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Open AccessJournal ArticleDOI

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

TLDR
The data showed that resistant genotypes were pre-existing and adaptively selected by NAC, while transcriptional profiles were acquired by reprogramming in response to chemotherapy in TNBC patients.
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This article is published in Cell.The article was published on 2018-05-03 and is currently open access. It has received 684 citations till now. The article focuses on the topics: Exome sequencing & Single cell sequencing.

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Insights into Molecular Classifications of Triple-Negative Breast Cancer: Improving Patient Selection for Treatment.

TL;DR: This work seeks to review the most recent efforts to classify TNBC based on the comprehensive profiling of tumors for cellular composition and molecular features to help improve risk stratification of patients, guide treatment decisions and surveillance, and help identify new targets for drug development.
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Resolving genetic heterogeneity in cancer.

TL;DR: An overview of the theoretical models of tumour evolution is provided and what to consider when inferring evolutionary dynamics from genomic data is discussed.
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Stem cell fate in cancer growth, progression and therapy resistance

TL;DR: Evidence showing that activation of stem cell programmes in cancers can lead to progression, therapy resistance and metastatic growth and that targeting these attributes may enable better control over a difficult disease is considered.
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Tumour heterogeneity and metastasis at single-cell resolution.

TL;DR: Recent advances in single-cell technologies are reviewed and discussed in detail how they can be leveraged to understand tumour heterogeneity and metastasis.
References
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Fast gapped-read alignment with Bowtie 2

TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
Journal Article

Visualizing Data using t-SNE

TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
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limma powers differential expression analyses for RNA-sequencing and microarray studies

TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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