Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 44

1.

LGP2 binds to PACT to regulate RIG-I- and MDA5-mediated antiviral responses.

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.

Sci Signal. 2019 Oct 1;12(601). pii: eaar3993. doi: 10.1126/scisignal.aar3993.

PMID:
31575732
2.

Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity.

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.

Cell Syst. 2019 Feb 27;8(2):109-121.e6. doi: 10.1016/j.cels.2019.01.001. Epub 2019 Feb 13.

PMID:
30772378
3.

The Cytoscape Automation app article collection.

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.

F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018.

4.

A Blood RNA Signature Detecting Severe Disease in Young Dengue Patients at Hospital Arrival.

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.

J Infect Dis. 2018 May 5;217(11):1690-1698. doi: 10.1093/infdis/jiy086.

5.

Network module identification-A widespread theoretical bias and best practices.

Nikolayeva I, Guitart Pla O, Schwikowski B.

Methods. 2018 Jan 1;132:19-25. doi: 10.1016/j.ymeth.2017.08.008. Epub 2017 Sep 21.

6.

Common and phylogenetically widespread coding for peptides by bacterial small RNAs.

Friedman RC, Kalkhof S, Doppelt-Azeroual O, Mueller SA, Chovancová M, von Bergen M, Schwikowski B.

BMC Genomics. 2017 Jul 21;18(1):553. doi: 10.1186/s12864-017-3932-y.

7.

From the exposome to mechanistic understanding of chemical-induced adverse effects.

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.

Environ Int. 2017 Feb;99:97-106. doi: 10.1016/j.envint.2016.11.029. Epub 2016 Dec 8. Review.

8.

Network-based analysis of omics data: the LEAN method.

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.

Bioinformatics. 2017 Mar 1;33(5):701-709. doi: 10.1093/bioinformatics/btw676.

9.

Detecting multi-way epistasis in family-based association studies.

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.

Brief Bioinform. 2017 May 1;18(3):394-402. doi: 10.1093/bib/bbw039.

PMID:
27178992
10.

Bacterial Internalization, Localization, and Effectors Shape the Epithelial Immune Response during Shigella flexneri Infection.

Lippmann J, Gwinner F, Rey C, Tamir U, Law HK, Schwikowski B, Enninga J.

Infect Immun. 2015 Sep;83(9):3624-37. doi: 10.1128/IAI.00574-15. Epub 2015 Jun 29.

11.

Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis.

Grange L, Bureau JF, Nikolayeva I, Paul R, Van Steen K, Schwikowski B, Sakuntabhai A.

BMC Genet. 2015 Feb 6;16:11. doi: 10.1186/s12863-015-0174-3.

12.

The Cytoscape app article collection.

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.

F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014.

13.

Automated flow cytometric analysis across large numbers of samples and cell types.

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; Milieu Intérieur Consortium.

Clin Immunol. 2015 Apr;157(2):249-60. doi: 10.1016/j.clim.2014.12.009. Epub 2015 Jan 7.

14.

The Cyni framework for network inference in Cytoscape.

Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.

Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18.

15.

Analysis of time-resolved gene expression measurements across individuals.

Elo LL, Schwikowski B.

PLoS One. 2013 Dec 9;8(12):e82340. doi: 10.1371/journal.pone.0082340. eCollection 2013.

16.

TLM-Quant: an open-source pipeline for visualization and quantification of gene expression heterogeneity in growing microbial cells.

Piersma S, Denham EL, Drulhe S, Tonk RH, Schwikowski B, van Dijl JM.

PLoS One. 2013 Jul 17;8(7):e68696. doi: 10.1371/journal.pone.0068696. Print 2013.

17.

Identification of additional proteins in differential proteomics using protein interaction networks.

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.

Proteomics. 2013 Apr;13(7):1065-76. doi: 10.1002/pmic.201200482.

18.

Automated phosphopeptide identification using multiple MS/MS fragmentation modes.

Vandenbogaert M, Hourdel V, Jardin-Mathé O, Bigeard J, Bonhomme L, Legros V, Hirt H, Schwikowski B, Pflieger D.

J Proteome Res. 2012 Dec 7;11(12):5695-703. doi: 10.1021/pr300507j. Epub 2012 Nov 7.

PMID:
23094866
19.

Feature detection with controlled error rates in LC/MS images.

Li-Thiao-Té S, Schwikowski B.

J Comput Biol. 2012 Apr;19(4):349-64. doi: 10.1089/cmb.2009.0125. Epub 2012 Mar 13.

PMID:
22414152
20.

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.

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.

Science. 2012 Mar 2;335(6072):1103-6. doi: 10.1126/science.1206848.

21.

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism.

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.

Science. 2012 Mar 2;335(6072):1099-103. doi: 10.1126/science.1206871.

22.

Fragmentation-free LC-MS can identify hundreds of proteins.

Bochet P, Rügheimer F, Guina T, Brooks P, Goodlett D, Clote P, Schwikowski B.

Proteomics. 2011 Jan;11(1):22-32. doi: 10.1002/pmic.200900765. Epub 2010 Dec 6.

PMID:
21182191
23.

Evolution of metabolic network organization.

Mazurie A, Bonchev D, Schwikowski B, Buck GA.

BMC Syst Biol. 2010 May 11;4:59. doi: 10.1186/1752-0509-4-59.

24.

MUDE: a new approach for optimizing sensitivity in the target-decoy search strategy for large-scale peptide/protein identification.

Cerqueira FR, Graber A, Schwikowski B, Baumgartner C.

J Proteome Res. 2010 May 7;9(5):2265-77. doi: 10.1021/pr901023v.

PMID:
20199108
25.

Phylogenetic distances are encoded in networks of interacting pathways.

Mazurie A, Bonchev D, Schwikowski B, Buck GA.

Bioinformatics. 2008 Nov 15;24(22):2579-85. doi: 10.1093/bioinformatics/btn503. Epub 2008 Sep 26.

26.

Alignment of LC-MS images, with applications to biomarker discovery and protein identification.

Vandenbogaert M, Li-Thiao-Té S, Kaltenbach HM, Zhang R, Aittokallio T, Schwikowski B.

Proteomics. 2008 Feb;8(4):650-72. doi: 10.1002/pmic.200700791. Review.

PMID:
18297649
27.

Integration of biological networks and gene expression data using Cytoscape.

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.

Nat Protoc. 2007;2(10):2366-82.

28.

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics.

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.

Mol Cell Proteomics. 2007 Oct;6(10):1741-8. Epub 2007 Jul 7.

29.

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.

Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, Aittokallio T.

Bioinformatics. 2007 Feb 1;23(3):394-6. Epub 2006 Nov 24.

PMID:
17127678
30.

Graph-based methods for analysing networks in cell biology.

Aittokallio T, Schwikowski B.

Brief Bioinform. 2006 Sep;7(3):243-55. Epub 2006 Jul 30. Review.

PMID:
16880171
31.

Signal maps for mass spectrometry-based comparative proteomics.

Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B.

Mol Cell Proteomics. 2006 Mar;5(3):423-32. Epub 2005 Nov 3.

32.
33.

Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection.

Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T.

BMC Bioinformatics. 2005 Jun 20;6:154.

34.

Towards optimally multiplexed applications of universal arrays.

Ben-Dor A, Hartman T, Karp RM, Schwikowski B, Sharan R, Yakhini Z.

J Comput Biol. 2004;11(2-3):476-92.

PMID:
15285903
35.

Predicting protein-peptide interactions via a network-based motif sampler.

Reiss DJ, Schwikowski B.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i274-82.

PMID:
15262809
36.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Genome Res. 2003 Nov;13(11):2498-504.

37.

The restriction scaffold problem.

Ben-Dor A, Karp RM, Schwikowski B, Shamir R.

J Comput Biol. 2003;10(3-4):385-98.

PMID:
12935335
38.
39.

Discovering regulatory and signalling circuits in molecular interaction networks.

Ideker T, Ozier O, Schwikowski B, Siegel AF.

Bioinformatics. 2002;18 Suppl 1:S233-40.

PMID:
12169552
40.

Algorithms for phylogenetic footprinting.

Blanchette M, Schwikowski B, Tompa M.

J Comput Biol. 2002;9(2):211-23.

PMID:
12015878
41.

Universal DNA tag systems: a combinatorial design scheme.

Ben-Dor A, Karp R, Schwikowski B, Yakhini Z.

J Comput Biol. 2000;7(3-4):503-19.

PMID:
11108476
42.

A network of protein-protein interactions in yeast.

Schwikowski B, Uetz P, Fields S.

Nat Biotechnol. 2000 Dec;18(12):1257-61.

PMID:
11101803
43.

An exact algorithm to identify motifs in orthologous sequences from multiple species.

Blanchette M, Schwikowski B, Tompa M.

Proc Int Conf Intell Syst Mol Biol. 2000;8:37-45.

PMID:
10977064
44.

The deferred path heuristic for the generalized tree alignment problem.

Schwikowski B, Vingron M.

J Comput Biol. 1997 Fall;4(3):415-31.

PMID:
9278068

Supplemental Content

Loading ...
Support Center