| Computation for ChIP-seq and RNA-seq studies S Pepke, B Wold, A Mortazavi Nature methods 6 (Suppl 11), S22-S32, 2009 | 754 | 2009 |
| Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming DH Kim, GK Marinov, S Pepke, ZS Singer, P He, B Williams, GP Schroth, ... Cell stem cell 16 (1), 88-101, 2015 | 176 | 2015 |
| A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II S Pepke, T Kinzer-Ursem, S Mihalas, MB Kennedy PLoS computational biology 6 (2), e1000675, 2010 | 101 | 2010 |
| Predictability of self-organizing systems SL Pepke, JM Carlson Physical Review E 50 (1), 236, 1994 | 84 | 1994 |
| Prediction of large events on a dynamical model of a fault SL Pepke, JM Carlson, BE Shaw Journal of Geophysical Research: Solid Earth 99 (B4), 6769-6788, 1994 | 84 | 1994 |
| High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation A Ozdemir, KI Fisher-Aylor, S Pepke, M Samanta, L Dunipace, K McCue, ... Genome research 21 (4), 566-577, 2011 | 62 | 2011 |
| Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps A Mortazavi, S Pepke, C Jansen, GK Marinov, J Ernst, M Kellis, ... Genome research 23 (12), 2136-2148, 2013 | 51 | 2013 |
| Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer S Pepke, G Ver Steeg BMC medical genomics 10 (1), 12, 2017 | 29 | 2017 |
| A portfolio approach to accelerate therapeutic innovation in ovarian cancer S Chaudhuri, K Cheng, AW Lo, S Pepke, S Rinaudo, L Roman, ... Available at SSRN 3286330, 2018 | 14 | 2018 |
| Electronic states in a disordered metal: Magnetotransport in doped germanium TF Rosenbaum, S Pepke, RN Bhatt, TV Ramakrishnan Physical Review B 42 (17), 11214, 1990 | 4 | 1990 |
| Using confidence set heuristics during topology search improves the robustness of phylogenetic inference SL Pepke, D Butt, I Nadeau, AJ Roger, C Blouin Journal of molecular evolution 64, 80-89, 2007 | 3 | 2007 |
| A User's Guide to the Encyclopedia of DNA Elements (ENCODE) B Wold, A Mortazavi, B Williams, G Marinov, D Trout, B King, K McCue, ... PLoS Biology 9 (4), 0 | 2 | |
| Multivariate information maximization yields hierarchies of expression components in tumors that are both biologically meaningful and prognostic S Pepke, GV Steeg bioRxiv, 043257, 2016 | 1 | 2016 |
| Multi-stage modeling of the kinetics of activation of CaMKII M Stefan, S Pepke, S Mihalas, T Bartol, T Sejnowski, M Kennedy Front. Neuroinform. Conference Abstract: 4th INCF Congress of …, 2011 | 1 | 2011 |
| Analyzing tumor gene expression factors with the corexplorer web portal S Pepke, WM Nelson, G Ver Steeg JoVE (Journal of Visualized Experiments), e60431, 2019 | | 2019 |
| Prediction Fault Studies of Earthquake Models and Applications to Seismic Catalogs JM Carlson, SL Pepke, V Kossobokov Reduction And Predictability Of Natural Disasters, 273, 2018 | | 2018 |
| Abstract NTOC-104: BEYOND RECIST1. 1: THE NEED FOR ALTERNATIVE DISEASE MEASUREMENT CRITERIA FOR CLINICAL TRIALS IN OVARIAN CANCER S Pepke, T Rucker Clinical Cancer Research 23 (11_Supplement), NTOC-104-NTOC-104, 2017 | | 2017 |
| Modelling calcium-dependent proteins in the spine-challenges and solutions M Stefan, S Pepke, S Mihalas, T Bartol, T Sejnowki, M Kennedy Front. Neuroinform. Conference Abstract: 5th INCF Congress of …, 2014 | | 2014 |
| Investigating ChIP-seq derived candidate cis-regulatory regions in two different developmental systems K Fisher, A Ozdemir, G Kwan, S Pepke, A Kirilusha, G DeSalvo, ... Developmental Biology 1 (344), 416, 2010 | | 2010 |
| Inferring Phylogenies by Confidence Set Optimization SL Pepke, D Butt, I Nadeau, AJ Roger, C Blouin Phylogeny 269, 18, 2002 | | 2002 |
