Epidermal growth factor receptor and EGFRvIII in glioblastoma: signaling pathways and targeted therapies

Z An, O Aksoy, T Zheng, QW Fan, WA Weiss - Oncogene, 2018 - nature.com
Amplification of epidermal growth factor receptor (EGFR) and its active mutant EGFRvIII
occurs frequently in glioblastoma (GBM). While EGFR and EGFRvIII play critical roles in …

Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders

NN Parikshak, MJ Gandal, DH Geschwind - Nature Reviews Genetics, 2015 - nature.com
Genetic and genomic approaches have implicated hundreds of genetic loci in
neurodevelopmental disorders and neurodegeneration, but mechanistic understanding …

Integrative analysis of drug response and clinical outcome in acute myeloid leukemia

D Bottomly, N Long, AR Schultz, SE Kurtz, CE Tognon… - Cancer cell, 2022 - cell.com
Acute myeloid leukemia (AML) is a cancer of myeloid-lineage cells with limited therapeutic
options. We previously combined ex vivo drug sensitivity with genomic, transcriptomic, and …

Sex-specific transcriptional signatures in human depression

B Labonté, O Engmann, I Purushothaman, C Menard… - Nature medicine, 2017 - nature.com
Major depressive disorder (MDD) is a leading cause of disease burden worldwide. While the
incidence, symptoms and treatment of MDD all point toward major sex differences, the …

JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom

A Sreedasyam, C Plott, MS Hossain… - Nucleic acids …, 2023 - academic.oup.com
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying
trait variation. Conversely, plant responses to environmental cues represent important …

An anatomically comprehensive atlas of the adult human brain transcriptome

MJ Hawrylycz, ES Lein, AL Guillozet-Bongaarts… - Nature, 2012 - nature.com
Neuroanatomically precise, genome-wide maps of transcript distributions are critical
resources to complement genomic sequence data and to correlate functional and genetic …

Molecular ecological network analyses

Y Deng, YH Jiang, Y Yang, Z He, F Luo, J Zhou - BMC bioinformatics, 2012 - Springer
Background Understanding the interaction among different species within a community and
their responses to environmental changes is a central goal in ecology. However, defining …

[HTML][HTML] Fast R functions for robust correlations and hierarchical clustering

P Langfelder, S Horvath - Journal of statistical software, 2012 - ncbi.nlm.nih.gov
Many high-throughput biological data analyses require the calculation of large correlation
matrices and/or clustering of a large number of objects. The standard R function for …

WGCNA application to proteomic and metabolomic data analysis

G Pei, L Chen, W Zhang - Methods in enzymology, 2017 - Elsevier
Progresses in mass spectrometric instrumentation and bioinformatics identification
algorithms made over the past decades allow quantitative measurements of relative or …

Aging effects on DNA methylation modules in human brain and blood tissue

S Horvath, Y Zhang, P Langfelder, RS Kahn… - Genome biology, 2012 - Springer
Background Several recent studies reported aging effects on DNA methylation levels of
individual CpG dinucleotides. But it is not yet known whether aging-related consensus …