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Organic substrate diffusibility governs microbial community composition, nutrient removal performance and kinetics of granulation of aerobic granular sludge.

Layer M, Adler A, Reynaert E, Hernandez A, Pagni M, Morgenroth E, Holliger C, Derlon N.

Water Res X. 2019 May 20;4:100033. doi: 10.1016/j.wroa.2019.100033. eCollection 2019 Aug 1.


Expression and Immunostaining Analyses Suggest that Pneumocystis Primary Homothallism Involves Trophic Cells Displaying Both Plus and Minus Pheromone Receptors.

Luraschi A, Richard S, Almeida JMGCF, Pagni M, Cushion MT, Hauser PM.

MBio. 2019 Jul 9;10(4). pii: e01145-19. doi: 10.1128/mBio.01145-19.


Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression.

Kirchner FR, Littringer K, Altmeier S, Tran VDT, Schönherr F, Lemberg C, Pagni M, Sanglard D, Joller N, LeibundGut-Landmann S.

Front Immunol. 2019 Feb 27;10:330. doi: 10.3389/fimmu.2019.00330. eCollection 2019.


Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.

Tran VDT, Moretti S, Coste AT, Amorim-Vaz S, Sanglard D, Pagni M.

Bioinformatics. 2019 Jul 1;35(13):2258-2266. doi: 10.1093/bioinformatics/bty929.


Inferring gene expression networks with hubs using a degree weighted Lasso approach.

Sulaimanov N, Kumar S, Burdet F, Ibberson M, Pagni M, Koeppl H.

Bioinformatics. 2019 Mar 15;35(6):987-994. doi: 10.1093/bioinformatics/bty716.


A systems genetics resource and analysis of sleep regulation in the mouse.

Diessler S, Jan M, Emmenegger Y, Guex N, Middleton B, Skene DJ, Ibberson M, Burdet F, Götz L, Pagni M, Sankar M, Liechti R, Hor CN, Xenarios I, Franken P.

PLoS Biol. 2018 Aug 9;16(8):e2005750. doi: 10.1371/journal.pbio.2005750. eCollection 2018 Aug.


Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis.

Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA.

MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18.


A new species of genus Eulimnadia Packard, 1874 (Branchiopoda: Spinicaudata: Limnadiidae) from India with an updated key for some Indian species.

Padhye SM, Rabet N, Kulkarni MR, Pagni M.

Zootaxa. 2018 Mar 21;4399(3):341-350. doi: 10.11646/zootaxa.4399.3.4.


Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs.

Richard S, Almeida JMGCF, Cissé OH, Luraschi A, Nielsen O, Pagni M, Hauser PM.

MBio. 2018 Feb 20;9(1). pii: e02201-17. doi: 10.1128/mBio.02201-17.


Low number of fixed somatic mutations in a long-lived oak tree.

Schmid-Siegert E, Sarkar N, Iseli C, Calderon S, Gouhier-Darimont C, Chrast J, Cattaneo P, Schütz F, Farinelli L, Pagni M, Schneider M, Voumard J, Jaboyedoff M, Fankhauser C, Hardtke CS, Keller L, Pannell JR, Reymond A, Robinson-Rechavi M, Xenarios I, Reymond P.

Nat Plants. 2017 Dec;3(12):926-929. doi: 10.1038/s41477-017-0066-9. Epub 2017 Dec 4.


Mechanisms of Surface Antigenic Variation in the Human Pathogenic Fungus Pneumocystis jirovecii.

Schmid-Siegert E, Richard S, Luraschi A, Mühlethaler K, Pagni M, Hauser PM.

MBio. 2017 Nov 7;8(6). pii: e01470-17. doi: 10.1128/mBio.01470-17.


Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center.

Kytola V, Topaloglu U, Miller LD, Bitting RL, Goodman MM, D Agostino RB Jr, Desnoyers RJ, Albright C, Yacoub G, Qasem SA, DeYoung B, Thorsson V, Shmulevich I, Yang M, Shcherban A, Pagni M, Liu L, Nykter M, Chen K, Hawkins GA, Grant SC, Petty WJ, Alistar AT, Levine EA, Staren ED, Langefeld CD, Miller V, Singal G, Petro RM, Robinson M, Blackstock W, Powell BL, Wagner LI, Foley KL, Abraham E, Pasche B, Zhang W.

Theranostics. 2017 Jul 12;7(11):2914-2923. doi: 10.7150/thno.20355. eCollection 2017.


Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages.

Yang M, Topaloglu U, Petty WJ, Pagni M, Foley KL, Grant SC, Robinson M, Bitting RL, Thomas A, Alistar AT, Desnoyers RJ, Goodman M, Albright C, Porosnicu M, Vatca M, Qasem SA, DeYoung B, Kytola V, Nykter M, Chen K, Levine EA, Staren ED, D'Agostino RB Jr, Petro RM, Blackstock W, Powell BL, Abraham E, Pasche B, Zhang W.

J Hematol Oncol. 2017 May 4;10(1):100. doi: 10.1186/s13045-017-0468-1.


Vps13F links bacterial recognition and intracellular killing in Dictyostelium.

Leiba J, Sabra A, Bodinier R, Marchetti A, Lima WC, Melotti A, Perrin J, Burdet F, Pagni M, Soldati T, Lelong E, Cosson P.

Cell Microbiol. 2017 Jul;19(7). doi: 10.1111/cmi.12722. Epub 2017 Feb 21.


Updates in Rhea - an expert curated resource of biochemical reactions.

Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A.

Nucleic Acids Res. 2017 Apr 20;45(7):4279. doi: 10.1093/nar/gkw1299. No abstract available.


Identification and Functional Ascertainment of the Pneumocystis jirovecii Potential Drug Targets Gsc1 and Kre6 Involved in Glucan Synthesis.

Luraschi A, Cissé OH, Pagni M, Hauser PM.

J Eukaryot Microbiol. 2017 Jul;64(4):481-490. doi: 10.1111/jeu.12385. Epub 2016 Dec 14.


RNA Sequencing-Based Genome Reannotation of the Dermatophyte Arthroderma benhamiae and Characterization of Its Secretome and Whole Gene Expression Profile during Infection.

Tran VD, De Coi N, Feuermann M, Schmid-Siegert E, Băguţ ET, Mignon B, Waridel P, Peter C, Pradervand S, Pagni M, Monod M.

mSystems. 2016 Aug 2;1(4). pii: e00036-16. eCollection 2016 Jul-Aug.


Updates in Rhea - an expert curated resource of biochemical reactions.

Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A.

Nucleic Acids Res. 2017 Jan 4;45(D1):D415-D418. doi: 10.1093/nar/gkw990. Epub 2016 Oct 26. Erratum in: Nucleic Acids Res. 2017 Apr 20;45(7):4279.


The salivary microbiome for differentiating individuals: proof of principle.

Leake SL, Pagni M, Falquet L, Taroni F, Greub G.

Microbes Infect. 2016 Jun;18(6):399-405. doi: 10.1016/j.micinf.2016.03.011. Epub 2016 Apr 8.


Population genomics reveals that within-fungus polymorphism is common and maintained in populations of the mycorrhizal fungus Rhizophagus irregularis.

Wyss T, Masclaux FG, Rosikiewicz P, Pagni M, Sanders IR.

ISME J. 2016 Oct;10(10):2514-26. doi: 10.1038/ismej.2016.29. Epub 2016 Mar 8.


MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

Moretti S, Martin O, Van Du Tran T, Bridge A, Morgat A, Pagni M.

Nucleic Acids Res. 2016 Jan 4;44(D1):D523-6. doi: 10.1093/nar/gkv1117. Epub 2015 Nov 2.


RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans.

Amorim-Vaz S, Tran Vdu T, Pradervand S, Pagni M, Coste AT, Sanglard D.

MBio. 2015 Sep 22;6(5):e00942-15. doi: 10.1128/mBio.00942-15.


Functional characterization of the Pneumocystis jirovecii potential drug targets dhfs and abz2 involved in folate biosynthesis.

Luraschi A, Cissé OH, Monod M, Pagni M, Hauser PM.

Antimicrob Agents Chemother. 2015 May;59(5):2560-6. doi: 10.1128/AAC.05092-14. Epub 2015 Feb 17.


Comparative genomics suggests primary homothallism of Pneumocystis species.

Almeida JM, Cissé OH, Fonseca Á, Pagni M, Hauser PM.

MBio. 2015 Jan 13;6(1). pii: e02250-14. doi: 10.1128/mBio.02250-14.


Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss.

Cissé OH, Pagni M, Hauser PM.

Genome Biol Evol. 2014 Jul 24;6(8):1938-48. doi: 10.1093/gbe/evu155.


Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps.

Pellissier L, Niculita-Hirzel H, Dubuis A, Pagni M, Guex N, Ndiribe C, Salamin N, Xenarios I, Goudet J, Sanders IR, Guisan A.

Mol Ecol. 2014 Sep;23(17):4274-90. doi: 10.1111/mec.12854. Epub 2014 Aug 1.


Highly cited works in radiology: the top 100 cited articles in radiologic journals.

Pagni M, Khan NR, Cohen HL, Choudhri AF.

Acad Radiol. 2014 Aug;21(8):1056-66. doi: 10.1016/j.acra.2014.03.011. Epub 2014 May 13.


Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing.

Hauser PM, Bernard T, Greub G, Jaton K, Pagni M, Hafen GM.

PLoS One. 2014 Mar 5;9(3):e90934. doi: 10.1371/journal.pone.0090934. eCollection 2014.


Plant species distributions along environmental gradients: do belowground interactions with fungi matter?

Pellissier L, Pinto-Figueroa E, Niculita-Hirzel H, Moora M, Villard L, Goudet J, Guex N, Pagni M, Xenarios I, Sanders I, Guisan A.

Front Plant Sci. 2013 Dec 10;4:500. doi: 10.3389/fpls.2013.00500. eCollection 2013.


Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis.

Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Bécard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22. doi: 10.1073/pnas.1313452110. Epub 2013 Nov 25. Erratum in: Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):563. Young, Peter W [corrected to Young, J Peter W].


Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

Cissé OH, Almeida JM, Fonseca A, Kumar AA, Salojärvi J, Overmyer K, Hauser PM, Pagni M.

MBio. 2013 Apr 30;4(3):e00055-13. doi: 10.1128/mBio.00055-13.


Density-based hierarchical clustering of pyro-sequences on a large scale--the case of fungal ITS1.

Pagni M, Niculita-Hirzel H, Pellissier L, Dubuis A, Xenarios I, Guisan A, Sanders IR, Goudet J, Guex N.

Bioinformatics. 2013 May 15;29(10):1268-74. doi: 10.1093/bioinformatics/btt149. Epub 2013 Mar 28.


pfsearchV3: a code acceleration and heuristic to search PROSITE profiles.

Schuepbach T, Pagni M, Bridge A, Bougueleret L, Xenarios I, Cerutti L.

Bioinformatics. 2013 May 1;29(9):1215-7. doi: 10.1093/bioinformatics/btt129. Epub 2013 Mar 16.

34. a website and repository for accessing, analysing and manipulating metabolic networks.

Ganter M, Bernard T, Moretti S, Stelling J, Pagni M.

Bioinformatics. 2013 Mar 15;29(6):815-6. doi: 10.1093/bioinformatics/btt036. Epub 2013 Jan 28.


De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient.

Cissé OH, Pagni M, Hauser PM.

MBio. 2012 Dec 26;4(1):e00428-12. doi: 10.1128/mBio.00428-12.


Reconciliation of metabolites and biochemical reactions for metabolic networks.

Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M.

Brief Bioinform. 2014 Jan;15(1):123-35. doi: 10.1093/bib/bbs058. Epub 2012 Nov 19. Review.


Complete genome sequence of the dog commensal and human pathogen Capnocytophaga canimorsus strain 5.

Manfredi P, Pagni M, Cornelis GR.

J Bacteriol. 2011 Oct;193(19):5558-9. doi: 10.1128/JB.05853-11.


Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host's lungs.

Hauser PM, Burdet FX, Cissé OH, Keller L, Taffé P, Sanglard D, Pagni M.

PLoS One. 2010 Dec 20;5(12):e15152. doi: 10.1371/journal.pone.0015152.


Can hyperbaric oxygenation therapy (HOT) modify the blood testosterone concentration?

Passavanti G, Tanasi P, Brauzzi M, Pagni MR, Aloisi AM.

Urologia. 2010 Jan-Mar;77(1):52-6.


PDB_REDO: automated re-refinement of X-ray structure models in the PDB.

Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G.

J Appl Crystallogr. 2009 Jun 1;42(Pt 3):376-384. Epub 2009 Apr 3.


Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources.

Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Médigue C, Lidstrom ME.

PLoS One. 2009;4(5):e5584. doi: 10.1371/journal.pone.0005584. Epub 2009 May 18.


The Microbe browser for comparative genomics.

Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W296-9. doi: 10.1093/nar/gkp268. Epub 2009 Apr 30.


[Pulmonary arterial hypertension in Health District 11: a patient-oriented drug utilization analysis].

Ipponi A, Moriconi S, Pelagotti F, Lombardo G, Pagni M, Colombai R, Donati MG, Banfi R, Roccato E.

Recenti Prog Med. 2008 Sep;99(9):443-50. Italian.


The Wnt modulator sFRP2 enhances mesenchymal stem cell engraftment, granulation tissue formation and myocardial repair.

Alfaro MP, Pagni M, Vincent A, Atkinson J, Hill MF, Cates J, Davidson JM, Rottman J, Lee E, Young PP.

Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18366-71. doi: 10.1073/pnas.0803437105. Epub 2008 Nov 18.


Experience using web services for biological sequence analysis.

Stockinger H, Attwood T, Chohan SN, Côté R, Cudré-Mauroux P, Falquet L, Fernandes P, Finn RD, Hupponen T, Korpelainen E, Labarga A, Laugraud A, Lima T, Pafilis E, Pagni M, Pettifer S, Phan I, Rahman N.

Brief Bioinform. 2008 Nov;9(6):493-505. doi: 10.1093/bib/bbn029. Epub 2008 Jul 11.


A downstream mediator in the growth repression limb of the jasmonate pathway.

Yan Y, Stolz S, Chételat A, Reymond P, Pagni M, Dubugnon L, Farmer EE.

Plant Cell. 2007 Aug;19(8):2470-83. Epub 2007 Aug 3.


MyHits: improvements to an interactive resource for analyzing protein sequences.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W433-7. Epub 2007 Jun 1.


HitKeeper, a generic software package for hit list management.

Hau J, Muller M, Pagni M.

Source Code Biol Med. 2007 Mar 28;2:2.


The PROSITE database.

Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D227-30.

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