Matt Regner (he/him) @RegnerMJ

PhD Candidate at UNC Chapel Hill | #singlecell & #compbio | https://t.co/oEPUqd2BP8 Joined January 2020

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Matt Regner (he/him) @RegnerMJ

2 years ago

@TheHectorFranco Thanks for your guidance and support!

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𝕐 @nomad421

3 years ago

Did @10xGenomics just make newer versions of Cell Ranger open source? github.com/10XGenomics/ce… (cc @sjackman, @luizirber). This is a huge win for open, transparent, and reproducible science if it’s the case!

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Nancy Zhang @NancyZh60672287

3 years ago

What gets erased when you integrate #singlecell data across samples/studies, and can you get it back? When samples are from e.g. healthy & disease, should you simply massage cells together? FINALLY, I feel we can answer this question: doi.org/10.1101/2023.0…

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Rafael Irizarry @rafalab

3 years ago

Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s4159…

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Cell Genomics @CellGenomics

3 years ago

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes dlvr.it/Sqvk60

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Tirosh Lab @TiroshLab

3 years ago

1. Excited to share our new paper in @Nature! With over 1000 tumors analyzed by scRNA-seq, we provide a systematic pan-cancer characterization of transcriptional intra-tumor heterogeneity (ITH) nature.com/articles/s4158…

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Scott Tyler (@[email protected]) @ScienceScottT

3 years ago

Even so, thorough mixing after an 'integration' method only means "good" if you're analyzing technical replicates. Beta-cells w/beta-cells is fitting priors on what's important variation; 27% of the beta-cell transcriptome is circadian regulated. science.org/doi/abs/10.112…

Lior Pachter @lpachter

3 years ago

To be fair, the Jaccard similarity calculation wasn't the only benchmarking. The authors also made UMAPs, which they claim show that "bridge integration most consistently and effectively matched cells in the same biological state across modalities". 4/

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Nature News & Views @NatureNV

3 years ago

A human reference pangenome has been generated. In this Forum,@AryaMassarat & @mgymrek tell us how it was built, and Brian McStay & Hakon Jonsson discuss the insights into repetitive sequence that we are already gaining from it go.nature.com/3VRwM7Y

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Nature Biotechnology @NatureBiotech

3 years ago

Reactivated transposable elements generate chimeric tumor-specific antigens that are shared among different cancers and could provide potential pan-therapeutic targets. #NBThighlight nature.com/articles/s4158…

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dana_peer @dana_peer

3 years ago

@shyam_lab @lawrensonlab @SashaGusevPosts @themis_brown Batch correction is the WORST for cancer because each cancer IS different and unique. Batch correction is ALWAYS terrible in cancer and we NEVER do it. The number of times we had to argue with reviewers on this point!!!

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Dr. Jamshaid A. Shahir @jamshaid_shahir

3 years ago

As I reflect on my grad school experience during Carolina's day of giving, I'm very grateful to one of my professors @natstann for her mentorship this past year, which resulted in me submitting my first first-author paper! #UNCGradStudents @UNC_GradSchool tinyurl.com/2p8tp2fk

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Nature Biotechnology @NatureBiotech

3 years ago

SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data go.nature.com/42GNoCu

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Garth Kong | Computational Biologist @KongGarth

3 years ago

How reproducible are #bioinformatic pipelines really? 🤔 In pursuit of this question, I asked three lab members to run my pipeline on the same CUT&Tag data (4 conditions, 3 biological replicates, and 2 epigenetic marks). 💻 #Genomics #snakemake #AcademicChatter

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Vivek Patel, MD @vpatelmd

3 years ago

Hey #MedTwitter Here are the basics of survival curve and hazard ratio interpretation. Trust me it's conceptually easy. Dreaded terminology will be decoded. Ever wondered what a hazard ratio really means? What is a survival function? What is cox proportional hazards? 🧵

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Nana Matoba @NanaMatoba

3 years ago

Excited to share our new preprint, where we investigated context-specific gene regulation and QTLs by stimulating 🪄⚡️ the Wnt pathway in human neural progenitor cells🧠 (co-led with two wonderful grad students @brandonDLe @jmvalone4 in @jsteinlab) biorxiv.org/content/10.110… 1/🧵

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Henri Niskanen @henri_niskanen

3 years ago

Happy to share our work published today in @Nature, where we show that a subset of disease-associated variants in intrinsically disordered regions (IDRs) result in aberrant phase separation and nucleolar dysfunction. nature.com/articles/s4158…

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Adrian Liston @LabListon

4 years ago

We have an exciting #computational paper out in @CellRepMethods. Ever use a #tSNE or #UMAP in #scSeq, #flowcytometry or #masscytometry? It doesn't have to be just a pretty picture anymore - we've developed a statistical test to check for differences. 1/6 cell.com/cell-reports-m…

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sugarciare @sugarciare

4 years ago

After 100s of meetings and discussions with our multidisciplinary group, I’m excited to share the 1st AURORA US network study, which I'm honored to co-lead.go.nature.com/3XhJU5X @BCRFccure @TheTBCRC @UNC_Lineberger @DrLisaCarey @TomasPascual @youli_xia @kahoadley #CharlesPerou

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Katie Hoadley @kahoadley

4 years ago

Newest work from the @HoadleyLab and @MelissaTroester Lab by @AlinaHamilton. @UNC_Lineberger @CompMedUNC

Cancer Research Communications @CRC_AACR

4 years ago

#ICYMI— Incorporating #RNA-based risk scores for genomic instability to predict #breastcancer recurrence and immunogenicity in a diverse population, by @AlinaHamilton et al. bit.ly/3WGcRbF @UNCPathology #openaccess

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Ming "Tommy" Tang @tangming2005

4 years ago

protip: when ask for help with a bioinformatics problem, explain what you want, what you have tried, and what's the problem. Better to include the data and code. If you are not willing to put effort into asking a good question, do not expect people to make an effort to answer.