Heejung Shim retweeted
I am pleased to announce the establishment of an African Bioinformatics Institute thanks to funding from Wellcome Trust and CZI. We seek stakeholder input to shape the ABI to meet the needs of the bioinformatics and user communities. Join us for engagement sessions to contribute.
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Heejung Shim retweeted
PROGRAM RELEASED: Discover the latest advances in whole-cell modelling, machine learning and AI for genomics, and emerging technologies at #AMSIBioInfoSummer 2024.
View program: bis.amsi.org.au/program/
View program: bis.amsi.org.au/program/
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Heejung Shim retweeted
We are now hiring into our new Biostatistical Machine Learning theme @MRC_BSU ! We are looking for: (1) a Junior Group Leader in AI/ML for Biomedicine (w/ startup package including an RA) who will help shape the theme; and (2) an RA to join my group. Details below. Please RT :)
📢 Our exciting new Biostatistical Machine Learning theme is recruiting for 2 new roles 👇
Independent Junior Group Leader
jobs.cam.ac.uk/job/48012/
Research Associate
jobs.cam.ac.uk/job/48013/
#MachineLearning #ArtificialIntelligence #DataScience @pauldwkirk @Cambridge_Uni
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Heejung Shim retweeted
Registrations are open for #AMSIBioInfoSummer2024 hosted by MACSYS and Melbourne Integrative Genomics at @unimelb from 3-5 December.
Learn more and register: bis.amsi.org.au/register/
Learn more and register: bis.amsi.org.au/register/
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Heejung Shim retweeted
It’s time for the official announcement: the Luca Lab is moving to UChicago @HGEN_UChicago - get in touch if you are interested in studying GxE in the Windy City!
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Heejung Shim retweeted
We're thrilled to share our collaborative work with @Jothi_Lab on the human embryo atlas for human blastoid assessment (biorxiv.org/content/10.110…). This much-needed work by @hani_jieun provides insights into popular human blastoid models.
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Heejung Shim retweeted
Congratulations to Prof Gordon Smyth, finalist in the @austmus #EurekaPrizes!
For 20+ years Prof Smyth has led development of limma, software that helps detect changes in gene activity, and has helped make discoveries in more than 70k papers!
Learn more👇wehi.edu.au/news/prestigio…
For 20+ years Prof Smyth has led development of limma, software that helps detect changes in gene activity, and has helped make discoveries in more than 70k papers!
Learn more👇wehi.edu.au/news/prestigio…
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Heejung Shim retweeted
#ASCS2024 is all set to provide an amazing platform to aspiring Early Career Researchers (ECRs). Grab the opportunity to meet with pioneer bioinformaticians like @KiyoshiAsai and @heejungshim.
Abstract submission is open only until 5th August!
ascs2024.iscbsc.org
@iscbsc
Abstract submission is open only until 5th August!
ascs2024.iscbsc.org
@iscbsc
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Heejung Shim retweeted
In a new work led by @bound_to_love, joint with @calizavi and his lab, we introduce a method based on kallisto for accurate quantification of @nanopore or @PacBio long-read RNA-seq, and demonstrate its accuracy with numerous comparisons and benchmarks 1/🧵 biorxiv.org/content/10.110…
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Looking for a postdoc with a background in computational/Bayesian stats, ML, comp bio (will consider promising applicants from other fields), and a strong interest in genomic data analysis. If interested, please email me or apply here (deadline: 21 July): jobs.unimelb.edu.au/en/job/917200/…
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Heejung Shim retweeted
Excited to share our new preprint. In ST feature imputation (incl unprobed genes, unseen modality or cell type labels), we found spatial regularization can help retain more reliable downstream analysis: spatial variable genes, co-expressed pairs, etc.
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
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Heejung Shim retweeted
Excited to share our new preprint CellContrast, a computational method to infer the spatial location for single-cell RNAseq data. Based on contrastive learning, this method is particularly powerful in preserving the local neighbourhood.
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
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Heejung Shim retweeted
Pleased to share our latest paper describing @Bioconductor package for analysis of DamID sequencing data. Congratulations Caitlin Page who finished this BEFORE starting a PhD with me this year!
Damsel: Analysis and visualisation of DamID sequencing in R biorxiv.org/content/10.110…
Damsel: Analysis and visualisation of DamID sequencing in R biorxiv.org/content/10.110…
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Heejung Shim retweeted
It's finally published. This one took a long time to get through reviewers: Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications link.springer.com/article/10.103…
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Heejung Shim retweeted
A bit slow on X but still super excited to share our Hist2Cell, predicting fine-grained cell types (e.g., 80 subtypes in lung) solely from histology images. For less funded labs to go for spatial RNAs, you can observe a lot more just from H&E stains (1/4) biorxiv.org/content/10.110…
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Heejung Shim retweeted
The first paper from the Phipson lab has been published today in Genome Biology! Very proud to share this work, led by the talented @givanna90. SuperCellCyto: efficient analysis of cytometry data. A quick summary follows.
genomebiology.biomedcentral.com/articles/10.11…
genomebiology.biomedcentral.com/articles/10.11…
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Heejung Shim retweeted
New paper thread (a week late), with @syzmath, Tom Needham and @theosysbio. We combine ideas from topological data analysis and optimal transport to define a 𝐓𝐨𝐩𝐨𝐥𝐨𝐠𝐢𝐜𝐚𝐥 𝐎𝐩𝐭𝐢𝐦𝐚𝐥 𝐓𝐫𝐚𝐧𝐬𝐩𝐨𝐫𝐭 (𝐓𝐩𝐎𝐓) framework.
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Heejung Shim retweeted
Interested in @10xGenomics Visium technology and how different tissue handling protocols compare? Check out the SpatialBench project👇 A huge thank you to @mei__du @Changqing_Vme50 Charity Law @zalcenstein @DrDiHansen @rorybowden @WEHI_research & their teams for data + analysis
Spotlight on 10x Visium: a multi-sample protocol comparison of spatial technologies biorxiv.org/cgi/content/sh… #biorxiv_genomic
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Heejung Shim retweeted
Want an easy to use and fast error/SNP tolerate grep-like tool? Have complex barcodes or indices to demultiplex from raw `omics data? Flexiplex is now published, 🥳academic.oup.com/bioinformatics…, with some great software updates for even more flexibility, github.com/DavidsonGroup/… 1/3
Pleased to report the very first paper from my research group at WEHI is now up on bioRxiv. Flexiplex is a new tool for raw sequencing data that allowed you to identify and error correct barcodes, and can even be used as a general "grep-like" search tool.
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