%% This BibTeX bibliography file was created using BibDesk. %% http://bibdesk.sourceforge.net/ %% Created for Ryan C. Thompson at 2017-03-31 14:12:45 -0700 %% Saved with string encoding Unicode (UTF-8) @comment{x-kbibtex-personnameformatting=<%l><, %f>} @article{eiv-2017, Author = {Kurian, Sunil and Velazquez, Enrique and \textbf{Ryan Thompson} and Whisenant, Thomas and Rose, Stanley and Riley, Nicole and Harrison, Frank and Gelbart, Terri and Friedewald, John and Brietigam, Susan and Abecassis, Michael and Salomon, Daniel}, Date-Added = {2017-01-26 21:41:09 +0000}, Date-Modified = {2017-01-26 21:41:40 +0000}, Journal = {American Journal of Transplantation}, Title = {Orthogonal Comparison of Molecular Signatures of Kidney Transplants with Subclinical and Clinical Acute Rejection -- Equivalent Performance is Agnostic to either Technology or Platform}, Year = {2017}} @article{lamere2017-JMJD3, Abstract = {The changes to the epigenetic landscape in response to antigen during CD4 T cell activation have not been well characterized. While CD4 T cell subsets have been mapped globally for numerous epigenetic marks, little has been done to study their dynamics early after activation. We have studied changes to promoter H3K27me3 during activation of human na{\"\i}ve and memory CD4 T cells. Our results show that these changes occur relatively early (1 day) after activation of both na{\"\i}ve and memory cells, and that H3K27 demethylation is the predominant change at this time point, reinforcing high expression of target genes. Additionally, we also examined bivalent gene promoters (i.e. those containing both H3K4me3 and H3K27me3) and show that this state is dynamic during activation with different outcomes comparing na{\"\i}ve and memory subsets, despite strong overlap between mapped functional pathways. Additionally, inhibition of the H3K27 demethylase, JMJD3, in na{\"\i}ve CD4 demonstrates how the critical JAK/STAT pathways are regulated during activation by H3K27 demethylation. Our results demonstrate that H3K27me3 is a dynamic and important epigenetic modification during CD4 T cell activation and differentiation, and that JMJD3-driven H3K27 demethylation is integral to CD4 T cell function.}, Author = {LaMere, Sarah and {\textbf{Ryan C. Thompson}} and Meng, Xiangzhi and Komori, H. Kiyomi and Mark, A. and Salomon, Daniel R.}, Date-Added = {2016-10-25 21:40:16 +0000}, Date-Modified = {2017-03-31 21:12:35 +0000}, Journal = {Journal of Immunology (in review)}, Title = {{{H3K27} methylation dynamics during {CD4} {T} cell activation: regulation of {JAK}/{STAT} and {IL12RB2} expression by {JMJD3}}}, Year = {2017}} @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, Sarah and {\textbf{Ryan C. Thompson}} and Komori, H. Kiyomi and Mark, Adam and Salomon, Daniel R.}, Date-Added = {2016-06-10 14:29:31 +0000}, Date-Modified = {2016-10-25 22:10:59 +0000}, Journal = {Genes \& Immunity}, 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, Abstract = {Primate blood contains high concentrations of globin messenger RNA. Globin reduction is a standard technique used to improve the expression results obtained by DNA microarrays on RNA from blood samples. However, with whole transcriptome RNA-sequencing (RNA-seq) quickly replacing microarrays for many applications, the impact of globin reduction for RNA-seq has not been previously studied. Moreover, no off-the-shelf kits are available for globin reduction in nonhuman primates. Here we report a protocol for RNA-seq in primate blood samples that uses complimentary oligonucleotides to block reverse transcription of the alpha and beta globin genes. In test samples from cynomolgus monkeys (Macaca fascicularis), this globin blocking protocol approximately doubles the yield of informative (non-globin) reads by greatly reducing the fraction of globin reads, while also improving the consistency in sequencing depth between samples. The increased yield enables detection of about 2000 more genes, significantly increases the correlation in measured gene expression levels between samples, and increases the sensitivity of differential gene expression tests. These results show that globin blocking significantly improves the cost-effectiveness of mRNA sequencing in primate blood samples by doubling the yield of useful reads, allowing detection of more genes, and improving the precision of gene expression measurements. Based on these results, a globin reducing or blocking protocol is recommended for all RNA-seq studies of primate blood samples.}, Author = {{\textbf{Ryan C. Thompson}} and Gelbart, Terri and Head, Steven R. and Ordoukhanian, Phillip and Mullen, Courtney and Han, Dongmei and Berman, Dora M. and Bartholomew, Amelia and Kenyon, Norma S. and Salomon, Daniel R.}, Date-Added = {2016-05-03 23:39:31 +0000}, Date-Modified = {2016-09-24 18:11:49 +0000}, Journal = {Journal of Biological Methods (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{math-history-paper, 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 Rushton, Paul J. and Laudeman, Tom W. and Timko, Michael P.}, 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}}