| Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk FR Day, DJ Thompson, H Helgason, DI Chasman, H Finucane, P Sulem, ... Nature Genetics 49 (6), 834-841, 2017 | 561 | 2017 |
| Enhancer-Promoter Interactions are Encoded by Complex Genomic Signatures on Looping Chromatin S Whalen, RM Truty, KS Pollard Nature Genetics 48 (5), 488–496, 2016 | 463 | 2016 |
| Analysis of transcriptional variability in a large human iPSC library reveals genetic and non-genetic determinants of heterogeneity I Carcamo-Orive, GE Hoffman, P Cundiff, ND Beckmann, SL D’Souza, ... Cell Stem Cell 20 (4), 518-532. e9, 2017 | 263 | 2017 |
| The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice DD Engle, H Tiriac, KD Rivera, A Pommier, S Whalen, TE Oni, B Alagesan, ... Science 364 (6446), 1156-1162, 2019 | 242 | 2019 |
| An Introduction to ARP Spoofing S Whalen, S Engle, D Romeo | 236 | 2001 |
| Navigating the pitfalls of applying machine learning in genomics S Whalen, J Schreiber, WS Noble, KS Pollard Nature Reviews Genetics, 1-13, 2021 | 214 | 2021 |
| Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition F Eduati Nature Biotechnology 33 (9), 933–940, 2015 | 121 | 2015 |
| We Have Met the Enemy and He is Us M Bishop, S Engle, S Peisert, S Whalen, C Gates Proceedings of the 2008 New Security Paradigms Workshop, 2008 | 113 | 2008 |
| lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements MG Gordon, F Inoue, B Martin, M Schubach, V Agarwal, S Whalen, ... Nature Protocols 15 (8), 2387-2412, 2020 | 106 | 2020 |
| Machine learning dissection of human accelerated regions in primate neurodevelopment S Whalen, F Inoue, H Ryu, T Fair, E Markenscoff-Papadimitriou, K Keough, ... Neuron 111 (6), 857-873. e8, 2023 | 102* | 2023 |
| A chromatin accessibility atlas of the developing human telencephalon E Markenscoff-Papadimitriou, S Whalen, P Przytycki, R Thomas, ... Cell 182 (3), 754-769. e18, 2020 | 83 | 2020 |
| A Comparative Analysis of Ensemble Classifiers: Case Studies in Genomics S Whalen, G Pandey Proceedings of the 13th IEEE International Conference on Data Mining, 2013 | 81 | 2013 |
| A Risk Management Approach to the Insider Threat M Bishop, S Engle, DA Frincke, C Gates, FL Greitzer, S Peisert, S Whalen Insider Threats in Cyber Security, 2010 | 74 | 2010 |
| Three-dimensional genome rewiring in loci with human accelerated regions KC Keough, S Whalen, F Inoue, PF Przytycki, T Fair, C Deng, M Steyert, ... Science 380 (6643), eabm1696, 2023 | 60 | 2023 |
| The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation SA Moquin, S Thomas, S Whalen, A Warburton, SG Fernandez, ... Journal of virology 92 (3), e01413-17, 2018 | 56 | 2018 |
| Case Studies of an Insider Framework M Bishop, S Engle, S Peisert, S Whalen, C Gates Proceedings of the 42nd Annual Hawaii International Conference on System …, 2009 | 51 | 2009 |
| Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes E Markenscoff-Papadimitriou, F Binyameen, S Whalen, J Price, K Lim, ... Cell reports 37 (10), 110089, 2021 | 47 | 2021 |
| Most chromatin interactions are not in linkage disequilibrium S Whalen, KS Pollard Genome research 29 (3), 334-343, 2019 | 45* | 2019 |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype PP Shah, KC Keough, K Gjoni, GT Santini, RJ Abdill, NM Wickramasinghe, ... Genome Biology 24 (1), 1-35, 2023 | 44* | 2023 |
| Unboxing cluster heatmaps S Engle, S Whalen, A Joshi, KS Pollard BMC Bioinformatics 18 (2), 63, 2017 | 44 | 2017 |
