User profiles for S. Pepke

Shirley Pepke

Principal Scientist, Lyrid LLC
Verified email at lyridllc.com
Cited by 1365

Computation for ChIP-seq and RNA-seq studies

S Pepke, B Wold, A Mortazavi - Nature methods, 2009 - nature.com
… Bottom left, P(s), probability of observing a location with s reads covering it. The bars represent
the control data distribution. A hypothetical Poisson distribution fit is shown with s thresh …

[PDF][PDF] Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming

DH Kim, GK Marinov, S Pepke, ZS Singer, P He… - Cell stem cell, 2015 - cell.com
Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long
noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential …

[HTML][HTML] A Dynamic Model of Interactions of Ca2+, Calmodulin, and Catalytic Subunits of Ca2+/Calmodulin-Dependent Protein Kinase II

S Pepke, T Kinzer-Ursem, S Mihalas… - PLoS computational …, 2010 - journals.plos.org
s represents the increase in affinity of the N lobe of CaM for Ca 2+ when CaM binds to mCaMKII.
Explicitly, s … (Figure 3), we show that s and r also represent the proportional decrease in …

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

A Ozdemir, KI Fisher-Aylor, S Pepke… - Genome …, 2011 - genome.cshlp.org
… The genome was segregated into four mutually exclusive categories: promoter proximal (relative
to the set of promoters from S. Celniker, including 500 bp upstream), exonic, intronic, …

Predictability of self-organizing systems

SL Pepke, JM Carlson - Physical Review E, 1994 - APS
… In each case we attempt to predict events with s f, where s is some characteristic size (in …
small (s & s ) and large (s ~X) events, while the others exhibit power laws cut off at s =s (…

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

A Mortazavi, S Pepke, C Jansen, GK Marinov… - Genome …, 2013 - genome.cshlp.org
We tested whether self-organizing maps (SOMs) could be used to effectively integrate, visualize,
and mine diverse genomics data types, including complex chromatin signatures. A fine-…

[HTML][HTML] Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer

S Pepke, G Ver Steeg - BMC medical genomics, 2017 - Springer
… As mentioned, we restrict Y j ’s to take three possible values so that, eg, Y j =0,1, and 2 might
correspond to relatively low, neutral, and high expression. For each sample of data, X=x l , …

Prediction of large events on a dynamical model of a fault

SL Pepke, JM Carlson, BE Shaw - Journal of Geophysical …, 1994 - Wiley Online Library
… the number of events predicted, S diverges as the alarm time and the fraction of events
predicted approach zero. We often observe this behavior in S when intermediate-term algorithms …

A portfolio approach to accelerate therapeutic innovation in ovarian cancer

S Chaudhuri, K Cheng, AW Lo, S Pepke… - Available at SSRN …, 2018 - papers.ssrn.com
Biomedical innovation in oncology has become riskier and more expensive, precipitating a
withdrawal of private sector funding from the sector. In this article, we consider a portfolio-…

Electronic states in a disordered metal: Magnetotransport in doped germanium

TF Rosenbaum, S Pepke, RN Bhatt, TV Ramakrishnan - Physical Review B, 1990 - APS
We observe a sharp feature in the ultra-low-temperature magnetoconductivity of degenerately
doped Ge: Sb at H∼ 25 kOe, which is robust up to at least three times the critical density …