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Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.
Published in:
Genome Biology & Evolution, 2024, v. 16, n. 4, p. 1, doi. 10.1093/gbe/evae067
By:
- Benham, Phred M;
- Cicero, Carla;
- Escalona, Merly;
- Beraut, Eric;
- Fairbairn, Colin;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sahasrabudhe, Ruta;
- King, Benjamin L;
- Thomas, W Kelley;
- Kovach, Adrienne I;
- Nachman, Michael W;
- Bowie, Rauri C K
Publication type:
Article
Environmental DNA reveals invasive crayfish microbial associates and ecosystem‐wide biodiversity before and after eradication.
Published in:
Environmental DNA, 2024, v. 6, n. 1, p. 1, doi. 10.1002/edn3.445
By:
- Ballare, Kimberly M.;
- Worth, Anna;
- Goodearly, Tyler;
- Ruiz‐Ramos, Dannise V.;
- Beraut, Eric;
- Nava, Hailey;
- Fairbairn, Colin;
- Wayne, Robert K.;
- Shapiro, Beth;
- Short, Ginny;
- Meyer, Rachel S.
Publication type:
Article
A genome assembly of the American black bear, Ursus americanus, from California.
Published in:
Journal of Heredity, 2024, v. 115, n. 5, p. 498, doi. 10.1093/jhered/esae037
By:
- Supple, Megan A;
- Escalona, Merly;
- Adkins, Jillian;
- Buchalski, Michael R;
- Alexandre, Nicolas;
- Sahasrabudhe, Ruta M;
- Nguyen, Oanh;
- Sacco, Samuel;
- Fairbairn, Colin;
- Beraut, Eric;
- Seligmann, William;
- Green, Richard E;
- Meredith, Erin;
- Shapiro, Beth
Publication type:
Article
A highly contiguous genome assembly for the Yellow Warbler (Setophaga petechia).
Published in:
Journal of Heredity, 2024, v. 115, n. 3, p. 317, doi. 10.1093/jhered/esae008
By:
- Tsai, Whitney L E;
- Escalona, Merly;
- Garrett, Kimball L;
- Terrill, Ryan S;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Beraut, Eric;
- Seligmann, William;
- Fairbairn, Colin W;
- Harrigan, Ryan J;
- McCormack, John E;
- Alfaro, Michael E;
- Smith, Thomas B;
- Bay, Rachael A
Publication type:
Article
The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.
Published in:
Journal of Heredity, 2024, v. 115, n. 2, p. 221, doi. 10.1093/jhered/esae002
By:
- Mead, Alayna;
- Fitz-Gibbon, Sorel T;
- Escalona, Merly;
- Beraut, Eric;
- Sacco, Samuel;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sork, Victoria L
Publication type:
Article
The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.
Published in:
Journal of Heredity, 2023, v. 114, n. 6, p. 707, doi. 10.1093/jhered/esad052
By:
- Adams, Julia N;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Fairbairn, Colin W;
- Beraut, Eric;
- Seligmann, William;
- Nguyen, Oanh;
- Chumchim, Noravit;
- Stajich, Jason E
Publication type:
Article
A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.
Published in:
Journal of Heredity, 2023, v. 114, n. 6, p. 690, doi. 10.1093/jhered/esad051
By:
- Westeen, Erin P;
- Escalona, Merly;
- Beraut, Eric;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Fisher, Robert N;
- Toffelmier, Erin;
- Shaffer, H Bradley;
- Wang, Ian J
Publication type:
Article
De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica.
Published in:
Journal of Heredity, 2023, v. 114, n. 6, p. 669, doi. 10.1093/jhered/esad047
By:
- DeRaad, Devon A;
- Escalona, Merly;
- Benham, Phred M;
- Marimuthu, Mohan P A;
- Sahasrabudhe, Ruta M;
- Nguyen, Oanh;
- Chumchim, Noravit;
- Beraut, Eric;
- Fairbairn, Colin W;
- Seligmann, William;
- Bowie, Rauri C K;
- Cicero, Carla;
- McCormack, John E;
- Wayne, Robert K
Publication type:
Article
A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex.
Published in:
Journal of Heredity, 2023, v. 114, n. 6, p. 681, doi. 10.1093/jhered/esad045
By:
- Westeen, Erin P;
- Escalona, Merly;
- Holding, Matthew L;
- Beraut, Eric;
- Fairbairn, Colin;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Perri, Ralph;
- Fisher, Robert N;
- Toffelmier, Erin;
- Shaffer, H Bradley;
- Wang, Ian J
Publication type:
Article
A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri).
Published in:
Journal of Heredity, 2023, v. 114, n. 5, p. 549, doi. 10.1093/jhered/esad042
By:
- Benham, Phred M;
- Cicero, Carla;
- DeRaad, Devon A;
- McCormack, John E;
- Wayne, Robert K;
- Escalona, Merly;
- Beraut, Eric;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Nachman, Michael W;
- Bowie, Rauri C K
Publication type:
Article
Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.
Published in:
Journal of Heredity, 2023, v. 114, n. 5, p. 521, doi. 10.1093/jhered/esad037
By:
- Bishop, Anusha P;
- Westeen, Erin P;
- Yuan, Michael L;
- Escalona, Merly;
- Beraut, Eric;
- Fairbairn, Colin;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Chumchim, Noravit;
- Toffelmier, Erin;
- Fisher, Robert N;
- Shaffer, H. Bradley;
- Wang, Ian J
Publication type:
Article
Reference genome of California walnut, Juglans californica, and resemblance with other genomes in the order Fagales.
Published in:
Journal of Heredity, 2023, v. 114, n. 5, p. 570, doi. 10.1093/jhered/esad036
By:
- Fitz-Gibbon, Sorel;
- Mead, Alayna;
- O'Donnell, Scott;
- Li, Zhi-Zhong;
- Escalona, Merly;
- Beraut, Eric;
- Sacco, Samuel;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sork, Victoria L
Publication type:
Article
Chromosome-level reference genome of stinkwort, Dittrichia graveolens (L.) Greuter: A resource for studies on invasion, range expansion, and evolutionary adaptation under global change.
Published in:
Journal of Heredity, 2023, v. 114, n. 5, p. 561, doi. 10.1093/jhered/esad033
By:
- McEvoy, Susan L;
- Lustenhouwer, Nicky;
- Melen, Miranda K;
- Nguyen, Oanh;
- Marimuthu, Mohan P A;
- Chumchim, Noravit;
- Beraut, Eric;
- Parker, Ingrid M;
- Meyer, Rachel S
Publication type:
Article
Reference genome of an iconic lizard in western North America, Blainville's horned lizard Phrynosoma blainvillii.
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 410, doi. 10.1093/jhered/esad032
By:
- Richmond, Jonathan Q;
- McGuire, Jimmy A;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Toffelmier, Erin;
- Fisher, Robert N;
- Wang, Ian J;
- Shaffer, H Bradley
Publication type:
Article
Reference genome for the American rubyspot damselfly, Hetaerina americana.
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 385, doi. 10.1093/jhered/esad031
By:
- Grether, Gregory F;
- Beninde, Joscha;
- Beraut, Eric;
- Chumchim, Noravit;
- Escalona, Merly;
- MacDonald, Zachary G;
- Miller, Courtney;
- Sahasrabudhe, Ruta;
- Shedlock, Andrew M;
- Toffelmier, Erin;
- Shaffer, H Bradley
Publication type:
Article
Reference genome of the Virginia rail, Rallus limicola.
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 428, doi. 10.1093/jhered/esad026
By:
- Hall, Laurie A;
- Wang, Ian J;
- Escalona, Merly;
- Beraut, Eric;
- Sacco, Samuel;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Toffelmier, Erin;
- Shaffer, H Bradley;
- Beissinger, Steven R
Publication type:
Article
Reference genome of the black rail, Laterallus jamaicensis.
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 436, doi. 10.1093/jhered/esad025
By:
- Hall, Laurie A;
- Wang, Ian J;
- Escalona, Merly;
- Beraut, Eric;
- Sacco, Samuel;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Toffelmier, Erin;
- Shaffer, H Bradley;
- Beissinger, Steven R
Publication type:
Article
A highly contiguous genome assembly for the California quail (Callipepla californica).
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 418, doi. 10.1093/jhered/esad008
By:
- Benham, Phred M;
- Cicero, Carla;
- Escalona, Merly;
- Beraut, Eric;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Nachman, Michael W;
- Bowie, Rauri C K
Publication type:
Article
Reference genome of the long-jawed orb-weaver, Tetragnatha versicolor (Araneae: Tetragnathidae).
Published in:
Journal of Heredity, 2023, v. 114, n. 4, p. 395, doi. 10.1093/jhered/esad013
By:
- Adams, Seira A;
- Graham, Natalie R;
- Holmquist, Anna J;
- Sheffer, Monica M;
- Steigerwald, Emma C;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Beraut, Eric;
- Fairbairn, Colin;
- Sacco, Samuel;
- Seligmann, William;
- Escalona, Merly;
- Shaffer, H Bradley;
- Toffelmier, Erin;
- Gillespie, Rosemary G
Publication type:
Article
Reference genome of the Woolly Sculpin, Clinocottus analis.
Published in:
Journal of Heredity, 2023, v. 114, n. 1, p. 60, doi. 10.1093/jhered/esac055
By:
- Wright, Daniel B;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Toffelmier, Erin;
- Miller, Courtney;
- Shaffer, H Bradley;
- Bernardi, Giacomo
Publication type:
Article
Reference genome of the Monkeyface Prickleback, Cebidichthys violaceus.
Published in:
Journal of Heredity, 2023, v. 114, n. 1, p. 52, doi. 10.1093/jhered/esac054
By:
- Wright, Daniel B;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Toffelmier, Erin;
- Miller, Courtney;
- Shaffer, H Bradley;
- Bernardi, Giacomo;
- German, Donovan P
Publication type:
Article
Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 712, doi. 10.1093/jhered/esac052
By:
- Anghel, Ioana G;
- Jacobs, Sarah J;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Fairbairn, Colin W;
- Beraut, Eric;
- Nguyen, Oanh;
- Toffelmier, Erin;
- Shaffer, H Bradley;
- Zapata, Felipe
Publication type:
Article
Reference genome assembly of the sunburst anemone, Anthopleura sola.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 699, doi. 10.1093/jhered/esac050
By:
- Cornwell, Brendan H;
- Beraut, Eric;
- Fairbairn, Colin;
- Nguyen, Oanh;
- Marimuthu, Mohan P A;
- Escalona, Merly;
- Toffelmier, Erin
Publication type:
Article
Reference genome of the rubber boa, Charina bottae (Serpentes: Boidae).
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 641, doi. 10.1093/jhered/esac048
By:
- Grismer, Jesse L;
- Escalona, Merly;
- Miller, Courtney;
- Beraut, Eric;
- Fairbairn, Colin W;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Toffelmier, Erin;
- Wang, Ian J;
- Shaffer, H Bradley
Publication type:
Article
draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 673, doi. 10.1093/jhered/esac047
By:
- Griffiths, Joanna S;
- Sahasrabudhe, Ruta M;
- Marimuthu, Mohan P A;
- Chumchim, Noravit;
- Nguyen, Oanh H;
- Beraut, Eric;
- Escalona, Merly;
- Whitehead, Andrew
Publication type:
Article
chromosome-level reference genome for the giant pink sea star, Pisaster brevispinus, a species severely impacted by wasting.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 689, doi. 10.1093/jhered/esac044
By:
- DeBiasse, Melissa B;
- Schiebelhut, Lauren M;
- Escalona, Merly;
- Beraut, Eric;
- Fairbairn, Colin;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sahasrabudhe, Ruta;
- Dawson, Michael N
Publication type:
Article
Reference genome of the California glossy snake, Arizona elegans occidentalis: A declining California Species of Special Concern.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 632, doi. 10.1093/jhered/esac040
By:
- Wood, Dustin A;
- Richmond, Jonathan Q;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Westphal, Michael;
- Fisher, Robert N;
- Vandergast, Amy G;
- Toffelmier, Erin;
- Wang, Ian J;
- Shaffer, H Bradley
Publication type:
Article
Reference Genome of the Black Surfperch, Embiotoca jacksoni (Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 657, doi. 10.1093/jhered/esac034
By:
- Bernardi, Giacomo;
- Toy, Jason A;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Toffelmier, Erin;
- Miller, Courtney;
- Shaffer, H Bradley
Publication type:
Article
Reference Genome of the California Sheephead, Semicossyphus pulcher (Labridae, Perciformes), A Keystone Fish Predator in Kelp Forest Ecosystems.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 649, doi. 10.1093/jhered/esac032
By:
- Bernardi, Giacomo;
- DeBiasse, Melissa;
- Escalona, Merly;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Sacco, Samuel;
- Beraut, Eric;
- Miller, Courtney;
- Toffelmier, Erin;
- Shaffer, H Bradley
Publication type:
Article
Reference Genome Assembly of the Bobcat, Lynx rufus.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 615, doi. 10.1093/jhered/esac031
By:
- Lin, Meixi;
- Escalona, Merly;
- Sahasrabudhe, Ruta;
- Nguyen, Oanh;
- Beraut, Eric;
- Buchalski, Michael R;
- Wayne, Robert K
Publication type:
Article
Reference Genome of the Northwestern Pond Turtle, Actinemys marmorata.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 624, doi. 10.1093/jhered/esac021
By:
- Todd, Brian D;
- Jenkinson, Thomas S;
- Escalona, Merly;
- Beraut, Eric;
- Nguyen, Oanh;
- Sahasrabudhe, Ruta;
- Scott, Peter A;
- Toffelmier, Erin;
- Wang, Ian J;
- Shaffer, H Bradley
Publication type:
Article
Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii.
Published in:
Journal of Heredity, 2022, v. 113, n. 6, p. 665, doi. 10.1093/jhered/esac024
By:
- Orland, Chloé;
- Escalona, Merly;
- Sahasrabudhe, Ruta;
- Marimuthu, Mohan P A;
- Nguyen, Oanh;
- Beraut, Eric;
- Marshman, Blythe;
- Moore, James;
- Raimondi, Peter;
- Shapiro, Beth
Publication type:
Article
Experimental DNA demethylation associates with changes in growth and gene expression of oak tree seedlings.
Published in:
G3: Genes | Genomes | Genetics, 2020, v. 10, n. 3, p. 1, doi. 10.1534/g3.119.400770
By:
- Browne, Luke;
- Mead, Alayna;
- Horn, Courtney;
- Chang, Kevin;
- Celikkol, Zeynep;
- Henriquez, Claudia;
- Feiyang Ma;
- Beraut, Eric;
- Meyer, Rachel;
- Sork, Victoria L.
Publication type:
Article

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