Search

Your search keyword '"Roder, Heinrich"' showing total 568 results
Start Over Author "Roder, Heinrich"
568 results on '"Roder, Heinrich"'

1. Exact Shapley Values for Local and Model-True Explanations of Decision Tree Ensembles

Author

Campbell, Thomas W., Roder, Heinrich, Georgantas III, Robert W., and Roder, Joanna

Subjects
Computer Science - Machine Learning
Abstract

Additive feature explanations using Shapley values have become popular for providing transparency into the relative importance of each feature to an individual prediction of a machine learning model. While Shapley values provide a unique additive feature attribution in cooperative game theory, the Shapley values that can be generated for even a single machine learning model are far from unique, with theoretical and implementational decisions affecting the resulting attributions. Here, we consider the application of Shapley values for explaining decision tree ensembles and present a novel approach to Shapley value-based feature attribution that can be applied to random forests and boosted decision trees. This new method provides attributions that accurately reflect details of the model prediction algorithm for individual instances, while being computationally competitive with one of the most widely used current methods. We explain the theoretical differences between the standard and novel approaches and compare their performance using synthetic and real data., Comment: 23 pages, 7 figures

Published
2021

11. The Tyrosine Kinase c-Src Specifically Binds to the Active Integrin αIIbβ3 to Initiate Outside-in Signaling in Platelets*

Author

Wu, Yibing, Span, Lisa M, Nygren, Patrik, Zhu, Hua, Moore, David T, Cheng, Hong, Roder, Heinrich, DeGrado, William F, and Bennett, Joel S

Subjects
Biochemistry and Cell Biology, Biological Sciences, 2.1 Biological and endogenous factors, Aetiology, Blood Platelets, CSK Tyrosine-Protein Kinase, Enzyme Activation, Humans, Peptides, Platelet Glycoprotein GPIIb-IIIa Complex, Protein Binding, Signal Transduction, src Homology Domains, src-Family Kinases, integrin, platelet, signal transduction, Src, Src homology 3 domain, Chemical Sciences, Medical and Health Sciences, Biochemistry & Molecular Biology, Biological sciences, Biomedical and clinical sciences, Chemical sciences
Abstract

It is currently believed that inactive tyrosine kinase c-Src in platelets binds to the cytoplasmic tail of the β3 integrin subunit via its SH3 domain. Although a recent NMR study supports this contention, it is likely that such binding would be precluded in inactive c-Src because an auto-inhibitory linker physically occludes the β3 tail binding site. Accordingly, we have re-examined c-Src binding to β3 by immunoprecipitation as well as NMR spectroscopy. In unstimulated platelets, we detected little to no interaction between c-Src and β3. Following platelet activation, however, c-Src was co-immunoprecipitated with β3 in a time-dependent manner and underwent progressive activation as well. We then measured chemical shift perturbations in the (15)N-labeled SH3 domain induced by the C-terminal β3 tail peptide NITYRGT and found that the peptide interacted with the SH3 domain RT-loop and surrounding residues. A control peptide whose last three residues where replaced with those of the β1 cytoplasmic tail induced only small chemical shift perturbations on the opposite face of the SH3 domain. Next, to mimic inactive c-Src, we found that the canonical polyproline peptide RPLPPLP prevented binding of the β3 peptide to the RT- loop. Under these conditions, the β3 peptide induced chemical shift perturbations similar to the negative control. We conclude that the primary interaction of c-Src with the β3 tail occurs in its activated state and at a site that overlaps with PPII binding site in its SH3 domain. Interactions of inactive c-Src with β3 are weak and insensitive to β3 tail mutations.

Published
2015

14. Slow Folding–Unfolding Kinetics of an Octameric β‑Peptide Bundle

Author

Montalvo, Geronda L, Gai, Feng, Roder, Heinrich, and DeGrado, William F

Subjects
Kinetics, Oligopeptides, Protein Folding, Protein Structure, Secondary, Temperature, Thermodynamics, Tyrosine, Chemical Sciences, Biological Sciences, Organic Chemistry
Abstract

β-Peptide foldamers offer attractive frameworks for examining the effect of backbone flexibility on the dynamics of protein folding. Herein, we study the folding-unfolding kinetics of a β-peptide, Acid-1Y,1 which folds in aqueous solution into an octameric bundle of peptides in a conformation known as the 14-helix. Acid-1Y is comprised exclusively of β-amino acids, which differ from α-amino acids by the addition of a single methylene into the backbone. We aim to understand how the additional degree of freedom and increased backbone flexibility in the β-amino acid affect folding dynamics and to measure folding rates of this octameric β-peptide. Previously, we found that the T-jump induced relaxation kinetics of a monomeric β-peptide that forms a monomeric 14-helix occurred on the nanosecond time scale2 and were noticeably slower than a similar alanine-based α-helical peptide.3 Additionally, in comparison to similar α-helices, the relaxation rates showed a weaker dependence on temperature. Here, we find that the T-jump induced relaxation kinetics of the octameric β-peptide occurs on an even slower time scale (minutes) and the unfolding relaxation rates show a large dependence on temperature. These differences indicate that folding energy landscapes of β-peptide secondary and quaternary structure are markedly distinct from one another and also from their α-helical counterparts.

Published
2014

24. Data from A Serum Protein Signature Associated with Outcome after Anti–PD-1 Therapy in Metastatic Melanoma

Author

Weber, Jeffrey S., primary, Sznol, Mario, primary, Sullivan, Ryan J., primary, Blackmon, Shauna, primary, Boland, Genevieve, primary, Kluger, Harriet M., primary, Halaban, Ruth, primary, Bacchiocchi, Antonietta, primary, Ascierto, Paolo A., primary, Capone, Mariaelena, primary, Oliveira, Carlos, primary, Meyer, Krista, primary, Grigorieva, Julia, primary, Asmellash, Senait G., primary, Roder, Joanna, primary, and Roder, Heinrich, primary

Published
2023
Full Text
View/download PDF

25. Supplemental Material, Supplementary Figures 1 and 2, Supplemental Tables 1 - 8 from A Serum Protein Signature Associated with Outcome after Anti–PD-1 Therapy in Metastatic Melanoma

Author

Weber, Jeffrey S., primary, Sznol, Mario, primary, Sullivan, Ryan J., primary, Blackmon, Shauna, primary, Boland, Genevieve, primary, Kluger, Harriet M., primary, Halaban, Ruth, primary, Bacchiocchi, Antonietta, primary, Ascierto, Paolo A., primary, Capone, Mariaelena, primary, Oliveira, Carlos, primary, Meyer, Krista, primary, Grigorieva, Julia, primary, Asmellash, Senait G., primary, Roder, Joanna, primary, and Roder, Heinrich, primary

Published
2023
Full Text
View/download PDF

30. Supplementary Tables 1-4 from Detection of Tumor Epidermal Growth Factor Receptor Pathway Dependence by Serum Mass Spectrometry in Cancer Patients

Author

Chung, Christine H., primary, Seeley, Erin H., primary, Roder, Heinrich, primary, Grigorieva, Julia, primary, Tsypin, Maxim, primary, Roder, Joanna, primary, Burtness, Barbara A., primary, Argiris, Athanassios, primary, Forastiere, Arlene A., primary, Gilbert, Jill, primary, Murphy, Barbara, primary, Caprioli, Richard M., primary, Carbone, David P., primary, and Cohen, Ezra E.W., primary

Published
2023
Full Text
View/download PDF

31. Data from Detection of Tumor Epidermal Growth Factor Receptor Pathway Dependence by Serum Mass Spectrometry in Cancer Patients

Author

Chung, Christine H., primary, Seeley, Erin H., primary, Roder, Heinrich, primary, Grigorieva, Julia, primary, Tsypin, Maxim, primary, Roder, Joanna, primary, Burtness, Barbara A., primary, Argiris, Athanassios, primary, Forastiere, Arlene A., primary, Gilbert, Jill, primary, Murphy, Barbara, primary, Caprioli, Richard M., primary, Carbone, David P., primary, and Cohen, Ezra E.W., primary

Published
2023
Full Text
View/download PDF

32. Supplementary Data from A Serum Protein Classifier Identifying Patients with Advanced Non–Small Cell Lung Cancer Who Derive Clinical Benefit from Treatment with Immune Checkpoint Inhibitors

Author

Muller, Mirte, primary, Hummelink, Karlijn, primary, Hurkmans, Daan P., primary, Niemeijer, Anna-Larissa N., primary, Monkhorst, Kim, primary, Roder, Joanna, primary, Oliveira, Carlos, primary, Roder, Heinrich, primary, Aerts, Joachim G., primary, and Smit, Egbert F., primary

Published
2023
Full Text
View/download PDF

33. Data from A Serum Protein Classifier Identifying Patients with Advanced Non–Small Cell Lung Cancer Who Derive Clinical Benefit from Treatment with Immune Checkpoint Inhibitors

Author

Muller, Mirte, primary, Hummelink, Karlijn, primary, Hurkmans, Daan P., primary, Niemeijer, Anna-Larissa N., primary, Monkhorst, Kim, primary, Roder, Joanna, primary, Oliveira, Carlos, primary, Roder, Heinrich, primary, Aerts, Joachim G., primary, and Smit, Egbert F., primary

Published
2023
Full Text
View/download PDF

36. Predictive value of a proteomic signature in patients with non-small-cell lung cancer treated with second-line erlotinib or chemotherapy (PROSE): a biomarker-stratified, randomised phase 3 trial

Author

Gregorc, Vanesa, Novello, Silvia, Lazzari, Chiara, Barni, Sandro, Aieta, Michele, Mencoboni, Manlio, Grossi, Francesco, Pas, Tommaso De, de Marinis, Filippo, Bearz, Alessandra, Floriani, Irene, Torri, Valter, Bulotta, Alessandra, Cattaneo, Angela, Grigorieva, Julia, Tsypin, Maxim, Roder, Joanna, Doglioni, Claudio, Levra, Matteo Giaj, Petrelli, Fausto, Foti, Silvia, Viganò, Mariagrazia, Bachi, Angela, and Roder, Heinrich

Published
2014
Full Text
View/download PDF

40. VeriStrat® has a prognostic value for patients with advanced non-small cell lung cancer treated with erlotinib and bevacizumab in the first line: Pooled analysis of SAKK19/05 and NTR528

Author

Gautschi, Oliver, Dingemans, Anne-Marie, Crowe, Susanne, Peters, Solange, Roder, Heinrich, Grigorieva, Julia, Roder, Joanna, Zappa, Francesco, Pless, Miklos, Brutsche, Martin, Baty, Florent, Bubendorf, Lukas, Hsu Schmitz, Shu-Fang, Na, Kyung-Jae, Carbone, David, Stahel, Rolf, and Smit, Egbert

Published
2012
Full Text
View/download PDF

42. Design of a switchable eliminase

Author

Korendovych, Ivan V., Kulp, Daniel W., Wu, Yibing, Cheng, Hong, Roder, Heinrich, DeGrado, William F., and Baker, David

Published
2011

Catalog

Books, media, physical & digital resources
See catalog results