User profiles for S. Pepke
Shirley PepkePrincipal 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 …
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
Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long
noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential …
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 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 …
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, …
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 (…
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
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-…
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 , …
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
… 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 …
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-…
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 …
doped Ge: Sb at H∼ 25 kOe, which is robust up to at least three times the critical density …