Job opportunity John Innes Centre! Join my lab to investigate the roles of circadian rhythms, light and temperature signalling in the senescence of plants. Collaboration with Kerry Franklin University of Bristol Biological Sciences supported by Biotechnology and Biological Sciences Research #circadian #plantsci jobs.jic.ac.uk/Details.asp?va…

New Algorithm!
Do you clone a lot of plasmids? Are you tired of aligning plasmid maps to sequencing data, one by one?
Introducing Context Aware AutoAlign!  Automated sequence alignments & model predictions for when cloning many protein expression plasmids.
denovodna.com/software/conte…

Research proposal flowchart #research #academia #AcademicTwitter

How can we use single stranded DNA, DNA tiles or DNA origami to engineer synthetic cytoskeletons? We summarized current efforts towards engineering DNA-based cytoskeletons for synthetic cells in this new (and also my first) review: royalsocietypublishing.org/doi/10.1098/rs… Kerstin Göpfrich

The hardest part about being an immigrant is not the immigration system but having to choose between pursuing a world class career and seeing your parents grow old

One of the greatest mysteries concerning the #OriginOfLife is how it has emerged so quickly after the formation of the earth. This tweetorial presents a sketch on how the physics of chemically #activematter can help understand this puzzle better: nature.com/articles/s4146…

A literature review helps you build on existing knowledge, identify gaps and provide direction for future research.

Here is a list of simple tools you can use for your next literature review project.

Which one is your favorite?

Ten quick tips for bioinformatics analyses using an Apache Spark distributed computing environment | PLOS Computational Biology
journals.plos.org/ploscompbiol/a…

#Bioinformatics

Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector | Nature Communications
nature.com/articles/s4146…

#Bioinformatics

IBAS: Interaction-bridged association studies discovering novel genes underlying complex traits biorxiv.org/content/10.110…

Large language models in medicine | Nature Medicine
nature.com/articles/s4159…

#LLM

Transmorph: a unifying computational framework for modular single-cell RNA-seq data integration academic.oup.com/nargab/article…

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender nature.com/articles/s4159…

How big are the cells? Microorganisms in perspective

Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2 | Nature Communications
nature.com/articles/s4146…

#Bioinformatics

#MembraneTrafficking online seminars are back with a stellar lineup for the fall season! Join Fèlix Campelo Francesca Bottanelli and me for a whole lot of great science.

RNAseq counting tools are not perfect. I simulated 240 GTEx samples to test multiple tools. Below I show the difference between actual and estimated counts for each simulated sample.

But, what is causing this? And will it affect differential expression? (1/7) #Bioinformatics

A Size Filter Regulates Apical Protein Sorting biorxiv.org/content/10.110…

MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylation regions from whole-genome datasets biorxiv.org/content/10.110…

The annotation and software you use to align/count RNAseq matters a lot for many genes.

Here is a quick comparison between STAR+feature counts and salmon. Most genes are correlated, but in this example we have around 900 that are not. What's going on?? (1/5) #Bioinformatics