Proteomics □s, Amol Prakash, Brian Piening, Jeff Whiteaker, Heidi Zhang, Scott A. Shaffer, ...
Mass spectrometry-based proteomics holds great promise as a discovery tool for biomarker candidates in the early detection of diseases. Recently much emphasis has been placed upon producing highly...
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
Assessing bias in experiment design for large-scale mass spectrometry-based (2008)
Amol Prakash, Brian Piening, Jeff Whiteaker, Heidi Zhang, Scott A. Shaffer, Daniel Martin, ...
quantitative proteomics
Phylogenetic distances are encoded in networks of interacting pathways (2008)
Mazurie, Aurélien, Bonchev, Danail, Schwikowski, Benno, Buck, Gregory A.
Motivation: Although metabolic reactions are unquestionably shaped by evolutionary processes, the degree to which the overall structure and complexity of their interconnections are linked to the...
A Clustering Approach to Generalized Tree Alignment with Application to Alu Repeats (2007)
Benno Schwikowski, Martin Vingron
. A formalization of the multiple sequence alignment problem that emphasizes the problem's evolutionary aspect is the Generalized Tree Alignment Problem. Given a set of sequences, this...
Better Tree Alignments through Near-Optimal Intermediates (2007)
Benno Schwikowski, Martin Vingron
The reconstruction of hypothetical ancestral sequences is a widely used means to guide algorithms for multiple alignment and phylogeny reconstruction on the basis of an evolutionary tree. We identify...
Attacking Generalized Tree Alignment By a Deferred Path Heuristic (2007)
Benno Schwikowski And Martin Vingron, Benno Schwikowski, Martin Vingron
Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a...
The restriction scaffold problem (2007)
Amir Ben-dor, Richard M. Karp, Benno Schwikowski, Ron Shamir
Most shotgun sequencing projects undergo a long and costly phase of finishing, in which a partial assembly forms several contigs whose order, orientation and relative distance is unknown. We propose...
Benno Schwikowski, Martin Vingron
Abstract: We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment.Instead of relying on the...
Benno Schwikowski, Martin Vingron
Abstract: We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment.Instead of relying on the...
On enumerating all minimal solutions of (2007)
Benno Schwikowski, Ewald Speckenmeyer
feedback problems
Database searching / Software Summary (2007)
Ning Zhang, Ruedi Aebersold, Benno Schwikowski, Correspondence Benno Schwikowski
this paper, we present a structurally simple and straightforward probabilistic score function for identifying peptides from CID spectra via database searching. The score function used is based on a...
Garcia, Olivier, Saveanu, Cosmin, Cline, Melissa, Fromont-Racine, Micheline, Jacquier, Alain, Schwikowski, Benno, ...
Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds...
Gene Ontology-based layout and coloring (2006)
Olivier Garcia, Cosmin Saveanu, Melissa Cline, Micheline Fromont-racine, Alain Jacquier, Benno Schwikowski, ...
doi:10.1093/bioinformatics/btl605 GOlorize: a Cytoscape plug-in for network visualization with
Graph-based methods for analysing networks in cell biology (2006)
Aittokallio, Tero, Schwikowski, Benno
Availability of large-scale experimental data for cell biology is enabling computational methods to systematically model the behaviour of cellular networks. This review surveys the recent advances in...
Reiss, David J, Avila-Campillo, Iliana, Thorsson, Vesteinn, Schwikowski, Benno, Galitski, Timothy
Abstract Background The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating...
Predicting protein-peptide interactions via a network-based motif sampler (2004)
Reiss, David J., Schwikowski, Benno
Motivation: Many protein–protein interactions are mediated by peptide recognition modules (PRMs), compact domains that bind to short peptides, and play a critical role in a wide array of biological...
Schwikowski,Benno, Vingron,Martin
We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment. Instead of relying on the unrealistic...
Schwikowski, Benno, Vingron, Martin
We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment. Instead of relying on the unrealistic...
Towards optimally multiplexed applications of universal DNA tag systems (2003)
Amir Ben-dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini
We study a design and optimization problem that occurs, for example, when single nucleotide polymorphisms (SNPs) are to be genotyped using a universal DNA tag array. The problem of optimizing the...
Towards optimally multiplexed applications of universal DNA tag systems (2003)
Amir Ben-dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini
We study a design and optimization problem that occurs, for example, when single nucleotide polymorphisms (SNPs) are to be genotyped using a universal DNA tag array. The problem of optimizing the...
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks (2003)
Shannon, Paul, Markiel, Andrew, Ozier, Owen, Baliga, Nitin S., Wang, Jonathan T., Ramage, Daniel, ...
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework....
Towards optimally multiplexed applications of universal DNA tag systems (2003)
Amir Ben-dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini
We study a design and optimization problem that occurs, for example, when single nucleotide polymorphisms (SNPs) are to be genotyped using a universal DNA tag array. The problem of optimizing the...
Discovering regulatory and signalling circuits in molecular interaction networks (2002)
Ideker, Trey, Ozier, Owen, Schwikowski, Benno, Siegel, Andrew F.
Motivation: In model organisms such as yeast, large databases of protein–protein and protein-DNA interactions have become an extremely important resource for the study of protein function,...
Algorithms for Phylogenetic Footprinting (2001)
Mathieu Blanchette, Benno Schwikowski, Martin Tompa
Phylogenetic footprinting is a technique that identi es regulatory elements by nding unusually well conserved regions in a set of orthologous non-coding DNA sequences from multiple species. We...
Algorithms for Phylogenetic Footprinting (2001)
Mathieu Blanchette Benno, Benno Schwikowski, Martin Tompa
Phylogenetic footprinting is a technique that identi es regulatory elements by nding unusually well conserved regions in a set of orthologous non-coding DNA sequences from multiple species. We...
An exact algorithm to identify motifs in orthologous sequences from multiple species (2000)
Mathieu Blanchette, Benno Schwikowski, Martin Tompa
The identication of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as genes, promoters, splice sites, binding sites, etc. We...
Universal DNA Tag Systems: A Combinatorial Design Scheme (2000)
Amir Ben-Dor, Richard Karp, Benno Schwikowski, Zohar Yakhini
Custom-designed DNA arrays offer the possibility of simultaneously monitoring thousands of hybridization reactions. These arrays show great potential for many medical and scientific applications such...
An Exact Algorithm to Identify Motifs in Orthologous Sequences from Multiple Species (2000)
Mathieu Blanchette, Benno Schwikowski, Martin Tompa
The identication of sequence motifs is a fundamental method for suggesting good candidates for biologically functional regions such as promoters, splice sites, binding sites, etc. We investigate the...
The Deferred Path Heuristic for the Generalized Tree Alignment Problem (1997)
Benno Schwikowski, Martin Vingron
Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a...
The Deferred Path Heuristic for the Generalized Tree Alignment Problem (1997)
Benno Schwikowski, Martin Vingron
Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a...
On Computing All Minimal Solutions for Feedback Problems (1997)
B. Schwikowski, B. Schwikowski, E. Speckenmeyer, E. Speckenmeyer, Benno Schwikowski, ...
We present an algorithm that generates all (inclusion-wise) minimal feedback vertex sets of a directed graph G = (V; E). The feedback vertex sets of G are generated with a polynomial delay of O...
On computing all minimal solutions for feedback problems (1997)
B. Schwikowski, B. Schwikowski, E. Speckenmeyer, E. Speckenmeyer, Benno Schwikowski, ...
We present an algorithm that generates all (inclusion-wise) minimal feedback vertex sets of a directed graph G = (V; E). The feedback vertex sets of G are generated with a polynomial delay of O...
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Shannon, Paul, Markiel, Andrew, Ozier, Owen, Baliga, Nitin S., Wang, Jonathan T., Ramage, Daniel, ...
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework....
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Shannon, Paul, Markiel, Andrew, Ozier, Owen, Baliga, Nitin S., Wang, Jonathan T., Ramage, Daniel, ...
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework....
Phylogenetic distances are encoded in networks of interacting pathways
Mazurie, Aurélien, Bonchev, Danail, Schwikowski, Benno, Buck, Gregory A.
Motivation: Although metabolic reactions are unquestionably shaped by evolutionary processes, the degree to which the overall structure and complexity of their interconnections are linked to the...