35 Integrating Information for Protein Function Prediction (2009)
William Stafford Noble, Asa Ben-hur
Most of the work on predicting protein function uses a single source of information – the most common being the amino acid sequence of the protein (see Chapter 30). There are, however, a number of...
The use of gene ontology evidence codes in preventing classifier assessment bias (2009)
Motivation: The biological community's reliance on computational annotations of protein function makes correct assessment of function prediction methods an issue of great importance. The fact that a...
Haidong Wang, Eran Segal, Asa Ben-hur, Daphne Koller, Douglas L. Brutlag
protein-protein interaction sites on a
Haidong Wang, Eran Segal, Asa Ben-hur, Daphne Koller, Douglas L. Brutlag
protein-protein interaction sites on a
Haidong Wang, Eran Segal, Asa Ben-hur, Daphne Koller, Douglas L. Brutlag
protein-protein interaction sites on a
Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
Abstract We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our...
A structural alignment kernel for protein structures (2007)
Qiu, Jian, Hue, Martial, Ben-Hur, Asa, Vert, Jean-Philippe, Noble, William Stafford
Motivation: This work aims to develop computational methods to annotate protein structures in an automated fashion. We employ a support vector machine (SVM) classifier to map from a given class of...
An alignment kernel for protein structures (2007)
Qiu, Jian, Hue, Martial, Ben-Hur, Asa, Vert, Jean-Philippe, Noble, William
Motivation: This work aims to develop computational methods to annotate protein structures in an automated fashion. We employ a support vector machine (SVM) classifier to map from a given class of...
interaction binding sites on a proteome-wide scale (2007)
Haidong Wang, Eran Segal, Asa Ben-hur, Qian-ru Li, Marc Vidal, Daphne Koller
InSite: a computational method for identifying protein-protein
Choosing negative examples for the prediction of protein-protein interactions (2006)
Abstract The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experimentalists...
Supplementary Material References E-mail Alerts Rights & Permissions Reprints (2006)
Soo-yon Rhee, Jonathan Taylor, Gauhar Wadhera, Asa Ben-hur, Douglas L. Brutlag, W. Shafer, ...
doi:10.1073/pnas.0607274103 This information is current as of November 2006. High-resolution figures, a citation map, links to PubMed and Google Scholar, etc., can be found at:...
Bmc Bioinformatics, Asa Ben-hur, William Stafford Noble, Open Access
Proceedings Choosing negative examples for the prediction of protein-protein interactions
Kernel methods for predicting protein-protein interactions (2005)
Ben-Hur, Asa, Noble, William Stafford
Motivation: Despite advances in high-throughput methods for discovering protein–protein interactions, the interaction networks of even well-studied model organisms are sketchy at best, highlighting...
Result Analysis of the NIPS 2003 Feature Selection Challenge (2004)
Guyon, Isabelle, Gunn, Steve, Ben-Hur, Asa, Dror, Gideon
The NIPS 2003 workshops included a feature selection competition organized by the authors. We provided participants with five datasets from different application domains and called for classification...
CREME: Cis-Regulatory Module Explorer for the human genome (2004)
Roded Sharan, Asa Ben-hur, Gabriela G. Loots, Ivan Ovcharenko
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Sequence motifs: highly predictive features of protein function (2004)
Summary. Protein function prediction, i.e. classification of protein sequences according to their biological function is an important task in bioinformatics. In this chapter we illustrate that the...
CREME: Cis-Regulatory Module Explorer for the human genome (2004)
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Probabilistic analysis of a differential equation for linear programming (2003)
Asa Ben-hur, B Joshua Feinberg, Shmuel Fishman
ARTICLE IN PRESS
Detecting stable clusters using principal component analysis (2003)
Clustering is one of the most commonly used tools in the analysis of gene expression data (1, 2). The usage in grouping genes is based on the premise that co-expression is a result of co-regulation....
Vol No Pages, Asa Ben-hur, Douglas Brutlag
Motivation: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases.
Vol Suppl Pages, Asa Ben-hur, Douglas Brutlag
Motivation: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases.
Detecting Stable Clusters Using Principal Component Analysis (2003)
Clustering is one of the most commonly used tools in the analysis of gene expression data (1, 2) . The usage in grouping genes is based on the premise that co-expression is a result of co-regulation....
Remote homology detection: a motif based approach (2003)
Ben-Hur, Asa, Brutlag, Douglas
Motivation: Remote homology detection is the problem of detecting homology in cases of low sequence similarity. It is a hard computational problem with no approach that works well in all cases....
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments (2003)
Sharan, Roded, Ovcharenko, Ivan, Ben-Hur, Asa, Karp, Richard M.
Motivation: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of...
A theory of complexity for continuous time systems (2002)
Asa Ben-hur, Hava T. Siegelmann
We present a model of computation with ordinary differential equations (ODEs) which converge to attractors that are interpreted as the output of a computation. We introduce a measure of complexity...
A theory of complexity for continuous time systems (2002)
Abstract We present a model of computation with ordinary differential equations (ODEs) which converge to attractors that are interpreted as the output of a computation. We introduce a measure of...
Probabilistic analysis of the phase space flow for linear programming (2001)
Ben-Hur, Asa, Feinberg, Joshua, Fishman, Shmuel, Siegelmann, Hava T.
The phase space flow of a dynamical system leading to the solution of Linear Programming (LP) problems is explored as an example of complexity analysis in an analog computation framework. An ensemble...
Probabilistic analysis of a differential equation for linear programming (2001)
Ben-Hur, Asa, Feinberg, Joshua, Fishman, Shmuel, Siegelmann, Hava T.
In this paper we address the complexity of solving linear programming problems with a set of differential equations that converge to a fixed point that represents the optimal solution. Assuming a...
Support vector clustering (2001)
Asa Ben-hur, David Horn, Hava T. Siegelmann, Vladimir Vapnik
We present a novel clustering method using the approach of support vector machines. Data points are mapped by means of a Gaussian kernel to a high dimensional feature space, where we search for the...
A support vector method for clustering (2001)
Asa Ben-hur, David Horn, Hava T. Siegelmann, Vladimir Vapnik
We present a novel method for clustering using the support vector machine approach. Data points are mapped to a high dimensional feature space, where support vectors are used to define a sphere...
A Support Vector Method for Hierarchical Clustering (2001)
Asa Ben-hur, David Horn, Hava Siegelmann, Vladimir Vapnik
We present a novel method for clustering using the support vector machine approach. Data points are mapped to a high dimensional feature space, where support vectors are used to define a sphere...
A support vector method for clustering (2001)
Asa Ben-hur, Hava T. Siegelmann, David Horn, Vladimir Vapnik
We present a novel method for clustering using the support vector machine approach. Data points are mapped to a high dimensional feature space, where support vectors are used to define a sphere...
CREME: Cis-Regulatory Module Explorer for the human genome
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Large-scale identification of yeast integral membrane protein interactions
Miller, John P., Lo, Russell S., Ben-Hur, Asa, Desmarais, Cynthia, Stagljar, Igor, Noble, William Stafford, ...
We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated...
CREME: Cis-Regulatory Module Explorer for the human genome
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Large-scale identification of yeast integral membrane protein interactions
Miller, John P., Lo, Russell S., Ben-Hur, Asa, Desmarais, Cynthia, Stagljar, Igor, Noble, William Stafford, ...
We carried out a large-scale screen to identify interactions between integral membrane proteins of Saccharomyces cerevisiae by using a modified split-ubiquitin technique. Among 705 proteins annotated...
Choosing negative examples for the prediction of protein-protein interactions
Ben-Hur, Asa, Noble, William Stafford
The protein-protein interaction networks of even well-studied model organisms are sketchy at best, highlighting the continued need for computational methods to help direct experimentalists in the...
Genotypic predictors of human immunodeficiency virus type 1 drug resistance
Rhee, Soo-Yon, Taylor, Jonathan, Wadhera, Gauhar, Ben-Hur, Asa, Brutlag, Douglas L., Shafer, Robert W.
Understanding the genetic basis of HIV-1 drug resistance is essential to developing new antiretroviral drugs and optimizing the use of existing drugs. This understanding, however, is hampered by the...
Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs.