Amit Rupani
@IAnalyzeGenomes
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Bioinformatician helping enable genome-informed precision medicine for cancers and rare diseases. RTs are stuff I read. Sometimes.
Cleveland, Ohio
Joined September 2012
RT @tangming2005: 1/ Even in the era of single-cell RNAseq, bulk-RNAseq data are still very valuable. 10 tools/papers related to bulk-RNAse….
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RT @simocristea: Incredible resource: analysis of Whole Genome Sequencing data on 10,478 cancer patients spanning 35 types identifies 330 c….
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RT @RiyueSunnyBao: Evolution of delayed resistance to #immunotherapy in a #melanoma #responder: "37 tumor samples over 9 years from a pati….
nature.com
Nature Medicine - Genetic and protein expression analyses of serially collected tumor biopsies from a patient with melanoma treated with immune checkpoint inhibitors provide insights into tumor...
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RT @mo_lotfollahi: Our multimodal model to combine TCR sequences with scRNA-seq is finally out. The most interesting part for me was observ….
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RT @StevenSalzberg1: The human chromosomes are numbered incorrectly (The fourth in an irregular series of threads about #Bioinformatics.) A….
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RT @EricTopol: A major problem with cell-free tumor DNA to detect cancer (Liquid biopsy) is its very low quantity. Today @NatureMedicine us….
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RT @simocristea: “NK cells are well-positioned to steal the immunotherapy spotlight away from T cells”. https://t.c….
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RT @razoralign: VILOCA: Sequencing quality-aware haplotype reconstruction and mutation calling for short- and long-read data .
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RT @jsantoyo: Figeno: multi-region genomic figures with long-read support. #GenomicsData #LongReads #FigureGenerator #PublicationGradeFigur….
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RT @tangming2005: MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions
academic.oup.com
AbstractMotivation. The dynamic transcriptional mechanisms that govern eukaryotic cell function can now be analyzed by RNA sequencing. However, the package
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RT @jsantoyo: Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing. #RareDiseases @Solve_RD #HiFi #LongReads @Pac….
medrxiv.org
Solve-RD is a pan-European rare disease (RD) research program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilised 10-fold coverage HiFi long-read...
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RT @tangming2005: Precise identification of cell states altered in disease using healthy single-cell references | Nature Genetics. https://t….
nature.com
Nature Genetics - In single-cell studies, combining healthy reference atlases and designed control datasets allows more precise identification of disease-associated cell states.
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RT @StevenSalzberg1: We analyzed all 5734 of the available WGS samples from The Cancer Genome Atlas, and find far, far smaller numbers of m….
biorxiv.org
In recent years, a growing number of publications have reported the presence of microbial species in human tumors and of mixtures of microbes that appear to be highly specific to different cancer...
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RT @tangming2005: The future of rapid and automated single-cell data analysis using reference mapping
cell.com
Single-cell datasets are increasing in number and size. To leverage this rich resource, new workflows can reveal novel insights and discoveries. This perspective discusses the computational challen...
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RT @tangming2005: chatomics! new blog post: Common mistakes when analyzing single-cell RNAseq data
divingintogeneticsandgenomics.com
To not miss a post like this, sign up for my newsletter to learn computational biology and bioinformatics. I recently was interviewed by the SEQanswers forum on single-cell RNAseq analysis. In your...
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RT @biorxiv_bioinfo: Empowering bioinformatics communities with Nextflow and nf-core #biorxiv_bioinfo.
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