JR
J. Graham Ruby
AgingecologyLongevityEvolution, MolecularaginglifespanMole Ratsnaked mole-ratAge-related pathologyBioinformatics
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
51 papers in the corpus · 2006–2026AP-1 specifies developmental versus fibrotic extracellular matrix transcriptional programs in the lung10.64898/2026.09.10.750752v1 · Kaiser, A. M., Luo, A., Sivasubramanian, K. et al.2026 · 0 citationsbioRxiv
Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes.42520801 · Torlai Triglia, Elena, Miller, Tyler E, Durand, Neva C et al.2026 · 0 citationsCell genomics. 2026;6(8):101304
Genetic correlation-guided mega-analysis of DO mice provides mechanistic insight and candidate genes for age-related pathologies.41758904 · Mullis, Martin N, Lefebvre, Austin E Y T, Sivasubramanian, Kathyayini et al.2026 · 2 citationsPLoS genetics. 2026;22(2):e1012037
Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells.40974519 · Kaiser, Alyssa M, Selahi, Amirali, Kong, Wenjun et al.2026 · 2 citationsGeroScience. 2026;48(3):4173-4193
Geographic distribution of genetic diversity of Heterocephalus glaber analyzed using whole genome sequencing and a chromosome-scale genome assembly10.1101/2025.07.22.666215v1 · Wright, K. M., Sood, P., Zemlemerova, E. D. et al.2025 · 2 citationsbioRxiv
Characterizing aging-related genetic and physiological determinants of spinal curvature.40652108 · Wang, Frances M, Ruby, J Graham, Sethi, Anurag et al.2025 · 1 citationCommunications medicine. 2025;5(1):291
Workshop Report-Heterogeneity and Successful Aging Part II: Approaches to Investigate Heterogeneity in Aging Research.40257451 · Kumar, Vivek, Hevener, Andrea L, Ruby, J Graham et al.2025 · 3 citationsThe journals of gerontology. Series A, Biological sciences and medical sciences. 2025;80(5)
Workshop Report-Heterogeneity and Successful Aging Part I: Heterogeneity in Aging-Challenges and Opportunities.40052564 · Kuchel, George A, Hevener, Andrea L, Ruby, J Graham et al.2025 · 5 citationsThe journals of gerontology. Series A, Biological sciences and medical sciences. 2025;80(4)
Analysis of lifespan across Diversity Outbred mouse studies identifies multiple longevity-associated loci.39605744 · Mullis, Martin N, Wright, Kevin M, Raj, Anil et al.2025 · 4 citationsbioRxiv : the preprint server for biology. 2024
Five years later, with double the demographic data, naked mole-rat mortality rates continue to defy Gompertzian laws by not increasing with age.38773057 · Ruby, J Graham, Smith, Megan, Buffenstein, Rochelle2024 · 25 citationsGeroScience. 2024;46(5):5321-5341
Aging of the Spine: Characterizing genetic and physiological determinants of spinal curvature10.1101/2024.02.27.24303450v1 · Wang, F. M., Ruby, J. G., Sethi, A. et al.2024 · 1 citationmedRxiv
3D mouse pose from single-view video and a new dataset.37604955 · Hu, Bo, Seybold, Bryan, Yang, Shan et al.2023 · 6 citationsScientific reports. 2023;13(1):13554
An Automated, Home-Cage, Video Monitoring-based Mouse Frailty Index Detects Age-associated Morbidity in C57BL/6 and Diversity Outbred Mice.36708182 · Ruby, J Graham, Di Francesco, Andrea, Ylagan, Paulo et al.2023 · 16 citationsThe journals of gerontology. Series A, Biological sciences and medical sciences. 2023;78(5):762-770
Genetics implicates overactive osteogenesis in the development of diffuse idiopathic skeletal hyperostosis.37156767 · Sethi, Anurag, Ruby, J Graham, Veras, Matthew A et al.2023 · 36 citationsNature communications. 2023;14(1):2644
Calcification of the abdominal aorta is an under-appreciated cardiovascular disease risk factor in the general population.36277789 · Sethi, Anurag, Taylor, D Leland, Ruby, J Graham et al.2025 · 50 citationsFrontiers in cardiovascular medicine. 2022;9:1003246
A home-cage, video monitoring-based mouse frailty index detects age-associated morbidity in the absence of handler-induced stress.10.1101/2022.07.19.500666v1 · Ruby, J. G., Ylagan, P., Di Francesco, A. et al.2022 · 0 citationsbioRxiv
The naked truth: a comprehensive clarification and classification of current 'myths' in naked mole-rat biology.34476892 · Buffenstein, Rochelle, Amoroso, Vincent, Andziak, Blazej et al.2022 · 123 citationsBiological reviews of the Cambridge Philosophical Society. 2022;97(1):115-140
Opportunities for new insight into aging from the naked mole-rat and other non-traditional models.37117998 · Buffenstein, Rochelle, Ruby, J Graham2023 · 27 citationsNature aging. 2021;1(1):3-4
Fully Phased Sequence of a Diploid Human Genome Determined de Novo from the DNA of a Single Individual.32631951 · Soifer, Llya, Fong, Nicole L, Yi, Nelda et al.2021 · 9 citationsG3 (Bethesda, Md.). 2020;10(9):2911-2925
A Prospective Analysis of Genetic Variants Associated with Human Lifespan.31484785 · Wright, Kevin M, Rand, Kristin A, Kermany, Amir et al.2020 · 62 citationsG3 (Bethesda, Md.). 2019;9(9):2863-2878
Response to comment on 'Naked mole-rat mortality rates defy Gompertzian laws by not increasing with age'.31287059 · Ruby, J Graham, Smith, Megan, Buffenstein, Rochelle2019 · 19 citationseLife. 2019;8
Acoel genome reveals the regulatory landscape of whole-body regeneration.30872491 · Gehrke, Andrew R, Neverett, Emily, Luo, Yi-Jyun et al.2019 · 172 citationsScience (New York, N.Y.). 2019;363(6432)
Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating.30401766 · Ruby, J Graham, Wright, Kevin M, Rand, Kristin A et al.2019 · 263 citationsGenetics. 2018;210(3):1109-1124
Naked Mole-Rat mortality rates defy gompertzian laws by not increasing with age.29364116 · Ruby, J Graham, Smith, Megan, Buffenstein, Rochelle2018 · 265 citationseLife. 2018;7
Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.28880960 · Grard, Gilda, Fair, Joseph N, Lee, Deanna et al.2019 · 1 citationPLoS pathogens. 2017;13(9):e1006583
The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.28190732 · Slabodnick, Mark M, Ruby, J Graham, Reiff, Sarah B et al.2018 · 127 citationsCurrent biology : CB. 2017;27(4):569-575
Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.26991269 · Grard, Gilda, Fair, Joseph N, Lee, Deanna et al.2016 · 2 citationsPLoS pathogens. 2016;12(3):e1005503
Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. [Corrected].25544562 · Wen, Jiayu, Duan, Hong, Bejarano, Fernando et al.2015 · 52 citationsMolecular cell. 2015;57(1):165-78
The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.24823688 · Slabodnick, Mark M, Ruby, J Graham, Dunn, Joshua G et al.2015 · 70 citationsPLoS biology. 2014;12(5):e1001861
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
PRICE: software for the targeted assembly of components of (Meta) genomic sequence data.23550143 · Ruby, J Graham, Bellare, Priya, Derisi, Joseph L2014 · 290 citationsG3 (Bethesda, Md.). 2013;3(5):865-80
The posttranslational modification cascade to the thiopeptide berninamycin generates linear forms and altered macrocyclic scaffolds.23650400 · Malcolmson, Steven J, Young, Travis S, Ruby, J Graham et al.2013 · 64 citationsProceedings of the National Academy of Sciences of the United States of America. 2013;110(21):8483-8
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.23363705 · Melters, Daniël P, Bradnam, Keith R, Young, Hugh A et al.2015 · 526 citationsGenome biology. 2013;14(1):R10
Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor.23030602 · Holmes, Tracy C, May, Aaron E, Zaleta-Rivera, Kathia et al.2013 · 59 citationsJournal of the American Chemical Society. 2012;134(42):17797-806
Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis.22998755 · Stenglein, Mark D, Velazquez, Eric, Greenacre, Cheryl et al.2013 · 27 citationsVirology journal. 2012;9:216
A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.23028323 · Grard, Gilda, Fair, Joseph N, Lee, Deanna et al.2013 · 214 citationsPLoS pathogens. 2012;8(9):e1002924
Merochlorins A-D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases.22784372 · Kaysser, Leonard, Bernhardt, Peter, Nam, Sang-Jip et al.2012 · 212 citationsJournal of the American Chemical Society. 2012;134(29):11988-91
Identification, characterization, and in vitro culture of highly divergent arenaviruses from boa constrictors and annulated tree boas: candidate etiological agents for snake inclusion body disease.22893382 · Stenglein, Mark D, Sanders, Chris, Kistler, Amy L et al.2013 · 187 citationsmBio. 2012;3(4):e00180-12
Assemblathon 1: a competitive assessment of de novo short read assembly methods.21926179 · Earl, Dent, Bradnam, Keith, St John, John et al.2012 · 507 citationsGenome research. 2011;21(12):2224-41
Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma.21490616 · Arron, Sarah T, Ruby, J Graham, Dybbro, Eric et al.2011 · 150 citationsThe Journal of investigative dermatology. 2011;131(8):1745-53
Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.21687739 · Runckel, Charles, Flenniken, Michelle L, Engel, Juan C et al.2011 · 448 citationsPloS one. 2011;6(6):e20656
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.21085120 · Jan, Calvin H, Friedman, Robin C, Ruby, J Graham et al.2011 · 481 citationsNature. 2011;469(7328):97-101
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.20413612 · Chiang, H Rosaria, Schoenfeld, Lori W, Ruby, J Graham et al.2010 · 809 citationsGenes & development. 2010;24(10):992-1009
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.18923076 · Babiarz, Joshua E, Ruby, J Graham, Wang, Yangming et al.2008 · 908 citationsGenes & development. 2008;22(20):2773-85
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans.18571452 · Batista, Pedro J, Ruby, J Graham, Claycomb, Julie M et al.2008 · 588 citationsMolecular cell. 2008;31(1):67-78
The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs.18463630 · Okamura, Katsutomo, Chung, Wei-Jen, Ruby, J Graham et al.2008 · 391 citationsNature. 2008;453(7196):803-6
The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.18941527 · Sorber, Katherine, Chiu, Charles, Webster, Dale et al.2009 · 29 citationsPloS one. 2008;3(10):e3495
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.17994088 · Stark, Alexander, Lin, Michael F, Kheradpour, Pouya et al.2008 · 632 citationsNature. 2007;450(7167):219-32
Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.17989254 · Ruby, J Graham, Stark, Alexander, Johnston, Wendy K et al.2008 · 595 citationsGenome research. 2007;17(12):1850-64
Intronic microRNA precursors that bypass Drosha processing.17589500 · Ruby, J Graham, Jan, Calvin H, Bartel, David P2007 · 1,639 citationsNature. 2007;448(7149):83-6
Career total: 91 works. 51 are in this corpus.Showing the 50 most recent.
Profile built from the corpus for this byline.
Author records are still filling in while the Hub is in alpha. If this is your page, you'll be able to claim it soon. Spot a mistake? Tell us.