Publications

*co-first-author, equal contribution; # corresponding author

  • Daifeng WangSystems Biology: Constraint-Based Reconstruction and Analysis by Bernhard O. Palsson, The Quarterly Review of Biology, 92:3303-304, 2017 (invited book review)
  • Pedro Alves, Shuang Liu, Daifeng Wang# and Mark Gerstein#, Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press, 2017
  • Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein, DREISS: Using state-space models to infer the dynamics of gene expression driven by external and internal regulatory networks, PLoS Computational Biology, 12(10): e1005146, 2016
  • Daifeng Wang, Koon-Kiu Yan, Joel Rozowsky, Eric Pan, Mark Gerstein, Temporal dynamics of collaborative networks driven by large scientific consortia, Trends in Genetics, 32, 251-253, 2016
  • Koon-Kiu Yan*, Daifeng Wang*, Anurag Sethi, Robert Kitchen, Paul Muir, Chao Cheng, Mark Gerstein, Matchmaking hairballs – insights from cross-disciplinary network comparison, Cell Systems, 2, 147-157, 2016 (featured front-matter)
  • Paul Muir, Shantao Li, Shaoke Lou, Daifeng Wang, Daniel Spakowicz, Leonidas Salichos, Jing Zhang, Farren Isaacs, George M. Weinstock, Joel Rozowsky, Mark Gerstein, The real cost of sequencing: scaling computation to keep pace with data generation, Genome Biology, 17:53, 2016
  • Fei He, Shinjae Yoo, Daifeng Wang, Sunita Kumari, Mark Gerstein, Doreen Ware, Sergei Maslov, Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis, The Plant Journal, 86(6), 472-480, 2016
  • The PsychENCODE Consortium including Daifeng Wang, The PsychENCODE Project Consortium, Nature Neuroscience, 18, 1707-1712, 2015
  • Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel Rozowsky, William Meyerson, Mark Gerstein, Loregic: A method to characterize the cooperative logic of regulatory factors, PLoS Computational Biology 11(4): e1004132, 2015 (featured article)
  • Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein, An Approach for Determining and Measuring Network Hierarchy: Application to Comparing the Phosphorylome and the Regulome, Genome Biology, 16:63, 2015
  • Shuang Liu, Anjali Datta, Derek Ho, Jordan Dwelle, Daifeng Wang, Thomas E. Milner, H. Grady Rylander III, Mia K. Markey, Effect of image registration on longitudinal analysis of retinal nerve fiber layer thickness of non-human primates using Optical Coherence Tomography (OCT), BMC Eye and Vision, 2:3, 2015
  • Mark Gerstein*, Joel Rozowsky*, Koon-Kiu Yan*, Daifeng Wang*, Chao Cheng*, …, Steven Brenner, Brenton Graveley, Susan Celniker, Thomas Gingeras, and Robert Waterston, Comparative Analysis of the Transcriptome across Distant Species, Nature 512, 445–448, 2014 (News & Views, Nature)
  • Alan P. Boyle*, Carlos L. Araya*, …, Daifeng Wang, …, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder, Comparative analysis of regulatory information and circuits across diverse species, Nature 512, 453–456, 2014 (News & Views, Nature)
  • Koon-Kiu Yan*, Daifeng Wang*, Joel Rozowsky, Henry Zheng, Mark Gerstein, OrthoClust: An orthology-based network framework for expression clustering across multiple species, Genome Biology 15:R100, 2014
  • Cristina Sisu, Baikang Pei, Jing Leng, Adam Frankish, Yan Zhang, Suganthi Balasubramanian, Rachel Harte, Daifeng Wang, Michael Rutenberg Schoenberg, Wyatt Clark, Mark Diekhans, Joel Rozowsky, Tim Hubbard, Jennifer Harrow, Mark Gerstein, Comparative analysis of pseudogenes across three phyla, Proceedings of the National Academy of Sciences (PNAS), vol. 111, no. 37, pp. 13361–13366, 2014
  • Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Koon-Kiu Yan, Doreen Ware, Sergei Maslov, Mark Gerstein, Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar, Proceedings of 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACM BCB 2013)
  • Daifeng Wang, Mia K. Markey, Claus O. Wilke and Ari Arapostathis, Eigen-genomic System Dynamic-pattern Analysis (ESDA): Modeling mRNA degradation and self-regulation, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 2, pp. 430-437, 2012
  • Daifeng Wang, Ari Arapostathis, Claus O. Wilke, and Mia K. Markey, Principal-Oscillation-Pattern Analysis of Gene Expression, PLoS ONE 7(1): e28805, 2012
  • Sean X. Shi, Anand Ramalingam, Daifeng Wang, and David Z. Pan, Latch Modeling for Statistical Timing Analysis, Proceedings of the IEEE Conference on Design, Automation and Test in Europe 2008
  • Wei Wu, Daifeng Wang, Ari Arapostathis and K. Davey, Optimal Power Generation Scheduling of a Shipboard Power System, Proceedings of the IEEE Electric Ship Technologies Symposium 2007