• 2022
  Trutschel D, Bost P, Mariette X, Bondet V, Llibre A, Posseme C, Charbit B, Thorball CW, Jonsson R, Lessard CJ, Felten R, Ng WF, Chatenoud L, Dumortier H, Sibilia J, Fellay J, Brokstad KA, Appel S, Tarn JR, Quintana-Murci L, Mingueneau M, Meyer N, Duffy D, Schwikowski B, Gottenberg JE, Variability of Primary Sjögren’s Syndrome Is Driven by Interferon-α and Interferon-α Blood Levels Are Associated With the Class II HLA-DQ Locus., Arthritis Rheumatol 2022 Dec; 74(12): 1991-2002.
• 2022
  Firoozbakht F, Yousefi B, Schwikowski B, , An overview of machine learning methods for monotherapy drug response prediction., Brief Bioinform 2022 01; 23(1): .
• 2021
  Farzaneh Firoozbakht, Behnam Yousefi and Benno Schwikowski, An overview of machine learning methods for monotherapy drug response prediction, Briefings in Bioinformatics.
• 2021
  Farzaneh Firoozbakht, Behnam Yousefi and Benno Schwikowski, An overview of machine learning methods for monotherapy drug response prediction, briefings in Bioinformatics.
• 2021
  Bondet V, Rodero MP, Posseme C, Bost P, Decalf J, Haljasmägi L, Bekaddour N, Rice GI, Upasani V, Herbeuval JP, Reynolds JA, Briggs TA, Bruce IN, Mauri C, Isenberg D, Menon M, Hunt D, Schwikowski B, Mariette X, Pol S, Rozenberg F, Cantaert T, Eric Gottenberg J, Kisand K, Duffy D, , Differential levels of IFNα subtypes in autoimmunity and viral infection., Cytokine 2021 Aug; 144(): 155533.
• 2021
  Soret P, Le Dantec C, Desvaux E, Foulquier N, Chassagnol B, Hubert S, Jamin C, Barturen G, Desachy G, Devauchelle-Pensec V, Boudjeniba C, Cornec D, Saraux A, Jousse-Joulin S, Barbarroja N, Rodríguez-Pintó I, De Langhe E, Beretta L, Chizzolini C, Kovács L, Witte T, , , Bettacchioli E, Buttgereit A, Makowska Z, Lesche R, Borghi MO, Martin J, Courtade-Gaiani S, Xuereb L, Guedj M, Moingeon P, Alarcón-Riquelme ME, Laigle L, Pers JO, , A new molecular classification to drive precision treatment strategies in primary Sjögren’s syndrome., Nat Commun 2021 06; 12(1): 3523.
• 2021
  Bost P, De Sanctis F, Canè S, Ugel S, Donadello K, Castellucci M, Eyal D, Fiore A, Anselmi C, Barouni RM, Trovato R, Caligola S, Lamolinara A, Iezzi M, Facciotti F, Mazzariol A, Gibellini D, De Nardo P, Tacconelli E, Gottin L, Polati E, Schwikowski B, Amit I, Bronte V, , Deciphering the state of immune silence in fatal COVID-19 patients., Nat Commun 2021 03; 12(1): 1428.
• 2021
  Desvaux E, Hamon A, Hubert S, Boudjeniba C, Chassagnol B, Swindle J, Aussy A, Laigle L, Laplume J, Soret P, Jean-François P, Dupin-Roger I, Guedj M, Moingeon P, , Network-based repurposing identifies anti-alarmins as drug candidates to control severe lung inflammation in COVID-19., PLoS One 2021 ; 16(7): e0254374.
• 2020
  Bost P, Giladi A, Liu Y, Bendjelal Y, Xu G, David E, Blecher-Gonen R, Cohen M, Medaglia C, Li H, Deczkowska A, Zhang S, Schwikowski B, Zhang Z, Amit I, , Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients., Cell 2020 Jun; 181(7): 1475-1488.e12.
• 2020
  Thibaut R, Bost P, Milo I, Cazaux M, Lemaître F, Garcia Z, Amit I, Breart B, Cornuot C, Schwikowski B, Bousso P, , Bystander IFN-γ activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment., Nat Cancer 2020 Mar; 1(3): 302-314.
• 2019
  Sanchez David RY, Combredet C, Najburg V, Millot GA, Beauclair G, Schwikowski B, Léger T, Camadro JM, Jacob Y, Bellalou J, Jouvenet N, Tangy F, Komarova AV, LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses., Sci Signal 2019 Oct; 12(601): .
• 2019
  Benno Schwikowski, The Cytoscape platform for network analysis and visualization, in: Computational Systems Biology Approaches in Cancer Research, CRC Press.
• 2019
  Blecher-Gonen R, Bost P, Hilligan KL, David E, Salame TM, Roussel E, Connor LM, Mayer JU, Bahar Halpern K, Tóth B, Itzkovitz S, Schwikowski B, Ronchese F, Amit I, Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity, Cell Syst 2019 Feb;.
• 2018
  Scepanovic P, Alanio C, Hammer C, Hodel F, Bergstedt J, Patin E, Thorball CW, Chaturvedi N, Charbit B, Abel L, Quintana-Murci L, Duffy D, Albert ML, Fellay J, , , Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines., Genome Med 2018 Jul; 10(1): 59.
• 2018
  Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T, The Cytoscape Automation app article collection, F1000Res 2018;7:800.
• 2018
  Nikolayeva I, Bost P, Casademont I, Duong V, Koeth F, Prot M, Czerwinska U, Ly S, Bleakley K, Cantaert T, Dussart P, Buchy P, Simon-Lorière E, Sakuntabhai A, Schwikowski B, , A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival., J Infect Dis 2018 May; 217(11): 1690-1698.
• 2018
  Patin E, Hasan M, Bergstedt J, Rouilly V, Libri V, Urrutia A, Alanio C, Scepanovic P, Hammer C, Jönsson F, Beitz B, Quach H, Lim YW, Hunkapiller J, Zepeda M, Green C, Piasecka B, Leloup C, Rogge L, Huetz F, Peguillet I, Lantz O, Fontes M, Di Santo JP, Thomas S, Fellay J, Duffy D, Quintana-Murci L, Albert ML, , , Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors., Nat Immunol 2018 Mar; 19(3): 302-314.
• 2018
  Piasecka B, Duffy D, Urrutia A, Quach H, Patin E, Posseme C, Bergstedt J, Charbit B, Rouilly V, MacPherson CR, Hasan M, Albaud B, Gentien D, Fellay J, Albert ML, Quintana-Murci L, , , Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges., Proc Natl Acad Sci U S A 2018 Jan; 115(3): E488-E497.
• 2017
  Nikolayeva I, Guitart Pla O, Schwikowski B, Network module identification-A widespread theoretical bias and best practices, Methods 2018 01;132:19-25.
• 2017
  Friedman RC, Kalkhof S, Doppelt-Azeroual O, Mueller SA, Chovancová M, von Bergen M, Schwikowski B, Common and phylogenetically widespread coding for peptides by bacterial small RNAs, BMC Genomics 2017 07;18(1):553.
• 2017
  Loucoubar C, Grant AV, Bureau JF, Casademont I, Bar NA, Bar-Hen A, Diop M, Faye J, Sarr FD, Badiane A, Tall A, Trape JF, Cliquet F, Schwikowski B, Lathrop M, Paul RE, Sakuntabhai A, , Detecting multi-way epistasis in family-based association studies., Brief Bioinform 2017 May; 18(3): 394-402.
• 2017
  Gwinner F, Boulday G, Vandiedonck C, Arnould M, Cardoso C, Nikolayeva I, Guitart-Pla O, Denis CV, Christophe OD, Beghain J, Tournier-Lasserve E, Schwikowski B, Network-based analysis of omics data: the LEAN method, Bioinformatics 2017 03;33(5):701-709.
• 2016
  Escher BI, Hackermüller J, Polte T, Scholz S, Aigner A, Altenburger R, Böhme A, Bopp SK, Brack W, Busch W, Chadeau-Hyam M, Covaci A, Eisenträger A, Galligan JJ, Garcia-Reyero N, Hartung T, Hein M, Herberth G, Jahnke A, Kleinjans J, Klüver N, Krauss M, Lamoree M, Lehmann I, Luckenbach T, Miller GW, Müller A, Phillips DH, Reemtsma T, Rolle-Kampczyk U, Schüürmann G, Schwikowski B, Tan YM, Trump S, Walter-Rohde S, Wambaugh JF, From the exposome to mechanistic understanding of chemical-induced adverse effects, Environ Int 2017 02;99:97-106.
• 2015
  Lippmann J, Gwinner F, Rey C, Tamir U, Law HK, Schwikowski B, Enninga J, Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection, Infect. Immun. 2015 Sep;83(9):3624-37.
• 2015
  Chen X, Hasan M, Libri V, Urrutia A, Beitz B, Rouilly V, Duffy D, Patin É, Chalmond B, Rogge L, Quintana-Murci L, Albert ML, Schwikowski B, , , Automated flow cytometric analysis across large numbers of samples and cell types., Clin Immunol 2015 Apr; 157(2): 249-60.
• 2015
  Yang F, Petsalaki E, Rolland T, Hill DE, Vidal M, Roth FP, , Protein domain-level landscape of cancer-type-specific somatic mutations., PLoS Comput Biol 2015 Mar; 11(3): e1004147.
• 2015
  Grange L, Bureau JF, Nikolayeva I, Paul R, Van Steen K, Schwikowski B, Sakuntabhai A, Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis, BMC Genet. 2015;16:11.
• 2014
  Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B, The Cyni framework for network inference in Cytoscape, Bioinformatics 2015 May;31(9):1499-501.
• 2014
  Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M, , A proteome-scale map of the human interactome network., Cell 2014 Nov; 159(5): 1212-1226.
• 2014
  Brehme M, Voisine C, Rolland T, Wachi S, Soper JH, Zhu Y, Orton K, Villella A, Garza D, Vidal M, Ge H, Morimoto RI, , A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease., Cell Rep 2014 Nov; 9(3): 1135-50.
• 2014
  Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM, , Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage., Genes Dev 2014 Sep; 28(17): 1957-75.
• 2014
  Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T, The Cytoscape app article collection, F1000Res 2014;3:138.
• 2013
  Elo LL, Schwikowski B, Analysis of time-resolved gene expression measurements across individuals, PLoS ONE 2013;8(12):e82340.
• 2013
  Munier S, Rolland T, Diot C, Jacob Y, Naffakh N, , Exploration of binary virus-host interactions using an infectious protein complementation assay., Mol Cell Proteomics 2013 Oct; 12(10): 2845-55.
• 2013
  Piersma S, Denham EL, Drulhe S, Tonk RH, Schwikowski B, van Dijl JM, TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells, PLoS ONE 2013;8(7):e68696.
• 2013
  Gwinner F, Acosta-Martin AE, Boytard L, Chwastyniak M, Beseme O, Drobecq H, Duban-Deweer S, Juthier F, Jude B, Amouyel P, Pinet F, Schwikowski B, Identification of additional proteins in differential proteomics using protein interaction networks, Proteomics 2013 Apr;13(7):1065-76.
• 2012
  Mathias Vandenbogaert, Veronique Hourdel, Olivia Jardin-Mathé, Jean Bigeard, Ludovic Bonhomme, Véronique Legros, Heribert Hirt, Benno Schwikowski, Delphine Pflieger, Automated Phosphopeptide Identification Using Multiple MS/MS Fragmentation Modes, Journal of Proteome Research, 2012, 11 (12), pp.5695 - 5703. ⟨10.1021/pr300507j⟩.
• 2012
  Rozenblatt-Rosen O, Deo RC, Padi M, Adelmant G, Calderwood MA, Rolland T, Grace M, Dricot A, Askenazi M, Tavares M, Pevzner SJ, Abderazzaq F, Byrdsong D, Carvunis AR, Chen AA, Cheng J, Correll M, Duarte M, Fan C, Feltkamp MC, Ficarro SB, Franchi R, Garg BK, Gulbahce N, Hao T, Holthaus AM, James R, Korkhin A, Litovchick L, Mar JC, Pak TR, Rabello S, Rubio R, Shen Y, Singh S, Spangle JM, Tasan M, Wanamaker S, Webber JT, Roecklein-Canfield J, Johannsen E, Barabási AL, Beroukhim R, Kieff E, Cusick ME, Hill DE, Münger K, Marto JA, Quackenbush J, Roth FP, DeCaprio JA, Vidal M, Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins, Nature 2012 Jul;487(7408):491-5.
• 2012
  Carvunis AR, Rolland T, Wapinski I, Calderwood MA, Yildirim MA, Simonis N, Charloteaux B, Hidalgo CA, Barbette J, Santhanam B, Brar GA, Weissman JS, Regev A, Thierry-Mieg N, Cusick ME, Vidal M, Proto-genes and de novo gene birth, Nature 2012 Jul;487(7407):370-4.
• 2012
  Li-Thiao-Té S, Schwikowski B, Feature detection with controlled error rates in LC/MS images, J. Comput. Biol. 2012 Apr;19(4):349-64.
• 2012
  Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RA, Nannapaneni P, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P, Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis, Science 2012 Mar;335(6072):1103-6.
• 2012
  Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Rügheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, Van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U, Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism, Science 2012 Mar;335(6072):1099-103.
• 2012
  Laura L. Elo, Benno Schwikowski, Mining proteomic data for biomedical research, WIREs Data Mining Knowl Discov 2012, 2: 1–13 doi: 10.1002/widm.45.
• 2011
  , Evidence for network evolution in an Arabidopsis interactome map, Science 2011 Jul;333(6042):601-7.
• 2011
  Rolland T, Dujon B, Yeasty clocks: dating genomic changes in yeasts, C. R. Biol. 2011 Aug-Sep;334(8-9):620-8.
• 2010
  Bochet P, Rügheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B, Fragmentation-free LC-MS can identify hundreds of proteins, Proteomics 2011 Jan;11(1):22-32.
• 2010
  Mazurie A, Bonchev D, Schwikowski B, Buck GA, Evolution of metabolic network organization, BMC Syst Biol 2010;4:59.
• 2010
  Cerqueira FR, Graber A, Schwikowski B, Baumgartner C, MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification, J. Proteome Res. 2010 May;9(5):2265-77.
• 2010
  Rolland T, Dujon B, Richard GF, Dynamic evolution of megasatellites in yeasts, Nucleic Acids Res. 2010 Aug;38(14):4731-9.
• 2009
  Rolland T, Neuvéglise C, Sacerdot C, Dujon B, Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes, PLoS ONE 2009;4(8):e6515.
• 2008
  Mazurie A, Bonchev D, Schwikowski B, Buck GA, Phylogenetic distances are encoded in networks of interacting pathways, Bioinformatics 2008 Nov;24(22):2579-85.
• 2008
  Vandenbogaert M, Li-Thiao-Té S, Kaltenbach HM, Zhang R, Aittokallio T, Schwikowski B, Alignment of LC-MS images, with applications to biomarker discovery and protein identification, Proteomics 2008 Feb;8(4):650-72.
• 2007
  Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, Paulovich A, Schwikowski B, Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics, Mol. Cell Proteomics 2007 Oct;6(10):1741-8.
• 2007
  Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD, Integration of biological networks and gene expression data using Cytoscape, Nat Protoc 2007;2(10):2366-82.
• 2006
  Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T, GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring, Bioinformatics 2007 Feb;23(3):394-6.
• 2006
  Aittokallio T, Schwikowski B, Graph-based methods for analysing networks in cell biology, Brief. Bioinformatics 2006 Sep;7(3):243-55.
• 2005
  Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B, Signal maps for mass spectrometry-based comparative proteomics, Mol. Cell Proteomics 2006 Mar;5(3):423-32.
• 2005
  Zhang N, Li XJ, Ye M, Pan S, Schwikowski B, Aebersold R, ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer, Proteomics 2005 Nov;5(16):4096-106.
• 2005
  Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T, Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection, BMC Bioinformatics 2005;6:154.
• 2004
  Reiss DJ, Schwikowski B, Predicting protein-peptide interactions via a network-based motif sampler, Bioinformatics 2004 Aug;20 Suppl 1:i274-82.
• 2004
  Ben-Dor A, Hartman T, Karp RM, Schwikowski B, Sharan R, Yakhini Z, Towards optimally multiplexed applications of universal arrays, J. Comput. Biol. 2004;11(2-3):476-92.
• 2003
  Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res. 2003 Nov;13(11):2498-504.
• 2003
  Ben-Dor A, Karp RM, Schwikowski B, Shamir R, The restriction scaffold problem, J. Comput. Biol. 2003;10(3-4):385-98.
• 2002
  Zhang N, Aebersold R, Schwikowski B, ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data, Proteomics 2002 Oct;2(10):1406-12.
• 2002
  Ideker T, Ozier O, Schwikowski B, Siegel AF, Discovering regulatory and signalling circuits in molecular interaction networks, Bioinformatics 2002;18 Suppl 1:S233-40.
• 2002
  Blanchette M, Schwikowski B, Tompa M, Algorithms for phylogenetic footprinting, J. Comput. Biol. 2002;9(2):211-23.
• 2000
  Schwikowski B, Uetz P, Fields S, A network of protein-protein interactions in yeast, Nat. Biotechnol. 2000 Dec;18(12):1257-61.
• 2000
  Ben-Dor A, Karp R, Schwikowski B, Yakhini Z, Universal DNA tag systems: a combinatorial design scheme, J. Comput. Biol. 2000;7(3-4):503-19.
• 2000
  Blanchette M, Schwikowski B, Tompa M, An exact algorithm to identify motifs in orthologous sequences from multiple species, Proc Int Conf Intell Syst Mol Biol 2000;8:37-45.
• 1997
  Schwikowski B, Vingron M, The deferred path heuristic for the generalized tree alignment problem, J. Comput. Biol. 1997;4(3):415-31.