Recent Publications

Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V: The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev Cell. 2014 Oct 27. PMID: 25373775

Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M: Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28. PMID: 25164757

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R: Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28. PMID: 25164755

Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 2014 Aug 28. PMID: 25164749

Byrne AB, Walradt T, Gardner KE, Hubbert A, Reinke V, Hammarlund M: Insulin/IGF1 signaling inhibits age-dependent axon regeneration. Neuron. 2014 Feb 5; 2014 Jan 16. PMID: 24440228

Kasper DM, Gardner KE, Reinke V: Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs. Epigenetics. 2014 Jan; 2013 Oct 22. PMID: 24149573

Doh JH, Jung Y, Reinke V, Lee MH: C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. Worm. 2013 Oct 1. PMID: 24744981

Reinke V, Krause M, Okkema P: Transcriptional regulation of gene expression in C. elegans. WormBook. 2013 Jun 4; 2013 Jun 4. PMID: 23801596

Fontrodona L, Porta-de-la-Riva M, Morán T, Niu W, Díaz M, Aristizábal-Corrales D, Villanueva A, Schwartz S Jr, Reinke V, Cerón J: RSR-2, the Caenorhabditis elegans ortholog of human spliceosomal component SRm300/SRRM2, regulates development by influencing the transcriptional machinery. PLoS Genet. 2013 Jun; 2013 Jun 6. PMID: 23754964

Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V: Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 2013 Jan 23; 2013 Jan 23. PMID: 23347407

Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M, Preston E, Zinke A, Enst S, Teichgraber T, Janette J, Reis K, Janosch S, Schloissnig S, Ejsmont RK, Slightam C, Xu X, Kim SK, Reinke V, Stewart AF, Snyder M, Waterston RH, Hyman AA: A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012 Aug 17. PMID: 22901814

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR, Shendure J, Waterston RH, Oliver B, Lieb JD, Disteche CM: Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23; 2011 Oct 23. PMID: 22019781

Nottke AC, Beese-Sims SE, Pantalena LF, Reinke V, Shi Y, Colaiácovo MP: SPR-5 is a histone H3K4 demethylase with a role in meiotic double-strand break repair. Proc Natl Acad Sci U S A. 2011 Aug 2; 2011 Jul 18. PMID: 21768382

Kapelle WS, Reinke V: C. elegans meg-1 and meg-2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival. Genesis. 2011 May. PMID: 21305687

Petrella LN, Wang W, Spike CA, Rechtsteiner A, Reinke V, Strome S: synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival. Development. 2011 Mar. PMID: 21343362

Schober CS, Aydiner F, Booth CJ, Seli E, Reinke V: The kinase VRK1 is required for normal meiotic progression in mammalian oogenesis. Mech Dev. 2011 Mar-Apr; 2011 Jan 26. PMID: 21277975

Waters KA, Reinke V: Extrinsic and intrinsic control of germ cell proliferation in Caenorhabditis elegans. Mol Reprod Dev. 2011 Mar; 2011 Feb 17. PMID: 21337453

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB: Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177971

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, Shaham S, Rätsch G, Miller DM 3rd: A spatial and temporal map of C. elegans gene expression. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177967

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177963

Engelmann I, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ: A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One. 2011; 2011 May 13. PMID: 21602919

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M: A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One. 2010 Dec 29; 2010 Dec 29. PMID: 21209968

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 2010 Dec 22. PMID: 21177976

Waters K, Yang AZ, Reinke V: Genome-wide analysis of germ cell proliferation in C.elegans identifies VRK-1 as a key regulator of CEP-1/p53. Dev Biol. 2010 Aug 15; 2010 Jun 23. PMID: 20599896

Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M: Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics. 2010 Jun 17; 2010 Jun 17. PMID: 20565764

Li X, Panea C, Wiggins CH, Reinke V, Leslie C: Learning "graph-mer" motifs that predict gene expression trajectories in development. PLoS Comput Biol. 2010 Apr 29; 2010 Apr 29. PMID: 20454681

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M: Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19; 2010 Feb 19. PMID: 20174564

Niwa R, Hada K, Moliyama K, Ohniwa RL, Tan YM, Olsson-Carter K, Chi W, Reinke V, Slack FJ: C. elegans sym-1 is a downstream target of the hunchback-like-1 developmental timing transcription factor. Cell Cycle. 2009 Dec 15; 2009 Dec 9. PMID: 19923914

Klerkx EP, Alarcón P, Waters K, Reinke V, Sternberg PW, Askjaer P: Protein kinase VRK-1 regulates cell invasion and EGL-17/FGF signaling in Caenorhabditis elegans. Dev Biol. 2009 Nov 1; 2009 Aug 11. PMID: 19679119

Chi W, Reinke V: DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans. Mech Dev. 2009 May-Jun; 2009 Feb 6. PMID: 19368797

Katz DJ, Edwards TM, Reinke V, Kelly WG: A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell. 2009 Apr 17. PMID: 19379696

Reinke V, Cutter AD: Germline expression influences operon organization in the Caenorhabditis elegans genome. Genetics. 2009 Apr; 2009 Feb 9. PMID: 19204375

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH: Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009 Apr; 2009 Jan 30. PMID: 19181841

Reinke V: Gene regulation: a tale of germline mRNA tails. Curr Biol. 2008 Oct 14. PMID: 18957237

Kudron MM, Reinke V: C. elegans nucleostemin is required for larval growth and germline stem cell division. PLoS Genet. 2008 Aug 22; 2008 Aug 22. PMID: 18725931

Boag PR, Atalay A, Robida S, Reinke V, Blackwell TK: Protection of specific maternal messenger RNAs by the P body protein CGH-1 (Dhh1/RCK) during Caenorhabditis elegans oogenesis. J Cell Biol. 2008 Aug 11. PMID: 18695045

Wang G, Reinke V: A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol. 2008 Jun 24; 2008 May 22. PMID: 18501605

Lin B, Reinke V: The candidate MAP kinase phosphorylation substrate DPL-1 (DP) promotes expression of the MAP kinase phosphatase LIP-1 in C. elegans germ cells. Dev Biol. 2008 Apr 1; 2008 Jan 8. PMID: 18304523

Spike CA, Bader J, Reinke V, Strome S: DEPS-1 promotes P-granule assembly and RNA interference in C. elegans germ cells. Development. 2008 Mar; 2008 Jan 30. PMID: 18234720

Leacock SW, Reinke V: MEG-1 and MEG-2 are embryo-specific P-granule components required for germline development in Caenorhabditis elegans. Genetics. 2008 Jan. PMID: 18202375

Derry WB, Bierings R, van Iersel M, Satkunendran T, Reinke V, Rothman JH: Regulation of developmental rate and germ cell proliferation in Caenorhabditis elegans by the p53 gene network. Cell Death Differ. 2007 Apr; 2006 Dec 22. PMID: 17186023

Reinke V: Think globally, act locally. Nat Genet. 2007 Mar. PMID: 17325676

Troemel ER, Chu SW, Reinke V, Lee SS, Ausubel FM, Kim DH: p38 MAPK regulates expression of immune response genes and contributes to longevity in C. elegans. PLoS Genet. 2006 Nov 10; 2006 Sep 11. PMID: 17096597

Leacock SW, Reinke V: Expression profiling of MAP kinase-mediated meiotic progression in Caenorhabditis elegans. PLoS Genet. 2006 Nov 10. PMID: 17096596

Bender LB, Suh J, Carroll CR, Fong Y, Fingerman IM, Briggs SD, Cao R, Zhang Y, Reinke V, Strome S: MES-4: an autosome-associated histone methyltransferase that participates in silencing the X chromosomes in the C. elegans germ line. Development. 2006 Oct. PMID: 16968818

Chi W, Reinke V: Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB). Development. 2006 Aug; 2006 Jul 19. PMID: 16854972

Reinke V: Germline genomics. WormBook. 2006 Jan 20; 2006 Jan 20. PMID: 18050476

Thoemke K, Yi W, Ross JM, Kim S, Reinke V, Zarkower D: Genome-wide analysis of sex-enriched gene expression during C. elegans larval development. Dev Biol. 2005 Aug 15. PMID: 15987632

Whetstine JR, Ceron J, Ladd B, Dufourcq P, Reinke V, Shi Y: Regulation of tissue-specific and extracellular matrix-related genes by a class I histone deacetylase. Mol Cell. 2005 May 13. PMID: 15893731

Fernandez AG, Gunsalus KC, Huang J, Chuang LS, Ying N, Liang HL, Tang C, Schetter AJ, Zegar C, Rual JF, Hill DE, Reinke V, Vidal M, Piano F: New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res. 2005 Feb. PMID: 15687288

Reinke V: Sex and the genome. Nat Genet. 2004 Jun. PMID: 15167926

Reinke V, Gil IS, Ward S, Kazmer K: Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Development. 2004 Jan; 2003 Dec 10. PMID: 14668411

Wiederkehr C, Basavaraj R, Sarrauste de Menthière C, Hermida L, Koch R, Schlecht U, Amon A, Brachat S, Breitenbach M, Briza P, Caburet S, Cherry M, Davis R, Deutschbauer A, Dickinson HG, Dumitrescu T, Fellous M, Goldman A, Grootegoed JA, Hawley R, Ishii R, Jégou B, Kaufman RJ, Klein F, Lamb N, Maro B, Nasmyth K, Nicolas A, Orr-Weaver T, Philippsen P, Pineau C, Rabitsch KP, Reinke V, Roest H, Saunders W, Schröder M, Schedl T, Siep M, Villeneuve A, Wolgemuth DJ, Yamamoto M, Zickler D, Esposito RE, Primig M: GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Res. 2004 Jan 1. PMID: 14681481