Transcriptional programs: Modelling higher order structure in transcriptional control (2009)
Reid, John E, Ott, Sascha, Wernisch, Lorenz
Abstract Background Transcriptional regulation is an important part of regulatory control in eukaryotes. Even if binding motifs for transcription factors are known, the task of finding binding sites...
Automatic Prediction of Functional Site Regions in Low-Resolution Protein Structures (2008)
Jaspreet Singh Sodhi, Liam J. Mcguffin, Kevin Bryson, Jonathan J. Ward, Lorenz Wernisch, David T. Jones
www.cs.ucl.ac.uk/staff/J.Sodhi World-wide structural genomics initiatives are rapidly accumulating structures for which limited functional information is available. Additionally, state-of-the art...
Richard Newton, Jason Hinds, Lorenz Wernisch, Richard Newton, Birkbeck College
Figure 1- Plot of M values with genome position A typical plot of M values with genome position for an array from the TB data set (test strain 2122/97). Figure 2- Density distribution of M values...
Jacques Van Helden, Lorenz Wernisch, David Gilbert
Introduction..............................................................................................................2 Sources of data on metabolic...
Predicting metal-binding site residues in low-resolution structural models (2008)
Jaspreet Singh Sodhi, Kevin Bryson, Liam J. Mcguffin, Jonathan J. Ward, Lorenz Wernisch, David T. Jones, ...
The accurate prediction of biological function on a genome-wide scale promises wide-ranging benefits in understanding complex biological processes. Such understanding will be a key
Iosifina Pournara, Lorenz Wernisch
Learning Bayesian networks from microarray data
Preprint version of the article published in Biol Chem 381(9-10), 921-35. (2008)
Jacques Van Helden, Avi Naim, Mattew Eldridge, Lorenz Wernisch, David Gilbert, Shoshana J. Wodak, ...
Representing function in biological databases27/12/00 21:12
AMAZE: A DATABASE OF MOLECULAR FUNCTION, INTERACTIONS AND BIOCHEMICAL PROCESSES (2008)
Christian Lemer, Avi Naim, Yong Zhang, Didier Croes, Georges N. Cohen, Gaurab Mukherjee, ...
The aMAZE database
Zhang, Yi, Hatch, Kim A, Wernisch, Lorenz, Bacon, Joanna
Abstract Background Low oxygen availability has been shown previously to stimulate M. tuberculosis to establish non-replicative persistence in vitro . The two component sensor/regulator dosRS is a...
Iosifina Pournara, Lorenz Wernisch
Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the...
Iosifina Pournara, Lorenz Wernisch
Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the...
Quantification of global transcription patterns in prokaryotes using spotted microarrays (2007)
Sidders, Ben, Withers, Mike, Kendall, Sharon L, Bacon, Joanna, Waddell, Simon J, Hinds, Jason, ...
Abstract We describe an analysis, applicable to any spotted microarray dataset produced using genomic DNA as a reference, that quantifies prokaryotic levels of mRNA on a genome-wide scale. Applying...
Markov Chains for Linear Extensions, (2007)
Stefan Felsner, Lorenz Wernisch
Abstract. We study the generation of uniformly distributed linear extensions using Markov chains. In particular we show that monotone coupling from the past can be applied in the case of linear...
A comparative study of S/MAR prediction tools (2007)
Evans, Kenneth, Ott, Sascha, Hansen, Annika, Koentges, Georgy, Wernisch, Lorenz
Abstract Background S/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs...
A comparative study of S/MAR prediction tools (2007)
Evans, Kenneth, Ott, Sascha, Hansen, Annika, Koentges, Georgy, Wernisch, Lorenz
Abstract Background S/MARs are regions of the DNA that are attached to the nuclear matrix. These regions are known to affect substantially the expression of genes. The computer prediction of S/MARs...
Factor analysis for gene regulatory networks and transcription factor activity profiles (2007)
Pournara, Iosifina, Wernisch, Lorenz
Abstract Background Most existing algorithms for the inference of the structure of gene regulatory networks from gene expression data assume that the activity levels of transcription factors (TFs)...
Diboun, Ilhem, Wernisch, Lorenz, Orengo, Christine, Koltzenburg, Martin
Abstract Background RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but...
Graham R. Stewart, Lorenz Wernisch, Richard Stabler, Joseph A. Mangan, Jason Hinds, Ken G. Laing, ...
The regulation of heat shock protein (HSP) expression is critically important to pathogens such as Mycobacterium tuberculosis and dysregulation of the heat shock response results in increased immune...
Can Replication Save Noisy Microarray Data? (2006)
Microarray experiments are multi-step processes. At each step—the growth of cultures, extraction of mRNA, reverse transcription, labelling, hybridization, scanning, and image...
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome (2006)
Withers, Mike, Wernisch, Lorenz, Reis, Mario Dos
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat...
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome (2006)
Withers, Mike, Wernisch, Lorenz, Reis, Mario Dos
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat...
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome (2006)
Withers, Mike, Wernisch, Lorenz, Reis, Mario Dos
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat...
Núria Domedel-puig, Lorenz Wernisch
Summary: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive...
Applying GIFT, a Gene Interactions Finder in Text, to fly literature (2005)
Domedel-Puig, Núria, Wernisch, Lorenz
Summary: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive...
Edwards, Martin T., Rison, Stuart C. G., Stoker, Neil G., Wernisch, Lorenz
An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of...
Applying GIFT, a gene interactions finder in text, to fly literature (2005)
Domedel-Puig, Núria, Wernisch, Lorenz
Summary: A number of freely available text mining tools have been put together to extract highly reliable Drosophila gene interaction data from text. The system has been tested with The Interactive...
Reconstruction of gene networks using Bayesian learning and manipulation experiments (2004)
Pournara, Iosifina, Wernisch, Lorenz
Motivation: The analysis of high-throughput experimental data, for example from microarray experiments, is currently seen as a promising way of finding regulatory relationships between genes....
Solving the riddle of codon usage preferences: a test for translational selection (2004)
Reis, Mario Dos, Savva, Renos, Wernisch, Lorenz
Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of...
Reconstruction of gene networks using Bayesian learning and manipulation experiments (2004)
Pournara, Iosifina, Wernisch, Lorenz
Motivation: The analysis of high-throughput experimental data, for example from microarray experiments, is currently seen as a promising way of finding regulatory relationships between genes....
Reconstruction of gene networks using Bayesian learning and manipulation experiments (2004)
Pournara, Iosifina, Wernisch, Lorenz
Motivation: The analysis of high-throughput experimental data, for example from microarray experiments, is currently seen as a promising way of finding regulatory relationships between genes....
Analysis of Whole-Genome Microarray Replicates Using Mixed Models (2003)
Lorenz Wernisch Birkbeck, Lorenz Wernisch, Andreas Wietzorrek, Philip D. Butcher, Sharon L. Kendall, Tanya Parish, ...
Motivation: Microarray experiments are inherently noisy. Replication is the key to estimating realistic fold-changes despite such noise. In the analysis of the various sources of noise the dependency...
Dos Reis, Mario, Wernisch, Lorenz, Savva, Renos
Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when...
Analysis of whole-genome microarray replicates using mixed models (2003)
Wernisch, Lorenz, Kendall, Sharon L., Soneji, Shamit, Wietzorrek, Andreas, Parish, Tanya, Hinds, Jason, ...
Motivation: Microarray experiments are inherently noisy. Replication is the key to estimating realistic fold-changes despite such noise. In the analysis of the various sources of noise the dependency...
Can Replication Save Noisy Microarray Data? (2002)
Microarray experiments are multi-step processes. At each step—the growth of cultures, extraction of mRNA, reverse transcription, labelling, hybridization, scanning, and image analysis—variation...
Graham R. Stewart, Lorenz Wernisch, Richard Stabler, Joseph A. Mangan, Jason Hinds, Ken G. Laing, ...
The regulation of heat shock protein (HSP) expression is critically important to pathogens such as Mycobacterium tuberculosis and dysregulation of the heat shock response results in increased immune...
Jacques Van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana Wodak
We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with...
Automatic procedures for protein design (2001)
Alfonso Jaramillo, Lorenz Wernisch, Stephanie Héry, Shoshana J. Wodak
Abstract: This review describes computational procedures for deriving the amino acid sequences that are compatible with a given protein backbone structure. Such procedures can be used to gain insight...
Jacques Van Helden, Lorenz Wernisch, Michael Schroeder, Shoshana Wodak
We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with...
Jacques Van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana Wodak
this paper, we present examples of applications and discuss some critical issues for obtaining suitable results.
Maximum k-chains in planar point sets: Combinatorial structure and algorithms (1999)
Stefan Felsner, Lorenz Wernisch
Germany. A chain of a set P of n points in the plane is a chain of the dominance order on P. A k-chain is a subset C of P that can be covered by k chains. A k-chain C is a maximum k-chain if no other...
Trapezoid graphs and generalizations, geometry and algorithms (1997)
Stefan Felsner, Rudolf M, Lorenz Wernisch
Trapezoid graphs are a class of cocomparability graphs containing interval graphs and permutation graphs as subclasses. They were introduced by Dagan, Golumbic and Pinter [DGP]. They propose an O(n...
Trapezoid graphs and generalizations, geometry and algorithms (1997)
Stefan Felsner, Rudolf M Uller, Lorenz Wernisch
Trapezoid graphs are a class of cocomparability graphs containing interval graphs and permutation graphs as subclasses. They were introduced by Dagan, Golumbic and Pinter [DGP]. They propose an O(n...
Dominance relation on point sets and aligned rectangles / (1996)
Zugl.: Berlin, Freie Univ., Diss., 1994.
Trapezoid Graphs and Generalizations, Geometry and Algorithms (1994)
Stefan Felsner, Rudolf Müller, Lorenz Wernisch
Trapezoid graphs are a class of cocomparability graphs containing interval graphs and permutation graphs as subclasses. They were introduced by Dagan, Golumbic and Pinter [DGP]. They propose an O(n 2...
Jaramillo, Alfonso, Wernisch, Lorenz, Héry, Stéphanie, Wodak, Shoshana J.
An automatic protein design procedure is used to select amino acid sequences that optimize the folding free energy function for a given protein. The only information used in designing the sequences...
Dos Reis, Mario, Wernisch, Lorenz, Savva, Renos
Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when...
Solving the riddle of codon usage preferences: a test for translational selection
Reis, Mario Dos, Savva, Renos, Wernisch, Lorenz
Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of...
Edwards, Martin T., Rison, Stuart C. G., Stoker, Neil G., Wernisch, Lorenz
An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of...
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
Withers, Mike, Wernisch, Lorenz, Reis, Mario Dos
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat...
Jaramillo, Alfonso, Wernisch, Lorenz, Héry, Stéphanie, Wodak, Shoshana J.
An automatic protein design procedure is used to select amino acid sequences that optimize the folding free energy function for a given protein. The only information used in designing the sequences...
Dos Reis, Mario, Wernisch, Lorenz, Savva, Renos
Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when...
Solving the riddle of codon usage preferences: a test for translational selection
Reis, Mario Dos, Savva, Renos, Wernisch, Lorenz
Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of...
Edwards, Martin T., Rison, Stuart C. G., Stoker, Neil G., Wernisch, Lorenz
An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of...
Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
Withers, Mike, Wernisch, Lorenz, Reis, Mario Dos
Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat...
A comparative study of S/MAR prediction tools
Evans, Kenneth, Ott, Sascha, Hansen, Annika, Koentges, Georgy, Wernisch, Lorenz
Quantification of global transcription patterns in prokaryotes using spotted microarrays
Sidders, Ben, Withers, Mike, Kendall, Sharon L, Bacon, Joanna, Waddell, Simon J, Hinds, Jason, ...
An analysis is described, applicable to any spotted microarray dataset that is produced using genomic DNA as a reference for quantifying prokaryotic levels of mRNA on a genome-wide scale.
Using Temporal Correlation in Factor Analysis for Reconstructing Transcription Factor Activities
Pournara, Iosifina, Wernisch, Lorenz
Two-level gene regulatory networks consist of the transcription factors (TFs) in the top level and their regulated genes in the second level. The expression profiles of the regulated genes are the...
Stewart, Graham R., Wernisch, Lorenz, Stabler, Richard, Mangan, Joseph A., Hinds, Jason, Laing, Ken G., ...
The regulation of heat shock protein (HSP) expression is critically important to pathogens such as Mycobacterium tuberculosis and dysregulation of the heat shock response results in increased immune...
Can Replication Save Noisy Microarray Data?
Microarray experiments are multi-step processes. At each step—the growth of cultures, extraction of mRNA, reverse transcription, labelling, hybridization, scanning, and image analysis—variation...
Estimating Translational Selection in Eukaryotic Genomes
Dos Reis, Mario, Wernisch, Lorenz
Natural selection on codon usage is a pervasive force that acts on a large variety of prokaryotic and eukaryotic genomes. Despite this, obtaining reliable estimates of selection on codon usage has...
A HaemAtlas: characterizing gene expression in differentiated human blood cells
Watkins, Nicholas A., Gusnanto, Arief, De Bono, Bernard, De, Subhajyoti, Miranda-Saavedra, Diego, Hardie, Debbie L., ...
Hematopoiesis is a carefully controlled process that is regulated by complex networks of transcription factors that are, in part, controlled by signals resulting from ligand binding to cell-surface...