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Items: 32

1.

A Prospective Analysis of Genetic Variants Associated with Human Lifespan.

Wright KM, Rand KA, Kermany A, Noto K, Curtis D, Garrigan D, Slinkov D, Dorfman I, Granka JM, Byrnes J, Myres N, Ball CA, Ruby JG.

G3 (Bethesda). 2019 Sep 4;9(9):2863-2878. doi: 10.1534/g3.119.400448.

2.

Response to comment on 'Naked mole-rat mortality rates defy Gompertzian laws by not increasing with age'.

Ruby JG, Smith M, Buffenstein R.

Elife. 2019 Jul 9;8. pii: e47047. doi: 10.7554/eLife.47047.

3.

Acoel genome reveals the regulatory landscape of whole-body regeneration.

Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M.

Science. 2019 Mar 15;363(6432). pii: eaau6173. doi: 10.1126/science.aau6173.

PMID:
30872491
4.

Estimates of the Heritability of Human Longevity Are Substantially Inflated due to Assortative Mating.

Ruby JG, Wright KM, Rand KA, Kermany A, Noto K, Curtis D, Varner N, Garrigan D, Slinkov D, Dorfman I, Granka JM, Byrnes J, Myres N, Ball C.

Genetics. 2018 Nov;210(3):1109-1124. doi: 10.1534/genetics.118.301613.

PMID:
30401766
5.

Naked Mole-Rat mortality rates defy gompertzian laws by not increasing with age.

Ruby JG, Smith M, Buffenstein R.

Elife. 2018 Jan 24;7. pii: e31157. doi: 10.7554/eLife.31157.

6.

Correction: Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.

Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM.

PLoS Pathog. 2017 Sep 7;13(9):e1006583. doi: 10.1371/journal.ppat.1006583. eCollection 2017 Sep.

7.

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.

Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P.

Curr Biol. 2017 Feb 20;27(4):569-575. doi: 10.1016/j.cub.2016.12.057. Epub 2017 Feb 9.

8.

Correction: A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa.

Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM.

PLoS Pathog. 2016 Mar 18;12(3):e1005503. doi: 10.1371/journal.ppat.1005503. eCollection 2016 Mar. No abstract available.

9.

Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. [Corrected].

Wen J, Duan H, Bejarano F, Okamura K, Fabian L, Brill JA, Bortolamiol-Becet D, Martin R, Ruby JG, Lai EC.

Mol Cell. 2015 Jan 8;57(1):165-78. doi: 10.1016/j.molcel.2014.11.025. Epub 2014 Dec 24. Erratum in: Mol Cell. 2015 Jun 18;58(6):1133.

10.

The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis.

Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF.

PLoS Biol. 2014 May 13;12(5):e1001861. doi: 10.1371/journal.pbio.1001861. eCollection 2014 May.

11.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF.

Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10.

12.

The posttranslational modification cascade to the thiopeptide berninamycin generates linear forms and altered macrocyclic scaffolds.

Malcolmson SJ, Young TS, Ruby JG, Skewes-Cox P, Walsh CT.

Proc Natl Acad Sci U S A. 2013 May 21;110(21):8483-8. doi: 10.1073/pnas.1307111110. Epub 2013 May 6.

13.

PRICE: software for the targeted assembly of components of (Meta) genomic sequence data.

Ruby JG, Bellare P, Derisi JL.

G3 (Bethesda). 2013 May 20;3(5):865-80. doi: 10.1534/g3.113.005967.

14.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

Melters DP, Bradnam KR, Young HA, Telis N, May MR, Ruby JG, Sebra R, Peluso P, Eid J, Rank D, Garcia JF, DeRisi JL, Smith T, Tobias C, Ross-Ibarra J, Korf I, Chan SW.

Genome Biol. 2013 Jan 30;14(1):R10. doi: 10.1186/gb-2013-14-1-r10.

15.

Molecular insights into the biosynthesis of guadinomine: a type III secretion system inhibitor.

Holmes TC, May AE, Zaleta-Rivera K, Ruby JG, Skewes-Cox P, Fischbach MA, DeRisi JL, Iwatsuki M, Ōmura S, Khosla C.

J Am Chem Soc. 2012 Oct 24;134(42):17797-806. doi: 10.1021/ja308622d. Epub 2012 Oct 10.

16.

A novel rhabdovirus associated with acute hemorrhagic fever in central Africa.

Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe JJ, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM.

PLoS Pathog. 2012 Sep;8(9):e1002924. doi: 10.1371/journal.ppat.1002924. Epub 2012 Sep 27. Erratum in: PLoS Pathog. 2016 Mar;12(3):e1005503. PLoS Pathog. 2017 Sep 7;13(9):e1006583.

17.

Complete genome sequence of an astrovirus identified in a domestic rabbit (Oryctolagus cuniculus) with gastroenteritis.

Stenglein MD, Velazquez E, Greenacre C, Wilkes RP, Ruby JG, Lankton JS, Ganem D, Kennedy MA, DeRisi JL.

Virol J. 2012 Sep 22;9:216. doi: 10.1186/1743-422X-9-216.

18.

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.

Stenglein MD, Sanders C, Kistler AL, Ruby JG, Franco JY, Reavill DR, Dunker F, Derisi JL.

MBio. 2012 Aug 14;3(4):e00180-12. doi: 10.1128/mBio.00180-12. Print 2012.

19.

Merochlorins A-D, cyclic meroterpenoid antibiotics biosynthesized in divergent pathways with vanadium-dependent chloroperoxidases.

Kaysser L, Bernhardt P, Nam SJ, Loesgen S, Ruby JG, Skewes-Cox P, Jensen PR, Fenical W, Moore BS.

J Am Chem Soc. 2012 Jul 25;134(29):11988-91. doi: 10.1021/ja305665f. Epub 2012 Jul 12. Erratum in: J Am Chem Soc. 2014 Oct 15;136(41):14626.

20.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol ─░, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

21.

Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia.

Runckel C, Flenniken ML, Engel JC, Ruby JG, Ganem D, Andino R, DeRisi JL.

PLoS One. 2011;6(6):e20656. doi: 10.1371/journal.pone.0020656. Epub 2011 Jun 7.

22.

Transcriptome sequencing demonstrates that human papillomavirus is not active in cutaneous squamous cell carcinoma.

Arron ST, Ruby JG, Dybbro E, Ganem D, Derisi JL.

J Invest Dermatol. 2011 Aug;131(8):1745-53. doi: 10.1038/jid.2011.91. Epub 2011 Apr 14.

23.

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.

Jan CH, Friedman RC, Ruby JG, Bartel DP.

Nature. 2011 Jan 6;469(7328):97-101. doi: 10.1038/nature09616. Epub 2010 Nov 17.

24.

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.

Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel DP.

Genes Dev. 2010 May 15;24(10):992-1009. doi: 10.1101/gad.1884710. Epub 2010 Apr 22.

25.

The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.

Sorber K, Chiu C, Webster D, Dimon M, Ruby JG, Hekele A, DeRisi JL.

PLoS One. 2008;3(10):e3495. doi: 10.1371/journal.pone.0003495. Epub 2008 Oct 22.

26.

Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.

Babiarz JE, Ruby JG, Wang Y, Bartel DP, Blelloch R.

Genes Dev. 2008 Oct 15;22(20):2773-85. doi: 10.1101/gad.1705308.

27.

PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans.

Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D Jr, Luo S, Schroth GP, Carrington JC, Bartel DP, Mello CC.

Mol Cell. 2008 Jul 11;31(1):67-78. doi: 10.1016/j.molcel.2008.06.002. Epub 2008 Jun 19.

28.

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs.

Okamura K, Chung WJ, Ruby JG, Guo H, Bartel DP, Lai EC.

Nature. 2008 Jun 5;453(7196):803-6. doi: 10.1038/nature07015. Epub 2008 May 7.

29.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J; Harvard FlyBase curators; Berkeley Drosophila Genome Project, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, Dewey CN, Pachter L, Kent WJ, Haussler D, Lai EC, Bartel DP, Hannon GJ, Kaufman TC, Eisen MB, Clark AG, Smith D, Celniker SE, Gelbart WM, Kellis M.

Nature. 2007 Nov 8;450(7167):219-32.

30.

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.

Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.

Genome Res. 2007 Dec;17(12):1850-64. Epub 2007 Nov 7.

31.

Intronic microRNA precursors that bypass Drosha processing.

Ruby JG, Jan CH, Bartel DP.

Nature. 2007 Jul 5;448(7149):83-6. Epub 2007 Jun 24.

32.

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.

Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP.

Cell. 2006 Dec 15;127(6):1193-207.

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