Papers about the TransgeneOme technology and its applications

Wu E, Vashisht AA, Chapat C, Flamand MN, Cohen E, Sarov M, Tabach Y, Sonenberg N, Wohlschlegel J, Duchaine TF. A continuum of mRNP complexes in embryonic microRNA-mediated silencing. Nucleic Acids Res. 2017 Feb 28;45(4)

Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, Stender B, Janosch S, K J VV, Krishnan RT, Krishnamoorthy A, Ferreira IR, Ejsmont RK, Finkl K, Hasse S, Kämpfer P, Plewka N, Vinis E, Schloissnig S, Knust E, Hartenstein V, Mann M, et al. A genome-wide resource for the analysis of protein localisation in Drosophila. Elife. 2016 Feb 20;5

Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, et al. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data Brief. 2015 Dec 12;6

Kalebic N, Taverna E, Tavano S, Wong FK, Suchold D, Winkler S, Huttner WB, Sarov M. CRISPR/Cas9-induced disruption of gene expression in mouse embryonic brain and single neural stem cells in vivo. EMBO Rep. 2016 Mar;17(3)

Hasse S, Hyman AA, Sarov M. TransgeneOmics--A transgenic platform for protein localization based function exploration. Methods. 2016 Mar 1;96

Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, et al. Panorama of ancient metazoan macromolecular complexes. Nature. 2015 Sep 17;525(7569)

Penkov S, Kaptan D, Erkut C, Sarov M, Mende F, Kurzchalia TV. Integration of carbohydrate metabolism and redox state controls dauer larva formation in Caenorhabditis elegans. Nat Commun. 2015 Aug 20;6

Cornes E, Porta-De-La-Riva M, Aristizábal-Corrales D, Brokate-Llanos AM, García-Rodríguez FJ, Ertl I, Díaz M, Fontrodona L, Reis K, Johnsen R, Baillie D, Muñoz MJ, Sarov M, Dupuy D, Cerón J. Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans. RNA. 2015 Sep;21(9)

Spletter ML, Barz C, Yeroslaviz A, Schönbauer C, Ferreira IR, Sarov M, Gerlach D, Stark A, Habermann BH, Schnorrer F. The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle. EMBO Rep. 2015 Feb;16(2)

Frøkjær-Jensen C, Davis MW, Sarov M, Taylor J, Flibotte S, LaBella M, Pozniakovsky A, Moerman DG, Jorgensen EM. Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon. Nat Methods. 2014 May;11(5)

Sudhakaran IP, Hillebrand J, Dervan A, Das S, Holohan EE, Hülsmeier J, Sarov M, Parker R, VijayRaghavan K, Ramaswami M. FMRP and Ataxin-2 function together in long-term olfactory habituation and neuronal translational control. Proc Natl Acad Sci U S A. 2014 Jan 7;111(1)

Preibisch S, Amat F, Stamataki E, Sarov M, Singer RH, Myers E, Tomancak P. Efficient Bayesian-based multiview deconvolution. Nat Methods. 2014 Jun;11(6)

Andréasson C, Schick AJ, Pfeiffer SM, Sarov M, Stewart F, Wurst W, Schick JA. Direct cloning of isogenic murine DNA in yeast and relevance of isogenicity for targeting in embryonic stem cells. PLoS One. 2013 Sep 13;8(9)

Ivanova A, Kalaidzidis Y, Dirkx R, Sarov M, Gerlach M, Schroth-Diez B, Müller A, Liu Y, Andree C, Mulligan B, Münster C, Kurth T, Bickle M, Speier S, Anastassiadis K, Solimena M. Age-dependent labeling and imaging of insulin secretory granules. Diabetes. 2013 Nov;62(11)

Nedelcheva-Veleva MN, Sarov M, Yanakiev I, Mihailovska E, Ivanov MP, Panova GC, Stoynov SS. The thermodynamic patterns of eukaryotic genes suggest a mechanism for intron-exon recognition. Nat Commun. 2013;4

Mihail Sarov, John I. Murray, Kristin Schanze, Andrei Pozniakovski, Wei Niu, Karolin Angermann, Susanne Hasse, Michaela Rupprecht, Elisabeth Vinis, Matthew Tinney, Elicia Preston, Andrea Zinke, Susanne Enst, Tina Teichgraber, Judith Janette, Kadri Reis, Stephan Janosch, Siegfried Schloissnig, Radoslaw K. Ejsmont, Cindie Slightam, Xiao Xu, Stuart K. Kim, Valerie Reinke, A. Francis Stewart, Michael Snyder, Robert H. Waterston, Anthony A. Hyman, A Genome-Scale Resource for In Vivo Tag-Based Protein Function Exploration in C. elegans. Cell Aug. 2012.; 150(4): 855-866.

Petersen SC, Watson JD, Richmond JE, Sarov M, Walthall WW, Miller DM. A transcriptional program promotes remodeling of GABAergic synapses in Caenorhabditis elegans. J Neurosci 2011 Oct.;31(43):15362–15375.

Nedelkova M, Maresca M, Fu J, Rostovskaya M, Chenna R, Thiede C, Anastasiadis K, Sarov M, Stewart AF. Targeted isolation of cloned genomic regions by recombineering for haplotype phasing and isogenic targeting. Nucleic Acids Res 2011 Aug.;

Elefsinioti A, Sarac OS, Hegele A, Plake C, Hubner NC, Poser I, Sarov M, Hyman A, Mann M, Schroeder M, Stelzl U, Beyer A. Large-scale de novo prediction of physical protein-protein association. Mol Cell Proteomics 2011 Aug.;

Ciotta G, Hofemeister H, Maresca M, Fu J, Sarov M, Anastassiadis K, Stewart AF. Recombineering BAC transgenes for protein tagging. Methods 2011 Feb.;53(2):113–119.

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.;21(2):245–254.

Ejsmont RK, Ahlfeld P, Pozniakovsky A, Stewart AF, Tomancak P, Sarov M. Recombination-mediated genetic engineering of large genomic DNA transgenes. Methods Mol Biol 2011;772:445–458.

Hofemeister H, Ciotta G, Fu J, Seibert PM, Schulz A, Maresca M, Sarov M, Anastassiadis K, Stewart AF. Recombineering, transfection, Western, IP and ChIP methods for protein tagging via gene targeting or BAC transgenesis. Methods 2010 Dec.;

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 M-S, 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, Muroyama A, Murray JI, Ooi S-L, 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 K-K, 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.;330(6012):1775–1787.

Hutchins JRA, Toyoda Y, Hegemann B, Poser I, Hériché J-K, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J, Conrad C, Comartin D, Schleiffer A, Sarov M, Pozniakovsky A, Slabicki MM, Schloissnig S, Steinmacher I, Leuschner M, Ssykor A, Lawo S, Pelletier L, Stark H, Nasmyth K, Ellenberg J, Durbin R, Buchholz F, Mechtler K, Hyman AA, Peters J-M. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010 Apr.;328(5978):593–599.

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;5(12):e15898.

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HYK, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein MB, 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;6(2):e1000848.

Ejsmont RK, Sarov M, Winkler S, Lipinski KA, Tomancak P. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nat Methods 2009 Jun.;6(6):435–437.

Poser I, Sarov M, Hutchins JRA, Hériché J-K, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW, Pelletier L, Kittler R, Hua S, Naumann R, Augsburg M, Sykora MM, Hofemeister H, Zhang Y, Nasmyth K, White KP, Dietzel S, Mechtler K, Durbin R, Stewart AF, Peters J-M, Buchholz F, Hyman AA. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods 2008 May;5(5):409–415.

Sarov M, Schneider S, Pozniakovski A, Roguev A, Ernst S, Zhang Y, Hyman A, Stewart A. A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat Methods 2006 Oct.;3(10):839–844.