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Inferring multi-target QSAR models with taxonomy-based multi-task learning.
Rosenbaum L, Dörr A, Bauer MR, Boeckler FM, Zell A. Rosenbaum L, et al. Among authors: zell a. J Cheminform. 2013 Jul 11;5(1):33. doi: 10.1186/1758-2946-5-33. J Cheminform. 2013. PMID: 23842210 Free PMC article.
CONCLUSIONS: Multi-task learning is a valuable approach for inferring multi-target QSAR models for lead optimization. The application of multi-task learning is most beneficial if knowledge can be transferred from a similar task with a lot of in-domain knowled …
CONCLUSIONS: Multi-task learning is a valuable approach for inferring multi-target QSAR models for lead optimization. The application …
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat.
Römer M, Eichner J, Metzger U, Templin MF, Plummer S, Ellinger-Ziegelbauer H, Zell A. Römer M, et al. Among authors: zell a. PLoS One. 2014 May 15;9(5):e97640. doi: 10.1371/journal.pone.0097640. eCollection 2014. PLoS One. 2014. PMID: 24830643 Free PMC article.
We trained and evaluated diverse machine learning-based models, differing in the incorporated features and learning algorithms on a cross-omics dataset encompassing mRNA, miRNA, and protein expression profiles obtained from rat liver samples treated with a heterogen …
We trained and evaluated diverse machine learning-based models, differing in the incorporated features and learning algorithms on a c …
Evaluation of toxicogenomics approaches for assessing the risk of nongenotoxic carcinogenicity in rat liver.
Eichner J, Wrzodek C, Römer M, Ellinger-Ziegelbauer H, Zell A. Eichner J, et al. Among authors: zell a. PLoS One. 2014 May 14;9(5):e97678. doi: 10.1371/journal.pone.0097678. eCollection 2014. PLoS One. 2014. PMID: 24828355 Free PMC article.
The current gold-standard method for cancer safety assessment of drugs is a rodent two-year bioassay, which is associated with significant costs and requires testing a high number of animals over lifetime. ...Both methods were evaluated on a dataset obtained …
The current gold-standard method for cancer safety assessment of drugs is a rodent two-year bioassay, which is associated with signif …
A ranking method for the concurrent learning of compounds with various activity profiles.
Dörr A, Rosenbaum L, Zell A. Dörr A, et al. Among authors: zell a. J Cheminform. 2015 Jan 16;7(1):2. doi: 10.1186/s13321-014-0050-6. eCollection 2015. J Cheminform. 2015. PMID: 25643067 Free PMC article.
BACKGROUND: In this study, we present a SVM-based ranking algorithm for the concurrent learning of compounds with different activity profiles and their varying prioritization. To this end, a specific labeling of each compound was elaborated in order to infer virtual …
BACKGROUND: In this study, we present a SVM-based ranking algorithm for the concurrent learning of compounds with different activity …
A toxicogenomic approach for the prediction of murine hepatocarcinogenesis using ensemble feature selection.
Eichner J, Kossler N, Wrzodek C, Kalkuhl A, Bach Toft D, Ostenfeldt N, Richard V, Zell A. Eichner J, et al. Among authors: zell a. PLoS One. 2013 Sep 10;8(9):e73938. doi: 10.1371/journal.pone.0073938. eCollection 2013. PLoS One. 2013. PMID: 24040119 Free PMC article.
As this assay is cost-intensive and time-consuming there is a high interest in developing approaches for the screening and prioritization of drug candidates in preclinical safety evaluations. ...This method was evaluated on a microarray dataset containing global gen …
As this assay is cost-intensive and time-consuming there is a high interest in developing approaches for the screening and prioritiza …
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.
Eichner J, Topf F, Dräger A, Wrzodek C, Wanke D, Zell A. Eichner J, et al. Among authors: zell a. PLoS One. 2013 Dec 12;8(12):e82238. doi: 10.1371/journal.pone.0082238. eCollection 2013. PLoS One. 2013. PMID: 24349230 Free PMC article.
We implemented a four-step classification workflow which for a given protein sequence (1) discriminates TFs from other proteins, (2) determines the structural superclass of TFs, (3) identifies the DNA-binding domains of TFs and (4) predicts their cis-acting DNA moti …
We implemented a four-step classification workflow which for a given protein sequence (1) discriminates TFs from other protein …
4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening.
Jahn A, Rosenbaum L, Hinselmann G, Zell A. Jahn A, et al. Among authors: zell a. J Cheminform. 2011 Jul 6;3(1):23. doi: 10.1186/1758-2946-3-23. J Cheminform. 2011. PMID: 21733172 Free PMC article.
The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarit …
The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational …
Interpreting linear support vector machine models with heat map molecule coloring.
Rosenbaum L, Hinselmann G, Jahn A, Zell A. Rosenbaum L, et al. Among authors: zell a. J Cheminform. 2011 Mar 25;3(1):11. doi: 10.1186/1758-2946-3-11. J Cheminform. 2011. PMID: 21439031 Free PMC article.
The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. Besides a strong performance, the interpretability of a machine learning model is a desired property to guide the optimization of …
The outcomes of high-throughput screenings are a valuable source for machine learning algorithms to infer such models. Besides a
jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints.
Hinselmann G, Rosenbaum L, Jahn A, Fechner N, Zell A. Hinselmann G, et al. Among authors: zell a. J Cheminform. 2011 Jan 10;3(1):3. doi: 10.1186/1758-2946-3-3. J Cheminform. 2011. PMID: 21219648 Free PMC article.
BACKGROUND: The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. ...The aim of this work is to introduce a library for exactly defined molecular decompositions, with a strong focus …
BACKGROUND: The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic …
Estimation of the applicability domain of kernel-based machine learning models for virtual screening.
Fechner N, Jahn A, Hinselmann G, Zell A. Fechner N, et al. Among authors: zell a. J Cheminform. 2010 Mar 11;2(1):2. doi: 10.1186/1758-2946-2-2. J Cheminform. 2010. PMID: 20222949 Free PMC article.
Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a disjoint screening data set according to the predicted activity. For each prediction, the applicability of the model for the respective compou …
Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a di …
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