Publications

Papers are hyperlinked below.

Asterisk (*) signifies that authors contributed equally to the work.

• Ashrifa Ali, Hannah Schriever, Dennis Kostka, Takaaki Kuwajima, Kristen M. Koenig*, Jeffrey Gross*. “Zebrafish optic nerve injury results in systemic retinal ganglion cell dedifferentiation.” PLOS Genetics 21.9 (2025): e1011879.

  • Originally on bioRxiv

• Kristen B. Hunter, Kristen M. Koenig, and Marie Abèle Bind. “Conceptualizing experimental controls using the potential outcomes framework” The American Statistician (2025).

  • Originally on arXiv

• Shea Heilman, Hannah Schriever, Dennis Kostka, Kristen M. Koenig, Jeffrey Gross. “tet2 and tet3 regulate cell fate specification and differentiation events during retinal development.” Scientific Reports 15, 10404 (2025).

  • Originally on bioRxiv

• Crystal D Rogers, Chris Amemiya, Swathi Arur, Leslie Babonis, Michael Barresi, Madelaine Bartlett, Richard Behringer, Blair Benham-Pyle, Dominique Bergmann, Ben Blackman, C Titus Brown, Bill Browne, Jasmin Camacho, Chiswili Yves Chabu, Ida Chow, Ondine Cleaver, Jonah Cool, Megan Y Dennis, Alexandra Jazz Dickinson, Stefano Di Talia, Margaret Frank, Stewart Gillmor, Eric S Haag, Iswar Hariharan, Richard Harland, Aman Husbands, Loydie Jerome-Majewska, Kristen Koenig, Carole Labonne, Michael Layden, Chris Lowe, Madhav Mani, Megan Martik, Katelyn McKown, Cecilia Moens, Christian Mosimann, Joyce Onyenedum, Robert Reed, Ajna Rivera, Dan Rokhsar, Loic Royer, Flora Rutaganira, Rachel Shahan, Neelima Sinha, Billie Swalla, Jaimie M Van Norman, Daniel E Wagner, Athula Wikramanayake, Sophia Zebell, Siobhán M Brady. “Pluripotency of a founding field: rebranding developmental biology.” Development 151.3 (2024).

• Kyle J McCulloch, Leslie S Babonis, Alicia Liu, Christina M Daly, Mark Q Martindale, Kristen M. Koenig. “Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia” EvoDevo 14, 14 (2023).

  • Originally on bioRxiv

• Kristen M. Koenig. “Chilling with Cephalopods: Temperature-responsive RNA editing in octopus and squid” Cell 186, no. 12 (2023): 2518-2520.

• Francesca R. Napoli*, Christina M. Daly*, Stephanie Neal, Kyle J. McCulloch, Alex Zaloga, Alicia Liu, Kristen M. Koenig. “Cephalopod Retinal Development Shows Vertebrate-like Mechanisms of Neurogenesis” Current Biology 32, no. 23 (2022): 5045-5056.

  *These authors contributed equally to this work

  • Originally on bioRxiv

  • Current Biology Dispatch article by Deirdre Lyons and Paul Katz

• Stephanie Neal*, Kyle J. McCulloch*, Francesca Napoli, Christina M. Daly, James Coleman, and Kristen M. Koenig. “Co-option of the Limb Patterning Program in Cephalopod Eye Development” BMC Biology 20, 1 (2022).

  *These authors contributed equally to this work

  • Originally on bioRxiv

• Kyle McCulloch and Kristen M. Koenig. “KLF/SP Transcription Factor Evolution in the Spiralia and the Implications for Cephalopod Visual System Novelties”. Proceedings of the Royal Society B 287.1937 (2020): 20202055.

• Kristen M. Koenig and Jeffrey Gross. “Evolution and Development of Complex Eyes: A Celebration of Diversity”. Development 147, no. 19 (2020): dev182923.

  
  

• Andrews Akwasi Agbleke, Assaf Amitai, Jason D. Buenrostro, Aditi Chakrabarti, Lingluo Chu, Anders S. Hansen, Kristen M. Koenig, Ajay S. Labade, Sirui Liu, Tadasu Nozaki, Sergey Ovchinnikov, Andrew Seeber, Haitham A. Shaban, Jan-Hendrik Spille, Andrew D. Stephens, Jun-Han Su, Dushan Wadduwage. “Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields”. Molecular Cell (2020).

  
  

• Crawford, Karen, Juan F. Diaz Quiroz, Kristen M. Koenig, Namrata Ahuja, Caroline B. Albertin, and Joshua JC Rosenthal. “Highly Efficient Knockout of a Squid Pigmentation Gene”. Current Biology (2020).

  • Current Biology Dispatch article by Robert Steele

    
    

• Kristen M. Koenig, Peter Sun, Eli Meyer and Jeffrey Gross. “Eye Development and photoreceptor differentiation in the cephalopod Doryteuthis (Loligo) pealeii”, Development (2016).

  
  

• Caroline B. Albertin, Laure Bonnaud, C. Titus Brown, Wendy J. Crookes-Goodson, Rute R. da Fonseca, Carlo Di Cristo, Brian P. Dilkes, Eric Edsinger-Gonzales, Robert M. Freeman, Jr., Roger T. Hanlon, Kristen M. Koenig, Annie R. Lindgren, Mark Q. Martindale, Patrick Minx, Leonid L. Moroz, Marie-Therese Nödl, Spencer V. Nyholm, Atsushi Ogura, Judit R. Pungor, Joshua J. C. Rosenthal, Erich M. Schwarz, Shuichi Shigeno, Jan M. Strugnell, Tim Wollesen, Guojie Zhang, Clifton W. Ragsdale. “Cephalopod Genomics: A Plan of Strategies and Organization”. Standards in Genomic Sciences (2012) DOI:10.4056/sigs.3136559