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Publications (Google Scholar, DBLP)

Journal

• Semi-nonparametric Modeling of Topological Domain Formation From Epigenetic Data   [  data & code]
  Emre Sefer  &  Carl Kingsford
  Algorithms for Molecular Biology, 2019.
  

• Selecting the most appropriate time points to profile in high-throughput studies   [  data & code]
  M Kleyman, Emre Sefer, Nicola, T., Espinoza, C., Chhabra, D., Hagood, J. S., Kaminski, N., Ambalavanan, N., and Ziv Bar-Joseph
  eLife Sciences, 2017.
  

• Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments   [  data & code]
  Emre Sefer, M Kleyman, and Ziv Bar-Joseph
  Cell Systems, 2016.
  

• Deconvolution Of Ensemble Chromatin Interaction Data Reveals The Latent Mixing Structures In Cell Subpopulations   [  data & code]
  Emre Sefer, Geet Duggal, and Carl Kingsford
  Journal of Computational Biology, 2016.
  

• Diffusion Archaeology for Diffusion Progression History Reconstruction   [  data & code]
  Emre Sefer  &  Carl Kingsford
  Knowledge of Information Systems, 2016.
  

• Resolving spatial inconsistencies in chromosome conformation measurements   [  data & code]
  Geet Duggal, Rob Patro, Sefer, Emre, Hao Wang, Darya Filippova, Samir Khuller, and Carl Kingsford.
  Algorithms for Molecular Biology, 2013
  

• Parsimonious reconstruction of network evolution   [  data & code]
  Rob Patro, Emre Sefer, Justin Malin, Guillaume Marcais, Saket Navlakha, Carl Kingsford
  Algorithms for Molecular Biology, 2012.
  

Conference

• Shall we dense? Comparing design strategies for time series expression experiments   [  data & code]
  Emre Sefer  &  Ziv Bar-Joseph
  RECOMB 2016, Los Angeles, USA.  
  Best Paper Award    

• Deconvolution Of Ensemble Chromatin Interaction Data Reveals The Latent Mixing Structures In Cell Subpopulations.   [  data & code]
  Emre Sefer, Geet Duggal, and Carl Kingsford
  RECOMB 2015, Warsaw, Poland.  
  

• Convex Risk Minimization To Infer Networks From Probabilistic Diffusion Data At Multiple Scales   [  data & code]
  Emre Sefer  &  Carl Kingsford
  ICDE 2015, Seoul, South Korea.  
  

• Semi-nonparametric Modeling of Topological Domain Formation From Epigenetic Data   [  data & code]
  Emre Sefer  &  Carl Kingsford
  WABI 2015, Atlanta, USA.  
  

• Diffusion Archaeology for Diffusion Progression History Reconstruction   [  data & code]
  Emre Sefer  &  Carl Kingsford
  ICDM 2014, Shenzhen, China.  
  

• Resolving spatial inconsistencies in chromosome conformation measurements   [  data & code]
  Geet Duggal, Rob Patro, Sefer, Emre, Hao Wang, Darya Filippova, Samir Khuller, and Carl Kingsford
  WABI 2012, Ljubljana, Slovenia.  
  

• The missing models: a data-driven approach for learning how networks grow   [  data & code]
  Robert Patro, Geet Duggal, Emre Sefer, Hao Wang, Darya Filippova, and Carl Kingsford
  KDD 2012, Beijing, China.  
  Best Video Award    

• Parsimonious reconstruction of network evolution   [  data & code]
  Rob Patro, Emre Sefer, Justin Malin, Guillaume Marcais, Saket Navlakha, Carl Kingsford
  WABI 2011, Ljubljana, Slovenia.  
  

• NetVisia: Heat map & matrix visualization of dynamic social network statistics & content   [  data & code]
  Robert Gove, Nick Gramsky, Emre Sefer, Ben Shneiderman
  Socialcom 2011,  
  

• Metric labeling and semi-metric embedding for protein annotation prediction   [  data & code]
  Emre Sefer  &  Carl Kingsford
  RECOMB 2011, Vancouver, Canada  
  

• Thinking ahead in real-time search   [  data & code]
  Dana Nau, Emre Sefer, and Ugur Kuter
  ICAPS 2009,  
  

• Real-time A* search with depth-k lookahead   [  data & code]
  Emre Sefer, Ugur Kuter, Dana Nau
  SoCS 2009,  
  

Code & Data

Ph.D. Thesis

• Inferring and Analyzing the Present and the Past of Networks from Limited Information   [  Proposal]
  Emre Sefer, Doctoral Dissertation, Carnegie Mellon University, 2015