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Table of Contents (PDF) Cancer Research Table of Contents November 1, 2017 Volume 77 Number 21 SPECIAL FEATURES e23 A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration FOCUS ON COMPUTER RESOURCES of Molecular Profiling Data Complimentary access to these online-only articles Bradley M. Broom, Michael C. Ryan, Robert E. Brown, describing freely available computing tools and resources: Futa Ikeda, Mark Stucky, David W. Kane, James Melott, cancerres.aacrjournals.org/compres Chris Wakefield, Tod D. Casasent, Rehan Akbani, and John N. Weinstein e1 Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research e27 Integrating DNA Methylation and Hydroxymethyl- Warren Kibbe, Juli Klemm, and John Quackenbush ation Data with the Mint Pipeline Raymond G. Cavalcante, Snehal Patil, Yongseok Park, e3 The Cancer Genomics Cloud: Collaborative, Laura S. Rozek, and Maureen A. Sartor Reproducible, and Democratized—A New Para- digm in Large-Scale Computational e31 Variant Review with the Integrative Genomics Research Viewer Jessica W. Lau, Erik Lehnert, Anurag Sethi, James T. Robinson, Helga Thorvaldsdóttir, Raunaq Malhotra, Gaurav Kaushik, Zeynep Onder, Aaron M. Wenger, Ahmet Zehir, and Jill P. Mesirov Nick Groves-Kirkby, Aleksandar Mihajlovic, Jack DiGiovanna, Mladen Srdic, Dragan Bajcic, e35 CRAVAT 4: Cancer-Related Analysis of Jelena Radenkovic, Vladimir Mladenovic, Variants Toolkit Damir Krstanovic, Vladan Arsenijevic, Djordje Klisic, David L. Masica, Christopher Douville, Collin Tokheim, Milan Mitrovic, Igor Bogicevic, Deniz Kural, and Rohit Bhattacharya, RyangGuk Kim, Kyle Moad, Brandi Davis-Dusenbery; for The Seven Bridges CGC Team Michael C. Ryan, and Rachel Karchin e7 The ISB Cancer Genomics Cloud: A Flexible e39 Software for the Integration of Multiomics Cloud-Based Platform for Cancer Genomics Experiments in Bioconductor Research Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Sheila M. Reynolds, Michael Miller, Phyliss Lee, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Kalle Leinonen, Suzanne M. Paquette, Zack Rodebaugh, Phil Chapman, Sean R. Davis, David Gomez-Cabrero, Abigail Hahn, David L. Gibbs, Joseph Slagel, Aedin C. Culhane, Benjamin Haibe-Kains, William J. Longabaugh, Varsha Dhankani, Madelyn Reyes, Kasper D. Hansen, Hanish Kodali, Marie S. Louis, Todd Pihl, Mark Backus, Matthew Bookman, Arvind S. Mer, Markus Riester, Martin Morgan, Vince Carey, Nicole Deflaux, Jonathan Bingham, David Pot, and and Levi Waldron Ilya Shmulevich e43 An Accessible Proteogenomics Informatics e11 WebMeV: A Cloud Platform for Analyzing and Resource for Cancer Researchers Visualizing Cancer Genomic Data Matthew C. Chambers, Pratik D. Jagtap, James E. Johnson, Yaoyu E. Wang, Lev Kutnetsov, Antony Partensky, Thomas McGowan, Praveen Kumar, Getiria Onsongo, Jalil Farid, and John Quackenbush Candace R. Guerrero, Harald Barsnes, Marc Vaudel, Lennart Martens, Bjorn€ Gruning,€ Ira R. Cooke, e15 Developing Cancer Informatics Applications and Mohammad Heydarian, Karen L. Reddy, and Tools Using the NCI Genomic Data Commons Timothy J. Griffin API Shane Wilson, Michael Fitzsimons, Martin Ferguson, e47 P-MartCancer–Interactive Online Software to Allison Heath, Mark Jensen, Josh Miller, Enable Analysis of Shotgun Cancer Proteomic Mark W. Murphy, James Porter, Himanso Sahni, Datasets Louis Staudt, Yajing Tang, Zhining Wang, Christine Yu, Bobbie-Jo M. Webb-Robertson, Lisa M. Bramer, Junjun Zhang, Vincent Ferretti, and Robert L. Grossman Jeffrey L. Jensen, Markus A. Kobold, Kelly G. Stratton, for the GDC Project Amanda M. White, and Karin D. Rodland e19 Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer e51 Explore, Visualize, and Analyze Functional Cancer Shenglin Mei, Clifford A. Meyer, Rongbin Zheng, Proteomic Data Using the Cancer Proteome Atlas Qian Qin, Qiu Wu, Peng Jiang, Bo Li, Xiaohui Shi, Jun Li, Rehan Akbani, Wei Zhao, Yiling Lu, Binbin Wang, Jingyu Fan, Celina Shih, Myles Brown, John N. Weinstein, Gordon B. Mills, and Han Liang Chongzhi Zang, and X. Shirley Liu v Downloaded from cancerres.aacrjournals.org on September 30, 2021. © 2017 American Association for Cancer Research. Table of Contents e55 DINC 2.0: A New Protein–Peptide Docking e83 An Image Analysis Resource for Cancer Research: Webserver Using an Incremental Approach PIIP—Pathology Image Informatics Platform for Dinler A. Antunes, Mark Moll, Didier Devaurs, Visualization, Analysis, and Management Kyle R. Jackson, Gregory Lizee, and Lydia E. Kavraki Anne L. Martel, Dan Hosseinzadeh, Caglar Senaras, Yu Zhou, Azadeh Yazdanpanah, Rushin Shojaii, e58 NDEx 2.0: A Clearinghouse for Research on Emily S. Patterson, Anant Madabhushi, and Cancer Pathways Metin N. Gurcan Dexter Pratt, Jing Chen, Rudolf Pillich, Vladimir Rynkov, Aaron Gary, Barry Demchak, and Trey Ideker e87 dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis e62 PDX-MI: Minimal Information for Patient- Results Using DICOM Derived Tumor Xenograft Models Christian Herz, Jean-Christophe Fillion-Robin, Terrence F. Meehan, Nathalie Conte, Theodore Goldstein, Michael Onken, Jorg€ Riesmeier, Andras Lasso, Giorgio Inghirami, Mark A. Murakami, Sebastian Brabetz, Csaba Pinter, Gabor Fichtinger, Steve Pieper, Zhiping Gu, Jeffrey A. Wiser, Patrick Dunn, Dale A. Begley, David Clunie, Ron Kikinis, and Andriy Fedorov Debra M. Krupke, Andrea Bertotti, Alejandra Bruna, Matthew H. Brush, Annette T. Byrne, Carlos Caldas, e91 Integrative Analysis of Histopathological Images Amanda L. Christie, Dominic A. Clark, Heidi Dowst, and Genomic Data Predicts Clear Cell Renal Jonathan R. Dry, James H. Doroshow, Olivier Duchamp, Cell Carcinoma Prognosis Yvonne A. Evrard, Stephane Ferretti, Kristopher K. Frese, Jun Cheng, Jie Zhang, Yatong Han, Xusheng Wang, Neal C. Goodwin, Danielle Greenawalt, Xiufen Ye, Yuebo Meng, Anil Parwani, Zhi Han, Melissa A. Haendel, Els Hermans, Peter J. Houghton, Qianjin Feng, and Kun Huang Jos Jonkers, Kristel Kemper, Tin O. Khor, Michael T. Lewis, K.C. Kent Lloyd, Jeremy Mason, Enzo Medico, e101 SlicerDMRI: Open Source Diffusion MRI Steven B. Neuhauser, James M. Olson, Daniel S. Peeper, Software for Brain Cancer Research Oscar M. Rueda, Je Kyung Seong, Livio Trusolino, Isaiah Norton, Walid Ibn Essayed, Fan Zhang, Emilie Vinolo, Robert J. Wechsler-Reya, Sonia Pujol, Alex Yarmarkovich, Alexandra J. Golby, David M. Weinstock, Alana Welm, S. John Weroha, Gordon Kindlmann, Demian Wasserman, Frederic Amant, Stefan M. Pfister, Marcel Kool, Raul San Jose Estepar, Yogesh Rathi, Steve Pieper, Helen Parkinson, Atul J. Butte, and Carol J. Bult Ron Kikinis, Hans J. Johnson, Carl-Fredrik Westin, and Lauren J. O'Donnell e67 The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models e104 Computational Radiomics System to Decode the of Human Cancer Radiographic Phenotype Debra M. Krupke, Dale A. Begley, John P. Sundberg, Joost J.M. van Griethuysen, Andriy Fedorov, Joel E. Richardson, Steven B. Neuhauser, and Carol J. Bult Chintan Parmar, Ahmed Hosny, Nicole Aucoin, Vivek Narayan, Regina G.H. Beets-Tan, e71 Platform for Quantitative Evaluation of Spatial Jean-Christophe Fillion-Robin, Steve Pieper, and Intratumoral Heterogeneity in Multiplexed Hugo J.W.L. Aerts Fluorescence Images Daniel M. Spagnolo, Yousef Al-Kofahi, Peihong Zhu, e108 TIMER: A Web Server for Comprehensive Ana- Timothy R. Lezon, Albert Gough, Andrew M. Stern, lysis of Tumor-Infiltrating Immune Cells Adrian V. Lee, Fiona Ginty, Brion Sarachan, Taiwen Li, Jingyu Fan, Binbin Wang, Nicole Traugh, D. Lansing Taylor, and S. Chakra Chennubhotla Qianming Chen, Jun S. Liu, Bo Li, and X. Shirley Liu e75 The Digital Slide Archive: A Software Platform e111 TumorMap: Exploring the Molecular Similarities for Management, Integration, and Analysis of of Cancer Samples in an Interactive Portal Histology for Cancer Research Yulia Newton, Adam M. Novak, Teresa Swatloski, David A. Gutman, Mohammed Khalilia, Sanghoon Lee, Duncan C. McColl, Sahil Chopra, Kiley Graim, Michael Nalisnik, Zach Mullen, Jonathan Beezley, Alana S. Weinstein, Robert Baertsch, Sofie R. Salama, Deepak R. Chittajallu, David Manthey, and Kyle Ellrott, Manu Chopra, Theodore C. Goldstein, Lee A.D. Cooper David Haussler, Olena Morozova, and Joshua M. Stuart e79 A Containerized Software System for Generation, e115 DeepPhe: A Natural Language Processing Management, and Exploration of Features from System for Extracting Cancer Phenotypes from Whole Slide Tissue Images Clinical Records Joel Saltz, Ashish Sharma, Ganesh Iyer, Erich Bremer, Guergana K. Savova, Eugene Tseytlin, Sean Finan, Feiqiao Wang, Alina Jasniewski, Tammy DiPrima, Melissa Castine, Timothy Miller, Olga Medvedeva, Jonas S. Almeida, Yi Gao, Tianhao Zhao, Mary Saltz, and David Harris, Harry Hochheiser, Chen Lin, Tahsin Kurc Girish Chavan, and Rebecca S. Jacobson vi Downloaded from cancerres.aacrjournals.org on September 30, 2021. © 2017 American Association for Cancer Research. Table of Contents e119 LesionTracker: Extensible Open-Source PRIORITY REPORT Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials 5721 Discovery of Human-Similar Gene Fusions in Trinity Urban, Erik Ziegler, Rob Lewis, Chris Hafey, Canine Cancers Cheryl Sadow, Annick D. Van den Abbeele, and Ronan Ulve, Melanie Rault, Mathieu Bahin, Gordon J. Harris Laetitia Lagoutte, Jerôme Abadie, Clotilde De Brito, Jean-Michel Coindre, Nadine Botherel, Audrey Rousseau, e123 ''Personalized Cancer Therapy'': A Publicly Valentin Wucher, Edouard Cadieu, Available Precision Oncology
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