[HTML][HTML] Loss of amino-terminal acetylation suppresses a prion phenotype by modulating global protein folding

WM Holmes, BK Mannakee, RN Gutenkunst… - Nature …, 2014 - nature.com
Amino-terminal acetylation is among the most ubiquitous of protein modifications in
eukaryotes. Although loss of N-terminal acetylation is associated with many abnormalities, the …

Sloppiness and the geometry of parameter space

BK Mannakee, AP Ragsdale, MK Transtrum… - Uncertainty in Biology: A …, 2016 - Springer
When modeling complex biological systems, exploring parameter space is critical, because
parameter values are typically poorly known a priori. This exploration can be Mannakee, …

Genomic landscape of lymphatic malformations: a case series and response to the PI3Kα inhibitor alpelisib in an N-of-1 clinical trial

…, AS Dobroff, TL Smith, TJ Bocklage, BK Mannakee… - Elife, 2022 - elifesciences.org
Background: Lymphatic malformations (LMs) often pose treatment challenges due to a large
size or a critical location that could lead to disfigurement, and there are no standardized …

[HTML][HTML] The impact of genome-wide association studies on biomedical research publications

TJ Struck, BK Mannakee, RN Gutenkunst - Human Genomics, 2018 - Springer
The past decade has seen major investment in genome-wide association studies (GWAS).
Among the many goals of GWAS, a major one is to identify and motivate research on novel …

[HTML][HTML] Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast

RA Hermansen, BK Mannakee, W Knecht… - BMC evolutionary …, 2015 - Springer
… changes are strongly purged from rate-limiting enzymes, because they alter pathway flux,
but such changes may accumulate in enzymes with less control over flux (Mannakee and …

Testing whether metazoan tyrosine loss was driven by selection against promiscuous phosphorylation

S Pandya, TJ Struck, BK Mannakee… - Molecular biology …, 2015 - academic.oup.com
Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the
corresponding kinase enzymes have diversified dramatically. This diversification is correlated …

Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors

BK Mannakee, U Balaji, AK Witkiewicz… - …, 2018 - academic.oup.com
Motivation Tumor genome sequencing offers great promise for guiding research and therapy,
but spurious variant calls can arise from multiple sources. Mouse contamination can …

[HTML][HTML] Selection on network dynamics drives differential rates of protein domain evolution

BK Mannakee, RN Gutenkunst - PLoS Genetics, 2016 - journals.plos.org
The long-held principle that functionally important proteins evolve slowly has recently been
challenged by studies in mice and yeast showing that the severity of a protein knockout only …

[PDF][PDF] Batcave: calling somatic mutations with a tumor-and site-specific prior

BK Mannakee, RN Gutenkunst - NAR genomics and …, 2020 - academic.oup.com
Detecting somatic mutations withins tumors is key to understanding treatment resistance,
patient prognosis and tumor evolution. Mutations at low allelic frequency, those present in only …

Statistical methods for improving low frequency variant calling in cancer genomics

BK Mannakee - 2020 - search.proquest.com
… My parents Bruce and Sandra Mannakee, and Lee and Nancy Mills, provided financial
and emotional support that made this journey possible. Without their generosity and …