flagellates (Kinetoplastida) based on small subunit rRNA gene sequences. Int. J. Syst. Evol. Microbiol. 50: 1943–1951.
• Yurchenko V., Kolesnikov A.A. & Lukeš J. (2000) Phylogenetic analysis of Trypanosomatina (Protozoa: Kinetoplastida) based on minicircle conserved regions. Folia Parasitol. 47:1–5.
• Avliyakulov N., Lukeš J., Kajava A.V., Liedberg B., Lundstrom I. & Svensson S.P.S. (2000) Suramin blocks nucleotide triphosphate binding to ribosomal protein L3 from Trypanoplasma borreli. Europ. J. Biochem. 267: 1723–1731.
• Lukeš J. & Maslov D.A. (2000) Unexpectedly high variability of histone H4 gene in Leishmania. Parasitol. Res. 86: 259–261. 
• Blom D., de Haan A., van den Burg J., van den Berg M., Sloof P., Jirků M., Lukeš J. & Benne R. (2000) Mitochondrial minicircles in the free–living bodonid Bodo saltans contain two gRNA gene cassettes and are not found in large networks. RNA 6: 1–15.
• Doležel D., Koudela B., Jirků M., Hypša V., Oborník M., Votýpka J.,Modrý D., Šlapeta J.R. & Lukeš J. (1999) Phylogenetic analysis of Sarcocystis spp. of mammals and reptiles support the coevolution of Sarcocystis spp. with their final hosts. Int. J. Parasitol.. 29: 795–798. 
• Yurchenko V., Hobza R., Benada O. & Lukeš J. (1999) Trypanosoma avium: Large minicircles in the kinetoplast DNA. Exp. Parasitol. 92: 215–218.
• Maslov D.A. & Lukeš J. (1998) Searching for a tree which can be trusted. Parasitol. Today 14: 334. 
• Hollar L., Lukeš J. & Maslov D.A. (1998) Monophyly of endosymbiont–containing trypanosomatids: Phylogeny versus Taxonomy. J. Euk. Microbiol. 45: 293–297.
• Votýpka J., Hypša V., Jirků M., Flegr J., Vávra J. & Lukeš J. (1998) Molecular phylogenetic relatedness of Frenkelia spp. (Protozoa, Apicomplexa) to Sarcocystis falcatula Stiles 1893: Is the genus Sarcocystis paraphyletic? J. Euk. Microbiol. 45: 137–141.
• Lukeš J., Jirků M., Avliyakulov N. & Benada O. (1998) Pankinetoplast DNA structure in a primitive bodonid flagellate, Cryptobia helicis. EMBO J. 17: 838–846.
• Blom D., de Haan A., van den Berg M., Sloof P., Jirků M., Lukeš J. & Benne R. (1998) RNA editing in the free–living bodonid Bodo saltans. Nucleic Acids Res. 26: 1205–1213.
• Král’ová I., van de Peer Y., Jirků M., van Ranst M., Scholz T. & Lukeš J. (1997) Phylogenetic analysis of a fish tapeworm, Proteocephalus exiguus, based on the small subunit rRNA gene. Mol. Biochem. Parasitol. 84: 263–266. 
• Lukeš J., Jirků M., Doležel D., Král’ová I., Hollar L. & Maslov D.A. (1997) Analysis of ribosomal RNA genes suggests that trypanosomes are monophyletic. J. Mol. Evol. 44: 521–527. 
• Maslov D.A., Lukeš J., Jirků M. & Simpson L. (1996) Phylogeny of trypanosomes as inferred from the small and large subunit rRNAs: Implications for the evolution of parasitism in the trypanosomatid protozoa. Mol. Biochem. Parasitol. 75:197–205.
• Jirků M., Kolesnikov A.A., Benada O. & Lukeš J. (1995) Marine fish and ray trypanosomes have large kinetoplast minicircle DNA. Mol. Biochem. Parasitol. 73: 279–283. 
• Lukeš J. (1995) Goussia chalupskyi n.sp. (Apicomplexa: Eimeriidae) from the chub Leuciscus cephalus (Cyprinidae). Syst. Parasitol. 30:27–30.
• Kolesnikov A.A., Jirků M., Pecková H., Polák A., Maslov D.A., Lukeš J. (1995) Analysis of kinetoplast DNA of freshwater fish trypanosomes. Folia Parasitol. 40: 424–428.
• Lukeš J., Arts G–J., van den Burg J., de Haan A., Opperdoes F., Sloof P. & Benne R. (1994) Novel pattern of editing regions in mitochondrial transcripts of the cryptobiid Trypanoplasma borreli. EMBO J. 13: 5086–5098.
• Lukeš J. (1994) A giant merogonial stage (Apicomplexa, Coccidia) in the intestine of Blicca bjoerkna (L.)(Cyprinidae). Parasite 1: 393–395.
• Lukeš J. (1994) Morphology of life cycle of Goussia bohemica n.sp. (Apicomplexa, Eimeriidae), a parasite of the goblet and epithelial cells of the gudgeon (Gobio gobio L.). Europ. J. Protistol. 30: 68–74.
• Lukeš J., Volf P. & Lom J. (1993) Detection of chitin in spores of Myxobolus muelleri and M. subepithelialis (Myxosporea, Myxozoa). Parasitol. Res. 79: 439–440.
• Lukeš J. (1993) A coccidian (Apicomplexa, Eimeriidae) with extracytoplasmally located stages in kidney tubules of golden carp (Carassius auratus gibelio L.)(Cyprinidae). Folia Parasitol. 40: 1–7.
• Lukeš J. & Starý V. (1992) Ultrastructure of life cycle stages of Goussia janae (Apicomplexa, Eimeriidae) and X–ray microanalysis of accompanying precipitates. Can. J. Zool. 70: 2382–2397.
• Zajíček P. & Lukeš J. (1992) Differentiation of freshwater and marine fish trypanosomes by lectin agglutinability. Folia Parasitol. 39: 195–200.
• Lukeš J. (1992) Life cycle of Goussia pannonica (Molnár, 1989) (Apicomplexa, Eimeriorina), an extracytoplasmic coccidium from the white bream, Blicca bjoerkna. J. Protozool. 39: 484–494.
• Lukeš J. & Kepr T. (1992) Eimeria lydiae n.sp. (Apicomplexa, Eimeriidae), a parasite of the brown trout, Salmo trutta m. fario (Salmonidae). Arch. Protistenkd. 141: 219–222.
• Lukeš J. & Vávra J. (1991) Microsporidium aedium n.sp., from the mosquito Aedes cantans. J. Invertebr. Pathol. 58: 274–276.
• Lukeš J., Steinhagen D. & Körting W. (1991) Goussia carpelli (Apicomplexa, Eimeriorina) from cyprinid fish: Field observations and infection experiments. Angew. Parasitol. 32:149–153.
• Steinhagen D., Lukeš J. & Körting W. (1990) Ultrastructural observations on gamogonic stages of Goussia subepithelialis (Apicomplexa, Coccidia) from common carp Cyprinus carpio. Dis. aquat. Org. 9: 31–36.
• Lukeš J. & Dyková I. (1990) Goussia janae n.sp. (Apicomplexa,Eimeriorina) in dace Leuciscus leuciscus and chub L. cephalus. Dis. aquat. Org. 8: 85–90.
• Lukeš J. & Vávra J. (1990) Life cycle of Amblyospora weiseri n.sp. (Microsporidia) in Aedes cantans (Diptera, Culicidae). Europ. J. Protistol. 25: 200–208.
• Volf P., Lukeš J. & Srp V. (1990) Study on the population of the warble fly, Oestromyia leporina (Pallas 1778) (Diptera, Hypodermatidae) in Bohemia. Folia Parasitol. 37: 187–190.

Updated: May 2024