cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2558451
title: netDx: Interpretable patient classification using integrated patient similarity networks

description: Docker image containing installed netDx software in Ubuntu to reproduce examples from the published manuscript. The R implementation of netDx is hosted at: https://github.com/BaderLab/netDx

---<br>
Publication abstract: Patient classification has widespread biomedical and clinical applications, including diagnosis, prognosis and treatment response prediction. A clinically useful prediction algorithm should be accurate, generalizable, be able to integrate diverse data types, and handle sparse data. A clinical predictor based on genomic data needs to be easily interpretable to drive hypothesis-driven research into new treatments. We describe netDx, a novel supervised patient classification framework based on patient similarity networks. netDx meets the above criteria and particularly excels at data integration and model interpretability. We compared classification performance of this method against other machine-learning algorithms, using a cancer survival benchmark with four cancer types, each requiring integration of up to six genomic and clinical data types. In these tests, netDx has significantly higher average performance than most other machine-learning approaches across most cancer types. In comparison to traditional machine learning-based patient classifiers, netDx results are more interpretable, visualizing the decision boundary in the context of patient similarity space. When patient similarity is defined by pathway-level gene expression, netDx identifies biological pathways important for outcome prediction, as demonstrated in diverse data sets of breast cancer and asthma. Thus, netDx can serve both as a patient classifier and as a tool for discovery of biological features characteristic of disease. We provide a freely available software implementation of netDx along with sample files and automation workflows in R.
DOI: 10.5281/zenodo.2558452
title: netDx: Interpretable patient classification using integrated patient similarity networks

description: Docker image containing installed netDx software in Ubuntu to reproduce examples from the published manuscript. The R implementation of netDx is hosted at: https://github.com/BaderLab/netDx

---<br>
Publication abstract: Patient classification has widespread biomedical and clinical applications, including diagnosis, prognosis and treatment response prediction. A clinically useful prediction algorithm should be accurate, generalizable, be able to integrate diverse data types, and handle sparse data. A clinical predictor based on genomic data needs to be easily interpretable to drive hypothesis-driven research into new treatments. We describe netDx, a novel supervised patient classification framework based on patient similarity networks. netDx meets the above criteria and particularly excels at data integration and model interpretability. We compared classification performance of this method against other machine-learning algorithms, using a cancer survival benchmark with four cancer types, each requiring integration of up to six genomic and clinical data types. In these tests, netDx has significantly higher average performance than most other machine-learning approaches across most cancer types. In comparison to traditional machine learning-based patient classifiers, netDx results are more interpretable, visualizing the decision boundary in the context of patient similarity space. When patient similarity is defined by pathway-level gene expression, netDx identifies biological pathways important for outcome prediction, as demonstrated in diverse data sets of breast cancer and asthma. Thus, netDx can serve both as a patient classifier and as a tool for discovery of biological features characteristic of disease. We provide a freely available software implementation of netDx along with sample files and automation workflows in R.
DOI: 10.14469/hpc/5021
title: sdfasdfsdaf23

description: sdfsdfsdf33
DOI: 10.5517/ccdc.csd.cc213v89
title: CCDC 1880530: Experimental Crystal Structure Determination

description: Related Article: Gabriele Pupo,  Anna Chiara Vicini,  David M. H. Ascough,  Francesco Ibba,  Kirsten E. Christensen,  Amber L. Thompson,  John M. Brown,  Robert S. Paton,  Véronique Gouverneur|2019|J.Am.Chem.Soc.|141|2878|doi:10.1021/jacs.8b12568
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc214d0m
title: CCDC 1881049: Experimental Crystal Structure Determination

description: Related Article: Varvara V. Avdeeva, Irina N. Polyakova, Andrei V. Churakov, Anna V. Vologzhanina, Elena A. Malinina, Konstantin Yu. Zhizhin, Nikolay T. Kuznetsov|2019|Polyhedron|162|65|doi:10.1016/j.poly.2019.01.051
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21554k
title: CCDC 1881797: Experimental Crystal Structure Determination

description: Related Article: Malose J. Mphahlele, Mmakwena M. Mmonwa|2019|Org.Biomol.Chem.|17|2204|doi:10.1039/C8OB03040E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.14469/hpc/5022
title: sdfsdf

description: sdfsdfsdf
DOI: 10.5281/zenodo.2556798
title: Single-molecule source data files

description: This data archive contains single-molecule source data for "A Conserved Mcm4 Motif is Required for Mcm2-7 Double-hexamer Formation and Origin DNA Unwinding" by Kanokwan Champasa, Caitlin Blank, Larry J. Friedman, Jeff Gelles, and Stephen P. Bell.

The data archive (doi: 10.5281/zenodo.2556799) provides files for figure 5 and 6.  The ‘intervals’ files are readable by the imscroll program (https://github.com/gelles-brandeis/CoSMoS_Analysis).
DOI: 10.5281/zenodo.2556799
title: Single-molecule source data files

description: This data archive contains single-molecule source data for "A Conserved Mcm4 Motif is Required for Mcm2-7 Double-hexamer Formation and Origin DNA Unwinding" by Kanokwan Champasa, Caitlin Blank, Larry J. Friedman, Jeff Gelles, and Stephen P. Bell.

The data archive (doi: 10.5281/zenodo.2556799) provides files for figure 5 and 6.  The ‘intervals’ files are readable by the imscroll program (https://github.com/gelles-brandeis/CoSMoS_Analysis).
DOI: 10.5517/ccdc.csd.cc216mws
title: CCDC 1883215: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216mxt
title: CCDC 1883216: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216myv
title: CCDC 1883217: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216mzw
title: CCDC 1883218: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216n0y
title: CCDC 1883219: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216pfd
title: CCDC 1883263: Experimental Crystal Structure Determination

description: Related Article: Salvador Pérez-Estrada,  Braulio Rodríguez-Molina,  Emily F. Maverick,  Saeed I. Khan,  Miguel A. Garcia-Garibay|2019|J.Am.Chem.Soc.|141|2413|doi:10.1021/jacs.8b11385
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6073/pasta/c00351dec9298c02de9f100e2f25dec0
title: BGPVC Plant species composition in the Belowground Plot Experiment at Konza Prairie

description: Two permanent plant composition plots were marked with conduit in each of the 64 plots. Canopy cover was recorded in a 5 m2circular area surrounding each of the plots.Â  At approximately 5-year intervals, coverage is assessed in late July, using visual estimates of cover by species, based on a modified Daubenmire scale. NOTE:In 1989, sampling was done once in early July after mowing using one 10 m2 plot placed randomly in the approximate center of each plot. In 1994, plant composition sampling was done in early June in the unmowed plots; sampling in the mowed plots occurred in August. In 1999, two permanent conduits were placed in each plot, and sampling was conducted in June, before mowing, and again in August using 5 m2 plot sizes. In 2005 and afterward, sampling was reduced to one time in late July. Sampling occurred once every five years until 2015. Plots have been sampled annually since 2016.
DOI: 10.14469/hpc/5018
title: wrewrwer

description: werwerw
DOI: 10.14469/hpc/5019
title: sdfsdfsdfsdfsdfsfsdfsdf

description: fdfdffsf
DOI: 10.5517/ccdc.csd.cc216n1z
title: CCDC 1883220: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216n20
title: CCDC 1883221: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc216n31
title: CCDC 1883222: Experimental Crystal Structure Determination

description: Related Article: Madhusudan K. Pandey, Harish S. Kunchur, Guddekoppa S. Ananthnag, Joel T. Mague, Maravanji S. Balakrishna|2019|Dalton Trans.|48|3610|doi:10.1039/C8DT04819C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2175j0
title: CCDC 1883731: Experimental Crystal Structure Determination

description: Related Article: Yong-Li Li, Li-Jun Xue, Jie Li, Li-Ming Chen, Jian-Jun Wu, Zhuo-Ni Xu, Ying Chen, Yu-Ping Tian, Xian-Wen Yang|2019|Org.Biomol.Chem.|17|2107|doi:10.1039/C8OB03117G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc217rnq
title: CCDC 1884293: Experimental Crystal Structure Determination

description: Related Article: Lingru Gao, Jun Ni, Mengmeng Su, Jiajia Kang, Juanjun Zhang|2019|Dyes Pigm.|165|231|doi:10.1016/j.dyepig.2019.02.004
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc217rvx
title: CCDC 1884299: Experimental Crystal Structure Determination

description: Related Article: Lingru Gao, Jun Ni, Mengmeng Su, Jiajia Kang, Juanjun Zhang|2019|Dyes Pigm.|165|231|doi:10.1016/j.dyepig.2019.02.004
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc217s03
title: CCDC 1884304: Experimental Crystal Structure Determination

description: Related Article: Lingru Gao, Jun Ni, Mengmeng Su, Jiajia Kang, Juanjun Zhang|2019|Dyes Pigm.|165|231|doi:10.1016/j.dyepig.2019.02.004
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc217s14
title: CCDC 1884305: Experimental Crystal Structure Determination

description: Related Article: Lingru Gao, Jun Ni, Mengmeng Su, Jiajia Kang, Juanjun Zhang|2019|Dyes Pigm.|165|231|doi:10.1016/j.dyepig.2019.02.004
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc217vbh
title: CCDC 1884376: Experimental Crystal Structure Determination

description: Related Article: Natalia A. Protasenko, Andrey I. Poddel'sky, Artem S. Bogomyakov, Andrey G. Starikov, Ivan V. Smolyaninov, Nadezhda T. Berberova, Georgy K. Fukin, Vladimir K. Cherkasov|2019|Inorg.Chim.Acta|489|1|doi:10.1016/j.ica.2019.02.002
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21821g
title: CCDC 1884584: Experimental Crystal Structure Determination

description: Related Article: Michelle Montgomery, Harry M. O'Brien, Carolina Méndez-Gálvez, Caitlin R. Bromfield, Jack P. M. Roberts, Anna M. Winnicka, Andrew Horner, David Elorriaga, Hazel A. Sparkes, Robin B. Bedford|2019|Dalton Trans.|48|3539|doi:10.1039/C8DT04926B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21822h
title: CCDC 1884585: Experimental Crystal Structure Determination

description: Related Article: Michelle Montgomery, Harry M. O'Brien, Carolina Méndez-Gálvez, Caitlin R. Bromfield, Jack P. M. Roberts, Anna M. Winnicka, Andrew Horner, David Elorriaga, Hazel A. Sparkes, Robin B. Bedford|2019|Dalton Trans.|48|3539|doi:10.1039/C8DT04926B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21823j
title: CCDC 1884586: Experimental Crystal Structure Determination

description: Related Article: Michelle Montgomery, Harry M. O'Brien, Carolina Méndez-Gálvez, Caitlin R. Bromfield, Jack P. M. Roberts, Anna M. Winnicka, Andrew Horner, David Elorriaga, Hazel A. Sparkes, Robin B. Bedford|2019|Dalton Trans.|48|3539|doi:10.1039/C8DT04926B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21824k
title: CCDC 1884587: Experimental Crystal Structure Determination

description: Related Article: Michelle Montgomery, Harry M. O'Brien, Carolina Méndez-Gálvez, Caitlin R. Bromfield, Jack P. M. Roberts, Anna M. Winnicka, Andrew Horner, David Elorriaga, Hazel A. Sparkes, Robin B. Bedford|2019|Dalton Trans.|48|3539|doi:10.1039/C8DT04926B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2184fx
title: CCDC 1884658: Experimental Crystal Structure Determination

description: Related Article: osé Antônio do Nascimento Neto,  Ana Karoline Silva Mendanha Valdo,  Cameron Capeletti da Silva,  Freddy Fernandes Guimarães,  Luiz Henrique Keng Queiroz Júnior,  Lauro June Queiroz Maia,  Ricardo Costa de Santana,  Felipe Terra Martins|2019|J.Am.Chem.Soc.|141|3400|doi:10.1021/jacs.8b13561
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21919q
title: CCDC 1885522: Experimental Crystal Structure Determination

description: Related Article: Salvador Pérez-Estrada,  Braulio Rodríguez-Molina,  Emily F. Maverick,  Saeed I. Khan,  Miguel A. Garcia-Garibay|2019|J.Am.Chem.Soc.|141|2413|doi:10.1021/jacs.8b11385
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc21970m
title: CCDC 1885699: Experimental Crystal Structure Determination

description: Related Article: Sam Greatorex, Kevin B. Vincent, Amgalanbaatar Baldansuren, Eric J. L. McInnes, Nathan J. Patmore, Stephen Sproules, Malcolm A. Halcrow|2019|Chem.Commun.|55|2281|doi:10.1039/C8CC10122A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc219w7h
title: CCDC 1886326: Experimental Crystal Structure Determination

description: Related Article: Michelle A. Kroc, Maciej Markiewicz, Wiktoria H. Pace, Donald J. Wink, Laura L. Anderson|2019|Chem.Commun.|55|2309|doi:10.1039/C8CC10313E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.