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

Jun 18, 2026
Steven Roberts

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

Jun 15, 2026
Steven Roberts

Oyster Priming Week 2

Aquaculture

The FTR Edition

Jun 10, 2026
Steven Roberts

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

Jun 10, 2026
Steven Roberts

Mortality Trial on Wescott Oysters

Aquaculture

Weekly and Daily leftovers

Jun 4, 2026
Steven Roberts

Mortality Trial on SORMI Oysters

Aquaculture

Heating up in the incubator

Jun 4, 2026
Steven Roberts

Mortality Trial on Manchester Oysters

Aquaculture

Heating up in the incubator

Jun 3, 2026
Steven Roberts

Setting up 2026 prime

Aquaculture

10k 4mm

May 29, 2026
Steven Roberts

Initial YC25 Oyster assay runs

Aquaculture
Over the past month we have ran some initial SORMI assays on the USDA YC25 families.
May 8, 2026
Steven Roberts

Merry Linkmas

Lab Updates
Computing
Here are few tidbits to bring you cheer this Christmas Season!
Dec 24, 2025
Steven Roberts

Barnacle

Transcriptomics

more lamda values

Dec 4, 2025
Steven Roberts

Coefficient of Gene Expression and GBM

Epigenetics
Transcriptomics

and expression distribution by methylation

Dec 4, 2025
Steven Roberts

Context dependent DNA methylation :: miRNA regulation of gene expression

Epigenetics
Transcriptomics

Contra

Dec 1, 2025
Steven Roberts

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

Epigenetics
Transcriptomics

x-y

Dec 1, 2025
Steven Roberts

Barnacle

Transcriptomics

final push

Nov 29, 2025
Steven Roberts

Calcifying Contra

Transcriptomics

and beyond

Nov 29, 2025
Steven Roberts

Calcification Count Matrices

Transcriptomics

filtering timeseries

Nov 26, 2025
Steven Roberts

Timeseries Gene Level methylation

Epigenetics
Transcriptomics

finally

Nov 25, 2025
Steven Roberts

Biomineraliztion in dark matter

Transcriptomics

where in the WGCBNA and barnacle?

Nov 15, 2025
Steven Roberts

Functional annotation summary for WGCNA modules

Genomics
Transcriptomics

GOing with more

Nov 13, 2025
Steven Roberts

Contra on 24

Transcriptomics

Epigenetic factors on barnacle

Nov 13, 2025
Steven Roberts

More Random Please

Transcriptomics

GOing with more

Nov 13, 2025
Steven Roberts

More Sparsity?

Transcriptomics

Optimizing Rank 35

Nov 5, 2025
Steven Roberts

Deep Dive on Rank 35

Transcriptomics

Going through barnacle rank gene factors

Nov 2, 2025
Steven Roberts

Lets talk Cod

Epigenetics
Transcriptomics

A check-in with data files

Nov 1, 2025
Steven Roberts

Lake Trout PacBio Data

Epigenetics

QC

Oct 27, 2025
Steven Roberts

Ortholog Selection for Physiological Processes

Genomics

Selecting orthologs based on metabolic and reproductive GO terms

Oct 4, 2025
Steven Roberts

MOSAiC orthologs

Genomics

reciping

Aug 31, 2025
Steven Roberts

Next leveling RNAseq

Aquaculture
Transcriptomics

MinION nanopore sequencing analysis

Aug 4, 2025
Steven Roberts

Getting on with Nanopore cDNA data

Aquaculture
Transcriptomics

MinION nanopore sequencing analysis

Aug 1, 2025
Steven Roberts

Oyster Pickup and Cleaning

Aquaculture

Point Whitney shellfish operations

Jul 23, 2025
Steven Roberts

Cod alignment

Genomics

BWA alignment for cod genomic analysis

Jul 8, 2025
Steven Roberts

The lncRNA repertoire of Ptuh

Transcriptomics

Long non-coding RNA repertoire analysis

Jun 21, 2025
Steven Roberts

ROL-PI Day three

Epigenetics

Más sequence files to bismark, por favor

May 26, 2025
Steven Roberts

ROL-PI Day two

Epigenetics

Más CpGs, por favor

May 24, 2025
Steven Roberts

ROL-PI Day one

Epigenetics

Más citas, por favor

May 24, 2025
Steven Roberts

CpG Intersect

Epigenetics

Apul Motifs and matches

May 15, 2025
Steven Roberts

Megan it

Genomics

taxa id from seq reads

May 5, 2025
Steven Roberts

Energy staging

Epigenetics

Can we predict where they are on the curve?

Apr 10, 2025
Steven Roberts

Getting to GO with Phenotype

Genomics

A short list for machine learning

Mar 21, 2025
Steven Roberts

OA OA OA

Epigenetics
Aquaculture

Bringing diploid - triploid to an end?

Mar 12, 2025
Steven Roberts

Long non-coding RNA discovery pipeline

Transcriptomics

Long non-coding RNA discovery pipeline implementation

Feb 28, 2025
Steven Roberts

Please Klone me

Computing

Getting on the RStudio Klone machine

Feb 19, 2025
Steven Roberts

Apul Time Series Methylation

Epigenetics

It’s in the name…

Feb 8, 2025
Steven Roberts

We wish you a Merry Mytilus!

Epigenetics

Differentially methylated loci on PAHs

Dec 24, 2024
Steven Roberts

Time-series coral lncRNA count matrix

Transcriptomics

Coral lncRNA count matrix generation and analysis pathway

Dec 20, 2024
Steven Roberts

Mytilus DNA methylation calls

Epigenetics

associated with contaminants

Dec 19, 2024
Steven Roberts

Hip Hip Array

Epigenetics
Computing

Knocking out the code to get bismark happy

Nov 20, 2024
Steven Roberts

Running Bismark in SLURM Array for Methylation Analysis

Epigenetics
Computing

Bismark array processing workflow

Nov 10, 2024
Steven Roberts

Stats on E5 genomes

Genomics

Welcoming new Pulcra genome statistics

Oct 5, 2024
Steven Roberts

Connecting annotations

Genomics
Transcriptomics

Challenges post-HiSat

Oct 3, 2024
Steven Roberts

Re-prime

Aquaculture

Giving 10k seed more resiliency

Sep 14, 2024
Steven Roberts

R N A T O G O

Genomics

On the Roan to assigning GO to genes

Aug 27, 2024
Steven Roberts

Git that Pro GO

Genomics

Deep dive into protein annotation

Aug 25, 2024
Steven Roberts

Double header

Aquaculture

larvae, ploidy, and 10k seed start

Jun 26, 2024
Steven Roberts

Oyster bath

Aquaculture

When is it too hot?

Jun 20, 2024
Steven Roberts

Huddl Launch

Aquaculture

First of season day 3 larvae are a go!

Jun 17, 2024
Steven Roberts

Repro Repro

Genomics

Pipeline for Reproduction Annotation

Jun 15, 2024
Steven Roberts

Spring Cleaning

Aquaculture

Getting ready for spawning

Jun 12, 2024
Steven Roberts

Seed travels

Aquaculture

The Wescott Bay deployment

Jun 7, 2024
Steven Roberts

HiSat that SeaStar

Transcriptomics

finally overcoming gtf h$11

Jun 3, 2024
Steven Roberts

xargs

Computing

now with no reason for loops

May 27, 2024
Steven Roberts

That escalated quickly

Computing

going from 1 line script to cronning a sys log

May 27, 2024
Steven Roberts

Working with IGV

Genomics

IGV visualization for cod analysis

May 23, 2024
Steven Roberts

Getting appropriate IDs for Gene, Transcripts

Genomics

for cod, looking ahead to Uniprot Accessions

May 21, 2024
Steven Roberts

Differentially Expressed Transcripts

Transcriptomics

Differentially expressed transcripts in cod

May 21, 2024
Steven Roberts

Differentially Expressed Genes

Transcriptomics

Differentially expressed genes in cod

May 21, 2024
Steven Roberts

Looking at Apul miRNA

Transcriptomics
Genomics

Coral miRNA visualization in IGV

May 16, 2024
Steven Roberts

HiSat

Transcriptomics

to DESeq

May 14, 2024
Steven Roberts

Genome files

Genomics

Cod genome files and datasets

May 13, 2024
Steven Roberts

Launching more stress

Aquaculture

starting new seed and adult hardening

Mar 11, 2024
Steven Roberts

What I have been up to today

Lab Updates

rewind

Feb 8, 2024
Steven Roberts

February Daily

Lab Updates
Your text here…
Feb 1, 2024
Steven Roberts

Apul lncRNA Discovery

Transcriptomics

Coral long non-coding RNA discovery and analysis

Nov 3, 2023
Steven Roberts

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.
Nov 1, 2023
Steven Roberts

Correlating Matrices

Epigenetics
Genomics

Matrix correlation analysis for methylation and SNP data

Sep 10, 2023
Steven Roberts

Peve lncRNA alignment

Transcriptomics

Sea star long non-coding RNA alignment and characterization

Sep 8, 2023
Steven Roberts

Epidiverse GRM

Genomics
Computing

Re-evaluating the GRM

Jul 24, 2023
Steven Roberts

Myt Iso-seq Annotation

Genomics

Mytilus isothermal sequencing annotation workflow

Jul 24, 2023
Steven Roberts

ggplotting some qPCR

Transcriptomics
Computing

quick take on graphing out some of Noah’s data

Jul 21, 2023
Steven Roberts

Mytilus Iso-seq Data check

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

DNA Methylation and Species/Tissue Specific Considerations

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

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.…
May 31, 2023
Celeste Valdivia
 

DNA Methylation Analysis Methods

Epigenetics
[]
May 31, 2023
Chris
 

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
May 29, 2023
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
May 29, 2023
Zach Bengtsson

The Role of DNA Methylation and Context Dependence

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

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…
May 17, 2023
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:
May 16, 2023
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:
Apr 30, 2023
Celeste Valdivia

epigeneticPath

DNA Methylation Synthesis

Reading Notes
Epigenetics
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
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…
Apr 29, 2023
Chris
 

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.…
Apr 27, 2023
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)…
Feb 18, 2023
Steven Roberts

Post With Code

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

Welcome To My Blog

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