SeanPatrickWhalenMD

PubMed

• 70 citations
  Navigating the pitfalls of applying machine learning in genomics.
  Sean Whalen, Jacob Schreiber, William Stafford Noble, Katherine S. Pollard> ;Nature Reviews. Genetics. 2021 Nov 26
• 5 citations
  Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
  M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Geor...> ;Nature Protocols. 2021 Jul 1
• 44 citations
  A Chromatin Accessibility Atlas of the Developing Human Telencephalon.
  Eirene Markenscoff-Papadimitriou, Sean Whalen, Pawel F. Przytycki, Reuben Thomas, Fadya Binyameen, Tomasz J. Nowakowski, Arnold R. Kriegstein, Stephen Sanders, Matthew...> ;Cell. 2020 Aug 6
• 47 citations
  lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements
  M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Geor...> ;Nature Protocols. 2020 Jul 8
• 19 citations
  AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design
  Kathleen C. Keough, Svetlana Lyalina, Michael P. Olvera, Sean Whalen, Bruce R. Conklin, Katherine S. Pollard> ;Genome Biology. 2019 Aug 15
• 5 citations
  Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'.
  Sean Whalen, Katherine S. Pollard> ;Nature Genetics. 2019 Aug 1
• 132 citations
  The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice
  Dannielle D. Engle, Hervé Tiriac, Keith Rivera, Arnaud Pommier, Sean Whalen, Tobiloba E. Oni, Brinda Alagesan, Eun Jung Lee, Melissa Yao, Matthew S. Lucito, Benjamin S...> ;Science. 2019 Jun 21
• 18 citations
  Most chromatin interactions are not in linkage disequilibrium.
  Sean Whalen, Katherine S. Pollard> ;Genome Research. 2019 Jan 7
• 37 citations
  The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.
  Stephanie Moquin, Sean Thomas, Sean Whalen, Alix Warburton, Samantha G. Fernanadez, Alison A. McBride, Katherine S. Pollard, JJ L. Miranda> ;Journal of Virology. 2017 Nov 15
• 331 citations
  Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk
  Felix R. Day, Deborah J. Thompson, Hannes Helgason, Daniel I. Chasman, Hilary K. Finucane, Patrick Sulem, Katherine S. Ruth, Sean Whalen, Abhishek Sarkar, Eva Albrecht...> ;Nature Genetics. 2017 Apr 24
• 175 citations
  Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity
  Ivan Carcamo-Orive, Gabriel E. Hoffman, Paige Cundiff, Noam D. Beckmann, Sunita L. D’Souza, Joshua W. Knowles, Achchhe Patel, Dimitri Papatsenko, Fahim Abbasi, Gerald ...> ;Cell Stem Cell. 2017 Apr 6
• 14 citations
  Unboxing cluster heatmaps.
  Sophie Engle, Sean Whalen, Alark Joshi, Katherine S. Pollard> ;BMC Bioinformatics. 2017 Feb 15
• 244 citations
  Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
  Sean Whalen, Rebecca Truty, Katherine S. Pollard> ;Nature Genetics. 2016 May 1
• 17 citations
  Predicting protein function and other biomedical characteristics with heterogeneous ensembles.
  Sean Whalen, Om Prakash Pandey, Gaurav Pandey> ;Methods. 2016 Jan 15
• 4 citations
  Enhancing the functional content of eukaryotic protein interaction networks.
  Gaurav Pandey, Sonali Arora, Sahil Manocha, Sean Whalen> ;Plos One. 2014 Oct 2
• Structural Drift: The Population Dynamics of Sequential Learning
  James P. Crutchfield, Sean Whalen> ;Plos Computational Biology. 2012 Jun 7
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