L. Falquet publications

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2024

 

Yepes-Garcia J, Falquet L. (2024). Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG. F1000Research (submitted)

Louviot F, Abdelrahman O, Abou-Mansour E, L’Haridon F, Allard PM, Falquet L & Weisskopf L (2024). Oligomycin-producing Streptomyces sp. newly isolated from Swiss soils efficiently protect Arabidopsis thaliana against Botrytis cinerea. mSphere 2024 Jun 12:e0066723. doi: 10.1128/msphere.00667-23

Steiner M, Falquet L, Fragnière AL, Brown A, Bacher S. (2024). Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and grape quality in vineyards. Ecological Solutions and Evidence, 5, e12327. https://doi.org/10.1002/2688-8319.12327

Zimmermann P, Pittet LF, Jakob W, Messina NL, Falquet L, Curtis N. The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial. Pediatr Infect Dis J. 2023 Dec 25. doi: 10.1097/INF.0000000000004223

 
2023
 

Landi M, Shah T, Falquet L,, Niazi A, Stavolone L, Bongcam-Rudloff E, Gisel A. Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta). Sci Data. 2023 Dec 9;10(1):887. doi: 10.1038/s41597-023-02800-0.

Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E. Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. EMBO Rep. 2023 Nov 3:e57984. doi: 10.15252/embr.202357984 

Gillon A, Abdelrahman O, Abou-Mansour E, L’Haridon F, Falquet L, Allard P-M,  Weisskopf L. (2023). Comparative genomic and metabolomic study of three Streptomyces sp. differing in biological activity. MicrobiologyOpen, 12, e1389. https://doi.org/10.1002/mbo3.1389 

Baby V, Ambroset C, Gaurivaud P, Falquet L, Boury C, Guichoux E, Jores J, Lartigue C, Tardy F, Sirand-Pugnet P. Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae.  Microb Genom. 2023 Oct;9(10). doi: 10.1099/mgen.0.001112

D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action. Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002

Anand A, Falquet L, Abou-Mansour E, L’Haridon F, Keel C, Weisskopf L. (2023) Biological hydrogen cyanide emission globally impacts the physiology of both HCN-emitting and HCN-perceiving Pseudomonas. mBio. 2023 Aug 31:e0085723. doi: 10.1128/mbio.00857-23

Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P (2023) Metagenomics analysis of the neonatal intestinal resistome. Front. Pediatr. 11:1169651. doi: 10.3389/fped.2023.1169651

Gisel A., Stavolone L., Olagunju T., Landi M., van Damme R., Niazi A., Falquet L., Shah T., Bongcam-Rudloff E. (2023). EpiCass and CassavaNet4Dev Advanced Bioinformatics Workshop. EMBnet.journal 29, e1045. doi:https://doi.org/10.14806/ej.29.0.1045

Khachatryan L, Xiang Y, Ivanov A, Glaab E, Graham G, Granata I, Giordano M, Maddalena L, Piccirillo M, Manipur I, Baruzzo G, Cappellato M, Avot B, Stan A, Battey J, Lo Sasso G, Boue S, Ivanov NV, Peitsch MC, Hoeng J, Falquet L, Di Camillo B, Guarracino MR, Ulyantsev V, Sierro N, Poussin C. Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge. Sci Rep. 2023 Apr 18;13(1):6303. doi: 10.1038/s41598-023-33050–0

Leo S, Cetiner OF, Pittet LF, Messina NL, Jakob W, Falquet L, Curtis N, Zimmermann P (2023) The association between the composition of the early-life intestinal microbiome and eczema in the first year of life. Front. Microbiomes 2:1147082. doi: 10.3389/frmbi.2023.1147082

Steiner M, Pingel M, Falquet L, Giffard B, Griesser M, Leyer I, Preda C, Uzman D, Bacher S, Reineke A. Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards. PLoS One. 2023 Jan 27;18(1):e0280516. doi: 10.1371/journal.pone.0280516

 

 

2022

 
Carbonnel S, Falquet L, Hazak O. Deeper genomic insights into tomato CLE genes repertoire identify new active peptides. BMC Genomics. 2022 Nov 17;23(1):756. doi: 10.1186/s12864-022-08980-0
Akarsu H, Liljander A, Younan M, Brodard I, Overesch G, Glücks I, Labroussaa F, Kuhnert P, Perreten V, Monecke S, Drexler JF, Corman VM, Falquet L, Jores J. Genomic Characterization and Antimicrobial Susceptibility of Dromedary-Associated Staphylococcaceae from the Horn of Africa. Appl Environ Microbiol. 2022 Nov 8;88(21):e0114622. doi: 10.1128/aem.01146-22
Keppner A, Maric D, Orlando IMC, Falquet L, Hummler E, Hoogewijs D. Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCDcl1 Cells. Int J Mol Sci. 2022 Jun 30;23(13):7262. doi: 10.3390/ijms23137262
Mansour M, Giudice E, Xu X, Akarsu H, Bordes P, Guillet V, Bigot DJ, Slama N, D'urso G, Chat S, Redder P, Falquet L, Mourey L, Gillet R, Genevaux P. Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis. Nat Commun. 2022 May 12;13(1):2641. doi: 10.1038/s41467-022-30373-w
Bozza S, Scherz V, Greub G, Falquet L, Taroni F. Corrigendum to "A probabilistic approach to evaluate salivary microbiome in forensic science when the defense says: 'It is my twin brother'" [Forensic Sci. Int. Genet. 57, 102638]. Forensic Sci Int Genet. 2022 Jul;59:102701. doi: 10.1016/j.fsigen.2022.102701.
Pillet B, Méndez-Godoy A, Murat G, Favre S, Stumpe M, Falquet L, Kressler D. Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis. Elife. 2022 Mar 31;11:e74255. doi: 10.7554/eLife.74255.
 
2021
 
Marques F, Falquet L, Vandewyer E, Beets I, Glauser DA. Signaling via the FLP-14/FRPR-19 neuropeptide pathway sustains nociceptive response to repeated noxious stimuli in C. elegans. PLoS Genet. 2021 Nov 8;17(11):e1009880. doi: 10.1371/journal.pgen.1009880
Hill V, Akarsu H, Barbarroja RS, Cippà VL, Kuhnert P, Heller M, Falquet L, Heller M, Stoffel MH, Labroussaa F, Jores J. Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PLoS Genet. 2021 Oct 21;17(10):e1009365. doi: 10.1371/journal.pgen.1009365
Perna A, Marathe S, Dreos R, Falquet L, Akarsu Egger H, Auber LA. Revealing NOTCH-dependencies in synaptic targets associated with Alzheimer's disease. Mol Cell Neurosci. 2021 Sep;115:103657. doi: 10.1016/j.mcn.2021.103657
Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol. 2021 Jul;6(7):830-841. doi: 10.1038/s41564-021-00911-1
Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pašić L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truică CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ. Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Front Microbiol. 2021 Feb 22;12:635781. doi: 10.3389/fmicb.2021.635781.
 
2020
 
Dylus D, Pillonel T, Opota O, Wüthrich D, Seth-Smith HMB, Egli A, Leo S, Lazarevic V, Schrenzel J, Laurent S, Bertelli C, Blanc DS, Neuenschwander S, Ramette A, Falquet L, Imkamp F, Keller PM, Kahles A, Oberhaensli S, Barbié V, Dessimoz C, Greub G, Lebrand A. NGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test. Front Microbiol. 2020 Nov 24;11:591093. doi: 10.3389/fmicb.2020.591093.
Piza-Buitrago A, Rincón V, Donato J, Saavedra SY, Duarte C, Morero J, Falquet L, Reguero MT, Barreto-Hernández E. Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases. BMC Microbiol. 2020 Nov 12;20(1):345. doi: 10.1186/s12866-020-02030-z
Volery M, Scherz V, Jakob W, Bandeira D, Deggim-Messmer V, Lauber-Biason A, Wildhaber J, Falquet L, Curtis N, Zimmermann P. Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term. BMJ Open. 2020 Jun 23;10(6):e036275. doi: 10.1136/bmjopen-2019-036275.
Bouchemousse S, Falquet L, Müller-Schärer H. Genome Assembly of the Ragweed Leaf Beetle: A Step Forward to Better Predict Rapid Evolution of a Weed Biocontrol Agent to Environmental Novelties. Genome Biol Evol. 2020 Jul 1;12(7):1167-1173. doi: 10.1093/gbe/evaa102.

 

2018

 

Aguilar-Bultet L, Nicholson P, Rychener L, Dreyer M, Goezel B, Origgi FC, Overman A, Frey J & Falquet L (2018). Genetic separation of Listeria monocytogenes causing central nervous system infections in animals. Front. Cell. Infect. Microbiol. 8: (online doi: 10.3389/fcimb.2018.00020). 

Babatunde KA, Mbagwu S, Hernández-Castañeda MA, Adapa SR, Walch M, Filgueira L, Falquet L, Jiang RHY, Ghiran I & Mantel PE (2018). Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles. Scientific Reports 8, Article number: 884 (doi:10.1038/s41598-018-19149-9)

Thoms M, Mitterer V, Kater L, Falquet L, Beckmann R, Kressler D & Hurt E (2018).

Suppressor mutations in Rpf2-Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation. Nat Commun. 2018 Oct 5;9(1):4094. (doi: 10.1038/s41467-018-06660-w.)

 

2017

 

Gros-Balthazard M, Galimberti M, Kousathanas A, Newton C, Ivorra S, Paradis L, Vigouroux Y, Carter R, Tengberg M, Battesti V, Santoni S, Falquet L, Pintaud JC, Terral JF & Wegmann D (2017). The discovery of wild date palms in Oman reveals a complex domestication history involving centers in the Middle East and Africa. Current Biology 27: 2211-2218.e.8 (online http://dx.doi.org/10.1016/j.cub.2017.06.045).

Rychener L, In-Albon S, Djordjevic S, Piklu Roy Chowdhury PR, Ziech R, de Vargas AC, Frey J & Falquet L (2017). Clostridium chauvoei, an evolutionary dead-end pathogen. Front. Microbiol. 8: 1054 (doi: 10.3389/fmicb.2017.01054). See correction at Front. Microbiol. (2018) https://doi.org/10.3389/fmicb.2018.00421

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). Whole-genome sequence of a Colombian Acinetobacter baumannii strain, a coproducer of OXA-72 and OXA-255-like carbapenemases. Genome Annoncements 5:e01558-16 (online: doi:10.1128/genomeA.01558-16).

 

2016

 

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.

 

2015

 

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).

 

2014

 

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).

 

2013

 

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.

 

2012

 

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). 

 

2011

 

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.

 

2009

 

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.

 

2008

 

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.

 

2007

 

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. 

 

2006

 

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.

 

2005

 

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

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

 

2004

 

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

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. 

 

2003

 

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.

 

2002


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.

 

2001

 

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 

 

2000 and before

 

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.