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Hi there 👋

I am an associate research scientist in Verhaak lab at the Department of Neurosurgery, Yale School of Medicine. I am working in the comparative genomics field to study evolutionary history of spontaneous canine and human glioma. My current work is focused on characterizing and targeting evolutionarily constrained genetic elements and underlying tissue-specific selection pressures that can drive tumor progression and therapy resistance. More

You can reach me either via tweeting or direct messaging @sbamin or contact here.

Samir Amin's Projects

biscut-py3 icon biscut-py3

Code from Shih J, Sarmashghi S et al. 2023: https://pubmed.ncbi.nlm.nih.gov/37380777/

canine_gistic2 icon canine_gistic2

Canine CanFam3.1 GISTIC2 copy number analysis. For debugging GISTIC2 .mat file, please contact developers at https://www.genepattern.org/modules/docs/GISTIC_2.0) or https://groups.google.com/a/broadinstitute.org/g/gistic-forum

canineglioma icon canineglioma

Comparative molecular life history of spontaneous canine and human gliomas. Amin et al. Cancer Cell 2020

cellprofiler icon cellprofiler

R scripts to clean/analyse CellProfiler output, forked from

cgp_germline icon cgp_germline

(Beta) Germline workflow for Canine Glioma Project - Stage for Nextflow

code101 icon code101

My notes on programming, mostly using R, Python, and bash.

dndscv icon dndscv

dN/dS methods to quantify selection in cancer and somatic evolution; forked for canine genome. Original code is by @im3sanger at

flowr icon flowr

Robust and efficient workflows using a simple language agnostic approach

gdc-client icon gdc-client

docker container for running NCI GDC gdc-client

gwa_tutorial icon gwa_tutorial

Forked from https://github.com/MareesAT/GWA_tutorial. Cite: 1 Marees AT, de Kluiver H, Stringer S, Vorspan F, Curis E, Marie-Claire C, et al. A tutorial on conducting genome-wide association studies: Quality control and statistical analysis. Int J Methods Psychiatr Res 2018;27:e1608. https://doi.org/10.1002/mpr.1608.

ichorcna icon ichorcna

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

islr-tidymodels-labs icon islr-tidymodels-labs

Credir: Sourced from https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs ; Issues at the author's site, https://github.com/EmilHvitfeldt/ISLR-tidymodels-labs/issues

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