Chirag Nepal
@ChiragNepal
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#Father #Husband #Freeletics #PrecisionOncology #TranslationalGenomics #CompBiology Faculty: @LLUHealth PostDoc: @UCPH_BRIC Ph.D.: @UiB #RT!=Endorsement
Loma Linda University
Joined April 2014
Our simplified model of alternative promoter regulation. 13/15
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p53 reveals principles of chromatin remodeling and enhancer activation
academic.oup.com
Abstract. Pioneer transcription factors can bind to closed chromatin, initiating its opening and subsequent gene activation. However, the specific features
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It’s unlikely that the editors conducted the experiments themselves. The retraction decision was probably informed by concerns raised by multiple researchers and independent evaluations.
Science is retracting the December 2010 Research Article, “A bacterium that can grow by using arsenic instead of phosphorus.” (THREAD 🧵) https://t.co/4yeowZdeV0
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Integrating GWAS and spatial omics. Spatially resolved mapping of cells associated with human complex traits https://t.co/tXqa5iitlz Research highlight @naturemethods
https://t.co/dzGGkqFFDm Good methods will reveal novel biology.
nature.com
Nature Methods - Integrating GWAS and spatial omics
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Single-cell methylation data are generally much sparser than scRNA-seq, but it was fun exploring the analysis.
linkedin.com
Single-cell methylation data are generally much sparser than scRNA-seq, but it was fun exploring the analysis. I tried 3 tools: MethSCAn (Python): https://lnkd.in/gh33q7q9 aMethyst (R): https://lnk...
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Calling reliable mutations and CNV is tough on short reads, which is more complicated in long reads. We need better tools. Recent tool SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read https://t.co/yc0MJrhZ4h
@naturemethods
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Aberrantly expressed tumor-specific antigens are epigenetically regulated. @NatureCancer
https://t.co/S2KoQBo1wJ Congrats to authors !
nature.com
Nature Cancer - Based on a proteogenomic analysis, Perreault and colleagues report that the majority of predicted tumor antigens originate from unmutated genomic sequences in melanoma and non-small...
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My recent posts on @X are getting only 30–40 views, whereas earlier I used to get 2–3K views on average. Seems like posts are being hidden if you're not verified. Anyone else noticing the same trend?
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The same genetic mutation can exist within different epigenetic contexts, and effective treatment strategies must account for these differences to achieve better clinical outcomes. #StayTuned #PaperAlert
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Nice work- very comprehensive. It reminded me a 2009 paper, though ChIP-seq weren't widely available at the time.
academic.oup.com
ABSTRACT. Using a comparative genomics approach to reconstruct the fate of genomic regulatory blocks (GRBs) and identify exonic remnants that have survived
Exonic enhancers are a widespread class of dual-function regulatory elements https://t.co/Ho0TdalAsu
#biorxiv_genomic
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Before writing the paper, I was very very excited about the findings. Now i have written it, i am hardly enthusiastic about it anymore. Do you guys feel the same about your stories? #AcademicChatter
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https://t.co/iKbVDjXEnT Mechanistically, KMT2D localized to active enhancers and CpG-poor promoters that preferentially regulate the urothelial lineage program. CpG-poor promoters-> generally tissue spec promoters Enhancers->generally CpG-poor -> tissue spec expression 😀
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Somatic mutation as an explanation for epigenetic aging
nature.com
Nature Aging - Koch and colleagues report that epigenetic clocks mirror age predictions based on the accumulation of somatic mutations and show that somatic mutations at CpG sites coincide with...
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Latent Embedding Multivariate Regression (LEMUR) for single cell analysis
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Persistent mutation burden drives sustained anti-tumor immune responses https://t.co/LOtzakL8ef Periodic reminder that we need to consider both SNV and CNV/aneuploidy for understanding drug response.
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In comp bio faculty positions, almost everybody looking for generative AI theme, while two years ago, it was all about single cell. How quickly the trends are changing. Keep evolving.
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When a gene is mutated, what is the copy number status of that gene, in general. Any comprehensive studies or any suggestions.
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Excellent story on 3′UTR-derived RNAs originate from G-rich regions enriched in AGO2 and UPF1 binding sites from @BorisLenhard @NejcHaberman @carninci. https://t.co/9GYrO4T25R CAGE has revealed many interesting phenomenon on RNAbiology. Need to do more CAGE on cancer samples
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#PshycEncode #PshycScreen Missing Header for ADHD_meta_PGC.formatted.bed Any idea what numerical value on 4th column means. thanks !
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I was recently invited to review a paper with a 1-week deadline. I did not respond. After 2 weeks, I received a second request to review the same paper. 1-week timeline is a bit too short.
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Around ten miles from our place. Extremely bad situation there and sorry for the people in neighborhood.
Effective immediately there is an evacuation ORDER for the following area: All undeveloped land east of Hwy 330 to Summertrail Place and north of Highland Ave are now under an evacuation ORDER.
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