A synthetic synthesis to explore animal evolution and development.

Perkins ML, Gandara L, Crocker J

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2022

doi:10.1098/rstb.2020.0517.

Nuclear morphogenesis: forming a heterogeneous nucleus during embryogenesis.

Tsai A, Crocker J

Development (Cambridge, England), 2022

doi:10.1242/dev.200266.

An open-source semi-automated robotics pipeline for embryo immunohistochemistry.

Fuqua T, Jordan J, Halavatyi A, Tischer C, Richter K, Crocker J

Scientific reports, 2021

doi:10.1038/s41598-021-89676-5.

Dense and pleiotropic regulatory information in a developmental enhancer.

Fuqua T, Jordan J, van Breugel ME, Halavatyi A, Tischer C, Polidoro P, Abe N, Tsai A, Mann RS, Stern DL, Crocker J

Nature, 2020

doi:10.1038/s41586-020-2816-5.

Robust and efficient gene regulation through localized nuclear microenvironments.

Tsai A, Galupa R, Crocker J

Development (Cambridge, England), 2020

doi:10.1242/dev.161430.

Enhancer-promoter communication: thinking outside the TAD.

Galupa R, Crocker J

Trends in genetics : TIG, 2020

doi:10.1016/j.tig.2020.04.002.

Multi-enhancer transcriptional hubs confer phenotypic robustness.

Tsai A, Alves MRP, Crocker J

2019

doi:10.7554/eLife.45325.

Visualizing long-range enhancer-promoter interaction.

Tsai A, Crocker J

Nature genetics, 2018

doi:10.1038/s41588-018-0198-5.

Transvection goes live-visualizing enhancer-promoter communication between chromosomes.

Tsai A, Singer RH, Crocker J

Molecular cell, 2018

doi:10.1016/j.molcel.2018.04.004.

Using synthetic biology to study gene regulatory evolution.

Crocker J, Ilsley GR

Current opinion in genetics & development, 2017

doi:10.1016/j.gde.2017.09.001.

Nuclear microenvironments modulate transcription from low-affinity enhancers.

Tsai A, Muthusamy AK, Alves MR, Lavis LD, Singer RH, Stern DL, Crocker J

eLife, 2017

doi:10.7554/elife.28975.

Functional regulatory evolution outside of the minimal even-skipped stripe 2 enhancer.

Crocker J, Stern DL

Development (Cambridge, England), 2017

doi:10.1242/dev.149427.

Genetic and Transgenic Reagents for Drosophila simulans, D-mauritiana, D-yakuba, D-santomea, and D-virilis

Stern DL, Crocker J, Ding Y, Frankel N, Kappes G, Kim E, Kuzmickas R, Lemire A, Mast JD, Picard S

G3-GENES GENOMES GENETICS, 2017

doi:10.1534/g3.116.038885.

A Fully Synthetic Transcriptional Platform for a Multicellular Eukaryote

Crocker J, Tsai A, Stern DL

Cell reports, 2017

doi:10.1016/j.celrep.2016.12.025.

The Soft Touch: Low-Affinity Transcription Factor Binding Sites in Development and Evolution

Crocker J, Noon EP, Stern DL

Current topics in developmental biology, 2016

doi:10.1016/bs.ctdb.2015.11.018.

Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors

Crocker J, Ilsley GR, Stern DL

Nature genetics, 2016

doi:10.1038/ng.3509.

Low affinity binding site clusters confer hox specificity and regulatory robustness

Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, Wang S, Alsawadi A, Valenti P, Plaza S, Payre F, Mann RS, Stern DL

Cell, 2015

doi:10.1016/j.cell.2014.11.041.

TALE-mediated modulation of transcriptional enhancers in vivo

Crocker J, Stern DL

Nature methods, 2013

doi:10.1038/nmeth.2543.

A Schnurri/Mad/Medea complex attenuates the dorsal-twist gradient readout at vnd.

Crocker J, Erives A

Developmental biology, 2013

doi:10.1016/j.ydbio.2013.03.002.

Dynamic evolution of precise regulatory encodings creates the clustered site signature of enhancers.

Crocker J, Potter N, Erives A

Nature communications, 2010

doi:10.1038/ncomms1102.

Evolution acts on enhancer organization to fine-tune gradient threshold readouts.

Crocker J, Tamori Y, Erives A

PLOS BIOLOGY, 2008

doi:10.1371/journal.pbio.0060263.

A Closer Look at the eve Stripe 2 Enhancers of Drosophila and Themira

Crocker J, Erives A

PLOS GENETICS, 2008

doi:10.1371/journal.pgen.1000276.

Chromatin enables precise and scalable gene regulation with factors of limited specificity.

Perkins LM, Crocker J

Proceedings of the National Academy of Sciences , 2024

doi:10.1073/pnas.2411887121.

Spherical harmonics texture extraction for versatile analysis of biological objects.

Gros O, Passmore JB, Borst NO, Kutra D, Nijenhuis W, Fuqua T, Kapitein LC, Crocker JM, Kreshuk A, Köhler S

PLoS computational biology, 2025

doi:10.1371/journal.pcbi.1012349.

Using AI to prevent the insect apocalypse: toward new environmental risk assessment procedures.

Gandara L, Foreman AL, Crocker J

Current opinion in insect science, 2024

doi:10.1016/j.cois.2024.101324.

Pervasive sublethal effects of agrochemicals on insects at environmentally relevant concentrations.

Gandara L, Jacoby R, Laurent F, Spatuzzi M, Vlachopoulos N, Borst NO, Ekmen G, Potel CM, Garrido-Rodriguez M, Böhmert AL, Misunou N, Bartmanski BJ, Li XC, Kutra D, Hériché JK, Tischer C, Zimmermann-Kogadeeva M, Ingham VA, Savitski MM, Masson JB, Zimmermann M, Crocker J

Science (New York, N.Y.), 2024

doi:10.1126/science.ado0251.

TF-High-Evolutionary: in vivo mutagenesis of gene regulatory networks for the study of the genetics and evolution of the Drosophila regulatory genome.

Li XC, Srinivasan V, Laiker I, Misunou N, Frankel N, Pallares LF, Crocker J

Molecular biology and evolution, 2024

doi:10.1093/molbev/msae167.

LarvaTagger: Manual and automatic tagging of drosophila larval behaviour.

Laurent F, Blanc A, May L, Gándara L, Cocanougher BT, Jones BMW, Hague P, Barré C, Vestergaard CL, Crocker J, Zlatic M, Jovanic T, Masson JB

Bioinformatics (Oxford, England), 2024

doi:10.1093/bioinformatics/btae441.

Rapid response of fly populations to gene dosage across development and generations.

Li XC, Gandara L, Ekelöf M, Richter K, Alexandrov T, Crocker J

Nature communications, 2024

doi:10.1038/s41467-024-48960-4.

Interdisciplinary approaches to predicting evolutionary biology.

Crocker J, Payne JL, Walczak AM, Wittkopp PJ

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2023

doi:10.1098/rstb.2022.0042.

Mutational scans reveal differential evolvability of Drosophila promoters and enhancers.

Li XC, Fuqua T, van Breugel ME, Crocker J

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2023

doi:10.1098/rstb.2022.0054.

Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development.

Galupa R, Alvarez-Canales G, Borst NO, Fuqua T, Gandara L, Misunou N, Richter K, Alves MRP, Karumbi E, Perkins ML, Kocijan T, Rushlow CA, Crocker J

Developmental cell, 2023

doi:10.1016/j.devcel.2022.12.003.

Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness.

Gandara L, Tsai A, Ekelöf M, Galupa R, Preger-Ben Noon E, Alexandrov T, Crocker J

Cell reports, 2022

doi:10.1016/j.celrep.2022.111832.