Reproducibility in science: improving the standard for basic and preclinical research

CG Begley, JPA Ioannidis - Circulation research, 2015 - Am Heart Assoc
Medical and scientific advances are predicated on new knowledge that is robust and
reliable and that serves as a solid foundation on which further advances can be built. In …

Supervised, unsupervised, and semi-supervised feature selection: a review on gene selection

JC Ang, A Mirzal, H Haron… - IEEE/ACM transactions …, 2015 - ieeexplore.ieee.org
Recently, feature selection and dimensionality reduction have become fundamental tools for
many data mining tasks, especially for processing high-dimensional data such as gene …

Comprehensive molecular characterization of papillary renal-cell carcinoma

Cancer Genome Atlas Research … - New England Journal of …, 2016 - Mass Medical Soc
Background Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell
carcinomas, is a heterogeneous disease that consists of various types of renal cancer …

A landscape of pharmacogenomic interactions in cancer

F Iorio, TA Knijnenburg, DJ Vis, GR Bignell… - Cell, 2016 - cell.com
Systematic studies of cancer genomes have provided unprecedented insights into the
molecular nature of cancer. Using this information to guide the development and application …

A comprehensive transcriptional portrait of human cancer cell lines

C Klijn, S Durinck, EW Stawiski, PM Haverty… - Nature …, 2015 - nature.com
Tumor-derived cell lines have served as vital models to advance our understanding of
oncogene function and therapeutic responses. Although substantial effort has been made to …

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

J Barretina, G Caponigro, N Stransky, K Venkatesan… - Nature, 2012 - nature.com
The systematic translation of cancer genomic data into knowledge of tumour biology and
therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust …

Cancer transcriptome profiling at the juncture of clinical translation

M Cieślik, AM Chinnaiyan - Nature Reviews Genetics, 2018 - nature.com
Methodological breakthroughs over the past four decades have repeatedly revolutionized
transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to …

Adaptive huber regression

Q Sun, WX Zhou, J Fan - Journal of the American Statistical …, 2020 - Taylor & Francis
Big data can easily be contaminated by outliers or contain variables with heavy-tailed
distributions, which makes many conventional methods inadequate. To address this …

[HTML][HTML] Revisiting global gene expression analysis

J Lovén, DA Orlando, AA Sigova, CY Lin, PB Rahl… - Cell, 2012 - cell.com
Gene expression analysis is a widely used and powerful method for investigating the
transcriptional behavior of biological systems, for classifying cell states in disease, and for …

Tumor-derived cell lines as molecular models of cancer pharmacogenomics

A Goodspeed, LM Heiser, JW Gray… - Molecular Cancer …, 2016 - AACR
Compared with normal cells, tumor cells have undergone an array of genetic and epigenetic
alterations. Often, these changes underlie cancer development, progression, and drug …