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

Authors: Campbell, Thomas W., Roder, Heinrich, Georgantas III, Robert W., Roder, Joanna

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2112.10592

Folding of Staphylococcal Nuclease Induced by Binding of Chemically Modified Substrate Analogues Sheds Light on Mechanisms of Coupled Folding/Binding Reactions

Authors: Mori, Yujiro, Mizukami, Takuya, Segawa, Saho, Roder, Heinrich, Maki, Kosuke

Source: Biochemistry. 62(11):1670-1678

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632822430&indx=1&recIds=ETOCRN632822430

Molecular and translational biology of the blood-based VeriStrat® proteomic test used in cancer immunotherapy treatment guidance

Authors: Koc, Matthew A., Wiles, Timothy Aaron, Weinhold, Daniel C., Rightmyer, Steven, Weaver, Amanda L., McDowell, Colin T., Roder, Joanna, Asmellash, Senait, Pestano, Gary A., Roder, Heinrich, Georgantas III, Robert W.

Source: In Journal of Mass Spectrometry and Advances in the Clinical Lab November 2023 30:51-60

Effects of ionic strength on the folding and stability of SAMP1, a ubiquitin-like halophilic protein

Authors: Mizukami, Takuya, Bedford, John T., Liao, ShanHui, Greene, Lesley H., Roder, Heinrich

Source: Biophysical journal. 121(4):552-564

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100155652699.0x000001&indx=1&recIds=ETOCvdc_100155652699.0x000001

Exact Shapley values for local and model-true explanations of decision tree ensembles

Authors: Campbell, Thomas W., Roder, Heinrich, Georgantas III, Robert W., Roder, Joanna

Source: In Machine Learning with Applications 15 September 2022 9

Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach

Authors: Mizukami, Takuya, Furuzawa, Shunta, Itoh, Satoru G., Segawa, Saho, Ikura, Teikichi, Ihara, Kunio, Okumura, Hisashi, Roder, Heinrich, Maki, Kosuke

Source: Proceedings of the National Academy of Sciences of the United States of America, 2020 Aug . 117(33), 19953-19962.

Access URL: https://www.jstor.org/stable/26968592

Predicting prognosis in COVID-19 patients using machine learning and readily available clinical data

Authors: Campbell, Thomas W., Wilson, Melissa P., Roder, Heinrich, MaWhinney, Samantha, Georgantas, Robert W., III, Maguire, Laura K., Roder, Joanna, Erlandson, Kristine M.

Source: In International Journal of Medical Informatics November 2021 155

A proposal for score assignment to characterize biological processes from mass spectral analysis of serum

Authors: Roder, Joanna, Net, Lelia, Oliveira, Carlos, Meyer, Krista, Asmellash, Senait, Kasimir-Bauer, Sabine, Pass, Harvey, Weber, Jeffrey, Roder, Heinrich, Grigorieva, Julia

Source: In Clinical Mass Spectrometry November 2020 18:13-26

Application of protein set enrichment analysis to correlation of protein functional sets with mass spectral features and multivariate proteomic tests

Authors: Grigorieva, Julia, Asmellash, Senait, Oliveira, Carlos, Roder, Heinrich, Net, Lelia, Roder, Joanna

Source: In Clinical Mass Spectrometry January 2020 15:44-53

Conformational Changes in the Cytoplasmic Region of KIR3DL1 upon Interaction with SHP-2

Authors: Cheng, Hong, Schwell, Vered, Curtis, Brett R., Fazlieva, Ruzaliya, Roder, Heinrich, Campbell, Kerry S.

Source: In Structure 2 April 2019 27(4):639-650

Prognostic role of the VeriStrat test in first line patients with non-small cell lung cancer treated with platinum-based chemotherapy

Authors: Grossi, Francesco, Genova, Carlo, Rijavec, Erika, Barletta, Giulia, Biello, Federica, Dal Bello, Maria Giovanna, Meyer, Krista, Roder, Joanna, Roder, Heinrich, Grigorieva, Julia

Source: In Lung Cancer March 2018 117:64-69

Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities

Authors: Bai, Nan, Roder, Heinrich, Dickson, Alex, Karanicolas, John

Source: Scientific reports. 9(1):1-15

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100117621320.0x000001&indx=1&recIds=ETOCvdc_100117621320.0x000001

Proteomic test for anti-PD-1 checkpoint blockade treatment of metastatic melanoma with and without BRAF mutations

Authors: Ascierto, Paolo, Capone, Mariaelena, Grimaldi, Antonio, Mallardo, Domenico, Simeone, Ester, Madonna, Gabriele, Roder, Heinrich, Meyer, Krista, Asmellash, Senait, Oliveira, Carlos, Roder, Joanna, Grigorieva, Julia

Source: Journal for immunotherapy of cancer. 7(1):1-8

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190703956.0x000001&indx=1&recIds=ETOCvdc_100190703956.0x000001

A dropout-regularized classifier development approach optimized for precision medicine test discovery from omics data

Authors: Roder, Joanna, Oliveira, Carlos, Net, Lelia, Tsypin, Maxim, Linstid, Benjamin, Roder, Heinrich

Source: BMC bioinformatics. 20(1):1-14

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100188498556.0x000001&indx=1&recIds=ETOCvdc_100188498556.0x000001

Robust identification of molecular phenotypes using semi-supervised learning

Authors: Roder, Heinrich, Oliveira, Carlos, Net, Lelia, Linstid, Benjamin, Tsypin, Maxim, Roder, Joanna

Source: BMC bioinformatics. 20(1):1-25

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100188089797.0x000001&indx=1&recIds=ETOCvdc_100188089797.0x000001

Ultrarapid Mixing Experiments Shed New Light on the Characteristics of the Initial Conformational Ensemble during the Folding of Ribonuclease A

Authors: Welker, Ervin, Maki, Kosuke, Juminaga, Darmawi, Bhat, Rajiv, Scheraga, Harold A., Roder, Heinrich

Source: Proceedings of the National Academy of Sciences of the United States of America, 2004 Dec . 101(51), 17681-17686.

Access URL: https://www.jstor.org/stable/3374028

Ultrafast Folding of α 3 D: A de novo Designed Three-Helix Bundle Protein

Authors: Zhu, Yongjin, Maki, Kosuke, Huang, Cheng-Yen, Lahr, Steven J., Daggett, Valerie, Roder, Heinrich, DeGrado, William F., Gai, Feng

Source: Proceedings of the National Academy of Sciences of the United States of America, 2003 Dec . 100(26), 15486-15491.

Access URL: https://www.jstor.org/stable/3149032

NMR-Detected Hydrogen Exchange and Molecular Dynamics Simulations Provide Structural Insight into Fibril Formation of Prion Protein Fragment 106-126

Authors: Kuwata, Kazuo, Matumoto, Tomoharu, Cheng, Hong, Nagayama, Kuniaki, James, Thomas L., Roder, Heinrich

Source: Proceedings of the National Academy of Sciences of the United States of America, 2003 Dec 01. 100(25), 14790-14795.

Access URL: https://www.jstor.org/stable/3148513

Early Kinetic Intermediate in the Folding of Acyl-CoA Binding Protein Detected by Fluorescence Labeling and Ultrarapid Mixing

Authors: Teilum, Kaare, Maki, Kosuke, Kragelund, Birthe B., Poulsen, Flemming M., Roder, Heinrich

Source: Proceedings of the National Academy of Sciences of the United States of America, 2002 Jul . 99(15), 9807-9812.

Access URL: https://www.jstor.org/stable/3059290

Advances in Mixer Design and Detection Methods for Kinetics Studies of Macromolecular Folding and Binding on the Microsecond Time Scale.

Authors: Mizukami, Takuya¹ (AUTHOR) Takuya.Mizukami@fccc.edu, Roder, Heinrich¹ (AUTHOR) Heinrich.Roder@fccc.edu

Source: Molecules. Jun2022, Vol. 27 Issue 11, p3392-3392. 15p.

Subject Terms: *SOLID-state lasers, *LIGAND binding (Biochemistry), *ULTRAVIOLET lasers, *PROTEIN folding, *TRYPTOPHAN, *LASER-induced fluorescence, *CHANNEL flow, *CYTOCHROME c