Tumbling Oysters

The Pathogen Has a Plan, the Hosts Do Not

Genomics

Comparing three sea star genomes against the Vibrio pectenicida arsenal, and coming up mostly empty

62 CpGs Separate Quihua From Rio Pudeto

Epigenetics

Genomics

Site-level differential methylation in Ostrea chilensis at 4x coverage

Three Ostrea chilensis Assemblies Walk Into a Dot Plot

Genomics

Computing

minimap2 whole-genome comparison of Assembly 1.0, HapA, and HapB

What Genes Reveal About Sea Star Wasting Disease

Transcriptomics

Genomics

Comparing the disease response of three sea star species through shared genes

Reading Methylation on Each Fish’s Own Genome

Genomics

Computing

DNA methylation is a chemical “annotation” layered on top of the DNA sequence — small tags (methyl groups) attached to certain letters that can turn genes up or down without…

The case of the missing mussel

Genomics

Computing

recovering a lost sample and mapping the mussel methylome

Two-Genome Evidence

Genomics

Computing

Reciprocal PAV, Ecotype-Specific Genes, and What Survives

Mapping Structural Differences Between Lean and Siscowet Genomes

Genomics

Computing

Lean and siscowet lake trout are two ecotypes of the same species that look and behave differently — siscowet are deep-water, fat-rich fish; lean are shallower-water and…

Beyond AUC

Aquaculture

Computing

Looking at other curve aspects: a teaser

Gene-Anchored Synteny Between Lean and Siscowet Lake Trout

Computing

Genomics

Purging haplotigs, re-lifting genes, and building MCScanX synteny maps from shared gene IDs

Liftoff Annotation of Lean & Siscowet Lake Trout Ecotype Assemblies

Genomics

Computing

Transferring the SaNama_1.0 annotation onto two PacBio HiFi ecotype assemblies with Liftoff

Oyster Priming Week 3

Aquaculture

From DMRs and Deletions to Candidate Genes in Lake Trout

Computing

Genomics

Epigenetics

Annotating differential methylation and PAVs, then reasoning about lean vs siscowet phenotype

Oyster Priming Week 2

Aquaculture

The FTR Edition

Guidelines for Pathogen Detection Using qPCR in Aquatic Systems

Aquaculture

Reading Notes

A practical framework generalized from the Dermo and QPX assay-development work, aligned to MIQE

Mortality Trial on Wescott Oysters

Aquaculture

Weekly and Daily leftovers

Mortality Trial on SORMI Oysters

Aquaculture

Heating up in the incubator

Mortality Trial on Manchester Oysters

Aquaculture

Heating up in the incubator

Setting up 2026 prime

Aquaculture

Initial YC25 Oyster assay runs

Aquaculture

Over the past month we have ran some initial SORMI assays on the USDA YC25 families.

Merry Linkmas

Lab Updates

Computing

Here are few tidbits to bring you cheer this Christmas Season!

Barnacle

Transcriptomics

more lamda values

Coefficient of Gene Expression and GBM

Epigenetics

Transcriptomics

and expression distribution by methylation

Context dependent DNA methylation :: miRNA regulation of gene expression

Epigenetics

Transcriptomics

Plotting Biomineralization Gene Expression vs Gene Body Methylation in Three Coral Species

Epigenetics

Transcriptomics

Barnacle

Transcriptomics

Calcifying Contra

Transcriptomics

Calcification Count Matrices

Transcriptomics

filtering timeseries

Timeseries Gene Level methylation

Epigenetics

Transcriptomics

Biomineraliztion in dark matter

Transcriptomics

where in the WGCBNA and barnacle?

Functional annotation summary for WGCNA modules

Genomics

Transcriptomics

GOing with more

Contra on 24

Transcriptomics

Epigenetic factors on barnacle

More Random Please

Transcriptomics

GOing with more

More Sparsity?

Transcriptomics

Optimizing Rank 35

Deep Dive on Rank 35

Transcriptomics

Going through barnacle rank gene factors

Lets talk Cod

Epigenetics

Transcriptomics

A check-in with data files

Lake Trout PacBio Data

Epigenetics

QC

Ortholog Selection for Physiological Processes

Genomics

Selecting orthologs based on metabolic and reproductive GO terms

MOSAiC orthologs

Genomics

Next leveling RNAseq

Aquaculture

Transcriptomics

MinION nanopore sequencing analysis

Getting on with Nanopore cDNA data

Aquaculture

Transcriptomics

MinION nanopore sequencing analysis

Oyster Pickup and Cleaning

Aquaculture

Point Whitney shellfish operations

Cod alignment

Genomics

BWA alignment for cod genomic analysis

The lncRNA repertoire of Ptuh

Transcriptomics

Long non-coding RNA repertoire analysis

ROL-PI Day three

Epigenetics

Más sequence files to bismark, por favor

ROL-PI Day two

Epigenetics

Más CpGs, por favor

ROL-PI Day one

Epigenetics

Más citas, por favor

CpG Intersect

Epigenetics

Apul Motifs and matches

Megan it

Genomics

taxa id from seq reads

Energy staging

Epigenetics

Can we predict where they are on the curve?

Getting to GO with Phenotype

Genomics

A short list for machine learning

OA OA OA

Epigenetics

Aquaculture

Bringing diploid - triploid to an end?

Long non-coding RNA discovery pipeline

Transcriptomics

Long non-coding RNA discovery pipeline implementation

Please Klone me

Computing

Getting on the RStudio Klone machine

Apul Time Series Methylation

Epigenetics

It’s in the name…

We wish you a Merry Mytilus!

Epigenetics

Differentially methylated loci on PAHs

Time-series coral lncRNA count matrix

Transcriptomics

Coral lncRNA count matrix generation and analysis pathway

Mytilus DNA methylation calls

Epigenetics

associated with contaminants

Hip Hip Array

Epigenetics

Computing

Knocking out the code to get bismark happy

Running Bismark in SLURM Array for Methylation Analysis

Epigenetics

Computing

Bismark array processing workflow

Stats on E5 genomes

Genomics

Welcoming new Pulcra genome statistics

Connecting annotations

Genomics

Transcriptomics

Challenges post-HiSat

Re-prime

Aquaculture

Giving 10k seed more resiliency

R N A T O G O

Genomics

On the Roan to assigning GO to genes

Git that Pro GO

Genomics

Deep dive into protein annotation

Double header

Aquaculture

larvae, ploidy, and 10k seed start

Oyster bath

Aquaculture

When is it too hot?

Huddl Launch

Aquaculture

First of season day 3 larvae are a go!

Repro Repro

Genomics

Pipeline for Reproduction Annotation

Spring Cleaning

Aquaculture

Getting ready for spawning

Seed travels

Aquaculture

The Wescott Bay deployment

HiSat that SeaStar

Transcriptomics

finally overcoming gtf h$11

xargs

Computing

now with no reason for loops

That escalated quickly

Computing

going from 1 line script to cronning a sys log

Working with IGV

Genomics

IGV visualization for cod analysis

Getting appropriate IDs for Gene, Transcripts

Genomics

for cod, looking ahead to Uniprot Accessions

Differentially Expressed Transcripts

Transcriptomics

Differentially expressed transcripts in cod

Differentially Expressed Genes

Transcriptomics

Differentially expressed genes in cod

Looking at Apul miRNA

Transcriptomics

Genomics

Coral miRNA visualization in IGV

HiSat

Transcriptomics

Genome files

Genomics

Cod genome files and datasets

Launching more stress

Aquaculture

starting new seed and adult hardening

What I have been up to today

Lab Updates

February Daily

Lab Updates

Your text here…

Apul lncRNA Discovery

Transcriptomics

Coral long non-coding RNA discovery and analysis

November Daily

Lab Updates

Went to hatchery to clean oysters. A couple of pipes in control fell. Temperature was 13.9. Installed header heater to 16.

Correlating Matrices

Epigenetics

Genomics

Matrix correlation analysis for methylation and SNP data

Peve lncRNA alignment

Transcriptomics

Sea star long non-coding RNA alignment and characterization

Epidiverse GRM

Genomics

Computing

Re-evaluating the GRM

Myt Iso-seq Annotation

Genomics

Mytilus isothermal sequencing annotation workflow

ggplotting some qPCR

Transcriptomics

Computing

quick take on graphing out some of Noah’s data

Mytilus Iso-seq Data check

Transcriptomics

Lets take look at Isoseq fasta

DNA Methylation and Species/Tissue Specific Considerations

Reading Notes

Epigenetics

Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases

Epigenetic mechanisms in marine invertebrates

Reading Notes

Epigenetics

Trigg, S. A., Y. R. Venkataraman, M. R. Gavery, S. B. Roberts, D. Bhattacharya, A. Downey‐Wall, J. M. Eirin‐Lopez, K. M. Johnson, K. E. Lotterhos, J. B. Puritz, and H. M.…

Celeste Valdivia

DNA Methylation Analysis Methods

Epigenetics

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Tutorial #5 Reflection

Reading Notes

Epigenetics

For the last week of our tutorial, we came back to DNA methylation and read another Roberts lab joint: https://doi.org/10.1111/1755-0998.13542

Grace Leuchtenberger

Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

Reading Notes

Transcriptomics

Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra

The Role of DNA Methylation and Context Dependence

Reading Notes

Epigenetics

Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?

Molecular stress responses in marine intertebrates

Reading Notes

Roberts, S. B., and M. R. Gavery. 2012. Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? Frontiers in Physiology 2. https://doi.org…

Celeste Valdivia

Tutorial #4: DNA Methylation Station

Reading Notes

Epigenetics

For our tutorial this week, I read the paper assigned to everyone, a Roberts lab special:

Grace Leuchtenberger

Molecular stress responses in marine intertebrates

Reading Notes

Two weeks ago members of our FISH 600 reading group were asked to select papers to present that cited the following paper:

Celeste Valdivia

DNA Methylation Synthesis

Reading Notes

Epigenetics

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New Family on the Block

Week 4 Reflection

Reading Notes

This week we read Gleason & Burton’s 2015 RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snail Chlorostoma funebralis and found…

Tutorial #2 Reflection

Reading Notes

Last week, almost all the papers we talked about looked at different living conditions for marine invertebrates and how that influences gene expression or gene regulation.…

Grace Leuchtenberger

Genetics: Does it really matter?

Reading Notes

Epigenetics

Here I will describe a recent, cool paper and try to also highlight 1) some of the material covered in our class on Proposal Writing and Professional Development, and 2)…

Post With Code

Computing

This is a post with executable code.

Welcome To My Blog

Lab Updates

This is the first post in a Quarto blog. Welcome!

Tristan O’Malley