Benno Schwikowski
Benno Schwikowski
Head, Systems Biology Lab, Pasteur Institute, Paris
Verified email at pasteur.fr - Homepage
TitleCited byYear
Cytoscape: a software environment for integrated models of biomolecular interaction networks
P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, ...
Genome research 13 (11), 2498-2504, 2003
148702003
Integration of biological networks and gene expression data using Cytoscape
MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, ...
Nature protocols 2 (10), 2366, 2007
19642007
A network of protein–protein interactions in yeast
B Schwikowski, P Uetz, S Fields
Nature biotechnology 18 (12), 1257, 2000
15062000
Discovering regulatory and signalling circuits in molecular interaction networks
T Ideker, O Ozier, B Schwikowski, AF Siegel
Bioinformatics 18 (suppl_1), S233-S240, 2002
11932002
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis
P Nicolas, U Mäder, E Dervyn, T Rochat, A Leduc, N Pigeonneau, ...
Science 335 (6072), 1103-1106, 2012
5612012
Graph-based methods for analysing networks in cell biology
T Aittokallio, B Schwikowski
Briefings in bioinformatics 7 (3), 243-255, 2006
4002006
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data
N Zhang, R Aebersold, B Schwikowski
Proteomics 2 (10), 1406-1412, 2002
2702002
Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
JM Buescher, W Liebermeister, M Jules, M Uhr, J Muntel, E Botella, ...
Science 335 (6072), 1099-1103, 2012
2342012
Algorithms for phylogenetic footprinting
M Blanchette, B Schwikowski, M Tompa
Journal of computational biology 9 (2), 211-223, 2002
2312002
Signal maps for mass spectrometry-based comparative proteomics
A Prakash, P Mallick, J Whiteaker, H Zhang, A Paulovich, M Flory, H Lee, ...
Molecular & Cellular Proteomics 5 (3), 423-432, 2006
1302006
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
O Garcia, C Saveanu, M Cline, M Fromont-Racine, A Jacquier, ...
Bioinformatics 23 (3), 394-396, 2006
1112006
Alignment of LC‐MS images, with applications to biomarker discovery and protein identification
M Vandenbogaert, S Li‐Thiao‐Té, HM Kaltenbach, R Zhang, T Aittokallio, ...
Proteomics 8 (4), 650-672, 2008
1062008
Universal DNA tag systems: a combinatorial design scheme
A Ben-Dor, R Karp, B Schwikowski, Z Yakhini
Journal of computational Biology 7 (3-4), 503-519, 2000
1022000
Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli
D Duffy, V Rouilly, V Libri, M Hasan, B Beitz, M David, A Urrutia, A Bisiaux, ...
Immunity 40 (3), 436-450, 2014
972014
Mining viral protease data to extract cleavage knowledge
A Narayanan, X Wu, ZR Yang
Bioinformatics 18 (suppl_1), S5-S13, 2002
932002
ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision‐induced dissociation spectrum collected by a tandem mass spectrometer
N Zhang, X Li, M Ye, S Pan, B Schwikowski, R Aebersold
Proteomics 5 (16), 4096-4106, 2005
882005
On enumerating all minimal solutions of feedback problems
B Schwikowski, E Speckenmeyer
Discrete Applied Mathematics 117 (1-3), 253-265, 2002
872002
Predicting protein–peptide interactions via a network-based motif sampler
DJ Reiss, B Schwikowski
Bioinformatics 20 (suppl_1), i274-i282, 2004
652004
Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics
A Prakash, B Piening, J Whiteaker, H Zhang, SA Shaffer, D Martin, ...
Molecular & cellular proteomics 6 (10), 1741-1748, 2007
612007
An exact algorithm to identify motifs in orthologous sequences from multiple species.
M Blanchette, B Schwikowski, M Tompa
ISMB, 37-45, 2000
612000
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Articles 1–20