Dimension reduction techniques for the integrative analysis of multi-omics data

C Meng, OA Zeleznik, GG Thallinger… - Briefings in …, 2016 - academic.oup.com
State-of-the-art next-generation sequencing, transcriptomics, proteomics and other high-
throughput 'omics' technologies enable the efficient generation of large experimental data …

Enter the matrix: factorization uncovers knowledge from omics

GL Stein-O'Brien, R Arora, AC Culhane, AV Favorov… - Trends in Genetics, 2018 - cell.com
Omics data contain signals from the molecular, physical, and kinetic inter-and intracellular
interactions that control biological systems. Matrix factorization (MF) techniques can reveal …

A placental model of SARS-CoV-2 infection reveals ACE2-dependent susceptibility and differentiation impairment in syncytiotrophoblasts

J Chen, JA Neil, JP Tan, R Rudraraju, M Mohenska… - Nature Cell …, 2023 - nature.com
SARS-CoV-2 infection causes COVID-19. Several clinical reports have linked COVID-19
during pregnancy to negative birth outcomes and placentitis. However, the …

Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells

D Rosebrock, S Arora, N Mutukula, R Volkman… - Nature cell …, 2022 - nature.com
Cerebral organoids exhibit broad regional heterogeneity accompanied by limited cortical
cellular diversity despite the tremendous upsurge in derivation methods, suggesting …

[9] TM4 microarray software suite

AI Saeed, NK Bhagabati, JC Braisted, W Liang… - Methods in …, 2006 - Elsevier
Powerful specialized software is essential for managing, quantifying, and ultimately deriving
scientific insight from results of a microarray experiment. We have developed a suite of …

[LLIBRE][B] Henri Lefebvre: A critical introduction

A Merrifield - 2013 - books.google.com
Philosopher, sociologist and urban theorist, Henri Lefebvre is one of the great social
theorists of the twentieth century. This accessible and innovative introduction to the work of …

A multivariate approach to the integration of multi-omics datasets

C Meng, B Kuster, AC Culhane, AM Gholami - BMC bioinformatics, 2014 - Springer
Background To leverage the potential of multi-omics studies, exploratory data analysis
methods that provide systematic integration and comparison of multiple layers of omics …

Global patterns in ecological indicators of marine food webs: a modelling approach

JJ Heymans, M Coll, S Libralato, L Morissette… - PloS one, 2014 - journals.plos.org
Background Ecological attributes estimated from food web models have the potential to be
indicators of good environmental status given their capabilities to describe redundancy, food …

Changes in the endometrial transcriptome during the bovine estrous cycle: effect of low circulating progesterone and consequences for conceptus elongation

N Forde, ME Beltman, GB Duffy, P Duffy… - Biology of …, 2011 - academic.oup.com
In cattle, elevated concentrations of circulating progesterone (P4) in the immediate
postconception period are associated with advanced conceptus development, while low P4 …

MADE4: an R package for multivariate analysis of gene expression data

AC Culhane, J Thioulouse, G Perrière… - …, 2005 - academic.oup.com
MADE4, m icroarray ade4, is a software package that facilitates multivariate analysis of
microarray gene-expression data. MADE4 accepts a wide variety of gene-expression data …