Dr. Yocca (@Aeyocca) header
Dr. Yocca (@Aeyocca) profile picture

Dr. Yocca

@Aeyocca

Bayer Crop Science | Genomics Data Scientist | PhD | Complacent career student

Joined October 2013
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Alan's law of biology manuscripts: if a study species is never mentioned, or first mentioned after the first 500 words, it's humans
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I’m excited to share our preprint presenting a haplotype-resolved genome assembly for Amborella trichopoda, including phased ZW sex chromosomes!
A GENESPACE plot showing sliding windows of the gene and repeat landscape of all 13 chromosomes in both Amborella haplotypes. In Amborella, the chromosome arms are gene dense and the repeats increase towards the centromere. The haploypes are highly syntenic to one another, though some structural variants, like INDELs are visible. A second panel below zooms in on the non-recombining region of the sex chromosomes on Chr09. Here a peak of female-specific k-mers is plotted on haplotype 1, identifying it as the W chromosome. Some structural variants are shown between the W and Z, most notably a small inversion at the beginning of the non-recombining region.

ALT A GENESPACE plot showing sliding windows of the gene and repeat landscape of all 13 chromosomes in both Amborella haplotypes. In Amborella, the chromosome arms are gene dense and the repeats increase towards the centromere. The haploypes are highly syntenic to one another, though some structural variants, like INDELs are visible. A second panel below zooms in on the non-recombining region of the sex chromosomes on Chr09. Here a peak of female-specific k-mers is plotted on haplotype 1, identifying it as the W chromosome. Some structural variants are shown between the W and Z, most notably a small inversion at the beginning of the non-recombining region.

bioRxiv Genomics (@biorxiv_genomic) profile picturebioRxiv Genomics@biorxiv_genomic14 May 2024
ZW sex chromosome structure in Amborella trichopoda biorxiv.org/cgi/content/shor… #biorxiv_genomic
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Our Granny 🍏 manuscript is out on BioRxiv! Granny is not only a delicious apple that we all love, it’s also a machine learning and computer vision to detect fruit quality traits. biorxiv.org/content/10.1101/…
Rating Pome Fruit Quality Traits Using Deep Learning and Image Processing

Rating Pome Fruit Quality Traits Using Deep Learning and Image Processing

Quality assessment of pome fruits ( i.e. apples and pears) is used not only crucial for determining the optimal harvest time, but also the progression of fruit-quality attributes during storage....

biorxiv.org
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In May I will be starting my dream job at Bayer Crop Science @Bayer4CropsUS as a Genomics Data Scientist with Rebecca Lowdon's (@rebeccalowdon) team. I'm excited to work towards Health for all, Hunger for none while continuing to work with plant genomics. (1/5)
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I empathize with those on the academic job market because its certainly more difficult to obtain those positions. Thanks to the endless support and understanding from my advisors @aeharkess and Loren Honaas along with friends' help, I am lucky enough to get this opportunity (4/5)
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If you are currently or recently on the job market, check out and populate this repository if you can. My CV and job talk seem much less impressive than most in there. github.com/RILAB/statements (5/5)
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We’re excited to share the first publication of the ACTG: American Campus Tree Genomes Initiative! 🧵⤵️
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Thanks @GeneticsGSA for the ACTG-themed postcards at PAG! We're thrilled to partner together to put more ACTG courses in G3 Genome Reports and continue training students in long-read @PacBio assembly, annotation, and publication to democratize cutting-edge genomics.
Image from Alex Harkess (@aeharkess)
Image from Alex Harkess (@aeharkess)
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And here is our ‘WA 38’ genome, second ACTG genome close to publication!
Image from Huiting Zhang (@Yannian120)
Alex Harkess (@aeharkess) profile pictureAlex Harkess@aeharkess16 Jan 2024
Thanks @GeneticsGSA for the ACTG-themed postcards at PAG! We're thrilled to partner together to put more ACTG courses in G3 Genome Reports and continue training students in long-read @PacBio assembly, annotation, and publication to democratize cutting-edge genomics.
Image from Alex Harkess (@aeharkess)
Image from Alex Harkess (@aeharkess)
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The Harkess Lab @hudsonalpha is well-represented at #PAG31! Talks and posters galore! Come talk to us about all things plant reproductive biology 🍎🌸🧬 🌱@aeharkess @nature_of_words @sarahbcarey @Aeyocca
Image from Charity Goeckeritz, PhD (@CherrityG)
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A Phased, Chromosome-scale Genome for Malus domestica 'WA 38'. #AppleCultivarGenome #ChromosomeLevelAssembly #PassedGenome @biorxivpreprint biorxiv.org/content/10.1101/…
A Phased, Chromosome-scale Genome for Malus domestica ‘WA 38’

A Phased, Chromosome-scale Genome for Malus domestica ‘WA 38’

Genome sequencing for agriculturally important Rosaceous crops has made rapid progress both in completeness and annotation quality. Whole genome sequence and annotation gives breeders, researchers,...

biorxiv.org
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Glad to see Vaccinium in the pangenoma era. Great team work. Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts academic.oup.com/hr/article/…
Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts

Abstract. Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavor

academic.oup.com
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I am looking for a freelance remote informatician to help refine and improve our labs computational pipelines for sex testing and custom marker development, and build customer-facing deliverables. Please spread to anyone and reach out to me via email or DM.
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I'm proud that our first @NSF funded ACTG: American Campus Tree Genomes manuscript is live. We trained 20 scientists (undergrad/PhD/other) in plant genome assembly, annotation, analysis. This manuscript details the d'Anjou pear genome, driven by postdoc @Aeyocca who co-taught.
Image from Alex Harkess (@aeharkess)
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So grateful to share my research on sex determination in Morella species this year at #PlantBio2023. Come check out my poster at 800-125!
Image from Laramie (Smith) Aközbek (@nature_of_words)
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Also come check out the fantastic posters from our lab mates on @hmueller_96’s duckweed genome, @Zach_Meharg’s dahlia genome, @Aeyocca’s Rosaceae genomes, and Caroline Bendickson’s Trillium phylogeny! All also in the 800 block #PlantBio2023!
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New preprint for the Vaccinium "super" pangenome from The Vaccinium Coordinated Agricultural Project (VacCAP) vacciniumcap.org/ ! biorxiv.org/cgi/content/shor… (1/6)
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A huge endeavor was made to create these data accessible through vaccinium.org. You can analyze individual genomes or access the multiple sequence alignment to investigate structural variants and sequence polymorphisms. (5/6)
Image from Dr. Yocca (@Aeyocca)
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Special thank you to all of the coauthors and the VacCAP (too many to tag and I don't want to miss any, feel free to quote tweet if you helped!). This is the final chapter of my dissertation and it seems like 16 months after graduating isn't that late. (6/6)
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