@HachLab

@f_hach's lab. Based in Vancouver Prostate Centre. Computational algorithms for cancer genomics research. 🧬💻

 Vancouver, British Columbia
hachlab.org
Joined January 2019
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TKSM is now accepted by Bioinformatics and published as an advance article! doi.org/10.1093/bioinformati… Take a moment to check this quite cool and very modular long-read simulator built by our PhD students @fkaraoglan_cs and @baraaorabi 👇🏻

TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator

AbstractMotivation. Transcriptomic long-read (LR) sequencing is an increasingly cost-effective technology for probing various RNA features. Numerous tools

academic.oup.com
Hach Lab@HachLab13 Jun 2023
Our latest manuscript that's spearheaded by @fkaraoglan_cs and @baraaorabi (with the co-supervision of Cedric Chauve and collaboration of @RyanFlannigan00) is out! We are delighted for TKSM to say Hello World! 👋 💻: github.com/vpc-ccg/tksm 📄: biorxiv.org/content/10.1101/…

GitHub - vpc-ccg/tksm: Very modular, very cool long-read transcriptomic simulator

Very modular, very cool long-read transcriptomic simulator - vpc-ccg/tksm

github.com
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Nice work from two @BilkentCompGen alumni!
Hach Lab@HachLab13 Jun 2023
Our latest manuscript that's spearheaded by @fkaraoglan_cs and @baraaorabi (with the co-supervision of Cedric Chauve and collaboration of @RyanFlannigan00) is out! We are delighted for TKSM to say Hello World! 👋 💻: github.com/vpc-ccg/tksm 📄: biorxiv.org/content/10.1101/…

GitHub - vpc-ccg/tksm: Very modular, very cool long-read transcriptomic simulator

Very modular, very cool long-read transcriptomic simulator - vpc-ccg/tksm

github.com
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Our latest manuscript that's spearheaded by @fkaraoglan_cs and @baraaorabi (with the co-supervision of Cedric Chauve and collaboration of @RyanFlannigan00) is out! We are delighted for TKSM to say Hello World! 👋 💻: github.com/vpc-ccg/tksm 📄: biorxiv.org/content/10.1101/…

GitHub - vpc-ccg/tksm: Very modular, very cool long-read transcriptomic simulator

Very modular, very cool long-read transcriptomic simulator - vpc-ccg/tksm

github.com
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Hope you all give TKSM a try and find it useful for simulating your long-read experiments!
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And of course, this work would not have been possible without the funding and institutional support of @SFU_CompSci @UBC_CS @VanProstateCtr @UBCUrology @SFUMath @NSERC_CRSNG @HlthResearchBC
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I am extremely proud to share that our recent method's manuscript on functional testing of non-coding genetic variants got published. doi.org/10.1093/nar/gkac1198. (1/6)

Optimized high-throughput screening of non-coding variants identified from genome-wide association...

Abstract. The vast majority of disease-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies (GWAS) are localize

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This semester has been filled with proud moments; we had the pleasure of FOUR grad students defending their theses! MSc Ghazal Ebrahimi, MSc @ArmitaSafa, MSc Reza Soltani, and PhD @tuncmorova successfully defended their theses in @ubcscience Graduate Program in Bioinformatics!
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Congratulations on all your hard work and well deserved degrees! Can't wait to see what you go on to achieve next 🎉🥂 (when you have four grads defending in a row [including three in the same week!] mid-day celebration is absolutely a must!)
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Our work on Freddie, an annotation-indepented isoform discovery using long-reads tool, is finally published at @NAR_Open! Check the open access code and paper: 📄: academic.oup.com/nar/advance… 💾: github.com/vpc-ccg/freddie/ 🐍: conda install -c bioconda freddie

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing...

Abstract. Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role a

academic.oup.com
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Finally, we show in the paper, using real and simulated datasets that Freddie produces accurate and useful results without using the annotation database (e.g. ENSEMBL).
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This work was spearheaded by our PhD candidate @baraaorabi. Thanks for all the support from @VanProstateCtr, @UBC_CS, @SFUMath @UBCUrology and the funding from @NSERC_CRSNG, @HlthResearchBC, @CIHR_IRSC, and DoD Prostate Cancer Research Program Idea Development Award!
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Our latest manuscript by Ghazal Ebrahimi and @baraaorabi is now published by @iScience_CP! "Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments" 💾: github.com/vpc-ccg/scTagger 📃: sciencedirect.com/science/ar…

GitHub - vpc-ccg/scTagger: 10x single cell short- and long-read RNA sequencing

10x single cell short- and long-read RNA sequencing - vpc-ccg/scTagger

github.com
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In our manuscript, we show that scTagger is highly accurate and is much faster than the alternative methods and demonstrate that on both real and simulated datasets.
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This work could not have been possible without our close collaboration with @RyanFlannigan00 lab (including Meghan Robinson!) and Cedric Chauve And of course, all the intuitional support we got! @VCHResearch @VanProstateCtr @CRSNG_NSERC @HlthResearchBC @UBC_CS @SFUMath
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