resume/citations.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/

%% Created for Ryan C. Thompson at 2016-06-10 07:30:41 -0700 


%% Saved with string encoding Unicode (UTF-8) 



@article{lamere2016,
	Abstract = {The epigenetic determinants driving the responses of CD4 T cells to antigen are currently an area of active research. Much has been done to characterize helper T-cell subsets and their associated genome-wide epigenetic patterns. In contrast, little is known about the dynamics of histone modifications during CD4 T-cell activation and the differential kinetics of these epigenetic marks between naive and memory T cells. In this study, we have detailed the dynamics of genome-wide promoter H3K4me2 and H3K4me3 over a time course during activation of human naive and memory CD4 T cells. Our results demonstrate that changes to H3K4 methylation occur relatively late after activation (5 days) and reinforce activation-induced upregulation of gene expression, affecting multiple pathways important to T-cell activation, differentiation and function. The dynamics and mapped pathways of H3K4 methylation are distinctly different in memory cells, which have substantially more promoters marked by H3K4me3 alone, reinforcing their more differentiated state. Our study provides the first data examining genome-wide histone modification dynamics during CD4 T-cell activation, providing insight into the cross talk between H3K4 methylation and gene expression, and underscoring the impact of these marks upon key pathways integral to CD4 T-cell activation and function.Genes and Immunity advance online publication, 12 May 2016; doi:10.1038/gene.2016.19.},
	Author = {LaMere, S. A. and \textbf{Ryan C. Thompson} and Komori, H. K. and Mark, A. and Salomon, D. R.},
	Date-Added = {2016-06-10 14:29:31 +0000},
	Date-Modified = {2016-06-10 14:30:40 +0000},
	Journal = {Genes Immun.},
	Month = {May},
	Title = {{{P}romoter {H}3{K}4 methylation dynamically reinforces activation-induced pathways in human {C}{D}4 {T} cells}},
	Year = {2016}}

@article{globin-reduction,
	Author = {\textbf{Ryan C. Thompson} and Terri Gelbart and Steven R. Head and Phillip Ordoukhanian and Courtney Mullen and Dongmei Han and Dora M. Berman and Amelia Bartholomew and Norma S. Kenyon and Daniel R. Salomon},
	Date-Added = {2016-05-03 23:39:31 +0000},
	Date-Modified = {2016-05-03 23:44:47 +0000},
	Journal = {American Journal of Primatology (in review)},
	Title = {Optimizing yield of deep {RNA} sequencing for gene expression profiling of peripheral blood samples from cynomolgus monkeys ({Macaca} fascicularis)},
	Year = {2016}}

@article{Scott036061,
	Abstract = {RNA-mediated oligonucleotide Annealing, Selection, and Ligation (RASL-seq) is a method to measure the expression of hundreds of genes in thousands of samples for a fraction of the cost of competing methods. However, enzymatic inefficiencies of the original protocol and the lack of open source software to design and analyze RASL-seq experiments have limited its widespread adoption. We recently reported an Rnl2-based RASL-seq protocol (RRASL-seq) that offers improved ligation efficiency and a probe decoy strategy to optimize sequencing usage. Here, we describe an open source software package, RASLseqTools, that provides computational methods to design and analyze RASL-seq experiments. Furthermore, using data from a large RRASL-seq experiment, we demonstrate how normalization methods can be used for characterizing and correcting experimental, sequencing, and alignment error. We provide evidence that the three principal predictors of RRASL-seq reproducibility are barcode/probe sequence dissimilarity, sequencing read depth, and normalization strategy. Using dozens of technical and biological replicates across multiple 384-well plates, we find simple normalization strategies yield similar results to more statistically complex methods.},
	Author = {Scott, Erick R. and Larman, H. Benjamin and Torkamani, Ali and Schork, Nicholas J. and Wineinger, Nathan and Nanis, Max and \textbf{Ryan C. Thompson} and Beheshti Zavareh, Reza B. and Lairson, Luke L. and Schultz, Peter G. and Su, Andrew I.},
	Date-Added = {2016-02-08 23:51:09 +0000},
	Date-Modified = {2016-02-09 20:54:45 +0000},
	Doi = {10.1101/036061},
	Eprint = {http://biorxiv.org/content/early/2016/01/07/036061.full.pdf},
	Journal = {Nucleic Acids Research (in review)},
	Title = {{RASLseqTools}: open-source methods for designing and analyzing {RNA}-mediated oligonucleotide Annealing, Selection, and, Ligation sequencing ({RASL}-seq) experiments},
	Url = {http://biorxiv.org/content/early/2016/01/07/036061},
	Year = {2016},
	Bdsk-Url-1 = {http://biorxiv.org/content/early/2016/01/07/036061},
	Bdsk-Url-2 = {http://dx.doi.org/10.1101/036061}}

@article{Rangarajue08833,
	Abstract = {Longevity mechanisms increase lifespan by counteracting the effects of aging. However, whether longevity mechanisms counteract the effects of aging continually throughout life, or whether they act during specific periods of life, preventing changes that precede mortality is unclear. Here, we uncover transcriptional drift, a phenomenon that describes how aging causes genes within functional groups to change expression in opposing directions. These changes cause a transcriptome-wide loss in mRNA stoichiometry and loss of co-expression patterns in aging animals, as compared to young adults. Using Caenorhabditis elegans as a model, we show that extending lifespan by inhibiting serotonergic signals by the antidepressant mianserin attenuates transcriptional drift, allowing the preservation of a younger transcriptome into an older age. Our data are consistent with a model in which inhibition of serotonergic signals slows age-dependent physiological decline and the associated rise in mortality levels exclusively in young adults, thereby postponing the onset of major mortality.DOI: http://dx.doi.org/10.7554/eLife.08833.001},
	Author = {Rangaraju, Sunitha and Solis, Gregory M and \textbf{Ryan C Thompson} and Gomez-Amaro, Rafael L and Kurian, Leo and Encalada, Sandra E and Niculescu, Alexander B and Salomon, Daniel R and Petrascheck, Michael},
	Date-Added = {2016-02-08 23:48:29 +0000},
	Date-Modified = {2016-02-09 20:55:49 +0000},
	Doi = {10.7554/eLife.08833},
	Editor = {VijayRaghavan, K},
	Journal = {eLife},
	Publisher = {eLife Sciences Publications Limited},
	Title = {Suppression of transcriptional drift extends \textit{{C. elegans}} lifespan by postponing the onset of mortality},
	Volume = {4},
	Year = {2015},
	Bdsk-Url-1 = {http://dx.doi.org/10.7554/eLife.08833}}

@unpublished{mathpaper,
	Abstract = {Of all the systems of thinking that have made their way through the ages, Euclidean geometry remains one of the most appealing and intuitive. It is also one of the most successful, having been practiced continuously from Greek antiquity through modern-day schools. We will examine the aspects of geometry that account for this intuitiveness, as well as several innovations that allowed it to tackle new and more difficult problems. We begin with an analysis of Euclid's Elements, and then we will consider the contributions of two ancient authors, Archimedes and Apollonius. Lastly, we will see how two authors during the scientific revolution, Galileo Galilei and Ren{\'e} Descartes, pushed geometry into new areas, namely the realistic and the algebraic.},
	Author = {\textbf{Ryan C. Thompson}},
	Date-Added = {2015-08-26 05:17:44 +0000},
	Date-Modified = {2016-02-09 21:00:31 +0000},
	Month = {May},
	Title = {\href{http://mneme.homenet.org/~ryan/resume/examples/UVa/math-history-paper.pdf}{The sources and limits of geometric rigor from {Euclid} through {Descartes}}},
	Year = {2008},
	Bdsk-Url-1 = {https://mneme.homenet.org/~ryan/resume/examples/UVa/math-history-paper.pdf}}

@unpublished{cfarmer,
	Abstract = {Here we present Contig Farmer, a tool for improving the length and depth of coverage of contigs generated from a database of short sequence reads. Contig Farmer works without assembling the entire database and has only modest hardware requirements. The underlying methodology of Contig Farmer is itera- tive growth of seed contigs using repeated search and assembly. The utility of Contig Farmer is demon- strated on the sequences in TOBFAC, the database of tobacco transcription factors. Contig Farmer suc- cessfully grew the TOBFAC contigs, both in length and in depth of coverage, to yield a larger, higher- quality set of contigs.},
	Author = {\textbf{Ryan C. Thompson} and Paul J. Rushton and Tom W. Laudeman and Michael P. Timko},
	Date-Added = {2015-08-26 05:11:30 +0000},
	Date-Modified = {2016-02-09 20:59:38 +0000},
	Month = {June},
	School = {University of Virginia},
	Title = {\href{http://mneme.homenet.org/~ryan/resume/examples/UVa/contigfarmer.pdf}{{Contig} {Farmer}: a tool for extracting maximal-length contiguous sequences from a database of short sequence reads (Undergraduate Thesis)}},
	Year = {2009},
	Bdsk-Url-1 = {https://mneme.homenet.org/~ryan/resume/examples/UVa/contigfarmer.pdf}}

@article{kurian2014molecular,
	Author = {Kurian, SM and Williams, AN and Gelbart, T and Campbell, D and Mondala, TS and Head, SR and Horvath, S and Gaber, L and \textbf{R Thompson} and Whisenant, T and others},
	Date-Modified = {2015-08-26 05:52:31 +0000},
	Journal = {American Journal of Transplantation},
	Number = {5},
	Pages = {1164--1172},
	Publisher = {Wiley Online Library},
	Title = {Molecular Classifiers for Acute Kidney Transplant Rejection in Peripheral Blood by Whole Genome Gene Expression Profiling},
	Volume = {14},
	Year = {2014},
	Bdsk-Url-1 = {http://onlinelibrary.wiley.com/enhanced/doi/10.1111/ajt.12671/}}

@article{van2011illumina,
	Author = {Van Nieuwerburgh, Filip and \textbf{Ryan C. Thompson} and Ledesma, Jessica and Deforce, Dieter and Gaasterland, Terry and Ordoukhanian, Phillip and Head, Steven R},
	Date-Modified = {2016-02-09 20:53:21 +0000},
	Journal = {Nucleic Acids Research},
	Pages = {gkr1000},
	Publisher = {Oxford Univ Press},
	Title = {{Illumina} Mate-Paired {DNA} Sequencing Library Preparation Using {Cre}-{Lox} Recombination},
	Year = {2011},
	Bdsk-Url-1 = {http://nar.oxfordjournals.org/content/40/3/e24.full}}