Publications

Saavedra SY, Prada-Cardozo D, Rincón V, Pérez-Cardona H, Melissa Hidalgo AM, González MN, Reguero MT, Valenzuela de Silva EM, Mantilla JR, Falquet L, Barreto-Hernández E & Duarte C (2017). Genome Annoncements 5:e01558-16 (online: doi:10.1128/genomeA.01558-16).

Ardissone S, Redder P, Russo G, Frandi A, Fumeaux C, Patrignani A, Schlapbach R, Falquet L & Viollier PH (2016). Cell Cycle Constraints and Environmental Control of Local DNA Hypomethylation in α-Proteobacteria. PLoS Genet 12: e1006499 (online doi:10.1371/journal.pgen.1006499).

Falquet L, Caleron-Copete SP, Barreto-Hernandez E  & Castaneda JEM (2016). Report On The Swiss-Colombian Workshop: "Assembly, Annotation and Comparison of Bacterial Genomes". EMBnet Journal 22: e872.

Leake SL, Pagni M, Falquet L, Taroni F & Greub G (2016). The salivary microbiome for differentiating individuals: proof of principle. Microbes and Infection 18: 399-405.

Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux JP & L'Haridon F (2016). The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytologist 210: 1033-1043.

SIB Swiss Institute of Bioinformatics Members (including Falquet L) (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Research 44: D27-D37.

Pillet B, García-Gómez JJ, Pausch P, Falquet L, Bange G, de la Cruz J & Kressler D (2015) The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site. PLoS Genetics 11: e1005565. doi:10.1371/journal.pgen.1005565,

Liljander A, Yu M, O'Brien E, Heller M, Nepper JF, Weibel DB, Gluecks I, Younan M, Frey J, Falquet L & Jores J. (2015). A field-applicable recombinase polymerase amplification assay for rapid detection of Mycoplasma capricolum subsp. capripneumoniae. J Clin Microbiol. 53: 2810-2815.

Rich MK, Schorderet M, Bapaume L, Falquet L, Morel P, Vandenbussche & Reinhardt D (2015), A petunia GRAS transcription factor controls symbiotic gene expression and fungal morphogenesis in arbuscular mycorrhiza. Plant Physiology 168: 788-797. (online http://dx.doi.org/10.1104/pp.15.00310)

Leung WY, Marschall T, Paudel Y, Falquet L, Mei H, Schönhuth A & Maoz (Moss)TY (2015). SV-AUTOPILOT: optimized, automated construction of structural variation discovery and benchmarking pipelines. BMC Genomics 16:238 (online doi:10.1186/s12864-015-1376-9).

Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, Roelof van der Meer J & Greub G (2015). Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Frontiers in Microbiology 6: #101 (online doi: 10.3389/fmicb.2015.00101).

Frey J & Falquet L (2014). Patho-genetics of Clostridium chauvoei. Research in Microbiology 166:384-392(online doi:10.1016/j.resmic.2014.10.013).

Favre P, Bapaume L, Bossolini E, Delorenz M, Falquet L & Reinhardt D (2014). A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants. BMC Plant Biology 14: 333 (online doi:10.1186/s12870-014-0333-0).

Cannarozzi G, Plaza-Wuthrich S, Esfeld K , Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blosch R, Farinelli L , Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K & Tadele Z (2014). Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 15: 581 (online doi:10.1186/1471-2164-15-581).

Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Von Siebenthal A, Falquet L & van der Meer JR (2014). Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology 17: 91-104 (online DOI:10.1111/1462-2920.12498)   

Falquet L, Rossier G & Yael Maoz T (2014). Report on the ALLBIO minisymposium and workshop: "Next Generation Sequencing (NGS) methods for identification of mutations and largestructural variants". EMBnet Journal 20: e766 (online doi:10.14806/ej.20.0.766).

Barreto-Henandez E, Falquet L, Reguero MT, Mantilla JR, Valenzuela EM, Gonzalez E, Cepeda A & Escalante A (2013). Draft genome sequences of multidrug-resistant Acinetobacter sp. strains from Colombian hospitals. Genome announcements 01/2013; 1(6). DOI:10.1128/genomeA.00868-13.

Aguilar-Bultet L, Calderon-Copete SP, Frey J & Falquet L (2013). Draft genome sequence of the virulent Avibacterium paragallinarum serotype A strain JF4211 and identification of two toxins. Genome announcements 01/2013; 1(4). DOI:10.1128/genomeA.00592-13.

Falquet L, Calderon-Copete SP & Frey J (2013). Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335. Genome announcements 01/2013; 1(4) DOI:10.1128/genomeA.00593-13.

Vogel V, Falquet L, Calderon-Copete SP, Basset P & Blanc DS (2012). Short term evolution of a highly transmissible methicillin-resistant Staphylococcus aureus clone (ST228) in a tertiary care hospital. PLoS ONE 7: e38969 (DOI: 10.1371/journal.pone.0038969). 

Riba-Grognuz O, Keller L, Falquet L, Xenarios I & Wurm Y (2011). Visualization and quality assessment of de novo genome assemblies. Bioinformatics 27: 33425-3426. 

Andres-Barrao C, Falquet L, Calderon-Copete SP, Descombes P, Perez RO & Barj F (2011). Genome sequences of the high-acetic acid-resistant bacteria Gluconacetobacter europaeus LMG 18890(T) and G. europaeus LMG 18494 (reference strains), G. europaeus 5P3, and Gluconacetobacter oboediens 174Bp2 (isolated from vinegar). J Bacteriology 193: 2670-2671.  

Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MAD, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D & Keller L (2011). The genome of the fire ant Solenopsis invicta. PNAS 108: 5679-5684. 

Zhuang L, Falquet L & Trueb B (2010). Genome-wide comparison of FGFRL1 with structurally related surface receptors. Experimental 6 Therapeutic Medicine 1: 1611-168.

Wurm Y, (Wurm, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L & Keller L (2009). Fourmidable: a database for ant genomics. BMC Genomics 10: #5 (DOI: 10.1186/1471-2164-10-5).

Calderon-Copete SP, Sandra P, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA & Falquet L (2009). The Mycoplasma conjunctivae genome sequencing, annotation and analysis. BMC Bioinformatics 10: #S7 (DOI: 10.1186/1471-2105-10-S6-S7).

Koua D, Cerutti L, Falquet L, Sigrist CJA, Theiler G, Hulo N & Dunand C (2009). PeroxiBase: a database with new tools for peroxidase family classification Nucleic Acids Research 37: D261-D266.

Stockinger H, Attwood T, Chohan SN, Cote R, Cudre-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 (2008). Experience using web services for biological sequence analysis. Brief. Bioinformatics 9: 493-505.

Mathimaran N, Falquet L, Ineichen K, Picard C, Redecker D, Boller T & Wiemken A (2008). Microsatellites for disentangling underground networks: Strain-specific identification of Glomus intraradices, an arbuscular mycorrhizal fungus. Fungal Genetics & Biology 45: 812-817.

Mathimaran N, Falquet L, Ineichen K, Picard C, Redecker D, Wiemken A & Boller T (2008). Unexpected vagaries of microsatellite loci in Glomus intraradices: length polymorphisms are rarely caused by variation in repeat number only. New Phytologist 180: 568-570.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D & Falquet L (2007). MyHits: improvements to an interactive resource for analyzing protein sequences. Nucleic Acids Research 35: W433-W437.

Passardi F, Theiler G, Zamocky M, Cosio C, Rouhier N, Teixera F, Margis-Pinheiro M, Ioannidis V, Penel C, Falquet L & Dunand C (2007). PeroxiBase: The peroxidase database. Phytochemistry 68: 1605-1611. 

Bakalovic N, Passardi F, Ioannidis V, Cosio C, Penel C, Falquet L & Dunand C (2006). PeroxiBase: A class III plant peroxidase database. Phytochemistry 67: 534-539.

Matute DR,  Barreto-Hernandez E & Falquet L (2006). Hunting for insect-specific protein domains. In Silico Biology 6: 35-42.

Beckmann, J S, Maurer, F, Delorenzi, M & Falquet L (2005). On ubiquitin ligases and cancer. Human Mutation 26: 505-512.

Beckmann JS, Maurer F, Delorenzi M & Falquet L (2004). Ubiquitin ligases as cancer genes. Nature Reviews Cancer. Online Correspondence 

Köffel R, Tiwari R, Falquet L & Schneiter R. (2005). The Saccharomyces cerevisiae YLL012/YEH1, YLR020/YEH2 and TGL1 genes encode a novel family of membrane-anchored lipases that are required for steryl ester hydrolysis. Mol Cell Biol. 25: 1655-1668

de Fourmestraux V, Neubauer H, Poussin C, Farmer P, Falquet L, Burcelin R, Delorenzi M & Thorens B. (2004).Transcript profiling suggests that differential metabolic adaptation of mice to a high fat diet is associated with changes in liver to muscle lipid fluxes. J Biol Chem. 279:50743-53.

Beckmann J S, Maurer F, Delorenzi M & Falquet L (2004) Ubiquitin ligases as cancer genes Nature Reviews Cancer 

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV & Falquet L (2004). MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res. Jul 1;32 (Web Server issue): W332-5. 

Falquet L, Bordoli L, Ioannidis V, Pagni M & Jongeneel CV (2003) Swiss EMBnet node web server. Nucleic Acids Res. 31:3782-3. 

Mulder NJ, Apweiler R, Attwood TK, Bairoch A Barrell D, Bateman A, Binns D, Biswas M, Bra- dley P, Bork P, Bucher P, Copley RR, Courcelle E, Das U, Durbin R, Falquet L, Fleischmann W, Grif- fiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJ, Vaughan R & Zdobnov EM. (2003). The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res. 31: 315-318.

Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A & Bucher P (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3: 265-74.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ. (2002). InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform. ;3): 225-35. 

Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A & Bucher P (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3: 265-74.

Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley R, Courcelle E, Durbin R, Falquet L, Fleischmann W, Gouzy J, Griffith-Jones S, Haft D, Hermjakob H, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Orchard S, Pagni M, Peyruc D, Ponting CP, Servant F, Sigrist CJ (2002). InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform. (3): 225-35.

Falquet L , Pagni M,  Bucher P,  Hulo N, Sigrist C J A,  Hofmann K,  Bairoch A  (2002) The PROSITE database, its status in 2002.  Nucleic Acids Res. 30:235-238. 

Hofmann K & Falquet L (2001) A conserved ubiquitin interacting motif in multiple components of proteasomal and lysosomal protein degradation systems. Trends Biochem Sci. 26:347-50.

Pagni M, Iseli C, Junier T, Falquet L, Jongeneel V & Bucher P (2001) trEST, trGEN and hits: access to databases of predicted protein sequences. Nucleic Acids Res. 29:148-151. 

Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M & Servant F (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29: 37-40 

Apweiler R, AttwoodTK, BairochA, BatemanA, BirneyE, BiswasM, BucherP, CeruttiL, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ & Zdobnov EM (2000). InterPro - an integrated documentation resource for protein families, domains and functional sites. Bioinformatics 16:, 1145-1150. 

Hofmann K, Bucher P, Falquet L & Bairoch A (1999) The PROSITE database, its status in 1999. Nucleic Acids Res. 27: 215-219. 

Falquet L, Paquet N, Frutiger S, Hughes GJ, Hoang-Van K & Jaton JC. (1995). cDNA cloning of a human 100 kDa de-ubiquitinating enzyme: the 100 kDa human de-ubiquitinase belongs to the ubiquitin C-terminal hydrolase family 2 (UCH2). FEBS Lett. 376: 233-237. 

Falquet L, Paquet N, Frutiger S, Hughes GJ, Hoang-Van K & Jaton JC (1995). A human de-ubiquitinating enzyme with both isopeptidase and peptidase activities in vitro. FEBS Lett. 359: 73-77.

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