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Vincent, Benjamin G., Joseph D. Szustakowski, Parul Doshi, Michael Mason, Justin Guinney, and David P. Carbone. “Pursuing Better Biomarkers for Immunotherapy Response in Cancer Through a Crowdsourced Data Challenge.” JCO Precision Oncology, no. 5 (January 1, 2021): 51–54. https://doi.org/10.1200/PO.20.00371.
Coquet, Jean, Nicolas Bievre, Vincent Billaut, Martin Seneviratne, Christopher J. Magnani, Selen Bozkurt, James D. Brooks, and Tina Hernandez-Boussard. “Assessment of a Clinical Trial-Derived Survival Model in Patients With Metastatic Castration-Resistant Prostate Cancer.” JAMA Network Open 4, no. 1 (January 4, 2021): e2031730. https://doi.org/10.1001/jamanetworkopen.2020.31730. Download
Bergquist, Timothy, Thomas Schaffter, Yao Yan, Thomas Yu, Justin Prosser, Jifan Gao, Guanhua Chen, et al. “Evaluation of Crowdsourced Mortality Prediction Models as a Framework for Assessing AI in Medicine.” MedRxiv, January 20, 2021, 2021.01.18.21250072. https://doi.org/10.1101/2021.01.18.21250072. Download
Chen, Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler, and Jianlin Cheng. “DeepGRN: Prediction of Transcription Factor Binding Site across Cell-Types Using Attention-Based Deep Neural Networks.” BMC Bioinformatics 22, no. 1 (February 1, 2021): 38. https://doi.org/10.1186/s12859-020-03952-1. Download
Xiong, Zhaoping, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, et al. “Crowdsourced Identification of Multi-Target Kinase Inhibitors for RET- and TAU- Based Disease: The Multi-Targeting Drug DREAM Challenge.” BioRxiv, February 17, 2021, 2021.02.15.430538. https://doi.org/10.1101/2021.02.15.430538. Download
Xiong, Zhaoping, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, et al. “Crowdsourced Identification of Multi-Target Kinase Inhibitors for RET- and TAU-Based Disease: The Multi-Targeting Drug DREAM Challenge.” BioRxiv, February 17, 2021, 2021.02.15.430538. https://doi.org/10.1101/2021.02.15.430538. Download
Shang, Junliang, Jing Wang, Yan Sun, Feng Li, Jin-Xing Liu, and Honghai Zhang. “Multiscale Part Mutual Information for Quantifying Nonlinear Direct Associations in Networks.” Bioinformatics (Oxford, England), March 17, 2021. https://doi.org/10.1093/bioinformatics/btab182.
Roy, Subhrajit, Isabell Kiral, Mahtab Mirmomeni, Todd Mummert, Alan Braz, Jason Tsay, Jianbin Tang, et al. “Evaluation of Artificial Intelligence Systems for Assisting Neurologists with Fast and Accurate Annotations of Scalp Electroencephalography Data.” EBioMedicine, March 18, 2021, 103275. https://doi.org/10.1016/j.ebiom.2021.103275.
Sieberts, Solveig K., Jennifer Schaff, Marlena Duda, Bálint Ármin Pataki, Ming Sun, Phil Snyder, Jean-Francois Daneault, et al. “Crowdsourcing Digital Health Measures to Predict Parkinson’s Disease Severity: The Parkinson’s Disease Digital Biomarker DREAM Challenge.” NPJ Digital Medicine 4, no. 1 (March 19, 2021): 53. https://doi.org/10.1038/s41746-021-00414-7.
Gabor, Attila, Marco Tognetti, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, et al. “Cell-to-Cell and Type-to-Type Heterogeneity of Signaling Networks: Insights from the Crowd.” BioRxiv, March 23, 2021, 2021.03.23.436603. https://doi.org/10.1101/2021.03.23.436603. Download
Ma, Weiping, Sunkyu Kim, Shrabanti Chowdhury, Zhi Li, Mi Yang, Seungyeul Yoo, Francesca Petralia, et al. “DreamAI: Algorithm for the Imputation of Proteomics Data.” BioRxiv, May 19, 2021, 2020.07.21.214205. https://doi.org/10.1101/2020.07.21.214205. Download
Cichońska, Anna, Balaguru Ravikumar, Robert J. Allaway, Fangping Wan, Sungjoon Park, Olexandr Isayev, Shuya Li, et al. “Crowdsourced Mapping of Unexplored Target Space of Kinase Inhibitors.” Nature Communications 12, no. 1 (June 3, 2021): 3307. https://doi.org/10.1038/s41467-021-23165-1. Download
Tarca, Adi L., Bálint Ármin Pataki, Roberto Romero, Marina Sirota, Yuanfang Guan, Rintu Kutum, Nardhy Gomez-Lopez, et al. “Crowdsourcing Assessment of Maternal Blood Multi-Omics for Predicting Gestational Age and Preterm Birth.” BioRxiv, June 6, 2020, 2020.06.05.130971. https://doi.org/10.1101/2020.06.05.130971. Download Download
Carpenter, Kristy, Alexander Pilozzi, and Xudong Huang. “A Pilot Study of Multi-Input Recurrent Neural Networks for Drug-Kinase Binding Prediction.” Molecules (Basel, Switzerland) 25, no. 15 (July 24, 2020). https://doi.org/10.3390/molecules25153372. Download
Mason, Mike J., Carolina Schinke, Christine L. P. Eng, Fadi Towfic, Fred Gruber, Andrew Dervan, Brian S. White, et al. “Multiple Myeloma DREAM Challenge Reveals Epigenetic Regulator PHF19 as Marker of Aggressive Disease.” Leukemia 34, no. 7 (2020): 1866–74. https://doi.org/10.1038/s41375-020-0742-z. Download Download
Pham, Vu VH, Xiaomei Li, Buu Truong, Thin Nguyen, Lin Liu, Jiuyong Li, and Thuc D. Le. “The Winning Methods for Predicting Cellular Position in the DREAM Single Cell Transcriptomics Challenge.” BioRxiv, May 10, 2020, 2020.05.09.086397. https://doi.org/10.1101/2020.05.09.086397. Download
Douglass, Eugene F., Robert J. Allaway, Bence Szalai, Wenyu Wang, Tingzhong Tian, Adrià Fernández-Torras, Ron Realubit, et al. “A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data.” BioRxiv, December 23, 2020, 2020.12.21.423514. https://doi.org/10.1101/2020.12.21.423514. Download
Sieberts, Solveig K., Jennifer Schaff, Marlena Duda, Bálint Ármin Pataki, Ming Sun, Phil Snyder, Jean-Francois Daneault, et al. “Crowdsourcing Digital Health Measures to Predict Parkinson’s Disease Severity: The Parkinson’s Disease Digital Biomarker DREAM Challenge.” BioRxiv, February 20, 2020, 2020.01.13.904722. https://doi.org/10.1101/2020.01.13.904722. Download
Cichonska, Anna, Balaguru Ravikumar, Robert J. Allaway, Sungjoon Park, Fangping Wan, Olexandr Isayev, Shuya Li, et al. “Crowdsourced Mapping Extends the Target Space of Kinase Inhibitors.” BioRxiv, February 11, 2020, 2019.12.31.891812. https://doi.org/10.1101/2019.12.31.891812. Download
Salcedo, Adriana, Maxime Tarabichi, Shadrielle Melijah G. Espiritu, Amit G. Deshwar, Matei David, Nathan M. Wilson, Stefan Dentro, et al. “A Community Effort to Create Standards for Evaluating Tumor Subclonal Reconstruction.” Nature Biotechnology 38, no. 1 (2020): 97–107. https://doi.org/10.1038/s41587-019-0364-z. Download
Yang, Mi, Francesca Petralia, Zhi Li, Hongyang Li, Weiping Ma, Xiaoyu Song, Sunkyu Kim, et al. “Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics.” Cell Systems 11, no. 2 (August 26, 2020): 186-195.e9. https://doi.org/10.1016/j.cels.2020.06.013. Download
Tanevski, Jovan, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, et al. “Gene Selection for Optimal Prediction of Cell Position in Tissues from Single-Cell Transcriptomics Data.” Life Science Alliance 3, no. 11 (November 2020). https://doi.org/10.26508/lsa.202000867. Download
Schaffter, Thomas, Diana S. M. Buist, Christoph I. Lee, Yaroslav Nikulin, Dezso Ribli, Yuanfang Guan, William Lotter, et al. “Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms.” JAMA Network Open 3, no. 3 (02 2020): e200265. https://doi.org/10.1001/jamanetworkopen.2020.0265. Download
Ellrott, Kyle, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, et al. “Reproducible Biomedical Benchmarking in the Cloud: Lessons from Crowd-Sourced Data Challenges.” Genome Biology 20, no. 1 (10 2019): 195. https://doi.org/10.1186/s13059-019-1794-0. Download
Kueffner, Robert, Neta Zach, Maya Bronfeld, Raquel Norel, Nazem Atassi, Venkat Balagurusamy, Barbara Di Camillo, et al. “Stratification of Amyotrophic Lateral Sclerosis Patients: A Crowdsourcing Approach.” Scientific Reports 9, no. 1 (24 2019): 690. https://doi.org/10.1038/s41598-018-36873-4. Download
Menden, Michael P., Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, et al. “Community Assessment to Advance Computational Prediction of Cancer Drug Combinations in a Pharmacogenomic Screen.” Nature Communications 10, no. 1 (17 2019): 2674. https://doi.org/10.1038/s41467-019-09799-2. Download
Choobdar, Sarvenaz, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, et al. “Assessment of Network Module Identification across Complex Diseases.” Nature Methods 16, no. 9 (2019): 843–52. https://doi.org/10.1038/s41592-019-0509-5. Download
Davis, Sage, Katrina Button-Simons, Taoufik Bensellak, Eren Mehmet Ahsen, Lisa Checkley, Gabriel J. Foster, Xinzhuan Su, et al. “Leveraging Crowdsourcing to Accelerate Global Health Solutions.” Nature Biotechnology 37, no. 8 (2019): 848–50. https://doi.org/10.1038/s41587-019-0180-5. Download
Lee, Anna Y., Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, et al. “Combining Accurate Tumor Genome Simulation with Crowdsourcing to Benchmark Somatic Structural Variant Detection.” Genome Biology 19, no. 1 (06 2018): 188. https://doi.org/10.1186/s13059-018-1539-5. Download
Razzaq, Misbah, Loïc Paulevé, Anne Siegel, Julio Saez-Rodriguez, Jérémie Bourdon, and Carito Guziolowski. “Computational Discovery of Dynamic Cell Line Specific Boolean Networks from Multiplex Time-Course Data.” PLoS Computational Biology 14, no. 10 (2018): e1006538. https://doi.org/10.1371/journal.pcbi.1006538. Download
Sendorek, Dorota H., Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, et al. “Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection.” BMC Bioinformatics 19, no. 1 (31 2018): 28. https://doi.org/10.1186/s12859-018-2046-0. Download
Gönen, Mehmet, Barbara A. Weir, Glenn S. Cowley, Francisca Vazquez, Yuanfang Guan, Alok Jaiswal, Masayuki Karasuyama, et al. “A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.” Cell Systems 5, no. 5 (22 2017): 485-497.e3. https://doi.org/10.1016/j.cels.2017.09.004. Download
Henriques, David, Alejandro F. Villaverde, Miguel Rocha, Julio Saez-Rodriguez, and Julio R. Banga. “Data-Driven Reverse Engineering of Signaling Pathways Using Ensembles of Dynamic Models.” PLoS Computational Biology 13, no. 2 (2017): e1005379. https://doi.org/10.1371/journal.pcbi.1005379. Download
Laajala, Teemu D., Justin Guinney, and James C. Costello. “Community Mining of Open Clinical Trial Data.” Oncotarget 8, no. 47 (October 10, 2017): 81721–22. https://doi.org/10.18632/oncotarget.20853. Download
Azencott, Chloé-Agathe, Tero Aittokallio, Sushmita Roy, Thea Norman, Stephen Friend, Gustavo Stolovitzky, and Anna Goldenberg. “The Inconvenience of Data of Convenience: Computational Research beyond Post-Mortem Analyses.” Nature Methods 14, no. 10 (2017): 937–938. Download
Guinney, Justin, Tao Wang, Teemu D. Laajala, Kimberly Kanigel Winner, J. Christopher Bare, Elias Chaibub Neto, Suleiman A. Khan, Gopal Peddinti, Antti Airola, and Tapio Pahikkala. “Prediction of Overall Survival for Patients with Metastatic Castration-Resistant Prostate Cancer: Development of a Prognostic Model through a Crowdsourced Challenge with Open Clinical Trial Data.” The Lancet Oncology 18, no. 1 (2017): 132–142.
Keller, Andreas, Richard C. Gerkin, Yuanfang Guan, Amit Dhurandhar, Gabor Turu, Bence Szalai, Joel D. Mainland, Yusuke Ihara, Chung Wen Yu, and Russ Wolfinger. “Predicting Human Olfactory Perception from Chemical Features of Odor Molecules.” Science 355, no. 6327 (2017): 820–826.
F, Seyednasrollah, Koestler Dc, Wang T, Piccolo Sr, Vega R, Greiner R, Fuchs C, et al. “A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer,” November 2017. https://pubmed.ncbi.nlm.nih.gov/30657384/. Download
Keller, Andreas, Richard C. Gerkin, Yuanfang Guan, Amit Dhurandhar, Gabor Turu, Bence Szalai, Joel D. Mainland, et al. “Reverse-Engineering Human Olfactory Perception from Chemical Features of Odor Molecules.” BioRxiv, October 21, 2016, 082495. https://doi.org/10.1101/082495. Download
Sieberts, Solveig K., Fan Zhu, Javier García-García, Eli Stahl, Abhishek Pratap, Gaurav Pandey, Dimitrios Pappas, et al. “Crowdsourced Assessment of Common Genetic Contribution to Predicting Anti-TNF Treatment Response in Rheumatoid Arthritis.” Nature Communications 7 (23 2016): 12460. https://doi.org/10.1038/ncomms12460. Download
Hill, Steven M., Laura M. Heiser, Thomas Cokelaer, Michael Unger, Nicole K. Nesser, Daniel E. Carlin, Yang Zhang, et al. “Inferring Causal Molecular Networks: Empirical Assessment through a Community-Based Effort.” Nature Methods 13, no. 4 (April 2016): 310–18. https://doi.org/10.1038/nmeth.3773. Download
Allen, Genevera I., Nicola Amoroso, Catalina Anghel, Venkat Balagurusamy, Christopher J. Bare, Derek Beaton, Roberto Bellotti, et al. “Crowdsourced Estimation of Cognitive Decline and Resilience in Alzheimer’s Disease.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 12, no. 6 (2016): 645–53. https://doi.org/10.1016/j.jalz.2016.02.006. Download
Noren, David P., Byron L. Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth Hess, Chenyue Wendy Hu, Alex J. Bisberg, et al. “A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.” PLoS Computational Biology 12, no. 6 (2016): e1004890. https://doi.org/10.1371/journal.pcbi.1004890. Download
Saez-Rodriguez, Julio, James C. Costello, Stephen H. Friend, Michael R. Kellen, Lara Mangravite, Pablo Meyer, Thea Norman, and Gustavo Stolovitzky. “Crowdsourcing Biomedical Research: Leveraging Communities as Innovation Engines.” Nature Reviews Genetics 17, no. 8 (2016): 470.
Bilal, Erhan, Theodore Sakellaropoulos, Ioannis N. Melas, Dimitris E. Messinis, Vincenzo Belcastro, Kahn Rhrissorrakrai, Pablo Meyer, et al. “A Crowd-Sourcing Approach for the Construction of Species-Specific Cell Signaling Networks.” Bioinformatics (Oxford, England) 31, no. 4 (February 15, 2015): 484–91. https://doi.org/10.1093/bioinformatics/btu659. Download
Karr, Jonathan R., Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, et al. “Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.” PLoS Computational Biology 11, no. 5 (May 2015): e1004096. https://doi.org/10.1371/journal.pcbi.1004096. Download
Abdallah, Kald, Charles Hugh-Jones, Thea Norman, Stephen Friend, and Gustavo Stolovitzky. “The Prostate Cancer DREAM Challenge: A Community-Wide Effort to Use Open Clinical Trial Data for the Quantitative Prediction of Outcomes in Metastatic Prostate Cancer.” The Oncologist 20, no. 5 (May 2015): 459–60. https://doi.org/10.1634/theoncologist.2015-0054. Download
Eduati, Federica, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, et al. “Erratum: Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition.” Nature Biotechnology 33, no. 10 (October 2015): 1109. https://doi.org/10.1038/nbt1015-1109a. Download
Eduati, Federica, Lara M. Mangravite, Tao Wang, Hao Tang, J. Christopher Bare, Ruili Huang, Thea Norman, et al. “Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition.” Nature Biotechnology 33, no. 9 (September 2015): 933–40. https://doi.org/10.1038/nbt.3299. Download
Cokelaer, Thomas, Mukesh Bansal, Christopher Bare, Erhan Bilal, Brian M. Bot, Elias Chaibub Neto, Federica Eduati, et al. “DREAMTools: A Python Package for Scoring Collaborative Challenges.” F1000Research 4 (2015): 1030. https://doi.org/10.12688/f1000research.7118.2. Download
Ewing, Adam D., Kathleen E. Houlahan, Yin Hu, Kyle Ellrott, Cristian Caloian, Takafumi N. Yamaguchi, J. Christopher Bare, et al. “Combining Tumor Genome Simulation with Crowdsourcing to Benchmark Somatic Single-Nucleotide-Variant Detection.” Nature Methods 12, no. 7 (July 2015): 623–30. https://doi.org/10.1038/nmeth.3407. Download
Califano, AnDrea, Manolis Kellis, and Gustavo Stolovitzky. “Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 22, no. 4 (April 2015): 251–52. https://doi.org/10.1089/cmb.2015.020P.
Küffner, Robert, Neta Zach, Raquel Norel, Johann Hawe, David Schoenfeld, Liuxia Wang, Guang Li, Lilly Fang, Lester Mackey, and Orla Hardiman. “Crowdsourced Analysis of Clinical Trial Data to Predict Amyotrophic Lateral Sclerosis Progression.” Nature Biotechnology 33, no. 1 (2015): 51–57.
Boutros, Paul C., Adam A. Margolin, Joshua M. Stuart, Andrea Califano, and Gustavo Stolovitzky. “Toward Better Benchmarking: Challenge-Based Methods Assessment in Cancer Genomics.” Genome Biology 15, no. 9 (September 17, 2014): 462. https://doi.org/10.1186/s13059-014-0462-7. Download
Boutros, Paul C., Adam D. Ewing, Kyle Ellrott, Thea C. Norman, Kristen K. Dang, Yin Hu, Michael R. Kellen, et al. “Global Optimization of Somatic Variant Identification in Cancer Genomes with a Global Community Challenge.” Nature Genetics 46, no. 4 (April 2014): 318–19. https://doi.org/10.1038/ng.2932. Download
Meyer, Pablo, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, et al. “Network Topology and Parameter Estimation: From Experimental Design Methods to Gene Regulatory Network Kinetics Using a Community Based Approach.” BMC Systems Biology 8 (February 7, 2014): 13. https://doi.org/10.1186/1752-0509-8-13. Download
Califano, Andrea, Manolis Kellis, and Gustavo Stolovitzky. “RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 21, no. 5 (May 2014): 371–72. https://doi.org/10.1089/cmb.2014.009p.
Costello, James C., Laura M. Heiser, Elisabeth Georgii, Mehmet Gönen, Michael P. Menden, Nicholas J. Wang, Mukesh Bansal, Petteri Hintsanen, Suleiman A. Khan, and John-Patrick Mpindi. “A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms.” Nature Biotechnology 32, no. 12 (2014): 1202–1212.
Bansal, Mukesh, Jichen Yang, Charles Karan, Michael P. Menden, James C. Costello, Hao Tang, Guanghua Xiao, Yajuan Li, Jeffrey Allen, and Rui Zhong. “A Community Computational Challenge to Predict the Activity of Pairs of Compounds.” Nature Biotechnology 32, no. 12 (2014): 1213–1222.
Plenge, Robert M., Jeffrey D. Greenberg, Lara M. Mangravite, Jonathan M. J. Derry, Eli A. Stahl, Marieke J. H. Coenen, Anne Barton, et al. “Crowdsourcing Genetic Prediction of Clinical Utility in the Rheumatoid Arthritis Responder Challenge.” Nature Genetics 45, no. 5 (May 2013): 468–69. https://doi.org/10.1038/ng.2623. Download
Aghaeepour, Nima, Greg Finak, FlowCAP Consortium, DREAM Consortium, Holger Hoos, Tim R. Mosmann, Ryan Brinkman, Raphael Gottardo, and Richard H. Scheuermann. “Critical Assessment of Automated Flow Cytometry Data Analysis Techniques.” Nature Methods 10, no. 3 (March 2013): 228–38. https://doi.org/10.1038/nmeth.2365. Download
Califano, Andrea, Manolis Kellis, and Gustavo Stolovitzky. “Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 20, no. 5 (May 2013): 373–74. https://doi.org/10.1089/cmb.2013.008p.
Margolin, Adam A., Erhan Bilal, Erich Huang, Thea C. Norman, Lars Ottestad, Brigham H. Mecham, Ben Sauerwine, Michael R. Kellen, Lara M. Mangravite, and Matthew D. Furia. “Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer.” Science Translational Medicine 5, no. 181 (2013): 181re1–181re1.
Weirauch, Matthew T., Atina Cote, Raquel Norel, Matti Annala, Yue Zhao, Todd R. Riley, Julio Saez-Rodriguez, Thomas Cokelaer, Anastasia Vedenko, and Shaheynoor Talukder. “Evaluation of Methods for Modeling Transcription Factor Sequence Specificity.” Nature Biotechnology 31, no. 2 (2013): 126–134.
Califano, Andrea, Manolis Kellis, and Gustavo Stolovitzky. “Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 Special Issue.” Journal of Computational Biology: A Journal of Computational Molecular Cell Biology 19, no. 2 (February 2012): 101. https://doi.org/10.1089/cmb.2012.010p. Download
Marbach, Daniel, James C. Costello, Robert Küffner, Nicole M. Vega, Robert J. Prill, Diogo M. Camacho, Kyle R. Allison, Manolis Kellis, James J. Collins, and Gustavo Stolovitzky. “Wisdom of Crowds for Robust Gene Network Inference.” Nature Methods 9, no. 8 (2012): 796–804.
Prill, Robert J., Julio Saez-Rodriguez, Leonidas G. Alexopoulos, Peter K. Sorger, and Gustavo Stolovitzky. Crowdsourcing Network Inference: The DREAM Predictive Signaling Network Challenge. American Association for the Advancement of Science, 2011.
Prill, Robert J., Daniel Marbach, Julio Saez-Rodriguez, Peter K. Sorger, Leonidas G. Alexopoulos, Xiaowei Xue, Neil D. Clarke, Gregoire Altan-Bonnet, and Gustavo Stolovitzky. “Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges.” PloS One 5, no. 2 (2010): e9202.
Stolovitzky, Gustavo, Robert J. Prill, and Andrea Califano. “Lessons from the DREAM2 Challenges.” Annals of the New York Academy of Sciences 1158 (March 2009): 159–95. https://doi.org/10.1111/j.1749-6632.2009.04497.x.
Marbach, Daniel, Thomas Schaffter, Claudio Mattiussi, and Dario Floreano. “Generating Realistic in Silico Gene Networks for Performance Assessment of Reverse Engineering Methods.” Journal of Computational Biology 16, no. 2 (2009): 229–239. Download
Stolovitzky, Gustavo, Don Monroe, and Andrea Califano. “Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference.” Annals of the New York Academy of Sciences 1115 (December 2007): 1–22. https://doi.org/10.1196/annals.1407.021.