likelihood of identifying reproducible genetic associations using
prior knowledge from publicly available databases and expert
-information [#Armstrong2008:function2gene]. Using these methods, I
-was able to identify genes previously unassociated with SLE in a
-trio-based study [#Jacob2007:ar_lupus]. These genes were then
+information [^Armstrong2008:function2gene]. Using these methods, I was
+able to identify genes previously unassociated with SLE in a
+trio-based study [^Jacob2007:ar_lupus]. These genes were then
replicated in a larger case-control study which was funded by the NIH
-on the basis of the original findings
-[#Jacob2009:sle_irak1],[#Armstrong2009:sle_gi]. Among other findings,
-this larger study identified a missense allele in NCF2 (H389Q,
-rs17849502) which was associated with SLE. Collaborative work
-indicated that H389Q altered the binding energy of NCF2 with VAV1
-using docking simulations, and in vitro experiments confirmed that
-H389Q altered NADPH oxidase function [#Jacob2012:sle_ncf2], thus
-identifying it as a causative SLE mutation.
+on the basis of the original findings [^Jacob2009:sle_irak1],[^Armstrong2009:sle_gi].
+Among other findings, this larger study
+identified a missense allele in NCF2 (H389Q, rs17849502) which was
+associated with SLE. Collaborative work indicated that H389Q altered
+the binding energy of NCF2 with VAV1 using docking simulations, and in
+vitro experiments confirmed that H389Q altered NADPH oxidase function
+[^Jacob2012:sle_ncf2], thus identifying it as a causative SLE
+mutation.
## Cancer Stem Cells in Glioblastoma
including the Id1/Thsb1 inhibitory pathway. Additional experiments
indicated that the *in vitro* pathology of endothelial cells could be
partially rescued using extracellular Thsb1
-[#Stapleton2011:thbs1].
+[^Stapleton2011:thbs1].
# Future research directions
reinvent them.
-[#Armstrong2009:sle_gi]: D L Armstrong et al. “Identification of new SLE-associated genes with a two-step
+[^Armstrong2009:sle_gi]: D L Armstrong et al. “Identification of new SLE-associated genes with a two-step
Bayesian study design”. In: Genes Immun. 10.5 (July 2009), pp. 446–456. doi:
[10.1038/gene.2009.38](http://dx.doi.org/10.1038/gene.2009.38).
-[#Armstrong2008:function2gene]: Don L Armstrong, Chaim O Jacob, and Raphael Zidovetzki. “Function2Gene: a
+[^Armstrong2008:function2gene]: Don L Armstrong, Chaim O Jacob, and Raphael Zidovetzki. “Function2Gene: a
gene selection tool to increase the power of genetic association studies by utilizing
public databases and expert knowledge”. In: BMC Bioinformatics 9 (2008), p. 311.
doi: [10.1186/1471-2105-9-311](http://dx.doi.org/10.1186/1471-2105-9-311).
-[#Jacob2009:sle_irak1]: Chaim O Jacob et al. “Identification of IRAK1 as a risk gene with critical role
+[^Jacob2009:sle_irak1]: Chaim O Jacob et al. “Identification of IRAK1 as a risk gene with critical role
in the pathogenesis of systemic lupus erythematosus”. In: Proc. Natl. Acad. Sci.
U.S.A. 106.15 (Apr. 2009), pp. 6256–6261. doi: [10.1073/pnas.0901181106](http://dx.doi.org/10.1073/pnas.0901181106).
-[#Jacob2007:ar_lupus]: Chaim O Jacob et al. “Identification of novel susceptibility genes in childhood-
+[^Jacob2007:ar_lupus]: Chaim O Jacob et al. “Identification of novel susceptibility genes in childhood-
onset systemic lupus erythematosus using a uniquely designed candidate gene
pathway platform”. In: Arthritis Rheum. 56.12 (Dec. 2007), pp. 4164–4173. doi:
[10.1002/art.23060](http://dx.doi.org/10.1002/art.23060).
-[#Jacob2012:sle_ncf2]: Chaim O Jacob et al. “Lupus-associated causal mutation in neutrophil cytosolic
+[^Jacob2012:sle_ncf2]: Chaim O Jacob et al. “Lupus-associated causal mutation in neutrophil cytosolic
factor 2 (NCF2) brings unique insights to the structure and function of NADPH
oxidase”. In: Proc. Natl. Acad. Sci. U.S.A. 109.2 (Jan. 2012), pp. 59–67. doi:
[10.1073/pnas.1113251108](http://dx.doi.org/10.1073/pnas.1113251108).
-[#Stapleton2011:thbs1]: Christopher J Stapleton et al.
+[^Stapleton2011:thbs1]: Christopher J Stapleton et al.
“Thrombospondin-1 modulates the angiogenic phe- notype of human
cerebral arteriovenous malformation endothelial cells”. In:
Neurosurgery 68.5 (May 2011), pp. 1342–1353.
doi: [10.1227/NEU.0b013e31820c0a68](http://dx.doi.org/10.1227/NEU.0b013e31820c0a68).
-[survival_rate]: Only 4% of patients survive to 5 years after diagnosis
+[^survival_rate]: Only 4% of patients survive to 5 years after diagnosis
-[avm_definition]: Direct artery to vein connection without an
+[^avm_definition]: Direct artery to vein connection without an
intervening capilary bed; leads to high pressure arterial flow in
venous tissue and can lead to hemmorrhage and death.
-[extending_note]: and extending existing open source tools where they
+[^extending_note]: and extending existing open source tools where they
exist
projects / don.git / blobdiff