[38] Gómez-Palacio A, Cruz-Saavedra L, Van den Broeck F, Geerts M, Pita S, Vallejo G.A., Carranza J.C. & Ramírez J.D. High‑throughput analysis of the Trypanosoma cruzi minicirculome (mcDNA) unveils structural variation and functional diversity. SCIENTIFIC REPORTS. 14: 5578.
[37] Heeren S, Maes I, Sanders M, Lye L-F, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley S.M., Cotton J.A., Dujardin J-C & Van den Broeck F. Diversity and dissemination of viruses in pathogenic protozoa. NATURE COMMUNICATIONS. 4: 8343.
[36] Negreira GH, de Groote R, Van Giel D, Monsieurs P, Maes I, de Muylder G, Van den Broeck F, Dujardin JC, Domagalska M. The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress. EMBO REPORTS. 24:e57413
[35] Jara M, Arevalo J, Llanos-Cuentas A, Van den Broeck F, Domagalska M, Dujardin JC. Unveiling drug-tolerant and persister-like cells in Leishmania braziliensis lines derived from patients with cutaneous leishmaniasis. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY. 13:1253033.
[34] De Moraes L, Portilho M, Vrancken B, Van den Broeck F et al. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. VIRUSES. 2023. 15: 1236.
[33] Van den Broeck F, Heeren S, Maes I, Sanders M, Cotton J, Cupolillo E, Alvarez E, Garcia L, Tasia M, Marneffe A, Dujardin JC, Van der Auwera G. Genome Analysis of Triploid Hybrid Leishmania Parasite from the Neotropics. EMERGING INFECTIUOS DISEASES. 29: 1076-1077.
[32] Hadermann A, Heeren S, Maes I, Dujardin JC, Domagalska M and Van den Broeck F. Genome diversity of Leishmania aethiopica. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY. 13:1147998.
[31] Geerts M, Chen Z, Bebronne N, Savill NJ, Schnaufer A, Büscher P, Van Reet N, Van den Broeck F. Deep kinetoplast genome analyses result in a novel molecular assay for detecting Trypanosoma brucei gambiense-specific minicircles. NAR GENOMICS AND BIOINFORMATICS. 4: 1.
[30] Nguyen PT, Kant R, Van den Broeck F, et al. The phylodynamics of SARS-CoV-2 during 2020 in Finland. COMMUNICATIONS BIOLOGY. 2: 65.
[29] Boushaki D, Wallis K, Van den Broeck F, Schnaufer A. Molecular Analysis of Trypanosome Infections in Algerian Camels. ACTA PARASITOLOGICA.
[28] Negreira G, Monsieurs P, Imamura H, Maes I, Kuk N, Yagoubat A, Van den Broeck F, Sterkers Y, Dujardin JC, Domagalska A High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani. NUCLEIC ACIDS RESEARCH. 50 (1): 293-305
[27] Achtman M, Van den Broeck F, Cooper K, Lemey P, Parker C, Zhou Z. Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLOS GENETICS. 17(9):e1009820.
[26] Geerts M, Schnaufer A, Van den Broeck F. rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects. BMC BIOINFORMATICS. 22:468.
[25] Lemey P, Ruktanonchai N, Hong S, Colizza V, Poletto C, Van den Broeck F, Gill M, Ji X, Levasseur A, Oude Munnink B, Koopmans M, Sadilek A, Lai A, Tatem A, Baele G, Suchard M & Dellicour S. Untangling introductions and persistence in COVID-19 resurgence in Europe. NATURE. 595: 713–717.
[24] Rey O, Webster B, Huyse T, Rollinson D, Van den Broeck F, Kincaid-Smith J, Onyekwere A, Boissier J. Population genetics of African Schistosoma species. INFECTION GENETICS AND EVOLUTION. 89: 104727.
[23] Van den Broeck F, Savill N, Imamura H, Sanders M, Maes I, Cooper S, Mateus D, Jara M, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Cupolillo E, Miles M, Berriman M, Schnaufer A, Cotton J, Dujardin JC. Ecological divergence and hybridization of Neotropical Leishmania parasites. PROCEEDINGS OF NATIONAL ACADEMY OF SCIENCES. 117(40): 25159-25168.
[22] Van den Broeck F, Vanoverbeke J, Polman K, Huyse T. A Darwinian outlook on schistosomiasis elimination. BIORXIV. 2020.
[21] Domagalska M, Imamura H, Sander M, Van den Broeck F, Bhattarai N, Vanaerschot M, Maes I, D’Haenens E, Rai K, Rijal S, Berriman M, Cotton J, Dujardin JC. Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. PLOS NEGLECTED TROPICAL DISEASES. 13(12): e0007900.
[20] Schwabl P, Imamura H, Van den Broeck F, Costales JA, Maiguashca-Sánchez J, Miles MA, Andersson B, Grijalva MJ, Llewellyn MS. Meiotic sex in Chagas disease parasite Trypanosoma cruzi. NATURE COMMUNICATIONS. 10(1): 3972.
[19] Van den Broeck F, Tavernier LJM, Vermeiren L, Dujardin JC, Van Den Abbeele J. Mito-nuclear genomics challenges the theory of clonality in Trypanosoma congolense. Reply to Tibayrenc and Ayala. MOLECULAR ECOLOGY. 27: 3425-3431.
[18] Boon N, Van den Broeck F, Faye D, Volckaert FAM, Mboup S, Polman K, Huyse T. Barcoding hybrids: heterogeneous distribution of Schistosoma haematobium × Schistosoma bovis hybrids across the Senegal River Basin. PARASITOLOGY. 145 (5): 634-645.
[17] Huyse T, Boon N, Van den Broeck F, Mbow M, Chaturvedi A, Meurs L, Volckaert F, Polman K. Evolutionary epidemiology of schistosomiasis: linking parasite genetics with disease phenotype in humans. INTERNATIONAL JOURNAL OF PARASITOLOGY. 48 (2): 107-115.
[16] Tihon E, Imamura H, Van den Broeck F, Vermeiren L, Dujardin JC & Van Den Abbeele J. Genomic analysis of Isometamidium Chloride resistance in Trypanosoma congolense. INTERNATIONAL JOURNAL OF PARASITOLOGY: DRUGS AND DRUG RESISTANCE. 7 (3): 350-361.
[15] Tihon E, Imamura H, Dujardin JC, Van Den Abbeele J & Van den Broeck F. Discovery and genomic analyses of hybridization between divergent lineages of Trypanosoma congolense, causative agent of Animal African Trypanosomiasis. MOLECULAR ECOLOGY. 26 (23): 6524–6538.
[14] Cuypers B, Van den Broeck F, Van Reet N, Meehan C, Cauchard J, Wilkes JM, Claes F, Goddeeris B, Hadush B, Dujardin JC, Laukens K, BÜscher P & Deborggraeve S. Genome-wide SNP analysis reveals distinct origins of Trypanosoma evansi and Trypanosoma equiperdum. GENOME BIOLOGY AND EVOLUTION. 9 (8): 1990–1997.
[13] Zein Eddine R, Djuikwo-Teukeng F, Dar Y, Dreyfuss G & Van den Broeck F. Population genetics of the Schistosoma snail host Bulinus truncatus in Egypt. ACTA TROPICA. 172: 36-43.
[12] Cuypers B, Lecordier L, Meehan C, Van den Broeck F, Imamura H, Büscher P, Dujardin JC, Laukens K, Schnaufer A, Deward C, Lewise M, Balmer O, Azuragog T, Kjei-Faried S, Oheneh SA, Duahi B, Homiahi P, Mensah EK, Anleah F, Franco JR, Pays E & Deborggraeve S. Novel Apolipoprotein L-I Variant Associated with Increased Susceptibility to Trypanosome Infection. MBIO. 7 (2): e02198-15.
[11] Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, Rai K, Uranw S, Bhattarai NR, Khanal B, Prajapati VK, Sharma S, Stark O, Schönian G7, De Koning HP, Settimo L, Vanhollebeke B, Roy S, Ostyn B, Boelaert M, Maes L, Berriman M, Dujardin JC & Cotton JA. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. ELIFE. 5: e12613.
[10] Van den Broeck F, Maes G, Larmuseau M, Rollinson D, Sy I, Faye D, Volckaert F, Polman K & Huyse T. Reconstructing colonization dynamics of the human parasite Schistosoma mansoni following anthropogenic environmental changes in Northwest Senegal. PLOS NEGLECTED TROPICAL DISEASES. 9 (8): e0003998.
[9] Van den Broeck F, Meurs L, Raeymaekers JAM, Boon N, Tandakha N, Volckaert FAM, Polman K & Huyse T. Inbreeding within human Schistosoma mansoni: do host-specific factors shape the genetic composition of parasite populations? HEREDITY. 113: 32-41.
[8] Vanaerschot M, Huijben S, Van den Broeck F & Dujardin JC. Drug resistance in vector-borne parasites: multiple actors and scenarios for an evolutionary arms race. FEMS MICROBIOLOGY REVIEWS. 38 (1): 41-55.
[7] Huyse T, Van den Broeck F, Jombart T, Webster B, Diaw O, Volckaert F, Balloux F, Rollinson D & Polman K. Regular treatments of praziquantel do not impact on the genetic make-up of S. mansoni in northern Senegal: evidence for drug tolerance?. INFECTION GENETICS AND EVOLUTION. 18: 100–105.
[6] Huyse T, Van den Broeck F, Hellemans B, Volckaert F, Polman K. Hybridization between the two major African schistosome species of humans. INTERNATIONAL JOURNAL OF PARASITOLOGY. 43: 687–689.
[5] De Waele V, Van den Broeck F, Huyse T, McGrath G, Higgins I, Speybroeck N, Berzano M, Raleigh P, Mulcahy GM & Murphy TM. Panmictic structure of the Cryptosporidium parvum population in Irish calves: influence of prevalence and host movement. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 79 (8): 2534-2541.
[4] Meurs L, Mbow M, Boon N, Van den Broeck F, Vereecken K, Dièye TN, Abatih E, Huyse T, Mboup S, Polman K. Micro-geographical heterogeneity in Schistosoma mansoni and S. haematobium infection and morbidity in a co-endemic community in Northern Senegal. PLOS NEGLECTED TROPICAL DISEASES. 7 (12): e2608.
[3] Raeymaekers JAM, Lens L, Van den Broeck F, Van Dongen S & Volckaert FAM. Quantifying population structure on short timescales. MOLECULAR ECOLOGY. 21 (14): 3458-73
[2] Adaui V, Maes I, Huyse T, Van den Broeck F, Talledo M, Kuhls K, De Doncker S, Maes L, Llanos-Cuentas A, Schönian G, Arevalo J & Dujardin JC. Multilocus genotyping reveals a polyphyletic pattern among naturally antimony-resistant Leishmania braziliensis isolates from Peru. INFECTION GENETICS AND EVOLUTION. 11 (8): 1873-1880.
[1] Van den Broeck F, Geldof S, Polman K, Volckaert FAM & Huyse T. Optimal sample storage and extraction protocols for reliable multilocus genotyping of the human parasite Schistosoma mansoni. INFECTION GENETICS AND EVOLUTION. 11 (6): 1413-1418.