Tumbling Oysters
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Ortholog Selection for Physiological Processes

e5
coral

Selecting orthologs based on metabolic and reproductive GO terms

Oct 4, 2025
Steven Roberts

MOSAiC orthologs

e5
coral

reciping

Aug 31, 2025
Steven Roberts

Next leveling RNAseq

oyster
chile

MinION nanopore sequencing analysis

Aug 4, 2025
Steven Roberts

Getting on with Nanopore cDNA data

oyster
chile

MinION nanopore sequencing analysis

Aug 1, 2025
Steven Roberts

Oyster Pickup and Cleaning

oyster
aquaculture

Point Whitney shellfish operations

Jul 23, 2025
Steven Roberts

Cod alignment

cod
wgs

BWA alignment for cod genomic analysis

Jul 8, 2025
Steven Roberts

The lncRNA repertoire of Ptuh

lncRNA
e5

Long non-coding RNA repertoire analysis

Jun 21, 2025
Steven Roberts

ROL-PI Day three

methylation
e5

Más sequence files to bismark, por favor

May 26, 2025
Steven Roberts

ROL-PI Day two

methylation
e5

Más CpGs, por favor

May 24, 2025
Steven Roberts

ROL-PI Day one

methylation
e5

Más citas, por favor

May 24, 2025
Steven Roberts

CpG Intersect

methylation
e5

Apul Motifs and matches

May 15, 2025
Steven Roberts

Megan it

eDNA
fish546

taxa id from seq reads

May 5, 2025
Steven Roberts

Energy staging

e5
methylation

Can we predict where they are on the curve?

Apr 10, 2025
Steven Roberts

Getting to GO with Phenotype

e5
GO

A short list for machine learning

Mar 21, 2025
Steven Roberts

OA OA OA

oyster
methylation

Bringing diploid - triploid to an end?

Mar 12, 2025
Steven Roberts

Long non-coding RNA discovery pipeline

e5
lncRNA

Long non-coding RNA discovery pipeline implementation

Feb 28, 2025
Steven Roberts

Please Klone me

hyak
hpc
RStudio

Getting on the RStudio Klone machine

Feb 19, 2025
Steven Roberts

Apul Time Series Methylation

e5
methylation
coral
bismark

It’s in the name…

Feb 8, 2025
Steven Roberts

We wish you a Merry Mytilus!

mytilus
methylation
methylkit

Differentially methylated loci on PAHs

Dec 24, 2024
Steven Roberts

Time-series coral lncRNA count matrix

e5
lncRNA

Coral lncRNA count matrix generation and analysis pathway

Dec 20, 2024
Steven Roberts

Mytilus DNA methylation calls

mytilus
methylation
bismark

associated with contaminants

Dec 19, 2024
Steven Roberts

Hip Hip Array

methylation
klone

Knocking out the code to get bismark happy

Nov 20, 2024
Steven Roberts

Running Bismark in SLURM Array for Methylation Analysis

methylation
klone

Bismark array processing workflow

Nov 10, 2024
Steven Roberts

Stats on E5 genomes

e5

Welcoming new Pulcra genome statistics

Oct 5, 2024
Steven Roberts

Connecting annotations

blast
hisat
annotation

Challenges post-HiSat

Oct 3, 2024
Steven Roberts

Re-prime

oyster
stress

Giving 10k seed more resiliency

Sep 14, 2024
Steven Roberts

R N A T O G O

blast
e5

On the Roan to assigning GO to genes

Aug 27, 2024
Steven Roberts

Git that Pro GO

blast
e5

Deep dive into protein annotation

Aug 25, 2024
Steven Roberts

Double header

oyster
temperature

larvae, ploidy, and 10k seed start

Jun 26, 2024
Steven Roberts

Oyster bath

oyster
temperature

When is it too hot?

Jun 20, 2024
Steven Roberts

Huddl Launch

oyster
aquaculture

First of season day 3 larvae are a go!

Jun 17, 2024
Steven Roberts

Repro Repro

blast
GO

Pipeline for Reproduction Annotation

Jun 15, 2024
Steven Roberts

Spring Cleaning

oyster
aquaculture

Getting ready for spawning

Jun 12, 2024
Steven Roberts

Seed travels

oyster
aquaculture

The Wescott Bay deployment

Jun 7, 2024
Steven Roberts

HiSat that SeaStar

hisat
seastar

finally overcoming gtf h$11

Jun 3, 2024
Steven Roberts

xargs

xargs

now with no reason for loops

May 27, 2024
Steven Roberts

That escalated quickly

cron
rsync
log

going from 1 line script to cronning a sys log

May 27, 2024
Steven Roberts

Working with IGV

R
igv
cod

IGV visualization for cod analysis

May 23, 2024
Steven Roberts

Getting appropriate IDs for Gene, Transcripts

R
blast
cod

for cod, looking ahead to Uniprot Accessions

May 21, 2024
Steven Roberts

Differentially Expressed Transcripts

R
datasets
cod

Differentially expressed transcripts in cod

May 21, 2024
Steven Roberts

Differentially Expressed Genes

R
datasets
cod

Differentially expressed genes in cod

May 21, 2024
Steven Roberts

Looking at Apul miRNA

R
datasets
cod

Coral miRNA visualization in IGV

May 16, 2024
Steven Roberts

HiSat

R
hisat

to DESeq

May 14, 2024
Steven Roberts

Genome files

R
datasets
cod

Cod genome files and datasets

May 13, 2024
Steven Roberts

Launching more stress

oyster
hardening
aquaculture

starting new seed and adult hardening

Mar 11, 2024
Steven Roberts

What I have been up to today

thoughts

rewind

Feb 8, 2024
Steven Roberts

February Daily

notebook
Your text here…
Feb 1, 2024
Steven Roberts

Apul lncRNA Discovery

deepdive
R
lncRNA
e5

Coral long non-coding RNA discovery and analysis

Nov 3, 2023
Steven Roberts

November Daily

notebook
Went to hatchery to clean oysters. A couple of pipes in control fell. Temperature was 13.9. Installed header heater to 16.
Nov 1, 2023
Steven Roberts

Correlating Matrices

ceabigr
R
tidyverse
methylation
snp

Matrix correlation analysis for methylation and SNP data

Sep 10, 2023
Steven Roberts

Peve lncRNA alignment

deepdive
R
lncRNA
e5

Sea star long non-coding RNA alignment and characterization

Sep 8, 2023
Steven Roberts

Epidiverse GRM

ceabigr
R
tidyverse
ggplot
snp

Re-evaluating the GRM

Jul 24, 2023
Steven Roberts

Myt Iso-seq Annotation

mytilus
R
tidyverse
blast
GO

Mytilus isothermal sequencing annotation workflow

Jul 24, 2023
Steven Roberts

ggplotting some qPCR

Quarto
R
tidyverse
ggplot
qPCR

quick take on graphing out some of Noah’s data

Jul 21, 2023
Steven Roberts

Mytilus Iso-seq Data check

notebook
Lets take look at Isoseq fasta
Jul 19, 2023
Steven Roberts

DNA Methylation and Species/Tissue Specific Considerations

news
Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases
Jun 1, 2023
Zach Bengtsson

Epigenetic mechanisms in marine invertebrates

paper
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.…
May 31, 2023
Celeste Valdivia
 

DNA Methylation Analysis Methods

[]
May 31, 2023
Chris
 

Tutorial #5 Reflection

news
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
May 29, 2023
Grace Leuchtenberger

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

paper
Long non-coding RNAs are associated with spatiotemporal gene expression profiles in the marine gastropod Tegula atra
May 29, 2023
Zach Bengtsson

The Role of DNA Methylation and Context Dependence

paper
Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates?
May 17, 2023
Zach Bengtsson

Molecular stress responses in marine intertebrates

paper
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…
May 17, 2023
Celeste Valdivia

Tutorial #4: DNA Methylation Station

news
For our tutorial this week, I read the paper assigned to everyone, a Roberts lab special:
May 16, 2023
Grace Leuchtenberger

Molecular stress responses in marine intertebrates

paper
Two weeks ago members of our FISH 600 reading group were asked to select papers to present that cited the following paper:
Apr 30, 2023
Celeste Valdivia

epigeneticPath

DNA Methylation Synthesis

paper
ntic](“https://github.com/sr320/tumbling-oysters/blob/main/posts/ChrisPosts/epigenticPath.png?raw=true”) ---
Apr 30, 2023
Chris
 

New Family on the Block

Week 4 Reflection
paper
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…
Apr 29, 2023
Chris
 

Tutorial #2 Reflection

news
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.…
Apr 27, 2023
Grace Leuchtenberger

Genetics: Does it really matter?

paper
highlight
code
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)…
Feb 18, 2023
Steven Roberts

Post With Code

news
code
analysis
This is a post with executable code.
Feb 17, 2023
Harlow Malloc

Welcome To My Blog

news
This is the first post in a Quarto blog. Welcome!
Feb 15, 2023
Tristan O’Malley
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