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@@ -80,7 +80,7 @@ A graft is categorized based on the relationship between donor and recipient:
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![Kidney allograft survival rates in children by transplant year[^kim-marks]](graphics/presentation/kidney-graft-survival.png){ height=65% }
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-[^kim-marks]: [Kim & Marks. "Long-term outcomes of children after solid organ transplantation". In: Clinics (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
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+[^kim-marks]: [Kim & Marks (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3884158/?report=classic)
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## Rejection is treated with immune suppressive drugs
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@@ -203,7 +203,7 @@ unexplored
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{ height=70% }
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-[^chipseq]: [Furey. "ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions". In: Nature Reviews Genetics (2012)](http://www.nature.com/articles/nrg3306)
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+[^chipseq]: [Furey (2012)](http://www.nature.com/articles/nrg3306)
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## Experimental design
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@@ -241,7 +241,7 @@ Data generated by Sarah Lamere, published in GEO as
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![ChIP-seq coverage in IL2 gene[^lamerethesis]](graphics/presentation/LaMere-thesis-fig3.9-SVG-CROP.png){ height=65% }
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-[^lamerethesis]: Sarah LaMere. "Dynamic epigenetic regulation of CD4 T cell activation and memory formation". PhD thesis. TSRI, 2015.
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+[^lamerethesis]: Sarah LaMere. Ph.D. thesis (2015).
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## Histone modifications occur on consecutive histones
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@@ -257,13 +257,13 @@ Data generated by Sarah Lamere, published in GEO as
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![Finding "islands" of coverage with SICER[^sicer]](graphics/presentation/SICER-fig1-SVG.png)
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-[^sicer]: [Zang et al. “A clustering approach for identification of enriched domains from histone modification ChIP-Seq data”. In: Bioinformatics 25.15 (2009)](https://doi.org/10.1093/bioinformatics/btp340)
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+[^sicer]: [Zang et al. (2009)](https://doi.org/10.1093/bioinformatics/btp340)
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## IDR identifies *reproducible* enriched regions
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![Example irreproducible discovery rate[^idr] score consistency plot](graphics/presentation/IDR-example-CROP-RASTER.png){ height=65% }
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-[^idr]: [Li et al. “Measuring reproducibility of high-throughput experiments”. In: AOAS (2011)](https://doi.org/10.1214/11-AOAS466)
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+[^idr]: [Li et al. (2011)](https://doi.org/10.1214/11-AOAS466)
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## Finding enriched regions across the genome
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