Publications

Dommann J, Kerbl-Knapp J, Albertos Torres D, Egli A, Keiser J, Schneeberger P.H.H. A novel barcoded nanopore sequencing workflow of high-quality, full-length bacterial 16S amplicons for taxonomic annotation of bacterial isolates and complex microbial communities. mSystems. 2024;9(10):e0085924. DOI: 10.1128/msystems.00859-24

Hofer L.M, Kweyamba P.A, Sayi R.M, Chabo M.S, Mwanga R, Maitra S.L, Somboka M.M, Schnoz A, Golumbeanu M, Schneeberger P.H.H, Ross A, Habtewold T, Nsanzabana C, Moore S.J, Tambwe M.M. Additional blood meals increase sporozoite infection in Anopheles mosquitoes but not Plasmodium falciparum genetic diversity. Sci Rep. 2024;14:17467. DOI: 10.1038/s41598-024-67990-y

Welsche S, Schneeberger P.H.H, Hattendorf J, Sayasone S, Hürlimann E, Keiser J. Egg excretion patterns of soil-transmitted helminth infections in humans following albendazole-ivermectin and albendazole treatment. PLoS Negl Trop Dis. 2024;18(3):e0012073. DOI: 10.1371/journal.pntd.0012073

Spreafico A, Heirali A.A, Araujo D.V, Tan T.J, Oliva M, Schneeberger P.H.H, Chen B, Wong M.K, Stayner L.A, Hansen A.R, Saibil S.D, Wang B.X, Cochrane K, Sherriff K, Allen-Vercoe E, Xu W, Siu L.L, Coburn B. First-in-class Microbial Ecosystem Therapeutic 4 (MET4) in combination with immune checkpoint inhibitors in patients with advanced solid tumors (MET4-IO Trial). Ann Oncol. 2023;34(6):520-530. DOI: 10.1016/j.annonc.2023.02.011

Yersin S, Garneau J.R, Schneeberger P.H.H, Osman K.A, Cercamondi C.I, Muhummed A.M, Tschopp R, Zinsstag J, Vonäsch P. Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits. Sci Rep. 2023;13:21342. DOI: 10.1038/s41598-023-47748-8

Rooney A.M, Raphenya A.R, Melano R.G, Seah C, Yee N.R, MacFadden D.R, McArthur A.G, Schneeberger P.H.H, Coburn B. Performance characteristics of next-generation sequencing for the detection of antimicrobial resistance determinants in Escherichia coli genomes and metagenomes. mSystems. 2022;7(3):e0002222. DOI: 10.1128/msystems.00022-22

Schneeberger P.H.H, Gueuning M, Welsche S, Hürlimann E, Dommann J, Häberli C, Frey J.E, Sayasone S, Keiser J. Different gut microbial communities correlate with efficacy of albendazole-ivermectin against soil-transmitted helminthiases. Nat Commun. 2022;13:1063. DOI: 10.1038/s41467-022-28658-1

Schneeberger P.H.H, Zhang C.Y.K, Santilli J, Chen B, Xu W, Lee Y, Wijesinha Z, Reguera-Nuñez E, Yee N, Ahmed M, Boonstra K, Ramendra R, Frankel C.W, Palmer S.M, Todd J.L, Martinu T, Coburn B. Lung allograft microbiome association with gastroesophageal reflux, inflammation, and allograft dysfunction. Am J Respir Crit Care Med. 2022;206(12):1495-1507. DOI: 10.1164/rccm.202110-2413OC

Buchter V, Schneeberger P.H.H, Keiser J. Validation of a human-serum-based in vitro growth method for drug screening on juvenile development stages of Schistosoma mansoni. PLoS Negl Trop Dis. 2021;15(3):e0009313. DOI: 10.1371/journal.pntd.0009313

Cho M.Y, Oliva M, Spreafico A, Chen B, Wei X, Choi Y, Kaul R, Siu L.L, Coburn B, Schneeberger P.H.H. Two-target quantitative PCR to predict library composition for shallow shotgun sequencing. mSystems. 2021;6(4):e00552-21. DOI: 10.1128/mSystems.00552-21

Massart S, Chiumenti M, De Jonghe K, Glover R, Haegeman A, Koloniuk I, Kominek P, Kreuze J, Kutnjak D, Lotos L, Maclot F, Maliogka V.I, Maree H, Olivier T, Olmos A, Pooggin M, Reynard J.S, Ruiz-Garcia A.B, Safarova D, Schneeberger P.H, Sela N, Turco S, Vainio E.J, Varallyai E, Verdin E, Westenberg M, Brostaux Y, Candresse T. Virus detection by high-throughput sequencing of small RNAs: large scale performance testing of sequence analysis strategies. Phytopathology. 2019;109(3):488-497. DOI: 10.1094/PHYTO-02-18-0067-R

Schneeberger P.H.H, Fuhrimann S, Becker S.L, Pothier J.F, Duffy B, Beuret C, Frey J.E, Utzinger J. Qualitative microbiome profiling along a wastewater system in Kampala, Uganda. Sci Rep. 2019;9:17334. DOI: 10.1038/s41598-019-53569-5

Schneeberger P.H.H, Coulibaly J.T, Gueuning M, Moser W, Coburn B, Frey J.E, Keiser J. Off-target effects of tribendimidine, tribendimidine plus ivermectin, tribendimidine plus oxantel-pamoate, and albendazole plus oxantel-pamoate on the human gut microbiota. Int J Parasitol Drugs Drug Resist. 2018;8(3):372-378. DOI: 10.1016/j.ijpddr.2018.07.001

Schneeberger P.H.H, Coulibaly J.T, Panic G, Daubenberger C, Gueuning M, Frey J.E, Keiser J. Investigations on the interplays between Schistosoma mansoni, praziquantel and the gut microbiome. Parasit Vectors. 2018;11:168. DOI: 10.1186/s13071-018-2739-2

Gétaz M, Bühlmann A, Schneeberger P.H.H, Van Malderghem C, Duffy B, Maes M, Pothier J.F, Cottyn B. A diagnostic tool for improved detection of Xanthomonas fragariae using a rapid and highly specific LAMP assay designed with comparative genomics. Plant Pathology. 2017;66(7):1094-1102. DOI: 10.1111/ppa.12665

Schneeberger P.H.H, Pothier J.F, Bühlmann A, Duffy B, Beuret C, Utzinger J, Frey J.E. Development and evaluation of a bioinformatics approach for designing molecular assays for viral detection. PLoS One. 2017;12(5):e0178195. DOI: 10.1371/journal.pone.0178195

Schneeberger P.H.H. Development and application of -omics and bioinformatics approaches for a deeper understanding of infectious diseases systems. Basel: Univ. Basel, 2017. Doctoral Thesis, University of Basel, Faculty of Science DOI: 10.5451/unibas-006755006

Becker S.L, Yap P, Horié N.S, Alirol E, Barbé B, Bhatta N.K, Bhattarai N.R, Bottieau E, Chatigre J.K, Coulibaly J.T, Fofana H.K.M, Jacobs J, Karki P, Khanal B, Knopp S, Koirala K, Mahendradhata Y, Mertens P, Meyanti F, Murhandarwati E.H, N'Goran E.K, Peeling R.W, Pradhan B, Ravinetto R, Rijal S, Sacko M, Saye R, Schneeberger P.H.H, Schurmans C, Silué K.D, Steinmann P, van Loen H, Verdonck K, van Lieshout L, von Müller L, Yao J.A, Boelaert M, Chappuis F, Polman K, Utzinger J. Experiences and lessons from a multicountry NIDIAG study on persistent digestive disorders in the tropics. PLoS Negl Trop Dis. 2016;10(11):e0004818. DOI: 10.1371/journal.pntd.0004818

Boelaert M, NIDIAG Consortium. Clinical research on neglected tropical diseases: challenges and solutions. PLoS Negl Trop Dis. 2016;10(11):e0004853. DOI: 10.1371/journal.pntd.0004853

Schneeberger P.H.H, Becker S.L, Pothier J.F, Duffy B, N'Goran E.K, Beuret C, Frey J.E, Utzinger J. Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study. Infect Genet Evol. 2016;40:389-397. DOI: 10.1016/j.meegid.2015.08.044

Fuhrimann S, Stalder M, Winkler M.S, Niwagaba C.B, Babu M, Masaba G, Kabatereine N.B, Halage A.A, Schneeberger P.H.H, Utzinger J, Cissé G. Microbial and chemical contamination of water, sediment and soil in the Nakivubo wetland area in Kampala, Uganda. Environ Monit Assess. 2015;187(7):475. DOI: 10.1007/s10661-015-4689-x

Polman K, Becker S.L, Alirol E, Bhatta N.K, Bhattarai N.R, Bottieau E, Bratschi M.W, Burza S, Coulibaly J.T, Doumbia M.N, Horie N.S, Jacobs J, Khanal B, Landoure A, Mahendradhata Y, Meheus F, Mertens P, Meyanti F, Murhandarwati E.H, N'Goran E.K, Peeling R.W, Ravinetto R, Rijal S, Sacko M, Saye R, Schneeberger P.H, Schurmans C, Silué K.D, Thobari J.A, Traore M.S, van Lieshout L, van Loen H, Verdonck K, von Müller L, Yansouni C.P, Yao J.A, Yao P.K, Yap P, Boelaert M, Chappuis F, Utzinger J. Diagnosis of neglected tropical diseases among patients with persistent digestive disorders (diarrhoea and/or abdominal pain >/= 14 days): a multi-country, prospective, non-experimental case-control study. BMC Infect Dis. 2015;15:338. DOI: 10.1186/s12879-015-1074-x

Reynard J.S, Schneeberger P.H, Frey J.E, Schaerer S. Biological, serological, and molecular characterization of a highly divergent strain of grapevine leafroll-associated virus 4 causing grapevine leafroll disease. Phytopathology. 2015;105(9):1262-1269. DOI: 10.1094/PHYTO-12-14-0386-R

Fuhrimann S, Winkler M.S, Schneeberger P.H.H, Niwagaba C.B, Buwule J, Babu M, Medlicott K, Utzinger J, Cissé G. Health risk assessment along the wastewater and faecal sludge management and reuse chain in Kampala, Uganda: a visualization. Geospat Health. 2014;9:241-245. DOI: 10.4081/gh.2014.21