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

Authors: Gandara, Lautaro ¹, Foreman, Amy L ², Crocker, Justin ¹

Source: In Current Opinion in Insect Science April 2025 68

Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development

Authors: Galupa, Rafael, Alvarez-Canales, Gilberto, Borst, Noa Ottilie, Fuqua, Timothy, Gandara, Lautaro, Misunou, Natalia, Richter, Kerstin, Alves, Mariana R.P., Karumbi, Esther, Perkins, Melinda Liu, Kocijan, Tin, Rushlow, Christine A., Crocker, Justin

Source: In Developmental Cell 9 January 2023 58(1):51-62

Spherical harmonics texture extraction for versatile analysis of biological objects.

Authors: Gros, Oane, Passmore, Josiah B., Borst, Noa O., Kutra, Dominik, Nijenhuis, Wilco, Fuqua, Timothy, Kapitein, Lukas C., Crocker, Justin M., Kreshuk, Anna, Köhler, Simone

Source: PLoS Computational Biology; 1/29/2025, Vol. 21 Issue 1, p1-20, 20p

Subject Terms: SPHERICAL projection, SPHERICAL harmonics, CONVEX domains, DROSOPHILA melanogaster, CAENORHABDITIS elegans

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

Authors: Perkins, Mindy Liu¹, Crocker, Justin¹, Tkačik, Gašper² gtkacik@ist.ac.at

Source: Proceedings of the National Academy of Sciences of the United States of America. 1/7/2025, Vol. 122 Issue 1, p1-12. 24p.

Subject Terms: *GENE expression, *GENETIC regulation, *GENE silencing, *GENOME size, *TRANSCRIPTION factors

Enhancer–Promoter Communication: Thinking Outside the TAD

Authors: Galupa, Rafael, Crocker, Justin

Source: In Trends in Genetics July 2020 36(7):459-461

Dynamic evolution of precise regulatory encodings creates the clustered signature of developmental enhancers

Authors: Erives, Albert, Crocker, Justin

Source: Nat Commun. (2010) 1:99

Subject Terms: Quantitative Biology - Populations and Evolution, Quantitative Biology - Cell Behavior, Quantitative Biology - Genomics, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/1004.1028

TF-High-Evolutionary: In Vivo Mutagenesis of Gene Regulatory Networks for the Study of the Genetics and Evolution of the Drosophila Regulatory Genome.

Authors: Li, Xueying C, Srinivasan, Vani, Laiker, Ian, Misunou, Natalia, Frankel, Nicolás, Pallares, Luisa F, Crocker, Justin

Source: Molecular Biology & Evolution; Aug2024, Vol. 41 Issue 8, p1-10, 10p

Subject Terms: GENE regulatory networks, GENETIC testing, TRANSCRIPTION factors, PHENOTYPES, MUTAGENESIS

LarvaTagger: manual and automatic tagging of Drosophila larval behaviour.

Authors: Laurent, François^1,2,3, flaurent@pasteur.fr, Blanc, Alexandre^1,2, May, Lilly^1,4, Gándara, Lautaro⁵, Cocanougher, Benjamin T^6,7,8, Jones, Benjamin M W^6,7,8, Hague, Peter^6,7,8, Barré, Chloé^1,2, Vestergaard, Christian L^1,2, Crocker, Justin⁵, Zlatic, Marta^6,7,8, Jovanic, Tihana⁹, Masson, Jean-Baptiste^1,2

Source: Bioinformatics; Jul2024, Vol. 40 Issue 7, p1-8, 8p

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

Authors: Gandara, Lautaro, Tsai, Albert, Ekelöf, Måns, Galupa, Rafael, Preger-Ben Noon, Ella, Alexandrov, Theodore, Crocker, Justin

Source: Cell reports. 41(11)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190918946.0x000001&indx=1&recIds=ETOCvdc_100190918946.0x000001

Using synthetic biology to study gene regulatory evolution

Authors: Crocker, Justin, Ilsley, Garth R

Source: In Current Opinion in Genetics & Development December 2017 47:91-101

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

Authors: Li, Xueying C., Gandara, Lautaro, Ekelöf, Måns, Richter, Kerstin, Alexandrov, Theodore, Crocker, Justin

Source: Nature Communications; 6/1/2024, Vol. 15 Issue 1, p1-14, 14p

Subject Terms: DEVELOPMENTAL programs, ECOLOGICAL disturbances, MULTICELLULAR organisms, GENE expression, GENES

A Fully Synthetic Transcriptional Platform for a Multicellular Eukaryote

Authors: Crocker, Justin, Tsai, Albert, Stern, David L.

Source: Cell reports. 18(1):287-296

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100129128241.0x000001&indx=1&recIds=ETOCvdc_100129128241.0x000001

Low Affinity Binding Site Clusters Confer Hox Specificity and Regulatory Robustness

Authors: Crocker, Justin, Abe, Namiko, Rinaldi, Lucrezia, McGregor, Alistair P., Frankel, Nicolás, Wang, Shu, Alsawadi, Ahmad, Valenti, Philippe, Plaza, Serge, Payre, François, Mann, Richard S., Stern, David L.

Source: In Cell 15 January 2015 160(1-2):191-203

S264 A Prospective Study Evaluating Cologuard® Ordering in the Community Setting

Authors: Sachdeva, Eesha, Khatri, Vibhuti, Arora, Monica, Crocker, Justin, Jagannath, Sanjay

Source: American journal of gastroenterology. 117(10):e188-e189

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100194745294.0x000001&indx=1&recIds=ETOCvdc_100194745294.0x000001

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

Authors: Crocker, Justin, Noon, Ella Preger-Ben, Stern, David L.

Source: Current topics in developmental biology. 117:455-470

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN606261157&indx=1&recIds=ETOCRN606261157

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

Authors: Crocker, Justin, Erives, Albert

Source: In Developmental Biology 1 June 2013 378(1):64-72

Transvection Goes Live—Visualizing Enhancer-Promoter Communication between Chromosomes

Authors: Tsai, Albert, Singer, Robert H., Crocker, Justin

Source: In Molecular Cell 19 April 2018 70(2):195-196

Narcotic Use and Misuse in Crohn's Disease

Authors: Crocker, Justin A., Yu, Huimin, Conaway, Mark, Tuskey, Anne G., Behm, Brian W.

Source: Inflammatory bowel diseases. 20(12):2234-2238

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100031010799.0x000001&indx=1&recIds=ETOCvdc_100031010799.0x000001

Interdisciplinary approaches to predicting evolutionary biology.

Authors: Crocker, Justin¹ justin.crocker@embl.de, Payne, Joshua L.^2,3, Walczak, Aleksandra M.⁴, Wittkopp, Patricia J.⁵

Source: Philosophical Transactions of the Royal Society B: Biological Sciences. 5/22/2023, Vol. 378 Issue 1877, p1-4. 4p.

Subject Terms: *BIOLOGY, *BIOTIC communities, *BIOLOGICAL evolution, *COMPUTATIONAL biology, *MOLECULAR biology, *PHYSIOLOGICAL adaptation

Mutational scans reveal differential evolvability of Drosophila promoters and enhancers.

Authors: Li, Xueying C., Fuqua, Timothy, van Breugel, Maria Elize, Crocker, Justin

Source: Philosophical Transactions of the Royal Society B: Biological Sciences; 5/22/2023, Vol. 378 Issue 1877, p1-9, 9p

Subject Terms: DROSOPHILA, DROSOPHILA melanogaster, GENE expression, PHENOTYPIC plasticity, COMPARATIVE genomics