Shian Su

🏆 Professor Gordon Smyth @WEHI_research is awarded the @ARDC_AU Eureka Prize for Excellence in Research Software. #EurekaPrizes Learn more: youtu.be/ZYakgC2wkw8

Super nice when people asked me if they can use my repository for teaching. I always say yes. Friends don’t let friends make bad graphs repository: github.com/cxli233/Friend…

Our review paper on "Genome assembly in the telomere-to-telomere era" published online in @NatureRevGenet. It amazes me how much assembly has progressed in the past four years – often ~100X improvement in contiguity and base accuracy and with haplotypes and hard regions resolved!

Ten quick tips for avoiding pitfalls in multi-omics data integration analyses journals.plos.org/ploscompbiol/a…

Stop the video and tell me if you can locate the disk (I bet you can't). When even your eyes cannot identify cells in a still image, improving the segmentation method is pointless. A better approach is to use temporal information from previous frames and next frames.

Is this one of those AI hallucinations I keep hearing about?

@strnr @i000 In my experience, very few solvable problems are truly that niche. My workflow is to start with a chat with GPT-4 to break down a problem. Then annotate intent with comments as I code with co-pilot.

@i000 I already did! My point was that the useless suggestions I kept getting on what was such a niche bioinfo problem that couldn't have possibly been in the training set were more distracting than helpful.

OTOH, I haven't asked or answered a SO post in >1 year. Copilot and GPT-4 are great for problems that have been solved before, writing tests, documentation. I've just found copilot distracting for niche problems that it couldn't possibly understand without thorough explanation.

A nice review of long-read genome assemblers and its associated #bioinformatics terms sciencedirect.com/science/articl…

Join us in person or online to hear from @BlewittMarnie @WEHI_research as part of the ARMI External Seminar Series. Learn about the latest research in epigenetic silencing and its role in the neurodevelopmental disorder Prader Willi syndrome. More details: bit.ly/3xNYavB

I've been waiting for this moment and it has finally happened. I got a paper review back saying I need to familiarise myself more with the works of Heejung Chung and that my work should engage more with her work.

I am currently recruiting a computational postdoc in my lab at CU dashnowlab.org The candidate would develop and use computational genomics methods to understand the genetic underpinnings of rare diseases and increase diagnoses. Pay starts at $70k for recent PhD grads

Thrilled to announce Professor @MelanieBahlo has been awarded the @GeneticsAus MJD White Medal in recognition of her outstanding contributions to the field of genetics research 👏👏 #genetics #science #medicalresearch #research 🧵1/3

Very pleased to announce that our paper, "SuperCellCyto: enabling efficient analysis of large scale cytometry datasets" has just been published in Genome Biology!! Paper: genomebiology.biomedcentral.com/articles/10.11… Code: github.com/phipsonlab/sup… 🧵👇

Any function named read_csv should never have a "delimiter" argument and this is a hill I will die on.

what's the best statistics-focused bioinformatics book you have read? For me, it is Modern Statistics for Modern Biology huber.embl.de/msmb/ and Data Analysis for Life Sciences leanpub.com/dataanalysisfo…

WEHI lab head and @SnowMedical Fellow Dr Stephin Vervoort (@Vervoort_lab) has been announced as the recipient of the Ruth Stephens Gani Medal by the @Science_Academy for his work in gene regulation, focusing on the genetic regulator RNA Polymerase II. wehi.edu.au/news/prestigio…

A global team co-led by WEHI's Dr @AnnaCoussens, @hanifesmail_tb (@ucl), @Rein_Houben (@LSHTM) has developed a new classification framework for TB (ICE-TB) that aims to improve focus on early TB stages & lead to better diagnosis & treatment: wehi.edu.au/news/new-class… #WorldTBDay

Females are #epigenetic mosaics! as illustrated by 🐈. Knowing which X chromosome is active is essential to understand how X-linked disorders affect females. We show how this can be done efficiently with @nanopore long-read sequencing... doi.org/10.1101/2024.0…

(1/5) Attention, Cellular Imaging Enthusiasts! Thrilled to share that our Analysis "The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions" has been published in Nature Methods (@NatureMethods) 🎉🎉🎉 Cell segmentation is a critical component of microscopy image analysis, but existing algorithms are often specialized for particular types of images or demand users to manually set hyper-parameters, posing challenges for biologists without a strong computational background. To address these issues, we organized an international challenge at NeurIPS 2022 to promote the development of novel cell segmentation methods that excel across a wide array of microscopy images, imaging platforms, and tissue types. 🌐 Homepage: uni-cellseg.github.io 📄 Paper: nature.com/articles/s4159… 🔬Data: neurips22-cellseg.grand-challenge.org/dataset/ 🏅Competition website: neurips22-cellseg.grand-challenge.org 👇 👇👇👇