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Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms

Benjamin D. Weger, Cédric Gobet, Fabrice P. A. David, Florian Atger, Eva Martin, Nicholas E. Phillips, Aline Charpagne, Meltem Weger, Felix Naef, Frédéric Gachon

Proc Natl Acad Sci U S A. 2021 Jan 19; 118(3): e2015803118. Published online 2021 Jan 15. doi: 10.1073/pnas.2015803118

PMCID:: PMC7826335

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Transcriptional outcomes and kinetic patterning of gene expression in response to NF-κB activation

Mingming Zhao, Jaimy Joy, Weiqiang Zhou, Supriyo De, William H. Wood, III, Kevin G. Becker, Hongkai Ji, Ranjan Sen

PLoS Biol. 2018 Sep; 16(9): e2006347. Published online 2018 Sep 10. doi: 10.1371/journal.pbio.2006347

PMCID:: PMC6147668

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Select item 102594773.

Neural circuit-wide analysis of changes to gene expression during deafening-induced birdsong destabilization

Bradley M Colquitt, Kelly Li, Foad Green, Robert Veline, Michael S Brainard

eLife. 2023; 12: e85970. Published online 2023 Jun 7. doi: 10.7554/eLife.85970

PMCID:: PMC10259477

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Select item 57852114.

Natural changes in light interact with circadian regulation at promoters to control gene expression in cyanobacteria

Joseph Robert Piechura, Kapil Amarnath, Erin K O'Shea

eLife. 2017; 6: e32032. Published online 2017 Dec 14. doi: 10.7554/eLife.32032

PMCID:: PMC5785211

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Select item 50477495.

Chromosome-wide mechanisms to decouple gene expression from gene dose during sex-chromosome evolution

Bayly S Wheeler, Erika Anderson, Christian Frøkjær-Jensen, Qian Bian, Erik Jorgensen, Barbara J Meyer

eLife. 2016; 5: e17365. Published online 2016 Aug 30. doi: 10.7554/eLife.17365

PMCID:: PMC5047749

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Select item 105194066.

Variation in histone configurations correlates with gene expression across nine inbred strains of mice

Anna L. Tyler, Catrina Spruce, Romy Kursawe, Annat Haber, Robyn L. Ball, Wendy A. Pitman, Alexander D. Fine, Narayanan Raghupathy, Michael Walker, Vivek M. Philip, Christopher L. Baker, J. Matthew Mahoney, Gary A. Churchill, Jennifer J. Trowbridge, Michael L. Stitzel, Kenneth Paigen, Petko M. Petkov, Gregory W. Carter

Genome Res. 2023 Jun; 33(6): 857–871. doi: 10.1101/gr.277467.122

PMCID:: PMC10519406

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Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation

Isabel Ferreirós-Vidal, Thomas Carroll, Tianyi Zhang, Vincenzo Lagani, Ricardo N. Ramirez, Elizabeth Ing-Simmons, Alicia G. Gómez-Valadés, Lee Cooper, Ziwei Liang, Georgios Papoutsoglou, Gopuraja Dharmalingam, Ya Guo, Sonia Tarazona, Sunjay J. Fernandes, Peri Noori, Gilad Silberberg, Amanda G. Fisher, Ioannis Tsamardinos, Ali Mortazavi, Boris Lenhard, Ana Conesa, Jesper Tegner, Matthias Merkenschlager, David Gomez-Cabrero

PLoS Biol. 2019 Apr; 17(4): e2006506. Published online 2019 Apr 12. doi: 10.1371/journal.pbio.2006506

PMCID:: PMC6481923

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BRG1 HSA domain interactions with BCL7 proteins are critical for remodeling and gene expression

Nicholas Dietrich, Kevin Trotter, James M Ward, Trevor K Archer

Life Sci Alliance. 2023 May; 6(5): e202201770. Published online 2023 Feb 17. doi: 10.26508/lsa.202201770

PMCID:: PMC9939006

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Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes

Colleen M Palmateer, Catherina Artikis, Savannah G Brovero, Benjamin Friedman, Alexis Gresham, Michelle N Arbeitman

eLife. 2023; 12: e78511. Published online 2023 Feb 1. doi: 10.7554/eLife.78511

PMCID:: PMC9891730

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The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance

Dilip Kumar, Pulugurtha Bharadwaja Kirti

Front Plant Sci. 2023; 14: 1275854. Published online 2023 Oct 30. doi: 10.3389/fpls.2023.1275854

PMCID:: PMC10646159

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Select item 870174811.

Guillaume Bordet, Niraj Lodhi, Andrew Kossenkov, Alexei Tulin

Genes (Basel) 2021 Dec; 12(12): 1982. Published online 2021 Dec 14. doi: 10.3390/genes12121982

PMCID:: PMC8701748

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Gene expression variability in human and chimpanzee populations share common determinants

Benjamin Jung Fair, Lauren E Blake, Abhishek Sarkar, Bryan J Pavlovic, Claudia Cuevas, Yoav Gilad

eLife. 2020; 9: e59929. Published online 2020 Oct 21. doi: 10.7554/eLife.59929

PMCID:: PMC7644215

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Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Alexander L. Cope, Brian C. O’Meara, Michael A. Gilchrist

BMC Genomics. 2020; 21: 370. Published online 2020 May 20. doi: 10.1186/s12864-020-6761-3

PMCID:: PMC7240986

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The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Pedro G. Ferreira, Manuel Muñoz-Aguirre, Ferran Reverter, Caio P. Sá Godinho, Abel Sousa, Alicia Amadoz, Reza Sodaei, Marta R. Hidalgo, Dmitri Pervouchine, Jose Carbonell-Caballero, Ramil Nurtdinov, Alessandra Breschi, Raziel Amador, Patrícia Oliveira, Cankut Çubuk, João Curado, François Aguet, Carla Oliveira, Joaquin Dopazo, Michael Sammeth, Kristin G. Ardlie, Roderic Guigó

Nat Commun. 2018; 9: 490. Published online 2018 Feb 13. doi: 10.1038/s41467-017-02772-x

PMCID:: PMC5811508

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Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes

Rahulsimham Vegesna, Marta Tomaszkiewicz, Paul Medvedev, Kateryna D. Makova

PLoS Genet. 2019 Sep; 15(9): e1008369. Published online 2019 Sep 16. doi: 10.1371/journal.pgen.1008369

PMCID:: PMC6772104

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A concise guide to choosing suitable gene expression systems for recombinant protein production

Anja Schütz, Frank Bernhard, Nick Berrow, Johannes F. Buyel, Frederico Ferreira-da-Silva, Jurgen Haustraete, Joop van den Heuvel, Jan-Erik Hoffmann, Ario de Marco, Yoav Peleg, Sabine Suppmann, Tamar Unger, Martine Vanhoucke, Susanne Witt, Kim Remans

STAR Protoc. 2023 Dec 15; 4(4): 102572. Published online 2023 Oct 31. doi: 10.1016/j.xpro.2023.102572