Computational Transcriptomics
@goekelab
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Lab of Computational Transcriptomics @astar_gis. Software releases, publications, journal clubs, anything long read RNA-Seq by team members. PI @jonathangoeke
Singapore
Joined March 2021
The Asia RNA Club Symposium will be happening in Seoul Nov 3-5, bringing together RNA scientists from the Asia-Pacific region. Excellent speakers and a great opportunity to connect! Abstract submission by Sept 5 https://t.co/bovhcjE3YL
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🚀 Exciting News from Singapore! 🚀 Scientists at A*STAR's Genome Institute of Singapore (@astar_gis) have unveiled one of the world's largest long-read RNA sequencing datasets! 🌍🔬 This groundbreaking resource, known as SG-NEx, is set to revolutionize disease research by
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This Analysis presents benchmarking results from the Singapore Nanopore Expression consortium project, including a valuable resource of datasets generated from various long-read and short-read RNA sequencing technologies. https://t.co/zfoDNFfUAJ
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For the new release of SG-NEx v0.6.0, it now features updated fastq/bam files processed with Guppy 6.4.2 & Minimap2-2.22. Check out here for more details on the resource: https://t.co/oCBkcpzkDC.
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The project is a close collaboration with experts from multiple institutions, including @Hasindu2008, @aka_hpatel, @AliciaOshlack, @mikelove, and many others. We are grateful for their support and contributions to this study.
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The SG-NEx data is a comprehensive resource for enabling the development and benchmarking of computational methods for profiling complex transcriptional events at isoform-level resolution.
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The manuscript provides a systematic benchmark of long-read and short-read RNA-seq protocols, demonstrates the value of long-read RNA-seq data in understanding alternative isoforms, novel transcripts, fusion transcripts and m6A RNA modifications.
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We are happy to share that our SG-NEx manuscript (led by @chenying927, @nadia_davidson, @yukkeiwan and @JonathanGoeke), is now out with open access: https://t.co/om90nZHvlb, together with an update release of SG-NEx data v0.6.0!
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Great to see this software tool that enables long-read single cell and spatial transcriptomics!
Very happy to release the single cell and spatial long read RNA seq module for our transcript discovery and quantification tool Bambu (Bambu-clump)! The key challenges were dimensionality and accurate estimation of transcript expression with minimal data https://t.co/m9agMLFGCz
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Congratulations to our Bambu team: @JonathanGoeke, Andre Sim, Min Hao Ling, Ying Chen, Sui Yue, and @JayShin on the release of their new single-cell and spatial long-read RNA-seq module for Bambu!
This work was down by @Andresim8, @Lingminhao31Min @chenying927 together with @JayShin's team at GIS @astar_gis. Let us know your comments and feedback, we aim to improve Bambu with every release!
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The recommended way to run bambu-clump is through the nextflow pipeline (bambu-pipe), which optimises barcode detection, alignment, transcript discocery and quantification, and it also includes an option to identify fusion transcripts in single cells
github.com
Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu - GoekeLab/bambu-singlecell-spatial
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Very happy to release the single cell and spatial long read RNA seq module for our transcript discovery and quantification tool Bambu (Bambu-clump)! The key challenges were dimensionality and accurate estimation of transcript expression with minimal data https://t.co/m9agMLFGCz
biorxiv.org
Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq...
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Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump https://t.co/TLAY3j7ehN
#biorxiv_bioinfo
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Now online! An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
cell.com
Mapping transcription start sites across five mammalian species before, during, and after embryonic genome activation unveils widespread transposable element-driven transcription and co-option of...
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Congratulations @JonathanGoeke @J_i_n_g_m_e_i from @astar_gis, recipients of the 2024 A*STAR Fellows for their outstanding contributions, leadership and impact on the local and international scientific community! 🏅🧪🧬💻
New year, new issue of A*STAR Research 🎊 Learn about A*STAR’s strategies on acquiring and developing new talent, and read about the recipients of the A*STAR Distinguished Fellowships and Fellowships of 2024 in a special feature. 👉🏻 Grab your copy today! https://t.co/gLu9LfopzL
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Meet the latest recipient of the Young Scientist Award: @JonathanGoeke, Senior Principal Scientist at @astar_gis! 🏅 Göke was recognised for his pioneering work in developing computational methods for long read RNA sequencing data. 🔍 https://t.co/oj2H4W6Ae3
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Congratulations to @JonathanGoeke on achieving the Young Scientist Award, which recognizes young researchers who are actively engaged in R&D in Singapore and have shown great potential to be world-class researchers in their field. Read more about his work: https://t.co/O39taAD3WM
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Many thank to my team members and collaborators, without them this would not have been possible!
Congratulations to @JonathanGoeke on achieving the Young Scientist Award, which recognizes young researchers who are actively engaged in R&D in Singapore and have shown great potential to be world-class researchers in their field. Read more about his work: https://t.co/O39taAD3WM
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The brainchild of researchers at @astar_gis, Bambu can detect both known and previously unidentified gene patterns with high precision 🔍 Find out how Bambu helps address a critical limitation in traditional methods for measuring gene activity ⬇️ https://t.co/PtnGmomBWc
research.a-star.edu.sg
Bambu, a new computational tool for analysing genetic data, effectively identifies and quantifies complex gene patterns.
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This week, we celebrate with our GIS colleagues who were conferred various awards for their distinguished service and significant contributions to A*STAR and Singapore. Our heartiest congratulations to the following awardees!
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