publications

including a lab member (underlined) and are in reversed chronological order

2024

  1. Li2024.png
    Chromatin context-dependent regulation and epigenetic manipulation of prime editing
    Xiaoyi Li, Wei Chen, Beth K Martin, Diego Calderon, Choli Lee, Junhong Choi, Florence M Chardon, Troy A McDiarmid, Riza M Daza, Haedong Kim, Jean-Benoı̂t Lalanne, Jenny F Nathans, David S Lee, and Jay Shendure
    Cell, 2024
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    27 Google Scholar citations
  2. Lalanne2024.png
    Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters
    Jean-Benoı̂t Lalanne, Samuel G Regalado, Silvia Domcke, Diego Calderon, Beth K Martin, Xiaoyi Li, Tony Li, Chase C Suiter, Choli Lee, Cole Trapnell, and Jay Shendure
    Nature Methods, 2024
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    17 Google Scholar citations

2023

  1. Chardon2023_2.png
    Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements
    Florence M Chardon, Troy A McDiarmid, Nicholas F Page, Riza M Daza, Beth Martin, Silvia Domcke, Samuel G Regalado, Jean-Benoı̂t Lalanne, Diego Calderon, Xiaoyi Li, Lea M Starita, Stephan J Sanders, Nadav Ahituv, and Jay Shendure
    BioRxiv, 2023
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    13 Google Scholar citations
  2. Chardon2023.png
    A multiplex, prime editing framework for identifying drug resistance variants at scale
    Florence M Chardon, Chase Suiter, Riza Daza, Nahum T Smith, Phoebe Parrish, Troy McDiarmid, Jean-Benoı̂t Lalanne, Beth K Martin, Diego Calderon, Amira Ellison, Alice Berger, Jay Shendure, and Lea M Starita
    bioRxiv, 2023
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    5 Google Scholar citations

2022

  1. Qiu2022.jpg
    Systematic reconstruction of cellular trajectories across mouse embryogenesis
    Chengxiang Qiu, Junyue Cao, Beth K Martin, Tony Li, Ian C Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M Disteche, Stephen A Murray, Malte Spielmann, Cecilia B Moens, Cole Trapnell, and Jay Shendure
    Nature genetics, 2022
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    110 Google Scholar citations
  2. DEAP.gif
    The continuum of Drosophila embryonic development at single-cell resolution
    Diego Calderon, Ronnie Blecher-Gonen, Xingfan Huang, Stefano Secchia, James Kentro, Riza M Daza, Beth Martin, Alessandro Dulja, Christoph Schaub, Cole Trapnell, Erica Larschan, Kate M O’Connor-Giles, Eileen EM Furlong, and Jay Shendure
    Science, 2022
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    66 Google Scholar citations

2020

  1. Calderon2020.jpg
    TransMPRA: A framework for assaying the role of many trans-acting factors at many enhancers
    Diego Calderon, Andria Ellis, Riza M Daza, Beth Martin, Jacob M Tome, Wei Chen, Florence M Chardon, Anh Leith, Choli Lee, Cole Trapnell, and Jay Shendure
    BioRxiv, 2020
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2019

  1. Calderon2019.png
    Landscape of stimulation-responsive chromatin across diverse human immune cells
    Diego Calderon, Michelle LT Nguyen, Anja Mezger, Arwa Kathiria, Fabian Müller, Vinh Nguyen, Ninnia Lescano, Beijing Wu, John Trombetta, Jessica V Ribado, David A Knowles, Ziyue Gao, Franziska Blaeschke, Audrey V Parent, Trevor D Burt, Mark S Anderson, Lindsey A Criswell, William J Greenleaf, Alexander Marson, and Jonathan K Pritchard
    Nature genetics, 2019
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    250 Google Scholar citations
  2. Antonio2019.png
    Ancient Rome: A genetic crossroads of Europe and the Mediterranean
    Margaret L Antonio, Ziyue Gao, Hannah M Moots, Michaela Lucci, Francesca Candilio, Susanna Sawyer, Victoria Oberreiter, Diego Calderon, Katharina Devitofranceschi, Rachael C Aikens, Serena Aneli, Fulvio Bartoli, Alessandro Bedini, Olivia Cheronet, Daniel J Cotter, Daniel M Fernandes, Gabriella Gasperetti, Renata Grifoni, Alessandro Guidi, Francesco La Pastina, Ersilia Loreti, Daniele Manacorda, Giuseppe Matullo, Simona Morretta, Alessia Nava, Vincenzo Fiocchi Nicolai, Federico Nomi, Carlo Pavolini, Massimo Pentiricci, Philippe Pergola, Marina Piranomonte, Ryan Schmidt, Giandomenico Spinola, Alessandra Sperduti, Mauro Rubini, Luca Bondioli, Alfredo Coppa, Ron Pinhasi, and Jonathan K Pritchard
    Science, 2019
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    250 Google Scholar citations

2018

  1. Banovich2018.png
    Impact of regulatory variation across human iPSCs and differentiated cells
    Nicholas E Banovich, Yang I Li, Anil Raj, Michelle C Ward, Peyton Greenside, Diego Calderon, Po Yuan Tung, Jonathan E Burnett, Marsha Myrthil, Samantha M Thomas, Courtney K Burrows, Irene Gallego Romero, Bryan J Pavlovic, Anshul Kundaje, Jonathan K Pritchard, and Yoav Gilad
    Genome research, 2018
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    140 Google Scholar citations

2017

  1. Calderon2017.png
    Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression
    Diego Calderon, Anand Bhaskar, David A Knowles, David Golan, Towfique Raj, Audrey Q Fu, and Jonathan K Pritchard
    American Journal of Human Genetics, 2017
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    120 Google Scholar citations

2013

  1. Vonk2013.png
    The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system
    Freek J Vonk, Nicholas R Casewell, Christiaan V Henkel, Alysha M Heimberg, Hans J Jansen, Ryan JR McCleary, Harald ME Kerkkamp, Rutger A Vos, Isabel Guerreiro, Juan J Calvete, Wolfgang Wüster, Anthony E Woods, Jessica M Logan, Robert A Harrison, Todd A Castoe, AP Jason De Koning, David D Pollock, Mark Yandell, Diego Calderon, Camila Renjifo, Rachel B Currier, David Salgado, Davinia Pla, Libia Sanz, Asad S Hyder, José MC Ribeiro, Jan W Arntzen, Guido EEJM Thillart, Marten Boetzer, Walter Pirovano, Ron P Dirks, Herman P Spaink, Denis Duboule, Edwina McGlinn, R Manjunatha Kini, and Michael K Richardson
    Proceedings of the National Academy of Sciences, 2013
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    530 Google Scholar citations