Tags

• yeast 8
• codon usage 2
• translation 6
• selection 1
• collaboration 2
• evolution 3
• drosophila 1
• mistranslation 1
• chemistry 2
• mass spectrometry 1
• elongation 1
• high-throughput sequencing 3
• 5PSeq 1
• perspective 1
• data 3
• heat shock 4
• aggregation 4
• biochemistry 1
• disaggregation 1
• protein 1
• RNA 6
• northern 1
• blot 1
• ribosome 1
• polysome 1
• gradient 1
• sequencing 1
• splicing 1
• transcription 2
• riboviz 9
• ribosome profiling 2
• bioinformatics 6
• award 1
• vacancy 6
• postdoc 4
• labmanual 10
• newstart 7
• phd 8
• eastbio 8
• bbsrc 8
• alex 1
• undergrad 1
• people 10
• precision medicine 1
• personal 1
• team 1
• wellcome trust 3
• papers 4
• Cryptococcus 3
• start codons 2
• howto 1
• remote-work 1
• epidemic 1
• cyanobacteria 1
• sedimentation 1
• condensation 1
• metabolism 1
• circadian 1
• preprint 2
• Ssd1 3
• tidyqpcr 1
• software 3
• collaborations 1
• ssd1 3
• rna-binding protein 3
• pseudoenzyme 1
• paper 6
• honours 1
• PhDstudent 1
• workflows 3
• education 1
• wetlab 3
• UTRs 2
• sophie 1
• emma 1
• open science 3
• flic 1
• RNA-binding proteins 1
• fungi 3
• cell wall 1
• post-transcriptional regulation 2
• Ribo-seq 2
• utr 1
• motifs 1
• reporter genes 1
• qPCR 1
• darwin trust 2
• Phd 2
• exons 2
• introns 1
• UTR 1
• meetings 2
• Gat201 1
• music 2
• RNASeq 1
• azide 1
• ethanol 1
• stress 1
• Hsf1 1
• biomolecular condensation 1
• regulation 1

yeast

• PREPRINT: The type of carbon source not the growth rate it supports can determine diauxie
• RNATagSeq: multiplexed library preparation for Illumina RNA sequencing
• Yeast total RNA isolation protocol
• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress
• Supernatant/pellet fractionation of budding yeast cells by cryogenic lysis
• Disaggregation assay data visualization
• Aggregation assay data visualization
• Estimating selection on synonymous codon usage from noisy experimental data

codon usage

• A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus
• Estimating selection on synonymous codon usage from noisy experimental data

translation

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts
• Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress
• Dying mRNA tells a story of its life
• A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus
• Estimating selection on synonymous codon usage from noisy experimental data

selection

• Estimating selection on synonymous codon usage from noisy experimental data

collaboration

• Daily cycles of reversible protein condensation in cyanobacteria
• A Model for the Evolution of Biological Specificity: a Cross-Reacting DNA-Binding Protein Causes Plasmid Incompatibility

evolution

• Evolution of the Ssd1 pseudonuclease
• Repeated evolution of inactive pseudonucleases in a fungal branch of the Dis3/RNase II family of nucleases
• A Model for the Evolution of Biological Specificity: a Cross-Reacting DNA-Binding Protein Causes Plasmid Incompatibility

drosophila

• A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus

mistranslation

• A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus

chemistry

• RNATagSeq: multiplexed library preparation for Illumina RNA sequencing
• Chloroform-methanol extraction of proteins

mass spectrometry

• Chloroform-methanol extraction of proteins

elongation

• Dying mRNA tells a story of its life

high-throughput sequencing

• riboviz: analysis and visualization of ribosome profiling datasets.
• Extremely fast and incredibly close: co-transcriptional splicing in budding yeast
• Dying mRNA tells a story of its life

5PSeq

• Dying mRNA tells a story of its life

perspective

• Dying mRNA tells a story of its life

data

• Data Curation Days
• Disaggregation assay data visualization
• Aggregation assay data visualization

heat shock

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts
• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress
• Disaggregation assay data visualization
• Aggregation assay data visualization

aggregation

• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress
• Supernatant/pellet fractionation of budding yeast cells by cryogenic lysis
• Disaggregation assay data visualization
• Aggregation assay data visualization

biochemistry

• Supernatant/pellet fractionation of budding yeast cells by cryogenic lysis

disaggregation

• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress

protein

• Reversible, specific, active aggregates of endogenous proteins assemble upon heat stress

RNA

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts
• Extremely fast and incredibly close: co-transcriptional splicing in budding yeast
• RNATagSeq: multiplexed library preparation for Illumina RNA sequencing
• Yeast total RNA isolation protocol
• Sucrose gradient protocol for polysome profiles
• Anti-RNA blotting with chemiluminescent detection

northern

• Anti-RNA blotting with chemiluminescent detection

blot

• Anti-RNA blotting with chemiluminescent detection

ribosome

• Sucrose gradient protocol for polysome profiles

polysome

• Sucrose gradient protocol for polysome profiles

gradient

• Sucrose gradient protocol for polysome profiles

sequencing

• RNATagSeq: multiplexed library preparation for Illumina RNA sequencing

splicing

• Extremely fast and incredibly close: co-transcriptional splicing in budding yeast

transcription

• PREPRINT: A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201
• Extremely fast and incredibly close: co-transcriptional splicing in budding yeast

riboviz

• choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
• How to ask for data from a paper
• riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow
• The benefits of an open-science approach in student research projects
• How we combine open science and student research projects
• Using prototyping to choose a bioinformatics workflow management system
• Workflows paper accepted
• Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
• riboviz: analysis and visualization of ribosome profiling datasets.

ribosome profiling

• Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
• riboviz: analysis and visualization of ribosome profiling datasets.

bioinformatics

• choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
• tidyqpcr: Quantitative PCR analysis in the tidyverse
• riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow
• Using prototyping to choose a bioinformatics workflow management system
• Workflows paper accepted
• riboviz: analysis and visualization of ribosome profiling datasets.

award

• New Lab Website

vacancy

• PhD opportunities on RNA and environmental sensing
• PhD opportunities on RNA and fungal adaptation
• PhD opportunity on machine learning of multi-omics data
• PhD opportunity on machine learning of multi-omics data (past)
• Welcome lab manager Rosey Bayne
• Come work on RNA Systems Biology of Fungi

postdoc

• Welcome Sam Haynes
• Welcome Laura Tuck
• Welcome lab manager Rosey Bayne
• Come work on RNA Systems Biology of Fungi

labmanual

• Lab tips and tricks
• New start guide
• Meetings: Lab, subgroup, and 1-1
• Where data belongs
• Lab standup
• Lab jobs and responsibilities
• Data Curation Days
• Lab notebook guidelines
• Where lab stuff belongs
• Data Management Plan

newstart

• New start guide
• Meetings: Lab, subgroup, and 1-1
• Where data belongs
• Lab standup
• Data Curation Days
• Where lab stuff belongs
• Data Management Plan

phd

• Fungal PhD opportunities in Edinburgh 2024
• Fungal PhD opportunities in Edinburgh 2023
• PhD opportunities on RNA and environmental sensing
• Collaborative PhD opportunities for October 2020 entry (Archive)
• PhD opportunities on RNA and fungal adaptation
• PhD opportunities for October 2019 entry (Archive)
• PhD opportunity on machine learning of multi-omics data
• PhD opportunity on machine learning of multi-omics data (past)

eastbio

• Fungal PhD opportunities in Edinburgh 2024
• Fungal PhD opportunities in Edinburgh 2023
• PhD opportunities on RNA and environmental sensing
• Collaborative PhD opportunities for October 2020 entry (Archive)
• PhD opportunities on RNA and fungal adaptation
• PhD opportunities for October 2019 entry (Archive)
• PhD opportunity on machine learning of multi-omics data
• PhD opportunity on machine learning of multi-omics data (past)

bbsrc

• Fungal PhD opportunities in Edinburgh 2024
• Fungal PhD opportunities in Edinburgh 2023
• PhD opportunities on RNA and environmental sensing
• Collaborative PhD opportunities for October 2020 entry (Archive)
• PhD opportunities on RNA and fungal adaptation
• PhD opportunities for October 2019 entry (Archive)
• PhD opportunity on machine learning of multi-omics data
• PhD opportunity on machine learning of multi-omics data (past)

alex

• Welcome undergrad student Aliaksandr Damenikan

undergrad

• Welcome undergrad student Aliaksandr Damenikan

people

• Dr. Weronika Danecka
• Dr. Sam Haynes
• Farewell Jing Qi, Welcome Eleanor and Marcos
• Welcome Domenico
• Farewell Flic
• Farewell Emma and Sophie
• Welcoming new lab members for 2021
• Welcome Sam Haynes
• Welcome Laura Tuck
• Welcome undergrad student Aliaksandr Damenikan

precision medicine

• PhD opportunities for October 2019 entry (Archive)

personal

• Scientist and Parent: The Bereaved Parent

team

• Welcome new lab members

wellcome trust

• Fungal PhD opportunities in Edinburgh 2024
• Fungal PhD opportunities in Edinburgh 2023
• Collaborative PhD opportunities for October 2020 entry (Archive)

papers

• How to ask for data from a paper
• How we combine open science and student research projects
• Favourite Papers In The Lab
• New paper on protein synthesis in fungi

Cryptococcus

• PREPRINT: A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201
• Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
• New paper on protein synthesis in fungi

start codons

• Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom
• New paper on protein synthesis in fungi

howto

• Safe and Productive Science-ing During an Epidemic

remote-work

• Safe and Productive Science-ing During an Epidemic

epidemic

• Safe and Productive Science-ing During an Epidemic

cyanobacteria

• Daily cycles of reversible protein condensation in cyanobacteria

sedimentation

• Daily cycles of reversible protein condensation in cyanobacteria

condensation

• Daily cycles of reversible protein condensation in cyanobacteria

metabolism

• Daily cycles of reversible protein condensation in cyanobacteria

circadian

• Daily cycles of reversible protein condensation in cyanobacteria

preprint

• Preprint on combining regulatory elements
• Preprints on the Ssd1 RNA-binding protein

Ssd1

• Alternative RNA recognition by the Ssd1 RNA-binding protein
• Evolution of the Ssd1 pseudonuclease
• Preprints on the Ssd1 RNA-binding protein

tidyqpcr

• tidyqpcr - Quantitative PCR analysis in the tidyverse.

software

• tidyqpcr: Quantitative PCR analysis in the tidyverse
• Working with the Software Sustainability Institute
• tidyqpcr - Quantitative PCR analysis in the tidyverse.

collaborations

• Working with the Software Sustainability Institute

ssd1

• Post-transcriptional control of fungal cell wall synthesis
• Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface
• Repeated evolution of inactive pseudonucleases in a fungal branch of the Dis3/RNase II family of nucleases

rna-binding protein

• Post-transcriptional control of fungal cell wall synthesis
• Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition interface
• Repeated evolution of inactive pseudonucleases in a fungal branch of the Dis3/RNase II family of nucleases

pseudoenzyme

• Repeated evolution of inactive pseudonucleases in a fungal branch of the Dis3/RNase II family of nucleases

paper

• What is an exon?
• Review paper on control of cell walls
• Preprint on combining regulatory elements
• Alternative RNA recognition by the Ssd1 RNA-binding protein
• Workflows paper accepted
• Evolution of the Ssd1 pseudonuclease

honours

• Welcoming new lab members for 2021

PhDstudent

• Welcoming new lab members for 2021

workflows

• riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow
• Using prototyping to choose a bioinformatics workflow management system
• Workflows paper accepted

education

• Using prototyping to choose a bioinformatics workflow management system

wetlab

• Lab tips and tricks
• Lab jobs and responsibilities
• Lab notebook guidelines

UTRs

• What is an exon?
• Preprint on combining regulatory elements

sophie

• Farewell Emma and Sophie

emma

• Farewell Emma and Sophie

open science

• How to ask for data from a paper
• The benefits of an open-science approach in student research projects
• How we combine open science and student research projects

flic

• Farewell Flic

RNA-binding proteins

• Review paper on control of cell walls

fungi

• End of Sir Henry Dale Fellowship
• Fungi Sessions vol 1
• Post-transcriptional control of fungal cell wall synthesis

cell wall

• Post-transcriptional control of fungal cell wall synthesis

post-transcriptional regulation

• PREPRINT: Limitations of composability of cis-regulatory elements in messenger RNA
• Post-transcriptional control of fungal cell wall synthesis

Ribo-seq

• choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
• riboviz 2: A flexible and robust ribosome profiling data analysis and visualization workflow

utr

• PREPRINT: Limitations of composability of cis-regulatory elements in messenger RNA

motifs

• PREPRINT: Limitations of composability of cis-regulatory elements in messenger RNA

reporter genes

• PREPRINT: Limitations of composability of cis-regulatory elements in messenger RNA

qPCR

• tidyqpcr: Quantitative PCR analysis in the tidyverse

darwin trust

• Fungal PhD opportunities in Edinburgh 2024
• Fungal PhD opportunities in Edinburgh 2023

Phd

• Dr. Weronika Danecka
• Dr. Sam Haynes

exons

• Not all exons are protein coding: Addressing a common misconception
• What is an exon?

introns

• Not all exons are protein coding: Addressing a common misconception

UTR

• Not all exons are protein coding: Addressing a common misconception

meetings

• Meetings: Lab, subgroup, and 1-1
• Lab standup

Gat201

• PREPRINT: A trade-off between proliferation and defense in the fungal pathogen Cryptococcus at alkaline pH is controlled by the transcription factor GAT201

music

• End of Sir Henry Dale Fellowship
• Fungi Sessions vol 1

RNASeq

• PREPRINT: The type of carbon source not the growth rate it supports can determine diauxie

azide

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

ethanol

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

stress

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

Hsf1

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

biomolecular condensation

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts

regulation

• Transcriptome-wide mRNA condensation precedes stress granule formation and excludes stress-induced transcripts