Advance Access publication... (2008)
Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, ...
Received on …; revised on …; accepted on …
Data and text mining ROCR: visualizing classifier performance in R (2008)
Tobias Sing, Oliver S, Niko Beerenwinkel, Thomas Lengauer
Summary: ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to...
Tobias Sing, Niko Beerenwinkel
Starting with the work of Jaakkola and Haussler, a variety of approaches have been proposed for coupling domain-specific generative models with statistical learning methods. The link is established...
Tobias Sing, Niko Beerenwinkel, Thomas Lengauer, Valentina Svicher, Francesca Ceccherini-silberstein, Carlo-federico Perno
We present a case study on the discovery of clinically relevant domain knowledge in the field of HIV drug resistance. Novel mutations in the HIV genome associated with treatment failure were...
Low, Andrew J., Marchant, David, Brumme, Chanson J., Brumme, Zabrina L., Dong, Winnie, Sing, Tobias, ...
Svicher, Valentina, Sing, Tobias, Artese, Anna, Santoro, Maria Mercedes, Forbici, Federica, ...
Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y,...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage (2007)
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J. Low, Peter K. Cheung, P. Richard Harrigan, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage (2007)
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J Low, Peter K Cheung, P Richard Harrigan, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Model-based anti-HIV therapy (2007)
Modern combination drug therapy has substantially improved the clinical management of HIV-1 infection. Still, the emergence of drug-resistant variants eventually leads to therapy failure in most...
Low, Andrew J., Dong, Winnie, Chan, Dennison, Sing, Tobias, Swanstrom, Ronald, Jensen, Mark, ...
Objective: Integrating CCR5 antagonists into clinical practice would benefit from accurate assays of co-receptor usage (CCR5 versus CXCR4) with fast turnaround and low cost. Design: Published HIV...
Skrabal, Katharina, Low, Andrew J., Dong, Winnie, Sing, Tobias, Cheung, Peter K., Mammano, Fabrizio, ...
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates (2007)
Sing, Tobias, Low, Andrew J., Beerenwinkel, Niko, Sander, Oliver, Cheung, Peter K., Domingues, Francisco S., ...
Structural Descriptors of gp120 V3 Loop for the Prediction of {HIV-1} Coreceptor Usage (2007)
Sander, Oliver, Sing, Tobias, Sommer, Ingolf, Low, Andrew J., Cheung, Peter K., Harrigan, P. Richard, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Ceccherini-Silberstein, Francesca, Svicher, Valentina, Sing, Tobias, Artese, Anna, Santoro, Maria Mercedes, Forbici, Federica, ...
Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y,...
Altmann, Andre, Beerenwinkel, Niko, Sing, Tobias, Savenkov, Igor, Däumer, Martin, Kaiser, Rolf, ...
Background: The outcome of antiretroviral combination therapy depends on many factors involving host, virus, and drugs. We investigate prediction of treatment response from the applied drug...
Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype (2007)
Sing, Tobias, Beerenwinkel, Niko
Starting with the work of Jaakkola and Haussler, a variety of approaches have been proposed for coupling domain-specific generative models with statistical learning methods. The link is established...
Stable coreceptor usage of HIV in patients with ongoing treatment failure on {HAART} (2006)
Lehmann, Clara, Däumer, Martin, Bousaad, Ibrahim, Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, ...
Background Disease progression in HIV infection has been associated with switch of viral coreceptor usage from CCR5 to CXCR4. Objectives To investigate the relationship between HIV-coreceptor tropism...
Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV (2006)
Roomp, Kirsten, Beerenwinkel, Niko, Sing, Tobias, Schülter, Eugen, Büch, Joachim, Sierra-Aragon, Saleta, ...
Despite the availability of antiretroviral combination therapies, success in drug treatment of HIV-infected patients is limited. One reason for therapy failure is the development of drug-resistant...
Bioinformatics-assisted anti-HIV therapy (2006)
Lengauer, Thomas, Sing, Tobias
Highly active antiretroviral therapy (HAART), in which three or more drugs are given in combination, has substantially improved the clinical management of HIV-1 infection. Still, the emergence of...
Niko Beerenwinkel, Tobias Sing, Thomas Lengauer, Jörg Rahnenführer, Kirsten Roomp, Igor Savenkov, ...
Data and text mining Vol. 21 no. 21 2005, pages 3943–3950 doi:10.1093/bioinformatics/bti654 Computational methods for the design of effective therapies against drug resistant HIV strains
Svicher, Valentina, Ceccherini-Silberstein, Francesca, Sing, Tobias, Santoro, M., Gori, C., Beerenwinkel, Niko, ...
Svicher, Valentina, Ceccherini-Silberstein, Francesca, Sing, Tobias, Santoro, M., Gori, C., Beerenwinkel, Niko, ...
Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance (2005)
Beerenwinkel, Niko, Däumer, Martin, Sing, Tobias, Rahnenführer, Jörg, Lengauer, Thomas, Selbig, Joachim, ...
Stable coreceptor usage of HIV-1 in patients with ongoing treatment failure on HAART (2005)
Kaiser, Rolf, Boussaad, Ibo, Lehmann, C., Däumer, Martin, Sing, Tobias, Schmeisser, N., ...
ROCR: visualizing classifier performance in R (2005)
Sing, Tobias, Sander, Oliver, Beerenwinkel, Niko, Lengauer, Thomas
Summary: ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to...
ROCR: visualizing classifier performance in R (2005)
Sing, Tobias, Sander, Oliver, Beerenwinkel, Niko, Lengauer, Thomas
Summary: ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures which can be freely combined...
Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...
Motivation: The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective...
Beerenwinkel, Niko, Sing, Tobias, Lengauer, Thomas, Rahnenführer, Jörg, Roomp, Kirsten, Savenkov, Igor, ...
Summary: The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure...
Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)
Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, Hernández-Orallo, José, Ferri, César, Lachiche, Nicolas, ...
Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)
Tobias Sing, Niko Beerenwinkel, Thomas Lengauer
Abstract. We introduce a model class for statistical learning which is based on mixtures of propositional rules. In our mixture model, the weight of a rule is not uniform over the entire instance...
Learning mixtures of localized rules by maximizing the area under the ROC curve (2004)
Sing, Tobias, Beerenwinkel, Niko, Lengauer, Thomas, Hern{\'a}ndez-Orallo, Jos{\'e}, Ferri, C{\'e}sar, Lachiche, Nicolas, ...
Svicher, Valentina, Sing, Tobias, Santoro, Maria Mercedes, Forbici, Federica, Rodríguez-Barrios, Fátima, Bertoli, Ada, ...
We characterized 16 additional mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) whose role in drug resistance is still unknown by analyzing 1,906 plasma-derived...
Svicher, Valentina, Sing, Tobias, Santoro, Maria Mercedes, Forbici, Federica, Rodríguez-Barrios, Fátima, Bertoli, Ada, ...
We characterized 16 additional mutations in human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) whose role in drug resistance is still unknown by analyzing 1,906 plasma-derived...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
Sander, Oliver, Sing, Tobias, Sommer, Ingolf, Low, Andrew J, Cheung, Peter K, Harrigan, P. Richard, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
Skrabal, Katharina, Low, Andrew J., Dong, Winnie, Sing, Tobias, Cheung, Peter K., Mammano, Fabrizio, ...
Two recombinant phenotypic assays for human immunodeficiency virus (HIV) coreceptor usage and an HIV envelope genotypic predictor were employed on a set of clinically derived HIV type 1 (HIV-1)...
Ceccherini-Silberstein, Francesca, Svicher, Valentina, Sing, Tobias, Artese, Anna, Santoro, Maria Mercedes, Forbici, Federica, ...
Resistance to antivirals is a complex and dynamic phenomenon that involves more mutations than are currently known. Here, we characterize 10 additional mutations (L74V, K101Q, I135M/T, V179I, H221Y,...